tag:theconversation.com,2011:/au/topics/genetic-diversity-22986/articlesGenetic diversity – The Conversation2023-08-23T21:22:36Ztag:theconversation.com,2011:article/2110072023-08-23T21:22:36Z2023-08-23T21:22:36ZCoral reefs: How climate change threatens the hidden diversity of marine ecosystems<figure><img src="https://images.theconversation.com/files/543317/original/file-20230817-23-tvw75n.jpg?ixlib=rb-1.1.0&rect=0%2C0%2C3982%2C2976&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">A healthy reef on Kiritimati (Christmas Island, Republic of Kiribati).</span> <span class="attribution"><span class="source">(Danielle Claar)</span>, <span class="license">Author provided</span></span></figcaption></figure><iframe style="width: 100%; height: 100px; border: none; position: relative; z-index: 1;" allowtransparency="" allow="clipboard-read; clipboard-write" src="https://narrations.ad-auris.com/widget/the-conversation-canada/coral-reefs-how-climate-change-threatens-the-hidden-diversity-of-aquatic-ecosystems" width="100%" height="400"></iframe>
<p>Like the heat waves on land we have all grown familiar with, <a href="https://doi.org/10.1146/annurev-marine-032720-095144">marine heat waves</a> are being <a href="https://doi.org/10.1038/s41586-018-0383-9">amplified by climate change</a>. These extreme warm water events have <a href="https://doi.org/10.1038/s41558-019-0412-1">ushered in some of the most catastrophic impacts</a> of climate change and are now a major threat to ocean life. </p>
<p>Coral reefs, which are <a href="https://doi.org/10.1017/9781009157964.001">home to a quarter of all life in the ocean, are the most vulnerable</a>.
This is a dire situation, given the vast number of people who <a href="https://doi.org/10.1016/j.rsma.2019.100699">depend on coral reefs</a> for their sustenance and livelihoods. </p>
<p>As climate change pushes corals beyond their limits, a key question is <a href="https://doi.org/10.1016/j.cub.2017.04.047">why different corals vary in their sensitivity</a> to warm waters. </p>
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<span class="caption">A reef on Kiritimati (Christmas Island) at the end of the 2015-16 marine heat wave where some Porites lobata colonies survived (yellow/tan colours), some were alive but bleached (white colonies), and some died along with the rest of the reef (red/purple/pink colours of turf algae covering dead colonies). (Danielle Claar), Author provided.</span>
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<p>In our <a href="https://doi.org/10.1126/sciadv.adf0954">new study in <em>Science Advances</em></a>, we examined the genetics of hundreds of individual corals during the 2015-16 El Niño-driven heat wave. Our results suggest that heat waves have hidden impacts on the genetic composition of reef-building corals. Understanding this could help scientists bolster reef resilience to future heat waves. </p>
<h2>Pushing corals out of their comfort zones</h2>
<p>Corals are <a href="https://doi.org/10.1126/science.aan8048">highly adapted to the temperature</a> of their local waters, with temperatures even 1 C warmer than normal pushing them out of their comfort zone. </p>
<p>Unusually warm water <a href="https://doi.org/10.1146/annurev.ecolsys.34.011802.132417">disrupts the vital relationship</a> between stony corals (the reef-builders) and their symbiotic partners, microscopic algae that provide food to the corals. This causes coral bleaching, and in many cases mortality. </p>
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Read more:
<a href="https://theconversation.com/is-the-great-barrier-reef-reviving-or-dying-heres-whats-happening-beyond-the-headlines-210558">Is the Great Barrier Reef reviving – or dying? Here's what's happening beyond the headlines</a>
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<p>The tropical heat wave at our study site in the central Pacific Ocean, Kiritimati (Christmas Island), lasted for ten months, a world record. This led to extensive coral bleaching, presenting an opportunity to determine why some corals died and others survived. </p>
<h2>Cryptic diversity within a widespread coral species</h2>
<p>We focused on the widespread lobed coral (<em>Porites lobata</em>). This species is amongst the most heat-tolerant corals, and despite <a href="https://doi.org/10.1126/sciadv.abq5615">almost 90 per cent of all coral cover being lost</a> on Kiritimati, over half of lobed corals survived. </p>
<p>In fact, some <em>Porites</em> colonies didn’t bleach at all. </p>
<p>Why?</p>
<p>Using genomic tools, we identified three distinct types of <em>Porites lobata</em> on Kiritimati. These lineages, which may represent distinct species, are indistinguishable by eye but genetically different. </p>
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<img alt="" src="https://images.theconversation.com/files/542847/original/file-20230815-29-rh83z4.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/542847/original/file-20230815-29-rh83z4.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=401&fit=crop&dpr=1 600w, https://images.theconversation.com/files/542847/original/file-20230815-29-rh83z4.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=401&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/542847/original/file-20230815-29-rh83z4.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=401&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/542847/original/file-20230815-29-rh83z4.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=504&fit=crop&dpr=1 754w, https://images.theconversation.com/files/542847/original/file-20230815-29-rh83z4.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=504&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/542847/original/file-20230815-29-rh83z4.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=504&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
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<span class="caption">Two colonies of Porities growing side-by-side on Kiritimati (Christmas Island) during the 2015-16 marine heat wave. One colony appears healthy while the other is severely bleached. (Kieran Cox), Author provided.</span>
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<p>Such biodiversity is known as <a href="https://doi.org/10.1186/jbiol60">“cryptic diversity” or “hidden diversity.”</a> Although cryptic diversity is widespread across corals, its ecological implications remain unclear. </p>
<h2>Marine heat waves threaten cryptic diversity</h2>
<p>We found that one genetic lineage of <em>Porites</em> was highly sensitive to the heat wave: only 15 per cent of its colonies survived compared to 50-60 per cent in the other lineages. Thus, even in a coral widely considered to be stress tolerant, heat waves can have hidden impacts, threatening diversity that is invisible to the naked eye.</p>
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Read more:
<a href="https://theconversation.com/out-of-danger-because-the-un-said-so-hardly-the-barrier-reef-is-still-in-hot-water-210787">Out of danger because the UN said so? Hardly – the Barrier Reef is still in hot water</a>
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<p>If future marine heat waves continue to have similar effects, eventually sensitive genotypes like this one could be completely lost, reducing the genetic diversity of coral reefs. </p>
<p>Because interbreeding between cryptic lineages and species can offer a <a href="https://doi.org/10.1046/j.1365-294x.2001.01216.x">potential avenue for future adaptation</a>, losses of genetic diversity could make a bad problem even worse by limiting future adaptation to changing environments.</p>
<h2>A forced breakup</h2>
<p>So why did <em>Porites</em> lineages on Kiritimati differ in survival? </p>
<p>One hypothesis is that they house symbiotic partners with different heat sensitivities. Using metabarcoding, a technique that attempts to identify everything found living in the coral tissue, we identified which symbionts were partnered with which corals before, during and after the heat wave.</p>
<p>We found that the distinct <em>Porites</em> lineages had different partnerships before the heat wave. <em>Porites</em> species pass on their symbionts from <a href="https://doi.org/10.1111/j.1529-8817.2012.01220.x">one generation to the next</a> and so these relationships likely arose over many generations.</p>
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<img alt="two divers inspect a coral reef" src="https://images.theconversation.com/files/543319/original/file-20230817-29-myzq3d.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/543319/original/file-20230817-29-myzq3d.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/543319/original/file-20230817-29-myzq3d.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/543319/original/file-20230817-29-myzq3d.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/543319/original/file-20230817-29-myzq3d.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/543319/original/file-20230817-29-myzq3d.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/543319/original/file-20230817-29-myzq3d.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=566&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
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<span class="caption">Danielle Claar and a team member sample a tracked surviving colony at the end of the heat wave on Kiritimati (Christmas Island).</span>
<span class="attribution"><span class="source">(Julia K. Baum), Author provided.</span></span>
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<p>By the end of the heat wave, however, one of <em>Porites’</em> unique algal partners had been virtually eliminated. The survivors of all lineages had similar symbionts, suggesting specialized relationships between the partners had been lost under extreme temperatures. </p>
<p>Thus, not only was a cryptic coral lineage left teetering on the edge of local extinction, but its specialized symbiotic relationship had also been forcefully broken up.</p>
<h2>Implications for conserving coral reefs</h2>
<p>Due to climate change and other threats, we are currently experiencing a <a href="https://doi.org/10.1038/35002708">biodiversity crisis</a>. Our findings underscore that this crisis extends beyond what the eye can see.</p>
<p>Cryptic species often occupy <a href="https://doi.org/10.1111/1365-2664.12246">unique ecological niches and play specific roles within ecosystems</a>. Discovering these hidden differences can enhance our understanding of how ecosystems function. But worryingly, we may be losing this critical diversity before it is even discovered. </p>
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Read more:
<a href="https://theconversation.com/through-the-magnifying-glass-how-cutting-edge-technology-is-helping-scientists-understand-baby-corals-210372">Through the magnifying glass: how cutting-edge technology is helping scientists understand baby corals</a>
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<p>Continued study of cryptic diversity could prove essential to building climate resilient ecosystems. Using heat tolerant cryptic lineages in <a href="https://doi.org/10.3389/fmars.2020.00237">restoration approaches</a>, for example, could help make reefs more tolerant to future warming. </p>
<p>Ultimately, <a href="https://doi.org/10.1126/science.aaw6974">greenhouse gas emissions must be rapidly reduced to curb planetary warming</a>. While targeted efforts to bolster coral reefs against climate change may buy limited time, the current heat waves blanketing the world’s oceans underscore that the ocean is simply becoming too hot for corals and we need to act rapidly to mitigate the damage.</p><img src="https://counter.theconversation.com/content/211007/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Samuel Starko receives funding from the Forrest Research Foundation, The University of Western Australia, The Australian Research Council (ARC), and Revive & Restore.</span></em></p><p class="fine-print"><em><span>Julia K. Baum receives funding from the Natural Sciences and Engineering Research Council of Canada (NSERC), the U.S. National Science Foundation (NSF), the David and Lucile Packard Foundation, the Rufford Maurice Laing Foundation, the Canadian Foundation for Innovation, British Columbia Knowledge Development Fund, University of Victoria, The Pew Charitable Trusts, and the National Geographic Society.
</span></em></p>Exploring the often unseen, and poorly understood, nuances of diversity within coral reefs may prove essential for ensuring the long-term health of Earth’s oceans.Samuel Starko, Forrest Research Fellow, The University of Western AustraliaJulia K. Baum, Professor of Biology, University of VictoriaLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2072452023-06-08T15:50:57Z2023-06-08T15:50:57ZCrocodile’s ‘virgin birth’ is a first for science’s history books<figure><img src="https://images.theconversation.com/files/530871/original/file-20230608-29-dubp2y.jpg?ixlib=rb-1.1.0&rect=0%2C0%2C2872%2C1621&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/wildlife-crocodile-green-underwater-photography-open-2313030857">LuckyStep/Shutterstock </a></span></figcaption></figure><p>Stories of virgin births, where young are produced without fertilisation, have been told <a href="https://www.livescience.com/42187-miracle-birth-stories-beyond-jesus.html">throughout history</a>. Mars the ancient Roman god, Horus the ancient Egyptian god and Qi from ancient Chinese mythology were all born to virgins. But virgin births actually do happen in the natural world. </p>
<p>The first evidence of a <a href="https://royalsocietypublishing.org/doi/10.1098/rsbl.2023.0129">virgin birth in crocodiles</a> has been reported in a captive American crocodile, <em>Crocodylus acutus</em>, who was housed on her own for 16 years in a zoo in Costa Rica. She laid a clutch of 14 eggs, of which seven seemed viable and were artificially incubated. The eggs failed to hatch and the contents of six of them were indiscernible. But one contained a fully formed foetus, genetically identical to its mother, showing no evidence of input from any males. </p>
<p>This isn’t the first case of a virgin birth in the animal kingdom. Baby lizards, snakes, sharks and birds, including the <a href="https://www.allaboutbirds.org/news/parthenogenesis-in-california-condors-stuns-scientists/">California condor</a>, have all been documented hatching from unfertilised eggs. </p>
<h2>How do we explain virgin births?</h2>
<p>Species can reproduce either sexually, combining genetic material from two parents, or asexually. Our ancient ancestors were asexual and essentially made clones of themselves. Plants <a href="https://www.bbc.co.uk/bitesize/guides/zykp34j/revision/1">reproduce in a similar way</a>, including splitting, budding and fragmenting.</p>
<p>However, this produces lots of organisms that are genetically identical, and a lack of genetic variation means that individuals cannot adapt to changing conditions. If the environment is bad for one member of a species, it is bad for all, and could lead to extinction.</p>
<p>Sexual reproduction in species such as humans needs sperm to fertilise eggs and create an embryo. In terms of evolution, sexually reproducing species are thought of as being more advanced, as their offspring are genetically diverse, with unique gene combinations from their parents.</p>
<p>This diversity can be important if a species <a href="https://www.nhm.ac.uk/discover/what-is-natural-selection.html#:%7E:text=Natural%20selection%20is%20a%20mechanism,change%20and%20diverge%20over%20time">needs to adapt</a>. It also reduces <a href="https://www.bbcearth.com/news/what-are-the-effects-of-inbreeding">adverse genetic mutations</a>, which are often associated with inbreeding (when close relatives mate).</p>
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<img alt="American crocodile floating in a river in Costa Rica" src="https://images.theconversation.com/files/530874/original/file-20230608-15-n8rta6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/530874/original/file-20230608-15-n8rta6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/530874/original/file-20230608-15-n8rta6.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/530874/original/file-20230608-15-n8rta6.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/530874/original/file-20230608-15-n8rta6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/530874/original/file-20230608-15-n8rta6.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/530874/original/file-20230608-15-n8rta6.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
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<span class="caption">The virgin mother was an American crocodile like this one.</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/american-crocodile-floating-river-costa-rica-539288503">Uwe Bergwitz/Shutterstock</a></span>
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<p>Virgin births are a form of asexual reproduction as they do not require genetic information from sperm. But, unlike other forms of asexual reproduction, they need an egg. Unfertilised eggs are often produced by females – you may have had unfertilised eggs for breakfast this morning from a domestic hen – and if unfertilised eggs aren’t eaten, they eventually perish. But there’s an exception. Virgin births, known as <a href="https://www.livescience.com/9460-female-komodo-dragon-virgin-births.html">parthenogenesis</a>, happen when an unfertilised egg develops into an embryo. </p>
<p>It won’t necessarily be genetically identical to the mother though – this depends on how the egg cell develops. Parthenogenic young can be either full or half clones of the mother. Half clones are produced when embryonic cells split in half before multiplying. Full clones are created when an embryo multiples whole cells.</p>
<p>So half clones have even less genetic diversity than full clones. Not only do they lack the genetic diversity of organisms created in sexual reproduction but they only inherit half of their mother’s genetic diversity.</p>
<p>Some species, termed facultative parthenogens, alternate between sexual and asexual reproduction. They rely mainly on sexual reproduction, but can use asexual reproduction if necessary.</p>
<p>Virgin birth, which usually results in female offspring, is thought to be triggered in several situations. For example, when there aren’t many males around. This is often reported in captive animals, including the <a href="https://www.theguardian.com/science/2007/may/23/uknews.sciencenews">bonnethead shark</a>, where animals are kept in single-sex enclosures. </p>
<h2>Passing on genes</h2>
<p>Even when there are males around, females may still use parthenogenesis. For example, last year a female zebra shark hatched several young <a href="https://www.popsci.com/environment/shark-virgin-birth-shedd-aquarium/">with DNA that did not match any of the males</a> in the Chicago aquarium where she lived, baffling researchers. Perhaps the female simply didn’t fancy the males she lived with.</p>
<p>If environmental conditions are poor, asexual reproduction involves less effort than sexual reproduction, because the female doesn’t need to waste time and energy finding a mate. For example, <a href="https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1420-9101.1998.11060755.x">many cases of parthenogenesis</a> have been discovered in geckos, snakes and lizards that live in dry and harsh climates such as high altitudes.</p>
<p>Female animals can also reproduce asexually to take advantage of a favourable change in conditions. The spiny-cheek crayfish is native to the US but was introduced to Europe where the climate is more moderate. It invaded many European waterways by reproducing asexually. Although many invasive species are bigger and stronger than the locals, <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0020281">parthenogenesis is another factor</a> that can contribute to their success.</p>
<p>Genetic testing technology that can identify parthenogenesis more readily is helping researchers discover that more and more species are capable of virgin births. The revelation of parthenogenesis in the American crocodile suggests there is a common ancestral link between the <a href="https://www.britannica.com/animal/archosaur">archosaurs</a>, or ruling reptiles, which include dinosaurs, <a href="https://theconversation.com/fossil-study-brings-us-one-step-closer-to-revealing-how-flying-dinosaurs-took-flight-196086">pterosaurs</a> (flying reptiles), birds and crocodiles. As parthenogenesis occurs in the birds and crocodiles, it is possible that dinosaurs had virgin births too.</p>
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<p>The virgin mother crocodile is eerily reminiscent of a scene in Jurassic Park when scientists claim there is nothing to worry about, that they can control the park’s population by ensuring all the dinosaurs are born female, so there won’t be any young produced naturally.</p>
<p>But in the words of the film’s chaos theory expert, Dr Ian Malcolm (played by Jeff Goldblum): “life finds a way”.</p><img src="https://counter.theconversation.com/content/207245/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Louise Gentle works for Nottingham Trent University. </span></em></p>Virgin motherhood is no myth – sharks, birds and lizards can hatch from unfertilised eggs.Louise Gentle, Principal Lecturer in Wildlife Conservation, Nottingham Trent UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2005702023-02-23T19:20:26Z2023-02-23T19:20:26ZThe animals and plants that only exist in captivity – and why time is running out to restore them to the wild<figure><img src="https://images.theconversation.com/files/511958/original/file-20230223-16-qaypn5.jpg?ixlib=rb-1.1.0&rect=0%2C0%2C2400%2C1598&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">The Socorro dove (_Zenaida graysoni_) was confirmed to be extinct in the wild in 1981.</span> <span class="attribution"><a class="source" href="https://en.wikipedia.org/wiki/Socorro_dove#/media/File:Zenaida_graysoni_-_Socorrotaube_-_Wildfarbig_-_Deutscher_Kanarien-_und_Vogelz%C3%BCchterbund_(DKB)_-_Vogelbund_-_Johann_Alexi.jpg">Johann Alexi/Freigabe-Nachweis</a>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span></figcaption></figure><p>It was April in 1981 when a party of four camped for two days and nights on the forested slopes of Mount Evermann, the central peak of Socorro, a volcanic island in the Pacific some 400 kilometres southwest of Baja California, Mexico. Their fruitless search confirmed their suspicions: the <a href="https://www.iucnredlist.org/species/22690740/178409463">Socorro dove</a>, an endearingly tame bird unique to the island, had disappeared, eaten by the cats of Spanish colonists, pushed out by grazing sheep and shot from the sky by hunters.</p>
<p>But the species had not vanished. Fifty six years prior to this search, in 1925, 17 Socorro doves had been collected from the island and transported to a bird keeper in California in the US. Somehow, almost 100 years later, the descendants of these birds – the last Socorro doves on the planet – are still with us, distributed across captive facilities in Europe and North America.</p>
<p>It’s a strange liminal space: disappeared from the wild, yet not entirely extinct. And it’s one not peculiar to the Socorro dove. <a href="https://www.science.org/doi/10.1126/science.add2889">Our research</a> has confirmed that at least 33 animals and 39 plants no longer have wild populations, but survive under human care in places such as zoos, aquariums, botanic gardens and seed banks.</p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/511987/original/file-20230223-4215-pkp18l.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="A tall palm tree with feathery protrusions." src="https://images.theconversation.com/files/511987/original/file-20230223-4215-pkp18l.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/511987/original/file-20230223-4215-pkp18l.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=800&fit=crop&dpr=1 600w, https://images.theconversation.com/files/511987/original/file-20230223-4215-pkp18l.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=800&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/511987/original/file-20230223-4215-pkp18l.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=800&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/511987/original/file-20230223-4215-pkp18l.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=1005&fit=crop&dpr=1 754w, https://images.theconversation.com/files/511987/original/file-20230223-4215-pkp18l.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=1005&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/511987/original/file-20230223-4215-pkp18l.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=1005&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">The last known Tali palm in the wild.</span>
<span class="attribution"><a class="source" href="https://en.wikipedia.org/wiki/Corypha_taliera#/media/File:Corypha_taliera_Md_Sharif_Hossain_Sourav.jpg">Md Sharif Hossain Sourav</a>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span>
</figcaption>
</figure>
<p>These species are categorised as “extinct in the wild” under <a href="https://www.iucnredlist.org/">the IUCN Red List of Threatened Species</a>, the system conservation biologists use to evaluate and communicate extinction risk. It’s a diverse set that includes the <a href="https://www.inaturalist.org/guide_taxa/1395299">manicillo</a>, a relative of the peanut only found in Bolivia; the <a href="https://www.iucnredlist.org/species/38493/10118302">Tali palm</a> originally identified from a lone specimen on the campus of Dhaka University in Bangladesh; and a number of <a href="https://www.researchgate.net/publication/231906900_From_61_species_to_five_Endemic_tree_snails_of_the_Society_Islands_fall_prey_to_an_ill-judged_biological_control_programme">tree snails</a> from the remote Society Islands in the Pacific Ocean.</p>
<p>In one sense, here is something worth celebrating: a group that has given extinction the slip. But what does the future look like for these species? Human care will not preserve them indefinitely. On the contrary, the longer they spend in captivity the more they risk becoming inbred or losing the genetic diversity that helps them resist diseases and other threats. Eventually, outright extinction looms, especially if their populations are small.</p>
<h2>Life in captivity</h2>
<p>A quirk in the red list means that conservationists don’t systematically count the numbers of seeds, plants or animals in captivity or monitor any changes in their status in the same way we do for threatened species in the wild. An extinct in the wild species numbering in the thousands is indistinguishable from one represented by a handful of individuals. We have somehow contrived to ignore the extinction risk of the very group of species for which we are most responsible.</p>
<p>Our review of this group uncovered reasons to be concerned. For the most part, it seems that these populations were founded by a tiny number of individuals and would require large populations, ideally in the thousands, to best insure against future genetic deterioration and extinctions. Unfortunately, where known, most species are held in small numbers (in the hundreds or lower), and across a small number of institutions (fewer than eight in most cases).</p>
<p>There also tends to be a lack of coordinated planning across institutions and regions where the same species is held. This is especially true for plants, where it’s not always known how many collections exist and where they are. Fortunately, there have been recent efforts by botanical gardens to share data and collaborate more closely. Seed banks are also important facilities that can store threatened plants as seeds for many decades or even centuries. But most extinct in the wild plant species can’t easily be found in online databases that might allow conservationists in different regions to work on joint recovery programmes.</p>
<p>Conservationists, and society more widely, must do better. We know that outright extinction is a real threat. Of the 95 species that have found themselves extinct in the wild or restricted to human care since 1950, 11 have since been lost forever, like the <a href="https://www.iucnredlist.org/species/178595/101749951">Christmas Island whiptail-skink</a> and the <a href="https://www.iucnredlist.org/species/37598/67372241">Saint Helena
olive</a>, a tree endemic to the island of the same name in the southern Atlantic Ocean.</p>
<h2>Return to the wild</h2>
<p>Is there hope? Perhaps surprisingly, yes. The flip side to the 11 species we’ve lost is the 12 that have been restored to the wild. These include the European bison, which, having disappeared from the wild in 1927, is now thriving in its native range in Eastern Europe and Russia, thanks to reintroduction efforts starting in the 1950s using stock from European zoos.</p>
<p>Encouragingly, more should follow: two-thirds of extinct in the wild animals and just under a quarter of extinct in the wild plants have already been released back to natural habitats. These nascent populations may not yet have reached true “wild” status by, for example, producing viable young, but this is a promising start. They show that being Extinct in the Wild needn’t be a dead end: it can be a platform for long-term restoration.</p>
<p>But if this is the aim for all extinct in the wild species and others perched on the brink, there must be a transformation in the way they are regarded and resourced. Conservationists should continue to rescue species nearing extinction and care for them in captivity. But collectively, we must also commit to revitalising the precarious populations under our care, with more individuals in more institutions. </p>
<p>Where return to the wild is a challenge, we must redouble efforts to find and mitigate threats in native habitat, or explore whether populations can be set up in new areas. Continued care of these wild populations will probably be needed.</p>
<p>Extinction looms but recovery is achievable. Conservation biologists have the tools for success, but need the support and attention of decision makers, funders and the broader public to deliver it.</p>
<hr>
<figure class="align-right ">
<img alt="Imagine weekly climate newsletter" src="https://images.theconversation.com/files/434988/original/file-20211201-21-13avx6y.png?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/434988/original/file-20211201-21-13avx6y.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=600&fit=crop&dpr=1 600w, https://images.theconversation.com/files/434988/original/file-20211201-21-13avx6y.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=600&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/434988/original/file-20211201-21-13avx6y.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=600&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/434988/original/file-20211201-21-13avx6y.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=754&fit=crop&dpr=1 754w, https://images.theconversation.com/files/434988/original/file-20211201-21-13avx6y.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=754&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/434988/original/file-20211201-21-13avx6y.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=754&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption"></span>
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<p><strong><em>Don’t have time to read about climate change as much as you’d like?</em></strong>
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<p class="fine-print"><em><span>Donal Smith is affiliated with the Institute of Zoology, part of the Zoological Society of London (ZSL). ZSL operates two zoos, London Zoo and Whipsnade. The institute receives funding from Research England.</span></em></p><p class="fine-print"><em><span>Sarah Elizabeth Dalrymple is affiliated with the IUCN Species Survival Commission's Conservation Translocation Specialist Group. </span></em></p>Surviving solely in zoos and botanic gardens are 33 animal and 39 plant species.Donal Smith, Postdoctoral Researcher in Conservation, Zoological Society of LondonSarah Dalrymple, Senior Lecturer in Conservation Ecology, Liverpool John Moores UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1937072022-11-03T19:00:47Z2022-11-03T19:00:47ZA platypus can glow green and hunt prey with electricity – but it can’t climb dams to find a mate<figure><img src="https://images.theconversation.com/files/493180/original/file-20221103-20-i7d5kk.jpg?ixlib=rb-1.1.0&rect=0%2C559%2C5342%2C2902&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><span class="source">Shutterstock</span></span></figcaption></figure><p>The platypus is one of Earth’s most unique creatures. It sports a duck-like bill and flippers. It locates prey in murky water by emitting an electric charge. Males have venomous spurs on their legs, and the females lay eggs. And a platypus’ fur glows blue-green under UV light!</p>
<p>Sadly, however, this fascinating and irreplaceable animal is at risk of extinction. Among the human-caused threats are habitat loss, climate change, pollution and becoming prey for invasive species such as foxes and dogs. To that list, we can now add another threat: dams.</p>
<p><a href="https://www.nature.com/articles/s42003-022-04038-9">New research</a> by myself and colleagues, published today, found large river dams restrict platypus movements and separate communities. </p>
<p>This increases the risk of inbreeding and restricts the exchange of genes essential to maintaining healthy platypus populations.</p>
<figure class="align-center ">
<img alt="platypus swims through brown water" src="https://images.theconversation.com/files/493181/original/file-20221103-14-el8js4.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/493181/original/file-20221103-14-el8js4.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/493181/original/file-20221103-14-el8js4.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/493181/original/file-20221103-14-el8js4.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/493181/original/file-20221103-14-el8js4.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/493181/original/file-20221103-14-el8js4.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/493181/original/file-20221103-14-el8js4.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Research shows dams restrict platypus movements and separate communities.</span>
<span class="attribution"><span class="source">Shutterstock</span></span>
</figcaption>
</figure>
<h2>A spotlight on platypus genetics</h2>
<p>Dams pose a major threat to global freshwater biodiversity. In Australia, as many as 77% (383 out of 495) of major dams – those with walls higher than 10 metres – are in regions where platypuses are found.</p>
<p>Platypuses spend most of their time in the water. They can also move over land, however until now it was not certain if dams restrict platypus’ movement.</p>
<p>My colleagues and I set out to answer this question. We did this by examining the genetic makeup of platypuses in nine rivers in New South Wales and Victoria: five dammed and four free-flowing. They spanned the Upper Murray, Snowy Mountains, Central NSW and Border Rivers regions. </p>
<p>We captured platypuses across 81 sites. We weighed, measured, sexed and aged them, collected a blood sample then returned the animal to the water. DNA was later extracted from the blood. </p>
<p>So what did we find? Genetic differentiation between platypuses below and above dams was four to 20 times higher than along similar stretches of adjacent undammed rivers. This suggest hardly any platypuses have passed around the dams since they were built.</p>
<p>In fact, one platypus below the dam, and one platypus above the dam, were as genetically different as two platypuses living in different rivers. </p>
<p>Genetic differentiation is not necessarily good or bad. It just describes how genetically different two populations are. But the results mean we’re now far more confident that dams pose insurmountable barriers to platypuses.</p>
<p>Importantly, the genetic differentiation increased the longer the dam had been in place. This reflects the long-term impacts on platypus genetics.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/australias-next-government-must-tackle-our-collapsing-ecosystems-and-extinction-crisis-182048">Australia's next government must tackle our collapsing ecosystems and extinction crisis</a>
</strong>
</em>
</p>
<hr>
<figure class="align-center ">
<img alt="a dam wall" src="https://images.theconversation.com/files/493163/original/file-20221102-12-xwz79h.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/493163/original/file-20221102-12-xwz79h.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/493163/original/file-20221102-12-xwz79h.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/493163/original/file-20221102-12-xwz79h.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/493163/original/file-20221102-12-xwz79h.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/493163/original/file-20221102-12-xwz79h.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/493163/original/file-20221102-12-xwz79h.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">The results mean we’re now far more confident that dams pose insurmountable barriers to platypuses.</span>
<span class="attribution"><span class="source">Shutterstock</span></span>
</figcaption>
</figure>
<h2>What does all this mean?</h2>
<p>There a several downsides for a species when populations are unable to connect. </p>
<p>First, it restricts the ability for animals to move to new habitat if needed, and find individuals to reproduce with.</p>
<p>Second, it reduces population size and gene flow. This is likely to lead to increased inbreeding and a reduction in the genetic variation necessary for the species to adapt to threats. </p>
<p>Third, it can lead to “inbreeding depression” – the reduced survival and fertility of offspring of related individuals.</p>
<p>The platypus is currently listed as near threatened by the International Union for Conservation of Nature. It’s also listed as endangered in South Australia and vulnerable in Victoria.</p>
<p>Continued declines are predicted under climate change as a result of drought and hotter conditions, which could mean <a href="https://doi.org/10.1111/j.1365-2486.2011.02472.x">more than 30%</a> of suitable platypus habitat is lost by 2070.</p>
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<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/how-to-ensure-the-worlds-largest-pumped-hydro-dam-isnt-a-disaster-for-queenslands-environment-191758">How to ensure the world's largest pumped-hydro dam isn't a disaster for Queensland's environment</a>
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</em>
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<hr>
<figure class="align-center ">
<img alt="platypus swims through tropical river" src="https://images.theconversation.com/files/493162/original/file-20221102-20-pgaf8v.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/493162/original/file-20221102-20-pgaf8v.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=374&fit=crop&dpr=1 600w, https://images.theconversation.com/files/493162/original/file-20221102-20-pgaf8v.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=374&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/493162/original/file-20221102-20-pgaf8v.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=374&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/493162/original/file-20221102-20-pgaf8v.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=470&fit=crop&dpr=1 754w, https://images.theconversation.com/files/493162/original/file-20221102-20-pgaf8v.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=470&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/493162/original/file-20221102-20-pgaf8v.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=470&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Climate change could mean more than 30% of platypus habitat is lost by 2070.</span>
<span class="attribution"><span class="source">Shutterstock</span></span>
</figcaption>
</figure>
<p>So how can we protect the platypus? There are many steps we could take, such as:</p>
<ul>
<li><p>rehabilitating riverbanks by replanting trees and restricting livestock access</p></li>
<li><p>improving water quality and natural flow regimes in rivers</p></li>
<li><p>limiting dams, roads, weirs and other structures </p></li>
<li><p>building bypasses so platypuses can move across barriers</p></li>
<li><p>protecting platypuses from invasive predators when they move over land</p></li>
<li><p>reducing river pollution</p></li>
<li><p>establishing insurance populations to ensure genetic diversity</p></li>
<li><p>relocating individuals</p></li>
<li><p>more research to understand breeding requirements.</p></li>
</ul>
<figure class="align-center ">
<img alt="platypus clambers over rocks" src="https://images.theconversation.com/files/493170/original/file-20221102-12-vzhx54.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/493170/original/file-20221102-12-vzhx54.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=421&fit=crop&dpr=1 600w, https://images.theconversation.com/files/493170/original/file-20221102-12-vzhx54.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=421&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/493170/original/file-20221102-12-vzhx54.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=421&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/493170/original/file-20221102-12-vzhx54.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=529&fit=crop&dpr=1 754w, https://images.theconversation.com/files/493170/original/file-20221102-12-vzhx54.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=529&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/493170/original/file-20221102-12-vzhx54.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=529&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Limiting dams and other barriers would help protect platypuses.</span>
<span class="attribution"><span class="source">Shutterstock</span></span>
</figcaption>
</figure>
<h2>Platypus, be dammed</h2>
<p>Our results reinforce growing evidence that major dams contribute to a decline in platypus populations. </p>
<p>The problem extends beyond that identified in our study. Below major dams, altered natural flow regimes in rivers have been found to significantly impact the abundance of platypuses. And research has found conditions below and above major dams are poor for platypuses to forage and live.</p>
<p>We hope our research will inform conservation decision-making, and will help ensure the long-term survival of this Australian icon.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/money-for-dams-dries-up-as-good-water-management-finally-makes-it-into-a-federal-budget-193380">Money for dams dries up as good water management finally makes it into a federal budget</a>
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<img src="https://counter.theconversation.com/content/193707/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Luis Mijangos receives funding from UNSW Canberra, Australian Research Council, Taronga Conservation Society, and the Australian Government’s Environmental Water Holder.</span></em></p>Dams prevent platypus movements, which restricts the exchange of genes essential to maintaining healthy populations.Luis Mijangos, Researcher, Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, University of CanberraLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1907132022-09-15T18:01:59Z2022-09-15T18:01:59ZHumans evolved with their microbiomes – like genes, your gut microbes pass from one generation to the next<figure><img src="https://images.theconversation.com/files/484929/original/file-20220915-17-nhg34h.jpg?ixlib=rb-1.1.0&rect=0%2C0%2C3840%2C2155&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">The gut microbiome may also play a role in personalized medicine.</span> <span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/photo/bacteria-lactobacillus-in-human-intestine-royalty-free-image/1338810328">nopparit/iStock via Getty Images Plus</a></span></figcaption></figure><p>When the first humans moved out of Africa, they carried their gut microbes with them. Turns out, these microbes also evolved along with them.</p>
<p>The <a href="https://doi.org/10.1146/annurev-micro-090110-102830">human gut microbiome</a> is made up of hundreds to thousands of species of bacteria and <a href="https://microbiologysociety.org/why-microbiology-matters/what-is-microbiology/archaea.html">archaea</a>. Within a given species of microbe, different strains carry different genes that can <a href="https://doi.org/10.1016/j.chom.2022.08.009">affect your health and the diseases you’re susceptible to</a>. </p>
<p>There is <a href="https://doi.org/10.1016/j.cell.2019.01.001">pronounced variation</a> in the microbial composition and diversity of the gut microbiome between people living in different countries around the world. Although researchers are starting to understand what factors affect microbiome composition, such as diet, there is still limited understanding on why different groups have different strains of the same species of microbes in their guts. </p>
<p>We are researchers who study <a href="https://scholar.google.com/citations?user=KEmIhncAAAAJ&hl=en">microbial evolution</a> and <a href="https://scholar.google.com/citations?user=up7dycYAAAAJ&hl=en">microbiomes</a>. Our <a href="https://www.science.org/doi/10.1126/science.abm7759">recently published study</a> found that not only did microbes diversify with their early modern human hosts as they traveled across the globe, they followed human evolution by restricting themselves to life in the gut.</p>
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<figcaption><span class="caption">The gut microbiome plays a key role in many areas of your health.</span></figcaption>
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<h2>Microbes share evolutionary history with humans</h2>
<p>We hypothesized that as humans fanned out across the globe and diversified genetically, so did the microbial species in their guts. In other words, gut microbes and their human hosts “codiversified” and evolved together – just as human beings diversified so that people in Asia look different from people in Europe, so too did their microbiomes.</p>
<p>To assess this, we needed to pair human genome and microbiome data from people around the world. However, data sets that provided both the microbiome data and genome information for individuals were limited when we started this study. Most publicly available data was from North America and Western Europe, and we needed data that was more representative of populations around the world. </p>
<p>So our research team used existing data from Cameroon, South Korea and the United Kingdom, and additionally recruited mothers and their young children in Gabon, Vietnam and Germany. We collected saliva samples from the adults to ascertain their genotype, or genetic characteristics, and fecal samples to sequence the genomes of their gut microbes.</p>
<p>For our analysis, we used data from 839 adults and 386 children. To assess the evolutionary histories of humans and gut microbes, we created <a href="https://www.khanacademy.org/science/ap-biology/natural-selection/phylogeny/a/phylogenetic-trees">phylogenetic trees</a> for each person and as well as for 59 strains of the most commonly shared microbial species.</p>
<p>When we compared the human trees to the microbial trees, we discovered a gradient of how well they matched. Some bacterial trees didn’t match the human trees at all, while some matched very well, indicating that these species codiversified with humans. Some microbial species, in fact, have been along for the evolutionary ride for over hundreds of thousands of years. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/484917/original/file-20220915-26-syoolq.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Two phylogenetic trees comparing human genetic diversity across geographic regions to the genetic diversity of _Collinsella aerofaciens_" src="https://images.theconversation.com/files/484917/original/file-20220915-26-syoolq.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/484917/original/file-20220915-26-syoolq.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=273&fit=crop&dpr=1 600w, https://images.theconversation.com/files/484917/original/file-20220915-26-syoolq.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=273&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/484917/original/file-20220915-26-syoolq.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=273&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/484917/original/file-20220915-26-syoolq.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=344&fit=crop&dpr=1 754w, https://images.theconversation.com/files/484917/original/file-20220915-26-syoolq.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=344&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/484917/original/file-20220915-26-syoolq.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=344&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">These two phylogenetic trees of human participants (left) and one bacterial species (right) closely match, indicating that they likely diversified together over the course of evolution.</span>
<span class="attribution"><a class="source" href="http://www.doi.org/10.1126/science.abm7759">Reprinted with permission from Suzuki et al., Science Volume 377, abm7759 (2022)</a>, <a class="license" href="http://creativecommons.org/licenses/by-nc-nd/4.0/">CC BY-NC-ND</a></span>
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<p>We also found that microbes that evolved in tandem with people have a unique set of genes and traits compared with microbes that had not codiversified with people. Microbes that partnered up with humans have smaller genomes and greater oxygen and temperature sensitivity, mostly unable to tolerate conditions below human body temperature.</p>
<p>In contrast, gut microbes with weaker ties to human evolution have traits and genes characteristic of free-living bacteria in the external environment. This finding suggests that codiversified microbes are very much dependent on the environmental conditions of the human body and must be transmitted quickly from one person to the next, either passed down generationally or between people living in the same communities. </p>
<p>Confirming this mode of transmission, we found that mothers and their children had the same strains of microbes in their guts. Microbes that were not codiversified, in contrast, were more likely to survive well outside of the body and may be transmitted more widely through water and soil.</p>
<h2>Gut microbes and personalized medicine</h2>
<p>Our discovery that gut microbes evolved right along with their human hosts offers another way to view the human gut microbiome. Gut microbes have passed between people over hundreds to thousands of generations, such that <a href="https://doi.org/10.1126/science.aaz6827">as humans changed, so did their gut microbes</a>. As a result, some gut microbes behave as though they are part of the human genome: They are packages of genes that are passed between generations and shared by related individuals.</p>
<p><a href="https://www.genome.gov/genetics-glossary/Personalized-Medicine">Personalized medicine</a> and genetic testing are starting to make treatments more specific and effective for the individual. Knowing which microbes have had long-term partnerships with people may help researchers develop microbiome-based treatments specific to each population. Clinicians are already using <a href="https://doi.org/10.1126/scitranslmed.abk1107">locally sourced probiotics</a> derived from the gut microbes of community members to treat malnutrition.</p>
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<a href="https://images.theconversation.com/files/484949/original/file-20220915-19-qzu5f6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Illustration of gut bacteria on intestinal villi." src="https://images.theconversation.com/files/484949/original/file-20220915-19-qzu5f6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/484949/original/file-20220915-19-qzu5f6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=338&fit=crop&dpr=1 600w, https://images.theconversation.com/files/484949/original/file-20220915-19-qzu5f6.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=338&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/484949/original/file-20220915-19-qzu5f6.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=338&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/484949/original/file-20220915-19-qzu5f6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=424&fit=crop&dpr=1 754w, https://images.theconversation.com/files/484949/original/file-20220915-19-qzu5f6.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=424&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/484949/original/file-20220915-19-qzu5f6.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=424&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Gut bacteria could be used to help treat various diseases and conditions.</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/photo/gut-bacteria-probiotics-royalty-free-image/1325237120">Artur Plawgo/iStock via Getty Images Plus</a></span>
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<p>Our findings also help scientists better understand how microbes transition ecologically and evolutionarily from “free-living” in the environment to dependent on the conditions of the human gut. Codiversified microbes have traits and genes <a href="https://doi.org/10.1146/annurev.genet.41.110306.130119">reminiscent of bacterial symbionts</a> that live inside insect hosts. These shared features suggest that other animal hosts may also have gut microbes that codiversified with them over evolution.</p>
<p>Paying special attention to the microbes that share human evolutionary history can help improve understanding of the role they play in human well-being.</p><img src="https://counter.theconversation.com/content/190713/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>The authors do not work for, consult, own shares in or receive funding from any company or organization that would benefit from this article, and have disclosed no relevant affiliations beyond their academic appointment.</span></em></p>As early modern humans spread across the globe, their gut microbes genetically changed with them. Understanding the origins of gut microbes could improve understanding of their role in human health.Taichi A. Suzuki, Postdoctoral Research Associate in Microbiome Science, Max Planck Institute for BiologyRuth Ley, Director, Department of Microbiome Science, Max Planck Institute for BiologyLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1859972022-09-12T12:15:12Z2022-09-12T12:15:12ZUncovering the genetic basis of mental illness requires data and tools that aren’t just based on white people – this international team is collecting DNA samples around the globe<figure><img src="https://images.theconversation.com/files/483545/original/file-20220908-9329-hl0h3j.jpg?ixlib=rb-1.1.0&rect=0%2C0%2C2419%2C1238&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Ethical and equitable scientific collaboration could help increase the genetic diversity of genomic data.</span> <span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/illustration/scientists-on-world-map-discussing-during-royalty-free-illustration/1322363700">gmast3r/iStock via Getty Images Plus</a></span></figcaption></figure><p>Mental illness is a growing public health problem. In 2019, an estimated <a href="https://www.who.int/news-room/fact-sheets/detail/mental-disorders">1 in 8 people around the world</a> were affected by mental disorders like depression, schizophrenia or bipolar disorder. While scientists have long known that many of these disorders run in families, their genetic basis isn’t entirely clear. One reason why is that the majority of existing genetic data used in research is overwhelmingly from white people.</p>
<p>In 2003, the Human Genome Project generated the first “reference genome” of human DNA from a combination of samples donated by <a href="https://www.statnews.com/2019/03/11/human-reference-genome-shortcomings/">upstate New Yorkers</a>, all of whom were of European ancestry. Researchers across many biomedical fields still use this reference genome in their work. But it doesn’t provide a complete picture of human genetics. Someone with a different genetic ancestry will have a number of <a href="https://www.yourgenome.org/facts/what-is-genetic-variation/">variations</a> in their DNA that aren’t captured by the reference sequence. </p>
<p>When most of the world’s ancestries are not represented in genomic data sets, studies won’t be able to provide a true representation of how diseases manifest across all of humanity. Despite this, ancestral diversity in genetic analyses hasn’t improved in the two decades since the Human Genome Project announced its first results. As of June 2021, <a href="https://doi.org/10.1038/s41591-021-01672-4">over 80%</a> of genetic studies have been conducted on people of European descent. Less than 2% have included people of African descent, even though these individuals have the <a href="https://doi.org/10.1073/pnas.1017511108">most genetic variation</a> of all human populations.</p>
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<p>To uncover the <a href="https://doi.org/10.1038/s41586-022-04556-w">genetic factors</a> driving mental illness, <a href="https://scholar.google.com/citations?user=lWu2u8kAAAAJ&hl=en">I</a>, <a href="https://scholar.google.com/citations?view_op=list_works&hl=en&hl=en&user=iS0IoKgAAAAJ&sortby=pubdate">Sinéad Chapman</a> and our colleagues at the Broad Institute of MIT and Harvard have partnered with collaborators around the world to launch <a href="https://www.broadinstitute.org/stanley-center-psychiatric-research/stanley-global">Stanley Global</a>, an initiative that seeks to collect a more diverse range of genetic samples from beyond the U.S. and Northern Europe, and train the <a href="https://doi.org/10.1038/s41588-022-01095-y">next generation of researchers</a> around the world. Not only does the genetic data lack diversity, but so do the tools and techniques scientists use to sequence and analyze human genomes. So we are implementing a new sequencing technology that addresses the inadequacies of previous approaches that don’t account for the genetic diversity of global populations.</p>
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<figcaption><span class="caption">Ethically and equitably expanding the diversity of genomics data can help improve care and reduce disparities.</span></figcaption>
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<h2>Global partnerships for global data</h2>
<p>To study the genetics of psychiatric conditions, researchers use data from <a href="https://www.genome.gov/about-genomics/fact-sheets/Genome-Wide-Association-Studies-Fact-Sheet">genome-wide association studies</a> that compare the genetic variations between people with and without a particular disease. However, these data sets are mostly <a href="https://doi.org/10.1038/s41591-021-01672-4">based on people of European ancestry</a>, largely because research infrastructure and funding for large-scale genetics studies, and the scientists conducting these studies, have historically been concentrated in Europe and the United States.</p>
<p>One way to close this gap is to sequence genetic data from diverse populations. My colleagues and I are working in close partnership with geneticists, statisticians and epidemiologists in 14 countries across four continents to study the DNA of tens of thousands of people of African, Asian and Latino ancestries who are affected by mental illness. We work together to recruit participants and collect DNA samples that are sequenced at the Broad Institute in Massachusetts and shared with all partners for analysis.</p>
<p><iframe id="ZIVeg" class="tc-infographic-datawrapper" src="https://datawrapper.dwcdn.net/ZIVeg/4/" height="400px" width="100%" style="border: none" frameborder="0"></iframe></p>
<p><a href="https://doi.org/10.1038/d41586-021-01795-1">Prioritizing the voices and priorities</a> of local communities and scientists is foundational to our work. All partners have joint ownership of the project, including decision-making and sample and data ownership and control. To do this, we build relationships and trust with the local communities we are studying and the local university leaders and scientists with whom we are partnering. We work to understand local cultures and practices, and adapt our collection methods to ensure study participants are comfortable. For example, because there are different cultural sensitivities around providing saliva and blood samples, we have adapted our practices by location to ensure study participants are comfortable.</p>
<p>We also freely share knowledge and materials with our partners. There is a two-way exchange of information between the Broad Institute and local teams on study progress and results, enabling continual learning, teaching and unity between teams. We strive to meet each other where we are by exchanging practices and training scientists to support the development of locally grown and locally led research programs.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/474777/original/file-20220719-18-mu7fdh.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Researchers in the GINGER program looking at laptop together and smiling" src="https://images.theconversation.com/files/474777/original/file-20220719-18-mu7fdh.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/474777/original/file-20220719-18-mu7fdh.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=454&fit=crop&dpr=1 600w, https://images.theconversation.com/files/474777/original/file-20220719-18-mu7fdh.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=454&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/474777/original/file-20220719-18-mu7fdh.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=454&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/474777/original/file-20220719-18-mu7fdh.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=570&fit=crop&dpr=1 754w, https://images.theconversation.com/files/474777/original/file-20220719-18-mu7fdh.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=570&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/474777/original/file-20220719-18-mu7fdh.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=570&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
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<span class="caption">The Global Initiative for Neuropsychiatric Genetics Education in Research (GINGER) program is focused on training the next generation of scientists.</span>
<span class="attribution"><a class="source" href="https://gingerprogram.org/">Global Initiative for Neuropsychiatric Genetics Education in Research</a>, <a class="license" href="http://creativecommons.org/licenses/by-nc-nd/4.0/">CC BY-NC-ND</a></span>
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<p>Our collaboration with African research groups provides a prime example of <a href="https://doi.org/10.1038/s41588-022-01095-y">our model</a>. For example, our African research colleagues are co-leaders on the grants that fund the lab equipment, scientists and other staff for projects based at their study sites. And we help to support the next generation of African geneticists and bioinformaticians through a <a href="https://www.broadinstitute.org/stanley-center-psychiatric-research/neurogap/global-initiative-neuropsychiatric-genetics-education-research-ginger">dedicated training program</a>.</p>
<h2>Analyzing variation</h2>
<p>Collecting samples from more diverse populations is only half of the challenge. </p>
<p>Existing genomic sequencing and analysis technologies do not adequately capture genetic variation across populations from around the world. That’s because these technologies were designed to detect genetic variations based on reference DNA from people of European ancestry, and they <a href="https://doi.org/10.1126/science.abg8871">reduce accuracy</a> when analyzing sequences that aren’t derived from the reference genome. When these tools are applied to genetic data from other populations, they <a href="https://doi.org/10.1016/j.ajhg.2021.03.012">fail to detect much of the rich variation</a> in their genomes. This can lead researchers to miss out on important biomedical discoveries. </p>
<p>To address this issue, we developed an approach to genome sequencing that can detect more genetic variation from populations around the world. It works by sequencing the <a href="https://www.genome.gov/genetics-glossary/Exome">exome</a> – the less than 2% of the genome that codes for proteins – in high detail, as well as sequencing the 98% of the genome that does not code for proteins in less detail.</p>
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<iframe width="440" height="260" src="https://www.youtube.com/embed/gDdoGcGS014?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">Different types of sequencing methods have pros and cons.</span></figcaption>
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<p>This combined approach reduces the trade-offs geneticists often have to make in sequencing projects. <a href="https://medlineplus.gov/genetics/understanding/testing/sequencing/">High-depth whole genome sequencing</a>, which reads through the entire genome multiple times to get detailed data, is too costly to do on a large number of DNA samples. While <a href="https://www.cancer.gov/about-nci/organization/ccg/blog/2019/low-coverage-seq">low-coverage sequencing</a> reduces costs by reading smaller segments of the genome, it may miss some important genetic variation. With our new technology, geneticists can get the best of both worlds: <a href="https://www.broadinstitute.org/blog/what-exome-sequencing">sequencing the exome in depth</a> maximizes the likelihood of pinpointing <a href="https://doi.org/10.1038/s41586-022-04556-w">specific genes</a> that play a role in mental illness, while <a href="https://doi.org/10.1016%2Fj.ajhg.2021.03.012">sequencing the whole genome less in depth</a> allows researchers to process large numbers of whole genomes more cost-effectively.</p>
<h2>Personalizing medicine</h2>
<p>Our hope is that this new technology will allow researchers to sequence large sample sizes from a diverse range of ancestries to capture the full breadth of genetic variation. With a better understanding of the genetics of mental illness, clinicians and researchers will be better equipped to develop new treatments that work for everyone. </p>
<p>Genomic sequencing opened a new era of <a href="https://doi.org/10.1377%2Fhlthaff.2017.1624">personalized medicine</a>, which promises to deliver treatments tailored to each individual person. This can be done only if the genetic variations of all ancestries are represented in the data sets that researchers use to make new discoveries about disease and develop treatments.</p><img src="https://counter.theconversation.com/content/185997/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Hailiang Huang receives funding from the National Institutes of Health and the Brain & Behavior Research Foundation. He is a member of the board of directors with the International Society of Psychiatric Genetics.</span></em></p>Existing genetic data and sequencing tools are overwhelmingly based on people of European ancestry, which excludes much of the rich genetic variation of the world.Hailiang Huang, Assistant Professor of Medicine, Harvard UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1306362022-02-16T13:15:35Z2022-02-16T13:15:35ZAfrican wild dogs cope with human development using skills they rely on to compete with other carnivores<figure><img src="https://images.theconversation.com/files/446628/original/file-20220215-27-1h2k3xj.jpg?ixlib=rb-1.1.0&rect=782%2C684%2C3566%2C2353&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Wild dogs are usually with their pack mates.</span> <span class="attribution"><span class="source">Scott Creel</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span></figcaption></figure><p>Large carnivores in Africa are important from ecological, economic and cultural perspectives, but human activities put them at risk. Increasingly, lions, hyenas and African wild dogs are restricted to protected areas like national parks. Within these limited areas, they must compete for the same food sources.</p>
<p>Competition is, of course, nothing new. For several million years, African wild dogs have evolved within a set of large carnivores that all prey on the same large herbivore species, like wildebeest and warthogs. Wild dogs are lanky, long-distance hunters that always live in groups, usually of eight to 10 adults. Cooperation with pack mates allows them to hunt prey much larger than themselves. Weighing in at about 40-62 pounds (18-28 kilograms), wild dogs have been shaped by the necessity to compete with larger species like the lion and spotted hyena.</p>
<p>There may be a silver lining to being the bottom dog in the competitive hierarchy. Research that my <a href="https://scholar.google.com/citations?user=IiQjBP8AAAAJ&hl=en&oi=ao">colleagues with the Zambian Carnivore Programme</a> <a href="https://scholar.google.com/citations?user=IBEIw1QAAAAJ&hl=en&oi=ao">and I</a> have conducted in Zambia and Tanzania suggests why smaller, subordinate species like wild dogs are better able to move through human-modified landscapes. Understanding how is essential for their conservation.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/446658/original/file-20220215-24208-dkqqwr.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Four African wild dogs around a kill" src="https://images.theconversation.com/files/446658/original/file-20220215-24208-dkqqwr.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/446658/original/file-20220215-24208-dkqqwr.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/446658/original/file-20220215-24208-dkqqwr.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/446658/original/file-20220215-24208-dkqqwr.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/446658/original/file-20220215-24208-dkqqwr.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/446658/original/file-20220215-24208-dkqqwr.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/446658/original/file-20220215-24208-dkqqwr.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">A pack of African wild dogs makes a formidable hunting team.</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/photo/african-wild-dog-lycaon-pictus-herd-on-a-kill-a-royalty-free-image/1255884159">slowmotiongli/iStock via Getty Images Plus</a></span>
</figcaption>
</figure>
<h2>Meeting the African wild dog</h2>
<p>In the late 1980s, I was studying dwarf mongooses in Tanzania’s Serengeti National Park when an extraordinary thing happened. While I sat on the roof of an ancient Land Rover watching mongooses on a nearby termite mound, a wild dog trotted past. And then another, and another. Wild dogs had been missing from most (perhaps all) of the Serengeti for years due to a combination of intense competition from larger carnivores and outbreaks of rabies. But here they were, back again.</p>
<p>Over the next year, I occasionally followed the dogs to watch them hunt on the shortgrass plains, where they were <a href="https://doi.org/10.1006/anbe.1993.1059">constantly shadowed by spotted hyenas</a>. Several hyenas often trailed the dogs even as they set out to hunt, and hyenas quickly aggregated when the dogs killed a gazelle or wildebeest – often alerted by the unmistakable sound of vultures plummeting through the air in their own race to the fresh carcass. </p>
<p>Although they are half the size, wild dogs do not easily give up a kill to hyenas. A pack of wild dogs making a coordinated attack on one or two hyenas can easily drive them off. But hyenas are also social animals, and researchers found that the <a href="https://doi.org/10.1006/anbe.1993.1059">dogs generally lost their kills to hyenas</a> when their numbers were equal. Given the large population of hyenas in Serengeti, they took nine out of 10 kills that the dogs made. And lions are simply too dangerous to fight, so the big cats could always take over a kill from the dogs, and kill them surprisingly often. </p>
<p>At that time, very little was known about wild dogs in places other than Serengeti and South Africa’s Kruger National Park, a more wooded ecosystem where researchers had found a flourishing population that <a href="https://doi.org/10.1644/05-MAMM-A-304R2.1">often hunted impala</a>. Biologists started to rethink the prevailing view that wild dogs were specialized to live and hunt in open grasslands.</p>
<p>My colleagues and I spent six years in the 1990s observing wild dogs in the Selous Game Reserve, confirming the Tanzania Wildlife Department’s belief that this large ecosystem was a major stronghold for the species. We found that the density of wild dogs in Selous was very good, at least partly because <a href="https://doi.org/10.1046/j.1523-1739.1996.10020526.x">wild dogs were better able to avoid problems</a> with lions and spotted hyenas in the miombo woodland of Selous than in plains of the Serengeti. It was more evidence that not only could they survive outside of grasslands like in the Serengeti, but African wild dogs found advantages to other kinds of environments.</p>
<p>By the mid-1990s, a scientific consensus was emerging that the persistence of wild dogs in an area depends at least partly on their ability to avoid losing food to hyenas or being killed by lions.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/446660/original/file-20220215-13-1cwgtpf.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="African wild dog pack on the edge of a paved road" src="https://images.theconversation.com/files/446660/original/file-20220215-13-1cwgtpf.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/446660/original/file-20220215-13-1cwgtpf.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/446660/original/file-20220215-13-1cwgtpf.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/446660/original/file-20220215-13-1cwgtpf.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/446660/original/file-20220215-13-1cwgtpf.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/446660/original/file-20220215-13-1cwgtpf.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/446660/original/file-20220215-13-1cwgtpf.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">African wild dogs have been less separated by human development, like roads, than some other large carnivores.</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/photo/pack-of-african-wild-dogs-on-the-road-royalty-free-image/669588630">Simoneemanphotography/iStock via Getty Images Plus</a></span>
</figcaption>
</figure>
<h2>Being bottom dog can pay off</h2>
<p>Many studies, including our current research in Zambia, have confirmed that <a href="https://doi.org/10.1111/1365-2656.12231">wild dogs are adapted to “live in the cracks”</a> of a landscape where they are outnumbered and outsized by spotted hyenas and lions.</p>
<p>In the short term, wild dogs move quickly away from an encounter with lions – or an experimental playback of their roars over a loudspeaker – in a straight line that would be unusual under other circumstances. Over the long term, wild dogs avoid areas that are heavily used by larger competitors, even though this requires them to <a href="https://conbio.onlinelibrary.wiley.com/doi/full/10.1046/j.1523-1739.1997.96252.x">hunt in areas with fewer prey</a>.</p>
<p>But there may be a benefit to being at the bottom of the competitive hierarchy. Compared to most species, all of the large African carnivores live in small and isolated populations that <a href="https://conbio.onlinelibrary.wiley.com/doi/full/10.1046/j.1523-1739.1999.98366.x">must remain connected</a> to maintain genetic diversity. But humans have now modified <a href="https://doi.org/10.1038/ncomms12558">more than half of the Earth’s terrestrial surface</a>, cutting lines of movement and increasing the isolation of protected areas. Despite this general pattern, some species are better adapted than others to maintain connections between ecosystems. </p>
<p>Our research has used advances in genetic sequencing to test how well connected wild dogs and lions are in several ecosystems across Zambia and Tanzania. The basic idea is that well-connected populations remain genetically similar, but poorly connected populations become genetically distinct from one another over time.</p>
<p>We wondered whether the adaptations of wild dogs that allow them to move through a landscape dominated by lions and hyenas might <a href="https://doi.org/10.1038/s41598-019-52904-0">also help them move through a landscape altered by humans</a>. For example, wild dogs could move more quickly and in a straighter line after an encounter with people, just as they do after an encounter with lions. We hypothesized that genetic data would show that wild dogs have stronger connections between ecosystems than lions, and that their connections are less affected by humans.</p>
<p>And this is <a href="https://doi.org/10.1038/s41598-019-52904-0">just what the data showed</a> when we compared the genotypes of 96 wild dogs and, separately, 208 lions. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/446350/original/file-20220214-25-qsmcdz.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="map of where dogs were living and their genetic similarity" src="https://images.theconversation.com/files/446350/original/file-20220214-25-qsmcdz.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/446350/original/file-20220214-25-qsmcdz.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=370&fit=crop&dpr=1 600w, https://images.theconversation.com/files/446350/original/file-20220214-25-qsmcdz.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=370&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/446350/original/file-20220214-25-qsmcdz.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=370&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/446350/original/file-20220214-25-qsmcdz.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=465&fit=crop&dpr=1 754w, https://images.theconversation.com/files/446350/original/file-20220214-25-qsmcdz.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=465&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/446350/original/file-20220214-25-qsmcdz.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=465&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Each dot represents an individual wild dog, and similarity in their color represents genetic similarity.</span>
<span class="attribution"><span class="source">Scott Creel</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>Wild dogs in eastern, central and western Zambia were genetically quite similar, showing that these populations remain well connected. In contrast, lions were much less genetically similar, with distinct populations that were not well connected.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/446351/original/file-20220214-23-6h14xf.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="map of where lions were living and their genetic similarity" src="https://images.theconversation.com/files/446351/original/file-20220214-23-6h14xf.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/446351/original/file-20220214-23-6h14xf.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=418&fit=crop&dpr=1 600w, https://images.theconversation.com/files/446351/original/file-20220214-23-6h14xf.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=418&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/446351/original/file-20220214-23-6h14xf.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=418&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/446351/original/file-20220214-23-6h14xf.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=526&fit=crop&dpr=1 754w, https://images.theconversation.com/files/446351/original/file-20220214-23-6h14xf.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=526&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/446351/original/file-20220214-23-6h14xf.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=526&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Each dot represents an individual lion, and similarity in their color represents genetic similarity.</span>
<span class="attribution"><span class="source">Scott Creel</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>We also mapped the degree to which human effects such as land conversion, agriculture and roads hinder animal movement, differentiating between areas with relatively little resistance to animal movement and areas with strong human effects. The genetic differences between lion populations were strongly correlated with human resistance, but there was no such correlation for wild dogs. That is, places that were less hospitable to animal movement had more genetically isolated populations of lions, but didn’t affect the genetic diversity of the wild dogs in the area.</p>
<p>While it is still too early to know if this pattern will apply to other species, it suggests that eons of dealing with lions and hyenas have provided the wild dog with tools that help them maneuver through the unforgiving landscapes that humans create outside of national parks.</p>
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<p class="fine-print"><em><span>Scott Creel received funding from the US National Science Foundation and the Wallenberg Foundation.</span></em></p>African wild dogs are used to evading hyenas and lions. Genetic research suggests they are using the same strengths to get around human development as well.Scott Creel, Professor of Conservation Biology & Ecology, Montana State UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1663972021-11-23T13:30:30Z2021-11-23T13:30:30ZScientist at work: Endangered ocelots and their genetic diversity may benefit from artificial insemination<figure><img src="https://images.theconversation.com/files/432290/original/file-20211116-25-1e4gv3m.jpg?ixlib=rb-1.1.0&rect=1384%2C1010%2C3607%2C2267&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Wild ocelots hunt alone at night.</span> <span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/news-photo/ocelot-is-hunting-at-night-at-the-san-francisco-ranch-in-news-photo/1219080513">Wolfgang Kaehler/LightRocket via Getty Images</a></span></figcaption></figure><p>The female ocelot lay anesthetized on the exam table, behind the scenes at the Albuquerque Biopark Zoo. As a veterinarian on the team preparing to artificially inseminate this animal, my palms were sweating at the thought of missing a step, dropping the sperm sample, or finding out our sample did not survive freezing. Any of these possibilities would end the procedure.</p>
<p>It was the first time anyone was trying to produce a pregnancy in a zoo-born female ocelot using sperm recovered from a deceased wild male ocelot. If the July 2021 operation worked, it would give his genes a way to live on past his death. This procedure was an important step in efforts to conserve endangered cat species so they can persist into the future.</p>
<p>Ocelots are medium-sized felines weighing around 20 to 30 pounds (9 to 13 kilograms) with sleek spotted coats. Their diet consists of small mammals, rodents, amphibians, reptiles and birds. Ocelots are primarily solitary cats, most active in the evening from dusk to dawn.</p>
<p>While people manage zoo-housed ocelots’ reproduction to maintain genetic diversity, it’s a different story for their wild relatives. There are <a href="https://dx.doi.org/10.2305/IUCN.UK.2015-4.RLTS.T11509A50653476.en">currently only 50 to 80 ocelots</a> (<em>Leopardus pardalis</em>) known to exist in the wild in the U.S., and that population is too small to be sustainable long term. <a href="https://ecos.fws.gov/ecp/species/4474">These endangered animals</a> face ongoing threats of habitat loss and fragmentation, and vehicle strikes. And because of their diminished numbers, they are at risk of inbreeding. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/432291/original/file-20211116-17-y7xeen.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="street sign warning of ocelot crossing" src="https://images.theconversation.com/files/432291/original/file-20211116-17-y7xeen.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/432291/original/file-20211116-17-y7xeen.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/432291/original/file-20211116-17-y7xeen.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/432291/original/file-20211116-17-y7xeen.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/432291/original/file-20211116-17-y7xeen.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/432291/original/file-20211116-17-y7xeen.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/432291/original/file-20211116-17-y7xeen.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">With so few individuals left in the wild in the U.S., each ocelot hit by a car could affect the species’ survival.</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/photo/ocelot-crossing-road-sign-royalty-free-image/855966216">kzubrycki/iStock via Getty Images Plus</a></span>
</figcaption>
</figure>
<p>Over the past 25 years, scientists at the <a href="http://cincinnatizoo.org/conservation/crew/">Center for Conservation and Research of Endangered Wildlife</a>, or CREW, led by veterinarian Bill Swanson, have been working on technologies that may eventually help add some more genetic diversity to the wild ocelot population. They’ve <a href="https://doi.org/10.1111/rda.12069">developed and refined techniques</a> for sperm collection, <a href="https://doi.org/10.1530/jrf.0.1060087">frozen storage</a> and <a href="https://doi.org/10.1095/biolreprod.112.105353">artificial insemination of ocelots</a> and other endangered cat species.</p>
<p>These innovations have played a key role in sustaining the genetic diversity of cat populations within zoos. Now, we’re trying to go a step further and apply these techniques in wild ocelots.</p>
<p>By creating gene flow among zoo-based ocelots and wild ocelots in different regions, we can increase the genetic diversity of both populations. With wild ocelots, we hope to combat their declining ability to produce offspring, fight infection and maintain adequate numbers in the wild for conservation of the species in the U.S.</p>
<h2>Salvaging sperm to increase diversity</h2>
<p><a href="https://scholar.google.com/citations?user=JyYbknYAAAAJ&hl=en&oi=ao">As a recently graduated veterinarian</a>, I joined my mentor, Debra Miller, at the University of Tennessee’s Comparative and Experimental Medicine Department and in her work at UT’s Center for Wildlife Health. From there, my interests in wildlife conservation led me to this multi-institutional collaboration focusing on the conservation of wild Texas ocelots.</p>
<p>This project relies on the routine collection and freezing of semen from wild ocelots in the field – usually living animals, but sometimes ones that have been found dead. Our semen stockpile lets us preserve genetic material even if these cats are killed by disease, natural disasters or road collisions.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/430877/original/file-20211108-19-fkek42.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="tanks containing many frozen animal semen samples" src="https://images.theconversation.com/files/430877/original/file-20211108-19-fkek42.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/430877/original/file-20211108-19-fkek42.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=405&fit=crop&dpr=1 600w, https://images.theconversation.com/files/430877/original/file-20211108-19-fkek42.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=405&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/430877/original/file-20211108-19-fkek42.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=405&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/430877/original/file-20211108-19-fkek42.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=509&fit=crop&dpr=1 754w, https://images.theconversation.com/files/430877/original/file-20211108-19-fkek42.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=509&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/430877/original/file-20211108-19-fkek42.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=509&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">The CREW CryoBioBank at the Cincinnati Zoo currently holds over 20,000 total semen samples from 82 animal species ranging from elephants to salamanders – including 30 cat species/subspecies – at temperatures of -320 F (-196 C) in liquid nitrogen.</span>
<span class="attribution"><span class="source">Tom Uhlman</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>For the artificial insemination procedure this past summer, the sperm donor was <a href="https://tpwd.texas.gov/huntwild/wild/species/ocelot/">a Texas ocelot</a> that died after being hit by a car. While this male’s death was a tragedy, there is a chance his genes may live on in future offspring thanks to the quick report of his death and the retrieval, shipping and processing of his gonads.</p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/430875/original/file-20211108-21-1kd1vi0.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Placing cryovial of animal semen in a storage tank" src="https://images.theconversation.com/files/430875/original/file-20211108-21-1kd1vi0.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/430875/original/file-20211108-21-1kd1vi0.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=708&fit=crop&dpr=1 600w, https://images.theconversation.com/files/430875/original/file-20211108-21-1kd1vi0.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=708&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/430875/original/file-20211108-21-1kd1vi0.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=708&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/430875/original/file-20211108-21-1kd1vi0.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=890&fit=crop&dpr=1 754w, https://images.theconversation.com/files/430875/original/file-20211108-21-1kd1vi0.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=890&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/430875/original/file-20211108-21-1kd1vi0.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=890&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Thirteen 0.25-milliliter semen straws are in each goblet tube within the canisters inside the frozen storage tank.</span>
<span class="attribution"><span class="source">Tom Uhlman</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>Back at CREW in Cincinnati, Bill Swanson worked to recover the cat’s sperm for future artificial insemination procedures. He froze 20 plastic straws, each containing about 8 million viable sperm. In addition to this deceased male, I have collected and cryopreserved semen from several living wild males for future use. </p>
<p>By testing thawed semen, our team has found that many of these sperm samples were capable of fertilizing cat eggs in vitro. The next step is figuring out whether the frozen wild ocelot semen really can produce kittens via artificial insemination. So Swanson packed up three frozen straws to ship to Albuquerque in a liquid nitrogen dry shipper tank to make sure they remain at -320 F (-196 C) throughout the journey.</p>
<h2>After the thaw, hoping for kittens</h2>
<p><a href="https://doi.org/10.1002/zoo.1010">Ocelots are induced ovulators</a>, meaning <a href="https://doi.org/10.1016/j.theriogenology.2006.03.011">a female must mate in order to release an egg</a> into her reproductive tract. The female we were working with was treated with hormones to help her ovulate at the proper time relative to the insemination procedure. The relief was overwhelming when we confirmed, by laparoscopically looking at the surface of the ovary, that the female had ovulated multiple eggs. </p>
<p>After thawing the semen straws, my excitement began to increase because we could see the deceased ocelot’s sperm swimming rapidly across a slide under the microscope. The sperm had survived the freezing and thawing process and was still in great shape.</p>
<p>I took multiple deep breaths to steady my hands as my smile spread from ear to ear. Bill Swanson positioned the insemination needle within each oviduct, I injected the sperm into both sides of the female’s reproductive tract, and the procedure was complete. </p>
<p>Unfortunately, although the female responded well to the ovulation synchronization protocol, and the artificial insemination procedure was performed without a hitch, she did not conceive. That’s not an uncommon outcome when <a href="https://doi.org/10.1016/S0378-4320(00)00099-3">using frozen semen</a>.</p>
<p>However, we are optimistic that future procedures – using semen samples from this specific male and other frozen samples from living, wild ocelots – will successfully produce pregnancies. By the end of 2021, we plan to conduct two additional artificial insemination procedures with zoo-managed ocelots, followed by three or four more in 2022.</p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/431082/original/file-20211109-27-zdrke4.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="leashed ocelot stands atop cryo tanks" src="https://images.theconversation.com/files/431082/original/file-20211109-27-zdrke4.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/431082/original/file-20211109-27-zdrke4.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=772&fit=crop&dpr=1 600w, https://images.theconversation.com/files/431082/original/file-20211109-27-zdrke4.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=772&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/431082/original/file-20211109-27-zdrke4.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=772&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/431082/original/file-20211109-27-zdrke4.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=970&fit=crop&dpr=1 754w, https://images.theconversation.com/files/431082/original/file-20211109-27-zdrke4.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=970&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/431082/original/file-20211109-27-zdrke4.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=970&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Sihil the ocelot began life as a frozen embryo in one of these liquid nitrogen cold storage tanks. Kittens born via artificial insemination will be the next step.</span>
<span class="attribution"><span class="source">Tom Uhlman</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>If any of these artificial insemination procedures result in the birth of offspring, it will be the first time kittens have been produced with frozen semen from a wild ocelot. They’ll add greater diversity to the ocelot population managed in North American zoos, while improving our understanding of possibilities for increasing genetic diversity within wild ocelot populations. This success would help demonstrate the feasibility of producing kittens using frozen semen from the endangered Texas ocelot population.</p>
<p>Further refinement of the knowledge and techniques to create genetic exchange between wild and zoo-managed ocelot populations or among wild ocelot populations living in fragmented habitats will help ensure that these animals survive into the future.</p><img src="https://counter.theconversation.com/content/166397/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Ashley Reeves is a PhD student within the University of Tennessee Comparative and Experimental Medicine Department and The Center for Wildlife Health. She receives funding from The University of Tennessee and The East Foundation. </span></em></p>There are so few wild ocelots in the US that the cats are becoming inbred, with a bad prognosis for their ultimate survival. But researchers are perfecting ways to get new genes into the population.Ashley Reeves, DVM, PhD Candidate in Comparative and Experimental Medicine, University of TennesseeLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1645382021-08-22T12:00:20Z2021-08-22T12:00:20ZHow a few good apples spawned today’s top varieties — and why breeders must branch out<figure><img src="https://images.theconversation.com/files/416637/original/file-20210817-14-1a8zceh.jpg?ixlib=rb-1.1.0&rect=54%2C54%2C4834%2C2522&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">You can plant a seed from a delicious Honeycrisp apple from the grocery store — but the fruit that comes from that tree will not be Honeycrisp. </span> <span class="attribution"><span class="source">(Shutterstock)</span></span></figcaption></figure><p>You take a bite out of your midday apple and it’s just perfect: the right amount of crunch, juice, sweet and sour. You imagine saving its hard brown seeds and planting them in the ground. One day you’ll have a whole tree producing apples just like this one. Or will you? </p>
<p>There’s no reason you can’t plant a seed from your delicious Honeycrisp apple from the grocery store — but the fruit that comes from that tree will not be Honeycrisp apples. </p>
<p>Golden Delicious, Red Delicious, Granny Smith and McIntosh are some of the most widely eaten apples in the world, but they were all discovered more than 100 years ago. As the climate changes, pests and diseases attack trees and fruit, and consumer tastes shift, apple breeding could benefit from harnessing the immense amount of genetic diversity that is available. But only if breeders are willing to take a risk and create new varieties using less familiar apples.</p>
<h2>An orchard of clones</h2>
<p>Apples, like other fruiting plants, start with flowers. The flowers on an apple tree require pollen from another tree in order to set fruit. That fruit will look like the tree it is growing on, but the seeds inside of it now contain two copies of DNA in each cell, one from the tree it grew on and one from the tree the pollen came from. </p>
<p>Crabapple trees are sometimes planted among cultivated apples in commercial orchards to provide pollen. If the apple you picked off a grocery store shelf wasn’t pollinated by a crabapple tree, it could have been pollinated by another apple variety. So, if you plant an apple seed, you might get something really delicious and tasty, which is exactly what apple breeders aim for when they make targeted crosses between two apple trees. But most likely you will not. </p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/416846/original/file-20210818-26417-f8nmza.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="A researcher dusts pollen onto an apple flower." src="https://images.theconversation.com/files/416846/original/file-20210818-26417-f8nmza.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/416846/original/file-20210818-26417-f8nmza.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=503&fit=crop&dpr=1 600w, https://images.theconversation.com/files/416846/original/file-20210818-26417-f8nmza.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=503&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/416846/original/file-20210818-26417-f8nmza.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=503&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/416846/original/file-20210818-26417-f8nmza.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=632&fit=crop&dpr=1 754w, https://images.theconversation.com/files/416846/original/file-20210818-26417-f8nmza.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=632&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/416846/original/file-20210818-26417-f8nmza.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=632&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">The flowers on an apple tree require pollen from another to set fruit. That can be done by hand, or by pollinators, such as bees.</span>
<span class="attribution"><span class="source">(Beatrice Amyotte)</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>The odds of getting something delicious aren’t great even when you know who the two parents are. <a href="https://orgprints.org/id/eprint/13698/1/220-225.pdf">One German apple breeding program started with 52,000 seeds</a> and it was only after 26 years that it finally released three new apple varieties.</p>
<p>If we can’t plant their seeds, how is it possible to grow more Granny Smith apple trees? The secret is clonal propagation. </p>
<p>Clonal propagation involves taking a cutting of wood that includes a bud from a desirable tree to grow a new tree, called a clone. Any apple orchard composed of one variety, like Gala, Granny Smith or Honeycrisp, is actually an orchard of clones. </p>
<figure class="align-center ">
<img alt="Small pots of apple seedlings in a greenhouse." src="https://images.theconversation.com/files/416844/original/file-20210818-21-c8b933.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/416844/original/file-20210818-21-c8b933.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=338&fit=crop&dpr=1 600w, https://images.theconversation.com/files/416844/original/file-20210818-21-c8b933.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=338&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/416844/original/file-20210818-21-c8b933.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=338&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/416844/original/file-20210818-21-c8b933.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=424&fit=crop&dpr=1 754w, https://images.theconversation.com/files/416844/original/file-20210818-21-c8b933.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=424&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/416844/original/file-20210818-21-c8b933.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=424&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Planting an apple seed will give you a seedling that has two parents: the tree the fruit came from, and the tree the pollen came from.</span>
<span class="attribution"><span class="source">(Beatrice Amyotte)</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>Clonal propagation is so successful that <a href="https://doi.org/10.3732/ajb.1000522">more than 75 per cent of perennial fruit crops are grown this way</a>. But this means that only a handful of apple varieties are grown worldwide.</p>
<p>For example, <a href="https://agriculture.canada.ca/en/canadas-agriculture-sectors/horticulture/market-information-infohort/apple-reports?menupos=01.02.02.05">according to Canadian Apple Storage Reports</a>, Canada’s top four apple varieties (McIntosh, Ambrosia, Honeycrisp and Gala) were responsible for over 50 per cent of apple production, based on weight, for the 2020-21 crop year. </p>
<h2>Closely related</h2>
<p><a href="https://doi.org/10.1038/s41438-020-00441-7">In a recent study</a>, my colleagues and I looked at <a href="https://www.ars.usda.gov/northeast-area/geneva-ny/plant-genetic-resources-unit-pgru/docs/apple-collection/">one of the most diverse collections of apples in the world</a>, located in Geneva, N.Y. <a href="http://www.pubhort.org/aps/74/v74_n2_a4.htm">This living collection contains thousands of apple trees</a>, including both the domesticated apple we eat and its wild relatives. </p>
<p>Apple varieties have to be preserved in living collections because they are clonally propagated and not grown from seed, so <a href="https://doi.org/10.2135/cropsci2019.05.0353">collections like the one in Geneva are critical to conserving and maintaining apple diversity</a>. </p>
<p>Our research found that some of the most popular apples are often used in apple breeding, with both Red Delicious and Golden Delicious having over 60 putative first-degree relatives (parent, sibling, offspring) in the collection. </p>
<p>Sometimes using a commercially successful parent works well. For example, Gala is the offspring of Golden Delicious, and Red Delicious is one of its grandparents. </p>
<p>In our study, we found seven of the top eight apple varieties in the United States were interconnected by a series of first-degree relationships. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/417056/original/file-20210819-17-1vhy96e.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Diagram showing the relationships of the top nine apple varieties" src="https://images.theconversation.com/files/417056/original/file-20210819-17-1vhy96e.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/417056/original/file-20210819-17-1vhy96e.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=486&fit=crop&dpr=1 600w, https://images.theconversation.com/files/417056/original/file-20210819-17-1vhy96e.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=486&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/417056/original/file-20210819-17-1vhy96e.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=486&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/417056/original/file-20210819-17-1vhy96e.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=611&fit=crop&dpr=1 754w, https://images.theconversation.com/files/417056/original/file-20210819-17-1vhy96e.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=611&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/417056/original/file-20210819-17-1vhy96e.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=611&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Network of first-degree relationships with the top eight apple varieties sold in the United States. Each apple is represented by a dot and each line represents a first-degree relationship.</span>
<span class="attribution"><a class="source" href="https://doi.org/10.1038/s41438-020-00441-7">(Zoë Migicovsky, modified)</a>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<p>The only exception was Honeycrisp, an apple variety with a unique and crisp texture. <a href="https://doi.org/10.1038/hortres.2017.3">Honeycrisp’s parents were commercially unsuccessful</a>: Keepsake and a University of Minnesota selection called MN1627, which is no longer available and not in the apple collection we studied. However, if it were, Honeycrisp would be linked to the remaining top apples because one of the parents of MN1627 was Golden Delicious. </p>
<h2>Missed apple-tunities</h2>
<p>By using the same handful of parents repeatedly in apple breeding, we are missing out on a lot of the unusual and wonderful variation that is out there. Commercial orchards have the same apple variety planted side by side. But <a href="http://www.cultivatingdiversity.org">our research orchard in Kentville, N.S.,</a> has more than 1,000 unique apple trees. Walking among these trees in the fall, you can see, smell and taste the possibilities. </p>
<p>All the Honeycrisps in the world can be traced back to one single tree. Plant diversity is the foundation of crop improvement, and by expanding the breeding pool, apple breeders can introduce new traits for consumers and improve crop resilience in response to a changing climate. </p>
<p>Apple breeding is about taking two parents, dusting the pollen from one tree onto the flower of another and creating something brand new. This is the same process that happens (with the help of bees) to the trees that grow the apples you buy at the grocery store. So if you were to plant a seed from one of them in your garden? Well, who knows how far the apple would fall from the tree.</p><img src="https://counter.theconversation.com/content/164538/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Zoë Migicovsky receives funding from National Science Foundation Plant Genome Research Program 1546869.</span></em></p>Apple breeders have created crisp, juicy and tasty fruits, but the limited varieties leave crops vulnerable to diseases, pests and climate change. Introducing new traits could improve crop resilience.Zoë Migicovsky, Postdoctoral fellow, Faculty of Agriculture, Dalhousie UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1542182021-02-19T17:58:25Z2021-02-19T17:58:25ZHow hybrids could help save endangered species<figure><img src="https://images.theconversation.com/files/382541/original/file-20210204-18-e7yle5.JPG?ixlib=rb-1.1.0&rect=721%2C589%2C3342%2C2336&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">A hybrid of the Turkmen and Iranian wild ass, introduced to Israel in 1968.</span> <span class="attribution"><span class="source">Lilith Zecherle</span>, <span class="license">Author provided</span></span></figcaption></figure><p>What do you get when you cross two distinct lineages of an endangered species? For scientists hoping to revive an extinct population in Israel, the answer was a lucky accident – one that could upend longstanding ideas about how best to preserve biodiversity.</p>
<p>The Asiatic wild ass is a relative of the donkey that, as the name suggests, was never domesticated. This truly wild animal lives in the steppes and deserts of western and central Asia, from the Mediterranean to Mongolia. Because they vary slightly in size and colour (ranging from a pale sand colour to a dark ochre), Asiatic wild asses have been classified into five distinct subspecies: Mongolian, Indian, Iranian, Turkmen, and Syrian. The latter once roamed the Middle East, but overhunting drove it to extinction in the 1920s. </p>
<p>Hoping to return this species to the Negev desert, Israel started a reintroduction programme in 1968. The idea was not to resurrect the extinct Syrian wild ass, but to introduce an equivalent that was as similar as possible, which would fill the ecological role of the departed subspecies. And so, Israel imported 11 Asiatic wild asses from zoos in Iran and Europe.</p>
<p>Perhaps confusion regarding the species’ taxonomy was to blame, but the 11 imported asses weren’t all alike. In fact, they belonged to two different subspecies from Iran and Turkmenistan. And accidentally, a mixed breeding population was established in the HaiBar Yotvata reserve in Israel that created an entirely new hybrid ass.</p>
<figure class="align-center ">
<img alt="A black-and-white photograph of a donkey-like animal galloping in an enclosure." src="https://images.theconversation.com/files/385278/original/file-20210219-19-foa71v.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/385278/original/file-20210219-19-foa71v.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=528&fit=crop&dpr=1 600w, https://images.theconversation.com/files/385278/original/file-20210219-19-foa71v.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=528&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/385278/original/file-20210219-19-foa71v.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=528&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/385278/original/file-20210219-19-foa71v.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=663&fit=crop&dpr=1 754w, https://images.theconversation.com/files/385278/original/file-20210219-19-foa71v.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=663&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/385278/original/file-20210219-19-foa71v.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=663&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">The now-extinct Syrian wild ass in a Vienna zoo, 1915.</span>
<span class="attribution"><a class="source" href="https://en.wikipedia.org/wiki/Syrian_wild_ass#/media/File:Syrian_wild_ass.jpg">Conrad Keller/Wikipedia</a></span>
</figcaption>
</figure>
<p>Intentionally crossing two different subspecies risks creating offspring which are less healthy or viable. But, remarkably, this accident seems to have paid off. <a href="https://onlinelibrary.wiley.com/doi/full/10.1111/eva.13191">In new research</a>, we studied the genetics of the hybrid population and showed that mixing the subspecies might have actually helped make the reintroduction a success. </p>
<h2>What’s wrong with hybrids?</h2>
<p>Separate species and subspecies are genetically distinct. If they’re too different, their hybrid offspring are likely to be much less healthy than the parents. Genetic incompatibilities between horses and donkeys mean that their hybrids – mules and hinnies – <a href="https://www.bnd.com/living/liv-columns-blogs/answer-man/article135296594.html">are infertile</a>. Subspecies are more genetically similar than species and less likely to experience this problem, but there are other issues. </p>
<p>Different subspecies of the same species might have unique genetic adaptations that they’ve evolved in order to thrive within their particular environments. By crossing them, the next generation will carry fewer of these adaptations and might struggle as a result. Imagine crossing a tiger from Siberia with one from Sumatra – the genetic make-up of the offspring may make them less comfortable than their parents in either snowy northern climes or tropical rainforests.</p>
<p>But mixing different populations can also help counteract the problems of small population sizes. Many endangered species persist in small and isolated populations and as a result, lose their genetic diversity through inbreeding and a random process called <a href="https://www.khanacademy.org/science/ap-biology/natural-selection/population-genetics/a/genetic-drift-founder-bottleneck#:%7E:text=Genetic%20drift%20is%20a%20mechanism,are%20strongest%20in%20small%20populations.">genetic drift</a>. This spells danger for the whole species, as low genetic diversity means a lower potential for coping with sudden change, like a hotter climate or a new disease. </p>
<p>Think of it like playing scrabble, but your tiles contain just two letters. Your options are severely limited. A greater diversity of letters would give you much more flexibility to respond. Mixing subspecies seems to have given the reintroduced Israeli wild asses a more diverse genome.</p>
<figure class="align-center ">
<img alt="A horse-donkey hybrid stands in a field in winter." src="https://images.theconversation.com/files/385279/original/file-20210219-23-16bwati.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/385279/original/file-20210219-23-16bwati.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=481&fit=crop&dpr=1 600w, https://images.theconversation.com/files/385279/original/file-20210219-23-16bwati.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=481&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/385279/original/file-20210219-23-16bwati.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=481&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/385279/original/file-20210219-23-16bwati.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=604&fit=crop&dpr=1 754w, https://images.theconversation.com/files/385279/original/file-20210219-23-16bwati.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=604&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/385279/original/file-20210219-23-16bwati.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=604&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">An old hinny – the offspring of a female donkey and a male horse. Most hinnies are sterile.</span>
<span class="attribution"><a class="source" href="https://en.wikipedia.org/wiki/Hinny#/media/File:Old_hinny_in_Oklahoma.jpg">Ragesoss/Wikipedia</a>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<h2>Return to the Negev</h2>
<p>In Israel, the population of Asiatic wild asses grew rapidly from 11 founders in a mixed breeding group in 1968 to around 300 wild animals today. A fast-growing population is a sign of health. But starting with a small number of founder animals risks creating a reintroduced population with very low genetic diversity. Over time, this could cause it to shrink or even collapse.</p>
<p>We performed <a href="https://onlinelibrary.wiley.com/doi/full/10.1111/eva.13191">a DNA analysis</a> to learn more about the genetic makeup of this population and its chances of persisting in the long-term. We found that all tested individuals of wild ass roaming the Israeli desert today are genetic hybrids and inherited half of their genes from each of the two subspecies. </p>
<p>This is more surprising than it sounds. If genetic incompatibilities between two subspecies usually make hybrids less healthy or fertile, we’d expect them to produce fewer foals than wild asses of pure subspecies ancestry. So, after several generations, we’d still expect to see some purebred asses, as they’re presumably better suited to breeding healthy young than the hydrids. Yet we found no purebreds, suggesting there were no genetic barriers to interbreeding. </p>
<p>More importantly, the hybrid population became more genetically diverse over time. This may explain the population’s rapid growth, and indicate that Israel’s wild ass population is well-prepared for future challenges like disease and climate change. </p>
<figure class="align-center ">
<img alt="A herd of wild asses in the desert." src="https://images.theconversation.com/files/385280/original/file-20210219-15-1bk9mzx.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/385280/original/file-20210219-15-1bk9mzx.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/385280/original/file-20210219-15-1bk9mzx.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/385280/original/file-20210219-15-1bk9mzx.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/385280/original/file-20210219-15-1bk9mzx.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/385280/original/file-20210219-15-1bk9mzx.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/385280/original/file-20210219-15-1bk9mzx.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Rather than leading to a genetic dead end, mixing two subspecies created a thriving hybrid population.</span>
<span class="attribution"><span class="source">Lilith Zecherle</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<h2>Diversity versus purity</h2>
<p>The reintroduction in Israel is a rare success in the conservation of Asiatic wild asses. Other re-introductions have used only one subspecies and most of them have failed. </p>
<p>When 11 Turkmen wild asses were <a href="https://link.springer.com/article/10.1007/s10592-018-1086-3">reintroduced to a reserve in Turkmenistan</a>, the resulting population lost much of its genetic diversity over four generations. To date, only <a href="https://onlinelibrary.wiley.com/doi/full/10.1111/eva.13191">five out of 18 attempts</a> to reintroduce wild asses have succeeded, including the one in Israel.</p>
<p>Despite the potential benefits, many conservationists <a href="https://onlinelibrary.wiley.com/doi/full/10.1002/ece3.2595">oppose mixing different subspecies</a> as it means sacrificing genetic purity, which some consider a precious component of a population’s overall value. But our work suggests that focusing on genetic purity might not be the best strategy for saving an endangered species from extinction. Carefully assessing the potential risks is important, but hybrids can also form resilient populations with realistic chances of long-term survival.</p><img src="https://counter.theconversation.com/content/154218/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Lilith Zecherle receives funding from Liverpool John Moores University. </span></em></p><p class="fine-print"><em><span>Hazel Nichols receives funding from NERC Bioinformatics Facility.</span></em></p><p class="fine-print"><em><span>Richard Brown does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>By only focusing on preserving the genetic purity of a species, conservationists risk the extinction of isolated populations.Lilith Zecherle, PhD Candidate in Conservation Biology, Liverpool John Moores UniversityHazel Nichols, Senior Lecturer in Biosciences, Swansea UniversityRichard Brown, Professor of Animal Evolution, Liverpool John Moores UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1534732021-02-17T14:45:35Z2021-02-17T14:45:35ZIncreasing land use could turn Mount Kilimanjaro into an ecological island<figure><img src="https://images.theconversation.com/files/381974/original/file-20210202-23-16ahyfy.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">A herd of elephants walk in front of Mount Kilimanjaro in Amboseli National Park.</span> <span class="attribution"><span class="source">Photo by CARL DE SOUZA/AFP via Getty Images</span></span></figcaption></figure><p>Located in Tanzania, with a height of almost 6,000 metres, Mount Kilimanjaro is Africa’s tallest mountain. Over the years, there’s <a href="https://www.sciencedirect.com/science/article/abs/pii/S0308521X05000995?via%3Dihub">been extensive</a> urbanisation and development at the base of the mountain, which could change what lives on the mountain. </p>
<p>Satellite images <a href="https://www.usgs.gov/centers/eros">show</a> that, between 1976 and 2000, there have been dramatic changes to the strips of land between Mount Kilimanjaro and Mount Meru, which is located less than 100km to the east. Areas that originally had dense natural vegetation were forced to make room for intensive agriculture and residential development to accommodate a growing population. </p>
<p>Nowadays, Mount Kilimanjaro is almost completely surrounded by developed areas that include wheat farms, commercial sugar cane plantations and rice paddies. There are also smallholder farms all around and growing, built-up settlements.</p>
<p>This means the mountain’s ecosystem is at risk of turning into an “ecological island”, entirely surrounded by cultivation and development. When natural habitats are isolated in this way, species are less able to migrate, leading to less genetic variation and diversity. </p>
<p>Less genetic variation makes ecosystems more vulnerable during environmental changes. Diversity increases the ability to adapt. For instance, if there’s a warming event some plants or animals might not survive and others might. </p>
<p>We carried out <a href="https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.14078">a study</a> to uncover what the long‐term effects of this land‐cover change could be on biodiversity. Specifically, we wanted to know how important natural vegetation bridges are. </p>
<p>We did this by studying a group of insects called Orthoptera – commonly known as grasshoppers, crickets and bushcrickets. These serve as an early warning system because they are adapted to a very special microclimate. This means they’re affected by even small changes in environmental conditions and this is immediately reflected in which species are living in a certain community in a certain habitat. Any changes to grasshoppers can signal far-reaching effects for other animal groups, which are often difficult to study. </p>
<p>Grasshoppers can also easily be collected and identified. </p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/383505/original/file-20210210-21-h733zj.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/383505/original/file-20210210-21-h733zj.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=447&fit=crop&dpr=1 600w, https://images.theconversation.com/files/383505/original/file-20210210-21-h733zj.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=447&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/383505/original/file-20210210-21-h733zj.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=447&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/383505/original/file-20210210-21-h733zj.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=562&fit=crop&dpr=1 754w, https://images.theconversation.com/files/383505/original/file-20210210-21-h733zj.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=562&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/383505/original/file-20210210-21-h733zj.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=562&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Chromothericles kanga.</span>
<span class="attribution"><span class="source">Claudia Hemp</span></span>
</figcaption>
</figure>
<p>We found that – because of the distribution of different species – Orthoptera used vegetation between Mount Meru and Mount Kilimanjaro as natural bridges. These bridges allowed species in the area to develop to their current diversity levels. </p>
<p>If bridges of vegetation between the mountains weaken or vanish altogether, it is not just the mobility of these insects that is affected. Larger animals such as antelope, small mammals, snakes, or chameleons are at an even higher risk of becoming isolated and thus going extinct in the foreseeable future. They need genetic exchange and large habitats. </p>
<h2>Bridges of vegetation</h2>
<p>We studied the environments of Orthoptera at 500 selected sites on Mount Kilimanjaro and Mount Meru. </p>
<p>We wanted to know whether these insects used natural vegetation as bridges. Endemic species – species that are found only in this region of East Africa – were of particular interest. We studied flightless Orthoptera that have to crawl on the ground if they want to reach a new habitat on another mountain. Widespread, mobile species which can fly would have been not suitable for our study.</p>
<p>We found an especially high proportion of common endemic species in the forest areas at lower altitudes shared by these two mountains. We believe that this is a clear indication that the Orthoptera once used dense vegetation between the mountains as bridges to spread out in both regions.</p>
<p>Conspicuously, there are also a few endemic flightless species, shared by both mountains, that are only found in higher forest areas. These species share common ancestors and originated from the same place. This distribution pattern cannot be related to the recently disappeared forest corridor. Species living in a completely different climate zone with much cooler and wetter conditions could never use a migration corridor in the lowlands, at least under the current climate. </p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/383506/original/file-20210210-23-bhrrw9.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/383506/original/file-20210210-23-bhrrw9.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=327&fit=crop&dpr=1 600w, https://images.theconversation.com/files/383506/original/file-20210210-23-bhrrw9.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=327&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/383506/original/file-20210210-23-bhrrw9.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=327&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/383506/original/file-20210210-23-bhrrw9.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=411&fit=crop&dpr=1 754w, https://images.theconversation.com/files/383506/original/file-20210210-23-bhrrw9.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=411&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/383506/original/file-20210210-23-bhrrw9.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=411&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Parasphena pulchripes - endemic to the upper montane and alpine grass and bushland zone on Kilimanjaro. It is evidence of a once much colder climate connecting mountains via open land bridges to enable ancestors of this flightless and little mobile genus to spread.</span>
</figcaption>
</figure>
<p>We believe the reason for this disconnected distribution of high elevation endemics lies in <a href="https://onlinelibrary.wiley.com/doi/full/10.1111/jbi.13880">ancient</a> climate changes. Several tens of thousands of years ago, it was <a href="https://www.researchgate.net/publication/260031608_Pollen-based_temperature_and_precipitation_inferences_for_the_montane_forest_of_Mt_Kilimanjaro_during_the_last_Glacial_and_the_Holocene">considerably</a> cooler and damper in the lower areas than it is today. Thus, Orthoptera that preferred these climatic conditions settled at the foot of the mountains, travelling by foot via the wooded land route. It was only later, as the temperatures rose and precipitation diminished that they made their way to higher areas. They then no longer had contact with grasshoppers in neighbouring regions. </p>
<p>Our research findings corroborate <a href="https://onlinelibrary.wiley.com/doi/10.1111/syen.12092">the thesis</a> that animal and plant species spread out primarily via bridges of vegetation. In contrast, other ways of spreading over long distances, for instance seed transport via wind or the “air travel” of individual insects, play a subordinate role. </p>
<p>Our study showed that forest bridges between East African mountains acted as important migratory corridors and are not only a prehistoric phenomenon, but existed and disappeared in some places more recently. Similar to the missing <a href="https://onlinelibrary.wiley.com/doi/full/10.1111/j.1365-2028.2006.00679.x">bamboo belt</a> of Kilimanjaro, this is another example of the long-lasting and accelerating influence of humans on the African landscape.</p>
<p>It’s important for policymakers to address the growing isolation of Kilimanjaro as, without these bridges, many species of animals will be at risk of extinction. </p>
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Read more:
<a href="https://theconversation.com/how-border-walls-threaten-species-trying-to-escape-rising-temperatures-155007">How border walls threaten species trying to escape rising temperatures</a>
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</em>
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<hr>
<p>Examples of important bridges in this area include the wildlife corridors that connect <a href="https://www.nature.org/en-us/about-us/where-we-work/africa/stories-in-africa/keeping-wide-open-spaces-for-elephants/">Amboseli and Kilimanjaro National Park</a> or <a href="https://www.researchgate.net/figure/Kwakuchinja-wildlife-corridor-between-Lake-Manyara-National-park-and-Tarangire-national_fig1_283186916">Manyara and Tarangire National Park</a>. </p>
<p>In particular the so-called “<a href="http://www.lucideastafrica.org/publications/Noe_LUCID_WP31.pdf">Kitendeni corridor</a>”, a seven kilometre-wide strip of savanna bushland on the northern slope, is another bridge of major importance. This links Kilimanjaro with the Amboseli National Park in Kenya. </p>
<p>As a wildlife corridor, Kitendeni is meant to preserve access for elephants and other wild animals to the forests of the mountain’s northern slopes, as far even as the forests of West Kilimanjaro. </p>
<p>Yet increasing human pressure, from cultivation and livestock grazing in particular, is reducing this corridor. It’s forcing wildlife, especially elephants and buffaloes, to remain longer on Kilimanjaro, having a further impact on the forests.</p><img src="https://counter.theconversation.com/content/153473/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Andreas Hemp receives funding from German Research Foundation (Deutsche Forschungsgemeinschaft, DFG). </span></em></p><p class="fine-print"><em><span>Claudia Hemp does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>When natural habitats are isolated it means species are less able to migrate, leading to less genetic variation and species diversity.Andreas Hemp, Research Associate Plant Systematics, Bayreuth UniversityClaudia Hemp, Research associate, Bayreuth UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1524582021-01-18T09:07:27Z2021-01-18T09:07:27ZHepatitis D: how the virus made the jump from animals to humans<figure><img src="https://images.theconversation.com/files/378551/original/file-20210113-17-mbqge5.jpg?ixlib=rb-1.1.0&rect=22%2C0%2C4989%2C3710&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Vampire bats, a commonly deltavirus-infected host, feed on the blood of other mammals.</span> <span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/common-vampire-bat-desmodus-rotundus-hanging-376769797">Belizar/Shutterstock</a></span></figcaption></figure><p>Pandemics past and present have been caused when <a href="https://www.sciencedaily.com/terms/pathogen.htm#:%7E:text=A%20pathogen%20or%20infectious%20agent,all%20of%20the%20biological%20kingdoms.">pathogens</a> – germs that cause disease – move between animals and humans, as <a href="https://www.who.int/emergencies/diseases/novel-coronavirus-2019/technical-guidance/naming-the-coronavirus-disease-(covid-2019)-and-the-virus-that-causes-it">SARS-CoV-2</a> (the virus that causes COVID-19) did when it made its way from <a href="https://doi.org/10.1038/s41586-020-2012-7">bats to people</a>. But not all emerging pathogens have it so easy.</p>
<p><a href="https://talk.ictvonline.org/ictv-reports/ictv_9th_report/sub-viral-agents-2011/w/sub_viruses/302/3-satellites-and-other-virus-dependent-nucleic-acids">Satellites</a> are a peculiar group of tiny pathogens that hijack unrelated viruses (called their “helpers”) to spread. Satellites are notorious because they can make the disease caused by their helper viruses more severe.</p>
<p>One example is the <a href="https://www.hepb.org/research-and-programs/hepdeltaconnect/what-is-hepatitis-delta/">hepatitis delta virus</a>, better known as hepatitis D or HDV, which is the only satellite known to cause illness in humans. Hepatitis D exploits the <a href="https://www.nhs.uk/conditions/hepatitis-b/#overview">hepatitis B virus</a>, to enter and exit cells, and in the process causes the most severe form of viral hepatitis in 20 million people worldwide.</p>
<p>Where hepatitis D came from has long been a mystery. For a long time, it didn’t resemble any other virus known to science. And having an animal origin in the way that SARS-CoV-2 has seemed unlikely because the ancestor satellite would either need to bring along its old helper or switch to a new and unfamiliar helper in humans – either way adding a degree of difficulty that normal viruses don’t have to deal with.</p>
<p>Recently though, <a href="https://academic.oup.com/ve/article/5/2/vez021/5532287">virus-prospecting studies</a> have discovered hepatitis D relatives (known as “deltaviruses”) in a diverse range of animals including fish, amphibians and termites. This suggests the possibility that we were wrong and hepatitis D-like satellites could jump between animals more easily than we thought.</p>
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<h2>Data mining</h2>
<p><a href="https://doi.org/10.1073/pnas.2019907118">Our own recent study</a> discovered new, close animal relatives of hepatitis D by mining virus sequences from thousands of published genetic datasets. This means that, like COVID-19, hepatitis D is a zoonotic disease. The virus passed from animals to humans and then slowly travelled around the world – as hepatitis D can now be found on all continents. </p>
<p>We also found another big surprise. All of the new deltaviruses we found – along with one recently discovered in <a href="https://doi.org/10.1073/pnas.2006750117">rats from Panama</a> – came from the Americas. This was unexpected because hepatitis D was previously thought to have originated somewhere in Africa. </p>
<p>Instead, that means the long ago spread of the virus probably kicked off somewhere in the Americas. When this happened is still a mystery, but we think that the arrival of hepatitis B (a compatible human helper for hepatitis D) to the Americas via human migration might have facilitated hepatitis D’s leap into humans.</p>
<p>We still don’t know exactly which animal was the source of hepatitis D since the animal deltaviruses we found were still pretty different. Finding that “missing link” will require testing more animals, but at least we now know that an animal reservoir is out there, somewhere in the Americas.</p>
<h2>Host jumps and helpers</h2>
<p>We also found that deltaviruses had made jumps between non-human mammals. One deltavirus from a <a href="https://animaldiversity.org/accounts/Peropteryx_macrotis/">lesser dog-like bat</a> from Mexico was most similar to deltaviruses from <a href="https://www.britannica.com/animal/American-spiny-rat">spiny rats</a> in Panama. Meanwhile, two different deltaviruses were discovered in common <a href="https://www.nationalgeographic.com/animals/mammals/c/common-vampire-bat/">vampire bats</a> from Peru that were not closely related to one another or the other bat deltavirus. Multiple non-human mammal jumps show that this host-leaping habit is a rule rather than an exception for deltavirus evolution.</p>
<figure class="align-center ">
<img alt="Small golden coloured rat." src="https://images.theconversation.com/files/378554/original/file-20210113-13-1330iyl.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/378554/original/file-20210113-13-1330iyl.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/378554/original/file-20210113-13-1330iyl.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/378554/original/file-20210113-13-1330iyl.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/378554/original/file-20210113-13-1330iyl.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/378554/original/file-20210113-13-1330iyl.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/378554/original/file-20210113-13-1330iyl.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">The South American spiny rat.</span>
<span class="attribution"><a class="source" href="https://en.wikipedia.org/wiki/Echimyidae#/media/File:Mesomys_hispidus_female.jpg">Antoine Baglan/Wikipedia</a>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<p>Given that deltaviruses seem perfectly happy in many different kinds of animal hosts, how attached are they to their helpers (the other viruses they depend on)? Do the animal-infecting relatives of hepatitis D also exploit animal-infecting relatives of hepatitis B?</p>
<p>Our searches found that deltavirus-infected animals had plenty of other viruses but nothing that looked like hepatitis B. Along with <a href="https://doi.org/10.1038/s41467-019-10117-z">lab studies</a> showing that hepatitis D may be able to exploit several other human viruses, this suggests that deltaviruses probably jump between helpers as well as hosts. This means that, at least in theory, deltaviruses might alter the severity of many different viruses in many different animals.</p>
<p>Exactly which helpers are used by the new animal-infecting deltaviruses is still a mystery, but viruses related to <a href="https://www.nhs.uk/conditions/hepatitis-c/">hepatitis C virus</a> are emerging as strong candidates after being found in bat and rodent hosts along with deltaviruses. Regardless, the absence of hepatitis B-related helpers revealed another piece of the hepatitis D origin puzzle: somewhere along the journey into humans, the forebear of hepatitis D switched helpers, acquiring the modern association with hepatitis B.</p>
<p>Possibly the most intriguing question is whether the new mammal deltaviruses have already made jumps into humans. Deltaviruses were previously very difficult to detect, and if the jump to humans didn’t cause changes in disease severity, they might have gone unnoticed. With their ability to jump between hosts and make disease more severe, we think these tiny agents deserve more of our attention.</p><img src="https://counter.theconversation.com/content/152458/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Laura Bergner receives funding from the Wellcome Trust (Institutional Strategic Support Fund Early Career Researcher Catalyst Grant) and the Human Frontier Science Program (RGP0013/2018). </span></em></p><p class="fine-print"><em><span>Daniel Streicker receives funding from the Wellcome Trust (217221/Z/19/Z ), the BBSRC (BB/V003798/1), the Human Frontier Science Program (RGP0013/2018), and the Leverhulme Trust (PLP-2020-362). </span></em></p>The genome of hepatitis D doesn’t resemble any known virus, making its origin a mystery. But by mining virus sequences from genetic datasets, a new study may have found the answer.Laura Bergner, Postdoctoral Research Assistant Biodiversity, Animal Health & Comparative Medicine, University of GlasgowDaniel Streicker, Wellcome Trust Senior Research Fellow, University of GlasgowLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1351172020-04-06T15:33:29Z2020-04-06T15:33:29ZFew clinical trials are done in Africa: COVID-19 shows why this urgently needs to change<figure><img src="https://images.theconversation.com/files/324023/original/file-20200330-146719-9jnd21.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">More clinical trials in African countries can help ensure that any vaccines or treatments developed cater to the continent's genetic diversity.</span> <span class="attribution"><span class="source">CELLOU BINANI/AFP via Getty Images</span></span></figcaption></figure><p>The World Health Organisation (WHO), in its quest to find efficacious therapies to treat COVID-19, plans to conduct a multi-arm, <a href="https://www.statnews.com/2020/03/18/who-to-launch-multinational-trial-to-jumpstart-search-for-coronavirus-drugs/">multi-country clinical trial</a>. The trials have yet to begin, but ten countries have already signed up. Only one of them, South Africa, is on the African continent. </p>
<p>Of course, the WHO isn’t the only organisation trying to find treatments or even a vaccine for COVID-19. The United States National Institutes of Health maintains an <a href="https://clinicaltrials.gov/ct2/home">online platform</a> that lists all registered, ongoing clinical trials globally. On March 26, a quick search of the platform using the term “coronavirus” revealed 157 ongoing trials; 87 of these involve either a drug or a vaccine, while the rest are behavioural studies. Only three are registered in Africa – all of them in Egypt.</p>
<p>This low representation of African countries in clinical trials is not unusual. Poor visibility of existing sites, limited infrastructure and unpredictable clinical trial regulatory timelines are some of the key issues hindering investments in this area.</p>
<p>Africa’s virtual absence from the clinical trials map is a big problem. The continent displays an incredible amount <a href="https://www.bionews.org.uk/page_91054">of genetic diversity</a>. If this diversity is not well represented in clinical trials, the trial findings cannot be generalised to large populations.</p>
<p>The same goes for the outcomes of the COVID-19 studies. They too may not be relevant for people in African countries unless conducted locally. This is because responses to drugs or vaccines are complicated and can be influenced by, among other things, human genetics: different people will respond differently to different drugs and vaccines. </p>
<p>More countries on the African continent must urgently get involved in clinical trials so that the data collected will accurately represent the continent at a genetic level. </p>
<p>Time is of the essence. The usual approach, of developing site or country specific protocols, won’t work. Instead, African governments need to look at ways to harmonise the response towards COVID-19 across the continent. Now, more than ever, African countries need to work together.</p>
<h2>Centres of excellence</h2>
<p>Africa does have clinical trial infrastructure and capabilities. But the resources remain unevenly distributed. The vast majority are in Egypt and South Africa. That’s because these countries have invested more heavily in <a href="https://gh.bmj.com/content/4/2/e001047">research and development</a> than others on the continent.</p>
<p>Traditionally, clinical trials are conducted at centres of excellence, which are sites that have the appropriate infrastructure and human skills necessary to conduct good quality trials. These can be located at a single university or research organisation, or work can be split between a few locations. But setting up these centres requires significant time and financial investment. Most that I am aware of on the continent have developed over the years with heavy support from external partners or sponsors. In many cases, African governments have not been involved in these efforts.</p>
<p>Once such centres are set up, the hard work continues to maintain these centres and to ensure they’re able to attract clinical trial sponsors. They require continuous funding, the establishment of proper institutional governance and the creation of trusted, consistent networks.</p>
<p>Usually African scientists leading clinical trial sites can apply for funding to conduct a trial; if the site is well known the scientists may be approached by a sponsor such as a pharmaceutical company interested in conducting a trial. </p>
<p>Clearly this approach takes time and usually benefits well-known sites or triallists. So what alternatives are available in the face of an epidemic that’s moving as fast as COVID-19?</p>
<h2>How to change direction</h2>
<p>Key stakeholders should work together to expedite the rollout of trials in different countries. This would include inter-country collaborations such as working with different governments and scientists in co-designing trials; and providing harmonised guidelines on patient management, sample collection and tracking and sharing results in real time.</p>
<p>African governments, meanwhile, should provide additional funding to clinical research institutions and clinical trial sites. This would allow the sites to pull resources together and rapidly enrol patients to answer various research questions.</p>
<p>Because of the uneven distribution of skills and resources the continent should also adopt a hub-and-spoke model in its efforts. This would involve countries that don’t have much capacity being able to ship samples easily across borders for analysis in a centralised well-equipped laboratory, which then feeds back data to the country of sample origin.</p>
<p>Governments should also form a task force to quickly engage with key pharmaceutical companies with drug candidates for COVID-19. This team should establish the companies’ appetite for collaborations in conducting relevant trials on the continent.</p>
<p>Through all of this, it is necessary for stakeholders to identify and address key ethical issues that may arise. Ethics should not be compromised by haste.</p>
<h2>Beyond COVID-19</h2>
<p>Every country’s epidemic preparedness kit should contain funds set aside for clinical trials during epidemics or pandemics.</p>
<p>This would require governments on the continent to evaluate their role and level of investment in the general area of clinical trials. This will augment the quality and quantity of clinical trials in the face of the constant challenge of emerging and <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6205565/">re-emerging infectious diseases</a> as well as a steady rise in <a href="https://www.thelancet.com/journals/langlo/article/PIIS2214-109X(19)30370-5/fulltext">non-communicable diseases</a>.</p>
<p>On top of this, clinical trial centres, clinical research institutions and clinical triallists on the continent should strive to increase their visibility in the global space. This will make them easy to find in times of crisis, and enhance both south-south and north-south collaborations. </p>
<p>The African Academy of Sciences is currently building <a href="https://www.aasciences.africa/aesa/programmes/clinical-trials-community">an online platform</a> to facilitate this visibility and encourage greater collaboration.</p><img src="https://counter.theconversation.com/content/135117/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Jenniffer Mabuka-Maroa works for the African Academy of Sciences (AAS). The AAS receives funding from the Bill and Melinda Gates Foundation</span></em></p>More countries on the African continent must urgently get involved in clinical trials so that the data collected will accurately represent the continent at a genetic level.Jenniffer Mabuka-Maroa, Programme Manager, African Academy of SciencesLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1282732019-12-12T12:49:19Z2019-12-12T12:49:19ZAncient DNA confirms humans wiped out northern hemisphere’s version of the penguin<figure><img src="https://images.theconversation.com/files/306596/original/file-20191212-85371-1s78lgx.jpg?ixlib=rb-1.1.0&rect=0%2C848%2C2508%2C1670&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">The now extinct great auk.</span> <span class="attribution"><a class="source" href="https://commons.wikimedia.org/wiki/File:Keulemans-GreatAuk.jpg">John Gerrard Keulemans</a></span></figcaption></figure><p>The North Atlantic was once home to a bird that bore a remarkable similarity to penguins. The great auk, also known as “the <a href="https://www.lexico.com/explore/what-is-the-origin-of-the-word-penguin">original penguin</a>”, was a large, flightless, black and white bird, that is said to have existed in the <a href="https://books.google.co.uk/books?id=tldtUiRPTnEC&source=gbs_navlinks_s">millions</a>. Despite its appearance, the great auk is actually a relative of razorbills and puffins, not of penguins. However, since around 1844, the northern hemisphere has been without its version of the penguin and it looks like we are to blame. </p>
<p>The great auk had long provided humans with a source of meat and eggs. But from around 1500, hunting dramatically intensified when Europeans discovered the rich fishing grounds of Newfoundland. Within 350 years, the <a href="https://theconversation.com/how-were-using-ancient-dna-to-solve-the-mystery-of-the-missing-last-great-auk-skins-80650">last great auks</a> ever reliably seen were killed to be put in a museum, and the species was lost forever.</p>
<p>Given the relative speed of this extinction, it’s worth asking whether other factors such as environmental changes were involved. Was the great auk heading for extinction before intensive hunting began? Or could it have survived and still be around today if it hadn’t been for humans? </p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/306603/original/file-20191212-85397-b8sv6z.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/306603/original/file-20191212-85397-b8sv6z.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=439&fit=crop&dpr=1 600w, https://images.theconversation.com/files/306603/original/file-20191212-85397-b8sv6z.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=439&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/306603/original/file-20191212-85397-b8sv6z.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=439&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/306603/original/file-20191212-85397-b8sv6z.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=552&fit=crop&dpr=1 754w, https://images.theconversation.com/files/306603/original/file-20191212-85397-b8sv6z.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=552&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/306603/original/file-20191212-85397-b8sv6z.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=552&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Where the great auk lived.</span>
<span class="attribution"><span class="source">Esri, Garmin, NOAA NGDC and others</span>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<p>In our recent <a href="https://elifesciences.org/articles/47509">study</a>, my colleagues and I found no evidence that the great auk was already in decline or at risk of extinction prior to the intensive hunting. This suggests that no other factors were at play in their demise and human hunting pressure alone was enough to cause their extinction. </p>
<p>Our findings highlight how industrial-scale commercial exploitation of natural resources has the potential to drive even an abundant, wide-ranging, highly mobile species to extinction within a short period of time.</p>
<h2>Ancient DNA</h2>
<p>Through studying species that have become extinct we are able to learn things which <a href="https://books.google.co.uk/books/about/Vanishing_Birds.html?id=zS8iAAAAMAAJ&redir_esc=y">can help us</a> in the fight to conserve species still living today. One way to do this is to look at the genetics of extinct species. Using ancient DNA (aDNA) we can look at things like genetic diversity (how much genes varied between different individuals in a species), which can reveal trends in how genetically healthy the species is. It can also show us how a species may have responded to environmental change, hunting or the introduction of new species into its habitat.</p>
<p>There is <a href="https://books.google.co.uk/books/about/The_Great_Auk.html?id=GFQXAQAAIAAJ&redir_esc=y.">lots of evidence</a>, including archaeological records and written accounts, that shows the great auk was hunted throughout its existence. But until now we haven’t known what impact <a href="https://sora.unm.edu/sites/default/files/journals/auk/v101n01/p0001-p0012.pdf">environmental change</a> may have had on the bird’s extinction. If the species had been at risk of extinction prior to the onset of intensive hunting in the 16th century, we would expect to see signs in its DNA.</p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/306598/original/file-20191212-85386-19zg65m.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/306598/original/file-20191212-85386-19zg65m.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=358&fit=crop&dpr=1 600w, https://images.theconversation.com/files/306598/original/file-20191212-85386-19zg65m.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=358&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/306598/original/file-20191212-85386-19zg65m.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=358&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/306598/original/file-20191212-85386-19zg65m.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=450&fit=crop&dpr=1 754w, https://images.theconversation.com/files/306598/original/file-20191212-85386-19zg65m.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=450&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/306598/original/file-20191212-85386-19zg65m.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=450&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Great auk bones used to obtain ancient DNA.</span>
<span class="attribution"><span class="source">Jessica Thomas</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>For example, if a species has low genetic diversity and most individuals are very similar, then the species is less likely to have certain individuals that can survive an environmental change when others can’t. So the species as a whole will be less able to adapt to that change. </p>
<p>Meanwhile, big differences in the DNA of individuals from different locations can also indicate that a species was divided into isolated populations that didn’t migrate or mix their DNA with other groups. This is known as population structure and can lead to less genetic diversity, increased inbreeding and an accumulation of “bad” genes, making it an important factor in a species’ vulnerability to extinction.</p>
<p>These kind of changes in genetic diversity are among the signatures we look for when studying species extinction. If we can’t find a loss in diversity during the last few centuries before extinction then it suggests the population declined rapidly, something which would indicate humans as the culprit.</p>
<p>We can also use statistical models called <a href="https://www.nature.com/scitable/knowledge/library/population-viability-analysis-origins-and-contributions-16091427/">population viability analyses</a> that look at the probability of a species going extinct in a given time. These models can be used to show if a realistic amount of hunting could be the sole cause of an extinction.</p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/306415/original/file-20191211-95173-14x37u4.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/306415/original/file-20191211-95173-14x37u4.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/306415/original/file-20191211-95173-14x37u4.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=901&fit=crop&dpr=1 600w, https://images.theconversation.com/files/306415/original/file-20191211-95173-14x37u4.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=901&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/306415/original/file-20191211-95173-14x37u4.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=901&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/306415/original/file-20191211-95173-14x37u4.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=1133&fit=crop&dpr=1 754w, https://images.theconversation.com/files/306415/original/file-20191211-95173-14x37u4.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=1133&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/306415/original/file-20191211-95173-14x37u4.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=1133&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Great auk specimen held in Kelvingrove Museum in Glasgow.</span>
<span class="attribution"><a class="source" href="https://commons.wikimedia.org/wiki/File:Great_Auk_(Pinguinis_impennis)_specimen,_Kelvingrove,_Glasgow_-_geograph.org.uk_-_1108249.jpg">Mike Pennington/Wikimedia Commons</a>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span>
</figcaption>
</figure>
<p>To find out which of these scenarios applied in the case of the great auk, we sequenced part of the bird’s DNA known as its mitochondrial genome. This involved taking samples from bones found by archaeologists and mounted skins and organs stored in museums around the world. We successfully generated DNA sequences from 41 individuals, which represented birds from across the major areas of where the auk lived, spanning a period from around 15,000 years ago to around 170 years ago.</p>
<h2>No gradual decline</h2>
<p>We found that genetic diversity was high across the samples, with evidence for a constant population size and no evidence of a population decline or of pronounced population structure. This suggests the great auk was not at risk of extinction before intensive human hunting and that its extinction followed a population decline too rapid to show up in our data. Meanwhile, the population viability analysis revealed that hunting alone could have been enough to cause the extinction of the great auk. </p>
<p>Today, seabirds are more threatened than any comparable groups of birds, with a third of species at <a href="https://tokyo.birdlife.org/sites/wp-content/uploads/2012/03/Croxall-et-al-2012.pdf">risk of extinction</a> and half facing decline. <a href="https://tokyo.birdlife.org/sites/wp-content/uploads/2012/03/Croxall-et-al-2012.pdf.">Threats to seabirds include</a> climate change, habitat loss, pollution, human fishing and the direct exploitation from harvesting eggs, chicks and adult birds for food and trophy hunting. Seabirds play a <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0129342">globally important</a> role in ecosystems, acting as predators, scavengers, nutrient subsidisers and ecosystem engineers, so understanding more about why they are going extinct is very important. </p>
<p>Our research builds the case for human hunting as the main cause of the great auk’s extinction, as well as reminding us how real the threat to today’s seabirds is. The findings also show why we need to thoroughly monitor commercially harvested species, particularly in poorly researched environments such as our oceans. This will help us better understand what is happening to the world’s threatened species and hopefully act before they follow the great auk into history.</p><img src="https://counter.theconversation.com/content/128273/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Jessica Emma Thomas received funding from NERC PhD Studentship (NE/L501694/1), the Genetics Society-Heredity Fieldwork Grant, and European Society for Evolutionary Biology–Godfrey Hewitt Mobility Award.</span></em></p>Understanding why the great auk went extinct could help protect species still living today.Jessica Emma Thomas, Postdoctoral Researcher, Swansea UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1262932019-12-03T16:19:13Z2019-12-03T16:19:13ZWhat we’ve learnt from building Africa’s biggest genome library<figure><img src="https://images.theconversation.com/files/301545/original/file-20191113-77310-1vdia49.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><span class="source">Shutterstock</span></span></figcaption></figure><p>The human genome was <a href="https://www.nature.com/scitable/topicpage/dna-sequencing-technologies-key-to-the-human-828/">first sequenced in 2003</a> by multiple research centres across the world. The breakthrough was hailed as the dawn of a new era. Genetics would swiftly transform our response to disease and lead to personalised medicine.</p>
<p>In the past decade there has been substantial progress in terms of <a href="https://www.ncbi.nlm.nih.gov/books/NBK19932/">studying</a> genetic factors giving rise to disease. But much of this has been focused on European populations. Little progress has been made in examining the factors associated with disease among Africans.</p>
<p>Until very recently, only a few hundred whole genome sequences of individuals within Africa had been completed. <a href="https://www.genome.gov/Funded-Programs-Projects/Population-Architecture-Using-Genomics-and-Epidemiology">Researchers</a> largely relied on genetic data from African-Americans. These have provided many new insights. But they don’t reflect the continent’s full genetic diversity.</p>
<p>Africa is known to be where humans originated. From Africa, they migrated to other parts of the world. This makes it the most genetically diverse region in the world. Diversity among other populations represents a subset of the diversity within Africa. </p>
<p>This genetic diversity provides unique opportunities to examine genetic factors associated with disease that can’t be examined in Europeans where diversity is much lower. This highlights the need for much larger studies of genetic causes of disease within Africa.</p>
<p>We conducted a <a href="https://www.cell.com/cell/ppt/S0092-8674(19)31120-1.ppt">study</a> to build one of the largest genome resources from within Africa. We developed a rich, diverse resource using genome wide data from 6,400 Ugandans – the Uganda Genome Resource. It included whole genome sequencing of nearly 2,000 people.</p>
<p>The study built on the long standing research programme of the <a href="https://www.mrcuganda.org/about/our-mission">Medical Research Council Uganda and Uganda Virus Research Institute</a>. Its aim has been to establish a clinical and genomic data resource to understand population health and disease in the region. </p>
<p>The team also incorporated data on 14,000 individuals from different parts of the continent. It did this in collaboration with the <a href="https://www.ukzn.ac.za/">University of KwaZulu-Natal</a> and the <a href="https://www.genome.gov/about-nhgri/Center-for-Research-on-Genomics-and-Global-Health">Centre of Genomics and Global Health</a>, National Institutes of Health. This allowed us to examine genetic determinants of traits within the population.</p>
<p>Around a quarter of the genetic variation identified had not been discovered before. We found a higher level of genetic diversity in the Ugandan population than seen in similar <a href="https://www.uk10k.org/studies/cohorts.html">studies</a> of European populations.</p>
<p>Modern Uganda appears to be a complex mosaic of genetic flow from many different communities that have migrated from surrounding regions within Africa – and from Europe or the Middle East. This gene flow appears to have occurred repeatedly, dating back from around 100 years ago to as long as 4,500 years ago.</p>
<p>Our work is an important step forward in African medical genetics research. But much more research is needed to understand how these genetic variants affect disease traits. That means looking at the functional effects of genomes on gene expression and protein levels. </p>
<h2>What we found</h2>
<p>In our study, we discovered ten new associations with blood traits, liver function tests and indicators of diabetes. Most of these new associations relate to genetic variants that are unique to the Ugandan population or very rare in non-Africans. These would not have been discovered even in very large studies of Europeans.</p>
<p>For example, we identified an association between a genetic variant that causes alpha-thalassemia, a blood disorder that leads to anaemia, and glycated haemoglobin levels, which are commonly used for diagnosis of diabetes. This genetic variant is found in 22% of Africans. It has become very common in some regions within Africa because it also protects against severe malaria. It remains very rare in other populations where malaria isn’t endemic. Our findings suggest that the utility of glycated haemoglobin as a diagnostic tool for diabetes may require re-evaluation in regions where alpha-thalassemia – a blood disorder that reduces the production of haemoglobin – is common. </p>
<p>The richness of the Uganda resource also offered us other opportunities. For example, we were able to study the extent to which genetic differences influence differences in traits among Ugandans relative to <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1557782/">previous studies</a> in <a href="https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003520">European</a> populations. We found that heritability – the extent to which genetic differences encode differences in traits or diseases – may differ between Ugandans and Europeans. </p>
<p>We also found that height is less genetically determined in rural Ugandans relative to <a href="https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003520">previous</a> <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1557782/">European studies</a>. We think that this might relate to differences in the impact of environmental factors between rural Ugandan and European populations. For example, the genetic influences on height might be more limited by nutritional influences in early childhood.</p>
<p>Our findings highlight the usefulness of examining genetically diverse populations within Africa. They underscore how this can lead to new discoveries and help us understand the genetic encoding of traits that may be different within Africa relative to other populations.</p>
<h2>Next steps</h2>
<p>Africa is central to our understanding of human origins, genetic diversity and disease susceptibility. There is a clear scientific and public health need to develop large-scale projects that examine disease susceptibility across diverse populations across the continent. That work should be integrated with initiatives to improve research capacity in Africa.</p>
<p>We now need larger and more diverse studies of genetic causes of disease across the region. These will foster the development of new treatments that will benefit people living in Africa as well as people of African descent around the world.</p>
<p>Future work will look at individuals from other parts of Africa. The aim will be to get a deeper understanding of genetic diversity among indigenous hunter-gatherer populations. These include the Khoe-San populations in Namibia and South Africa and the rain forest populations in central Africa. In addition, we will be expanding current studies of genetic causes of disease to 100,000 individuals across the region.</p>
<p><em>The data was collected by researchers from universities and research institutes from Africa and the UK, including Queen Mary University of London, the University of KwaZulu-Natal, MRC/UVRI & London School of Hygiene & Tropical Medicine Uganda Research Unit, the US National Institute of Health and the University of Cambridge.</em></p><img src="https://counter.theconversation.com/content/126293/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Deepti Gurdasani receives funding from the Medical Research Council, and is currently a UKRI HDR-UK career development fellow. </span></em></p><p class="fine-print"><em><span>Ayesha Motala receives funding from the Wellcome Trust.</span></em></p><p class="fine-print"><em><span>Segun Fatumo receives salary support from NIH grant U01MH115485 and the Makerere University-Uganda Virus Research Institute Centre of Excellence for Infection and Immunity Research and Training (MUII). MUII is supported through the DELTAS Africa Initiative (grant 107743). The DELTAS Africa Initiative is an independent funding scheme of the African Academy of Sciences (AAS), Alliance for Accelerating Excellence in Science in Africa (AESA), and supported by the New Partnership for Africa’s Development Planning and Coordinating Agency (NEPAD Agency) with funding from the Wellcome Trust (107743) and the U.K. government.</span></em></p><p class="fine-print"><em><span>Pontiano Kaleebu does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>Africa is known to be where humans originated. This makes it the most genetically diverse region in the world. Diversity in other populations represents a subset of the diversity within Africa.Deepti Gurdasani, Postdoctoral Fellow, Queen Mary University of LondonAyesha Motala, Professor and Head Department of Diabetes and Endocrinology, University of KwaZulu-NatalPontiano Kaleebu, Director of the MRC/Uganda Virus Research Institute, London School of Hygiene & Tropical MedicineSegun Fatumo, Assistant Professor of Genetic epidemiology & Bioinformatics, London School of Hygiene & Tropical MedicineLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1235042019-09-25T12:12:37Z2019-09-25T12:12:37ZSneaky lions in Zambia are moving across areas thought uninhabitable for them<figure><img src="https://images.theconversation.com/files/293046/original/file-20190918-187980-1ekemtt.jpg?ixlib=rb-1.1.0&rect=117%2C64%2C1151%2C824&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Where has this Zambian lion been?</span> <span class="attribution"><span class="source">Paula White</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span></figcaption></figure><p>Zambia, a country in southeast Africa, has approximately <a href="http://www.africanliongroup.org/uploads/5/0/0/7/5007626/session_minutes_final.pdf">1,200 lions</a>, one of the largest lion populations on the continent. More than 40% of the U-shaped country is <a href="http://doi.org/10.1371/journal.pone.0094109">protected land</a>, with over 120,000 square miles of national parks, sanctuaries and game management areas for lions to roam.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/293818/original/file-20190924-51463-5pwiyp.PNG?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/293818/original/file-20190924-51463-5pwiyp.PNG?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/293818/original/file-20190924-51463-5pwiyp.PNG?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=519&fit=crop&dpr=1 600w, https://images.theconversation.com/files/293818/original/file-20190924-51463-5pwiyp.PNG?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=519&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/293818/original/file-20190924-51463-5pwiyp.PNG?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=519&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/293818/original/file-20190924-51463-5pwiyp.PNG?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=652&fit=crop&dpr=1 754w, https://images.theconversation.com/files/293818/original/file-20190924-51463-5pwiyp.PNG?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=652&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/293818/original/file-20190924-51463-5pwiyp.PNG?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=652&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Zambia’s lion populations benefit from lots of protected lands.</span>
<span class="attribution"><a class="source" href="https://doi.org/10.1371/journal.pone.0217179">Curry et al., PLOS ONE 2019</a>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>Zambian lions are split into two subpopulations, with one in the Greater Kafue Ecosystem in the west and the other in the Luangwa Valley Ecosystem in the east. Between these two geographically different regions lies Lusaka, Zambia’s largest city, which is surrounded by farmland.</p>
<p>People had assumed that the two groups of lions <a href="https://doi.org/10.1007/s10531-012-0381-4">did not – even could not – mix</a>. After all, they’re separated by a geographical barrier: the two regions feature different habitats, with the east an offshoot of the Great Rift Valley system and the west part of the southern savannas. The lions are also separated by what’s called an <a href="https://allafrica.com/stories/201308110044.html">anthropogenic barrier</a>: a big city that lacks wildlife protection, making it seemingly unsuitable for lions.</p>
<p><a href="https://scholar.google.com/citations?user=a_TzvI0AAAAJ&hl=en&oi=ao">So my</a> <a href="https://www.researchgate.net/profile/Paula_White4">colleagues</a> <a href="https://scholar.google.com/citations?user=vAkgkSsAAAAJ&hl=en&oi=ao">and I</a> were surprised when we found that a small number of lions are in fact <a href="https://doi.org/10.1371/journal.pone.0217179">moving across the area</a> in between presumed to be uninhabitable by lions. These sneaky lions – and their mating habits – are causing the high levels of genetic diversity we found in the entire Zambian lion population.</p>
<h2>Identifying which genes are where</h2>
<p>Working with the Zambian Wildlife Authority, <a href="http://safariclubfoundation.org/zambia-lion-project/">biologist Paula White</a> collected hundreds of biological samples from lions across Zambia between 2004 and 2012. Eventually a box of this hair, skin, bone and tissue, meticulously packaged and labeled with collection notes and sampling locations, arrived at my lab at Texas A&M University.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/293826/original/file-20190924-51463-1693ods.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/293826/original/file-20190924-51463-1693ods.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/293826/original/file-20190924-51463-1693ods.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/293826/original/file-20190924-51463-1693ods.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/293826/original/file-20190924-51463-1693ods.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/293826/original/file-20190924-51463-1693ods.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/293826/original/file-20190924-51463-1693ods.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/293826/original/file-20190924-51463-1693ods.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=566&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Unwrapping African samples in a Texas lab.</span>
<span class="attribution"><span class="source">Caitlin J. Curry</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>Our goal was to investigate genetic diversity and the movement of various genes across Zambia by extracting and analyzing DNA from the lion samples.</p>
<p>From 409 lions found inside and outside of protected lands, I looked at two kinds of genes, mitochondrial and nuclear. You inherit mitochondrial DNA only from your mom, while you inherit nuclear DNA from both of your parents. Because of these differences, mitochondrial and nuclear genes can tell different genetic stories that, when combined, paint a more complete picture of how a population behaves.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/293828/original/file-20190924-51410-1jwh2lh.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/293828/original/file-20190924-51410-1jwh2lh.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/293828/original/file-20190924-51410-1jwh2lh.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=338&fit=crop&dpr=1 600w, https://images.theconversation.com/files/293828/original/file-20190924-51410-1jwh2lh.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=338&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/293828/original/file-20190924-51410-1jwh2lh.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=338&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/293828/original/file-20190924-51410-1jwh2lh.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=424&fit=crop&dpr=1 754w, https://images.theconversation.com/files/293828/original/file-20190924-51410-1jwh2lh.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=424&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/293828/original/file-20190924-51410-1jwh2lh.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=424&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Both nuclear (left) and mitochondrial (right) analyses show two genetically distinct Zambian lion subpopulations.</span>
<span class="attribution"><a class="source" href="https://unsplash.com/photos/f5CFy6-FaC4">Photo by Wade Lambert, diagram by Caitlin J. Curry</a>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>My mitochondrial analysis verified that, genetically, there are <a href="https://doi.org/10.1371/journal.pone.0143827">two isolated subpopulations of lions</a> in Zambia, one in the east and one in the west. However, by also looking at the nuclear genes, we found evidence that small numbers of lions are moving across the “unsuitable” habitat. Including nuclear genes provided a more complex picture that tells us not only which lions were moving but also where.</p>
<h2>Genes on the move as lions roam</h2>
<p>The amount of variation from alternate forms of genes found within a population is known as genetic diversity. Genetic diversity is important for a wildlife population because more genetic options give animals a greater chance for adaptation in a changing environment. Genetic diversity can also tell biologists about ways a population can fluctuate.</p>
<p>To a geneticist, migration, also referred to as <a href="https://evolution.berkeley.edu/evolibrary/article/evo_21">gene flow</a>, is the movement of genes from one geographical place to another. Mitochondrial DNA, inherited from the mother, can only tell researchers where genes from mom have been.</p>
<p>In the lion mating system, males travel long distances to find new prides, while females remain in or close to the pride they were born in. So, for the lion, it’s primarily males that are responsible for the movement of genes between prides. This male-mediated gene flow explains the lack of gene flow seen in mitochondrial genes compared to that of nuclear genes – female lions aren’t making the journey, but they do mate with new males who come from far away.</p>
<p>Male-mediated gene flow has helped keep the lions of Zambia genetically healthy, increasing genetic diversity by introducing new genes to new areas as male lions move between subpopulations. The eastern and western subpopulations each have high levels of genetic diversity; since only a few lions move between the groups each generation, the subpopulations stay genetically distinct.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/293829/original/file-20190924-51434-1bwagis.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/293829/original/file-20190924-51434-1bwagis.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/293829/original/file-20190924-51434-1bwagis.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=366&fit=crop&dpr=1 600w, https://images.theconversation.com/files/293829/original/file-20190924-51434-1bwagis.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=366&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/293829/original/file-20190924-51434-1bwagis.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=366&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/293829/original/file-20190924-51434-1bwagis.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=460&fit=crop&dpr=1 754w, https://images.theconversation.com/files/293829/original/file-20190924-51434-1bwagis.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=460&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/293829/original/file-20190924-51434-1bwagis.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=460&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">How genetically similar are individual lions? Represented by dots, individuals clustered together share more genes than those far apart. Lion dots are colored based on which national park they were found in.</span>
<span class="attribution"><a class="source" href="https://doi.org/10.1371/journal.pone.0217179">Curry et al, PLOS ONE, 2019</a>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>My colleagues and I were also able to determine where the lions are moving based on which individuals are more <a href="https://en.wikipedia.org/wiki/Isolation_by_distance">genetically similar to each other</a>. Lions in the North and South Luangwa National Parks, part of the eastern subpopulation, appear completely separated from the western subpopulation. Gene flow is occurring through the southern regions of the eastern subpopulation.</p>
<p>Lions are most likely traveling a route between the Lower Zambezi National Park and eastern corridor to the Kafue National Park in the west, possibly along the Kafue River. We can’t tell which way they’re moving, but by looking at where lions are more closely related, we can see where genes are being moved.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/293833/original/file-20190924-51463-q5av8i.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/293833/original/file-20190924-51463-q5av8i.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/293833/original/file-20190924-51463-q5av8i.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=453&fit=crop&dpr=1 600w, https://images.theconversation.com/files/293833/original/file-20190924-51463-q5av8i.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=453&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/293833/original/file-20190924-51463-q5av8i.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=453&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/293833/original/file-20190924-51463-q5av8i.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=570&fit=crop&dpr=1 754w, https://images.theconversation.com/files/293833/original/file-20190924-51463-q5av8i.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=570&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/293833/original/file-20190924-51463-q5av8i.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=570&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">It’s male lions that travel to find new prides.</span>
<span class="attribution"><span class="source">Paula White</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<h2>Lion data can help manage wildlife overall</h2>
<p>Human-lion conflict is a big issue in Zambia, <a href="https://www.cms.int/sites/default/files/document/ac27_cites_periodic_rev_status_african_lion_across_range_e.pdf">particularly outside of protected land</a>. If lions were moving across human dominated areas, you’d think they’d be seen and reported. But these lions are sneaking through virtually undetected – until we look at their genes. </p>
<p>As a large, charismatic carnivore, lion research and conservation influences many other species that share their habitat.</p>
<p>Wildlife managers can use these findings to help with lion conservation and other wildlife management in and around Zambia. Now that we generally know where lions are moving, managers can focus on these areas to find the actual route the big cats are taking and work to maintain or even increase how many lions can move across these areas. One of the ways of doing this is by creating more protected land, like corridors, to better connect suitable habitat.</p>
<p>[ <em>You’re smart and curious about the world. So are The Conversation’s authors and editors.</em> <a href="https://theconversation.com/us/newsletters?utm_source=TCUS&utm_medium=inline-link&utm_campaign=newsletter-text&utm_content=youresmart">You can read us daily by subscribing to our newsletter</a>. ]</p><img src="https://counter.theconversation.com/content/123504/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>This project received funding from Zambia Wildlife Authority, Professional Hunters Association of Zambia, Safari Hunters and Outfitters Association of Zambia, the Boore Family Foundation, Dallas Safari Club, Safari Club International Foundation and the Texas A&M Foundation. </span></em></p>Male lions are responsible for the movement of genes between prides. New research confirmed that the genes are traveling long distances – even though no one has been spotting the lions on the journey.Caitlin J. Curry, Phd Student in absentia of Veterinary Pathobiology, Texas A&M UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1167592019-05-10T14:38:45Z2019-05-10T14:38:45ZBiodiversity collapse: the wild relatives of livestock and crops are disappearing<p><a href="https://theconversation.com/revolutionary-change-needed-to-stop-unprecedented-global-extinction-crisis-116166">“Transformative change” is needed</a> to prevent a million species going extinct, according to <a href="https://www.ipbes.net/sites/default/files/downloads/spm_unedited_advance_for_posting_htn.pdf">a new report on the world’s biodiversity</a>. Based on information gathered over three years from land, freshwater and marine ecosystems, and drawing heavily from the <a href="https://www.iucnredlist.org/">IUCN Red List of Threatened Species</a>, the report from the Intergovernmental Platform on Biodiversity and Ecosystem Services warns that Earth’s life-support systems may collapse if humanity doesn’t change the way it values and uses nature.</p>
<p>But what does this mean for everyday life? “Biodiversity” – which describes the variety and abundance of species living on Earth – is a term which doesn’t travel far outside debate between scientists and policymakers. The consequences of the biodiversity crisis can seem abstract and difficult for many people to understand, particularly the implications for their own lives.</p>
<p>Think food, though, and the implications become clear.</p>
<h2>Genetic diversity and food security</h2>
<p>Modern livestock breeds and crop species have been bred to be highly productive, which means accentuating particular traits. Chickens have been <a href="https://theconversation.com/mysterious-museum-shows-how-humans-have-modified-nature-for-themselves-with-important-consequences-114800">bred to maintain a uniform size</a> for cost effective production, while fruit and vegetables have been <a href="https://www.businessinsider.com/what-foods-looked-like-before-genetic-modification?r=US&IR=T">bred to have thick, juicy flesh</a>. To concentrate these features within livestock and crop populations, plants and animals are bred with ever more genetically similar partners, leaving a shallow and homogeneous gene pool that is a poor defence against disease and environmental change.</p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/273800/original/file-20190510-183106-hczg2f.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/273800/original/file-20190510-183106-hczg2f.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=338&fit=crop&dpr=1 600w, https://images.theconversation.com/files/273800/original/file-20190510-183106-hczg2f.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=338&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/273800/original/file-20190510-183106-hczg2f.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=338&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/273800/original/file-20190510-183106-hczg2f.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=424&fit=crop&dpr=1 754w, https://images.theconversation.com/files/273800/original/file-20190510-183106-hczg2f.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=424&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/273800/original/file-20190510-183106-hczg2f.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=424&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Selective breeding by humans has created livestock species with very low genetic diversity.</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/baby-chickens-just-born-on-tray-1159174228?src=2aUvmlykYUnPBMrv6TbBiA-1-22">C.Lotongkum/Shutterstock</a></span>
</figcaption>
</figure>
<p>Wild relatives of domesticated plants and animals are the ancestral species from which crops and livestock have descended, or their near relatives. The pigs we raise for food are descended from wild boar (<em>Sus scrofa</em>) and chickens are descended from red jungle fowl (<em>Gallus gallus</em>) – a species that is widespread in Asia. These wild species are thought to be sufficiently closely related to domestic varieties that they could crossbreed to <a href="http://www.fao.org/publications/sowangr/en/">increase their genetic diversity</a>.</p>
<p>The wild relatives of domesticated species inhabit the rocky and icebound fastness of high mountain ranges, dense tropical forests and arid deserts. They’ve continued to evolve under natural conditions and so might contain genes that will help food species fight diseases and remain productive in a changing environment. Genetic diversity helps species survive long into the future, by increasing the likelihood that individuals will have helpful genetic quirks, such as immunity to a new disease. </p>
<p>As climate change makes some growing regions hotter and drier, wild relatives of corn that are drought-resistant could be crossbred with farmed varieties to make them more resilient. As new pathogens emerge, wild relatives of cows could crossbreed with cattle to bolster the immune defences encoded in their DNA.</p>
<p>These ancestral species and wild relatives are however, not all as common as junglefowl or wild boar. A worryingly large number are little known and highly threatened, or even on the verge of extinction. <a href="https://www.iucnredlist.org/species/22680384/129599398">Baer’s pochard</a> (<em>Aythya baeri</em>) is a critically endangered duck species from South East-Asia that is closely related to the mallard, from which the domestic duck is derived. The <a href="https://www.iucnredlist.org/species/2890/46363360">Kouprey</a> (<em>Bos sauveli</em>) from central Vietnam is a wild relative of the cow and may even be extinct in the wild.</p>
<p>Humans are relying on a narrowing base of species for food, using more and more commercially-bred livestock and crops while losing the wild relatives – the reservoir of genetic diversity. These genetic resources <a href="http://www.fao.org/3/i1823t/i1823t00.pdf">may become increasingly important</a> for feeding some nine billion people by 2050, in a world shaped by climate change and all the knock-on effects this will have for agriculture. </p>
<h2>Protecting wild relatives</h2>
<p>The status of wild relatives is, overall, <a href="https://onlinelibrary.wiley.com/doi/full/10.1111/conl.12588">worse than for birds and mammals generally</a>. Whereas 25% of all mammal species are considered threatened with extinction, more than half of mammals that are wild relatives of domesticated mammals are threatened. The figures for birds, while overall less threatened, show a similar pattern. Some 13% of all birds are threatened, compared with 31% of birds which are wild relatives of domesticated species like chickens and turkeys. </p>
<p>It’s perhaps unsurprising given that these species, like their intensively farmed relatives, are large-bodied and so once caught or killed provide a good source of nourishing food. That’s certainly the case for <a href="https://www.cambridge.org/core/journals/oryx/article/informing-decisions-on-an-extremely-data-poor-species-facing-imminent-extinction/ED0BCD3795CB129F712676F32409C808">Edwards’s pheasant</a> (<em>Lophura edwardsi</em>) – a critically endangered species which belongs to the same subfamily as chickens, native to South East-Asia and widely snared. A further 30 species are considered endangered, such as the <a href="https://www.iucnredlist.org/species/3126/46364222">Lowland Anoa</a> (<em>Bubalus depressicornis</em>), a close relative of the river buffalo and native to Indonesia.</p>
<p>Losing these wild relatives of domesticated animals seriously threatens the resilience of our food systems, by leaving crops and livestock genetically poorer. The IPBES report <a href="https://www.ipbes.net/aichi-targets/target-13">highlights this threat</a>. Countries will agree targets for protecting biodiversity in 2020 and the wild relatives of domesticated species should be chief among them.</p>
<p>We really do need a transformation in our relationship with nature, and this will have to include serious change in our diets and how food is produced. We will need wild relatives of important food species to ensure that genetic diversity can enhance food security in an increasingly uncertain future.</p><img src="https://counter.theconversation.com/content/116759/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Philip McGowan is Chair of the IUCN Species Survival Commission Post-2020 Biodiversity Targets Task Force</span></em></p><p class="fine-print"><em><span>Friederike Bolam is a member of the IUCN Species Survival Commission Post-2020 Biodiversity Targets Task Force.</span></em></p><p class="fine-print"><em><span>Louise Mair is a member of the IUCN Species Survival Commission Post-2020 Biodiversity Targets Task Force.</span></em></p>Biodiversity is in crisis. Nowhere is this more serious than among the wild species which our livestock and crops descend from.Philip McGowan, Senior Lecturer in Biodiversity and Conservation, Newcastle UniversityFriederike Bolam, Post-doctoral Research Associate in Biodiversity Policy, Newcastle UniversityLouise Mair, Research Associate in Biodiversity Conservation and Policy, Newcastle UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1099822019-01-17T11:36:31Z2019-01-17T11:36:31ZCoffee: 60% of wild species are at risk of extinction due to climate change<figure><img src="https://images.theconversation.com/files/254313/original/file-20190117-32825-1mio4p5.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/cup-coffee-smoke-beans-burlap-sack-582329227?src=LF-5eBaFLgxMgQ8xUzJmeQ-1-29">Amenic181/Shutterstock</a></span></figcaption></figure><p>Is your morning coffee an espresso or a skinny latte? Is it from a darkly roasted French or Italian blend? If it’s a high quality brew, it’s almost certainly made with beans from the Arabica species (<em>Coffea arabica</em>), which is known for its finer flavours. Examples would be Javan coffees, Ethiopian sidamo, and the expensive Jamaican blue mountain.</p>
<p>If you’ve stirred together an instant blend, it’s probably from a different species, Robusta (<em>Coffea canephora</em>), <a href="https://www.cirad.fr/en/our-research/tropical-supply-chains/coffee/plant-and-uses">known for its harsher taste</a>. But there are <a href="https://doi.org/10.1111/j.1095-8339.2006.00584.x">more than 100 species of coffee</a> in the wild. All produce similar beans that you could make a recognisable coffee drink from.</p>
<p>Robusta is sometimes openly mixed with Arabica in commercial products – and is often <a href="https://doi.org/10.1016/j.foodchem.2017.12.034">secretly used to adulterate</a> “100% Arabica” products, too. A third species, <em>Coffea liberica</em>, native to west and central Africa, is widely grown for local use in tropical countries, but is not globally traded because of its more bitter taste. </p>
<p>A fourth species <em>Coffea eugenoides</em> bred with Robusta to give rise to Arabica, a crossbreed. Another 38 closely related species are known or assumed to have <a href="http://advances.sciencemag.org/content/5/1/eaav3473">fertile pollen transfer with commercial coffees</a>.</p>
<p>There are a further 82 species which are more distantly related to the commercial breeds, but scientists could interbreed them with commercial coffees in a lab. All these coffee relatives can help enhance the genetic diversity of commercial coffee species, making them more adaptable to changes in their environment.</p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/254131/original/file-20190116-163274-1u0u5re.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/254131/original/file-20190116-163274-1u0u5re.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/254131/original/file-20190116-163274-1u0u5re.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/254131/original/file-20190116-163274-1u0u5re.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/254131/original/file-20190116-163274-1u0u5re.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/254131/original/file-20190116-163274-1u0u5re.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/254131/original/file-20190116-163274-1u0u5re.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Arabica coffee beans growing in Colombia.</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/closeup-coffee-fruit-farm-plantations-manizales-325255673?src=DfSQ0C3IhkISjNQ_X49WKg-1-6">Fotos593/Shutterstock</a></span>
</figcaption>
</figure>
<h2>Dark days ahead for coffee</h2>
<p>Climate change is <a href="https://theconversation.com/climate-change-is-causing-havoc-for-global-coffee-yields-25685">threatening global coffee yields</a> as changing temperatures and rainfall patterns affect plant growth. The changing climate may also be leaving plants <a href="https://doi.org/10.1098/rstb.2015.0458">more vulnerable to disease</a>.</p>
<p>All major commercial coffee growing countries have been badly affected by the fungal disease “<a href="http://www.bbc.com/future/story/20171106-the-disease-that-could-change-how-we-drink-coffee">coffee leaf rust</a>”, which spread across Africa and into Asia during the early 20th century, then to South America, becoming entrenched globally by the turn of the millennium.</p>
<p>The <a href="https://worldcoffeeresearch.org/work/applied-rd-coffee-leaf-rust/">Central American coffee rust outbreak</a> that began in the 2011-2012 harvest season affected 70% of farms in the region, resulting in over 1.7m lost jobs and US$3.2 billion in damage and lost income.</p>
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<em>
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Read more:
<a href="https://theconversation.com/climate-change-is-causing-havoc-for-global-coffee-yields-25685">Climate change is causing havoc for global coffee yields</a>
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<p>Robusta varieties used for the instant blends have been key to <a href="https://doi.org/10.1007/s12571-015-0446-9">developing resistance to coffee leaf rust</a> in Arabica varieties through cross breeding. As climate change and disease risks escalate, wild coffee species offer a crucial resource for maintaining the world’s coffee supply. Arabica has tightly limited geographic ranges in which it grows well and Robusta, while resistant to leaf rust, is vulnerable to <a href="https://www.researchgate.net/publication/277890144_Compendium_of_coffee_pests">other diseases</a>.</p>
<p><a href="http://advances.sciencemag.org/content/5/1/eaav3473">A recent study</a> led by the UK’s Kew Royal Botanic Gardens set the value of this variety in context: over 60% of coffee species are <a href="https://www.iucnredlist.org/">threatened with extinction</a>.</p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/254546/original/file-20190118-100267-chbbjx.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/254546/original/file-20190118-100267-chbbjx.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=485&fit=crop&dpr=1 600w, https://images.theconversation.com/files/254546/original/file-20190118-100267-chbbjx.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=485&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/254546/original/file-20190118-100267-chbbjx.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=485&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/254546/original/file-20190118-100267-chbbjx.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=610&fit=crop&dpr=1 754w, https://images.theconversation.com/files/254546/original/file-20190118-100267-chbbjx.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=610&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/254546/original/file-20190118-100267-chbbjx.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=610&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Leaf rust (<em>Hemileia vastatrix</em>) on a coffee plant.</span>
<span class="attribution"><a class="source" href="https://en.wikipedia.org/wiki/Hemileia_vastatrix#/media/File:Hemileia_vastatrix.jpg">Howard F. Schwartz/Wikimedia Commons</a>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
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<p>The authors explained that wild relatives of coffee are already used as local substitutes for globally traded commercial crops. They offer different climatic tolerance ranges and disease resistance traits that can help ensure global coffee production continues to meet demand. </p>
<p>But coffee species are particularly vulnerable to extinction because they occur in a small numbers of small geographic ranges – such as pockets of <a href="https://theconversation.com/ethiopias-vulnerable-tropical-forests-are-key-to-securing-future-of-wild-coffee-56516">wild Arabica populations</a> between certain altitude ranges in the Ethiopian highlands.</p>
<p>Wild coffee species – and wild varieties of the commercial species – are almost all <a href="https://doi.org/10.1126/sciadv.aav3473">in decline</a> due to competition for land use and overharvesting of the coffee plant for timber or firewood. A number of wild coffee relatives haven’t been spotted for many decades and may be extinct. </p>
<p>One species, the <a href="http://globaltrees.org/threatened-trees/trees/cafe-marron/">cafe marron</a>, from the remote island of Rodrigues in the Indian Ocean, was known from only one sighting in 1877. A century later, a schoolboy drew an “unusual” tree while exploring and showed it to a teacher. They recognised it as a surviving cafe marron. The sole surviving specimen of that wild coffee has inspired wider forest conservation on Rodrigues. It is also being cultured in lab collections at Kew.</p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/254324/original/file-20190117-32825-1ys2vrf.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/254324/original/file-20190117-32825-1ys2vrf.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=399&fit=crop&dpr=1 600w, https://images.theconversation.com/files/254324/original/file-20190117-32825-1ys2vrf.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=399&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/254324/original/file-20190117-32825-1ys2vrf.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=399&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/254324/original/file-20190117-32825-1ys2vrf.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=502&fit=crop&dpr=1 754w, https://images.theconversation.com/files/254324/original/file-20190117-32825-1ys2vrf.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=502&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/254324/original/file-20190117-32825-1ys2vrf.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=502&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Genetic diversity should also be considered in sustainability campaigns like Fairtrade.</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/city-ljubljana-slovenia-europe-3-january-318452198?src=BAgreBZ5FY9FkOhNJtFwAg-1-13">Peacepix/Shutterstock</a></span>
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<p>Sadly, there may be less hope for other species. Coffee seeds don’t store well, unlike wild relatives of other crops such as wheat or maize. So we can’t rely on <a href="https://theconversation.com/after-svalbard-why-safety-of-world-seed-vaults-is-crucial-to-future-food-security-79586">storage in seed banks</a> to conserve coffee diversity and resilience. Freezing plant matter in labs or growing samples in test tubes might be an alternative, but not one that has been explored beyond existing commercial strains.</p>
<p>Preserving different coffee varieties in botanic gardens isn’t really viable for protecting genetic diversity either. Coffee species readily fertilise each other, “<a href="https://doi.org/10.1007/s10722-012-9898-3">contaminating</a>” the resource you’re trying to conserve.</p>
<p>While some experts suggest we <a href="https://worldcoffeeresearch.org/work/global-coffee-conservation-strategy/">preserve coffee diversity in collections</a>, the Kew Gardens study argues that the sustainability of coffee depends on conservation of these species where they grow, in protected areas and working with communities throughout their native distribution in Africa and Asia.</p>
<p>Conserving genetic diversity should be included in existing approaches for sustainable coffee production, such as <a href="https://theconversation.com/food-security-how-fairtrade-helps-level-the-playing-field-for-small-producers-70937">Fair Trade</a> and <a href="https://www.rainforest-alliance.org">Rainforest Alliance</a> certifications. Ensuring the continuity of the coffee trade means protecting the ecosystems coffee comes from and the livelihoods of people across the <a href="https://theconversation.com/wheres-that-bean-been-coffees-journey-from-crop-to-cafe-30207">bean to coffee cup economy</a>.</p>
<p>We can also expect new flavours and even coffees with naturally low or zero caffeine content. Naturally caffeine-free Indian Ocean island cafe marron anyone?</p><img src="https://counter.theconversation.com/content/109982/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Adam Moolna does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>There are over 100 species of wild coffee, but only a few supply the world’s morning caffeine kick. Sadly, climate change and disease could be about to change that.Adam Moolna, Teaching Fellow in Environment and Sustainability, Keele UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1064322018-11-19T11:37:09Z2018-11-19T11:37:09ZA sharing economy for plants: Seed libraries are sprouting up<figure><img src="https://images.theconversation.com/files/246005/original/file-20181116-194516-3q61w9.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Got a license for those seeds?</span> <span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/collection-grain-cereal-seed-bean-agriculture-279330770?src=wD2_hxn-sejl7mmr-ftDyg-1-7">xuanhuongho/Shutterstock.com</a></span></figcaption></figure><p>Humans have been holding late-year <a href="https://www.ancient-origins.net/history-ancient-traditions/american-tradition-thanksgiving-harvest-festival-roots-old-world-004694">harvest celebrations</a> for millennia. Beyond bulking up for winter, these events have an enduring theme: Being grateful for what one has, while noting a duty to share one’s good fortune. </p>
<p>In my book, <a href="https://islandpress.org/books/food-sharing-revolution">“The Food Sharing Revolution: How Start-Ups, Pop-Ups, and Co-Ops are Changing the Way We Eat</a>,” I look at sharing from a variety of angles – good, bad and downright ugly. One example is the custom of seed sharing, which can be traced from indigenous societies and the <a href="https://www.ancient-origins.net/history-ancient-traditions/american-tradition-thanksgiving-harvest-festival-roots-old-world-004694">earliest fall festivals</a> that ultimately inspired American Thanksgiving. </p>
<p>For centuries, people in agrarian societies shared seeds to help each other subsist from year to year. Today, thanks to intellectual property rights and often well-intentioned laws, our ability to share seeds is restricted. Realizing this, food activists, garden enthusiasts and community leaders are trying to make it easier by making seeds available through libraries. Surely there’s nothing controversial about that, right? Actually, there is.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/246023/original/file-20181116-194509-45mjpr.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/246023/original/file-20181116-194509-45mjpr.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/246023/original/file-20181116-194509-45mjpr.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/246023/original/file-20181116-194509-45mjpr.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/246023/original/file-20181116-194509-45mjpr.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/246023/original/file-20181116-194509-45mjpr.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/246023/original/file-20181116-194509-45mjpr.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/246023/original/file-20181116-194509-45mjpr.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Seed swap at the ‘Harvesting Change: Food and Community’ gathering in Detroit, Michigan, May 20, 2014.</span>
<span class="attribution"><a class="source" href="https://flic.kr/p/nFP5ry">W.K. Kellogg Foundation</a>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<h2>Free seeds by mail</h2>
<p>Until the early 1800s, U.S. farmers either saved seed from their own crops or obtained it through personal networks. Then in 1819, Treasury Secretary William Crawford called upon all ambassadors and military officers stationed overseas to <a href="https://www.deltafarmpress.com/us-seed-law-history-primer">collect seeds and bring them home</a>, where they would be shared freely. </p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/246026/original/file-20181116-194494-oitvwj.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/246026/original/file-20181116-194494-oitvwj.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/246026/original/file-20181116-194494-oitvwj.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=994&fit=crop&dpr=1 600w, https://images.theconversation.com/files/246026/original/file-20181116-194494-oitvwj.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=994&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/246026/original/file-20181116-194494-oitvwj.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=994&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/246026/original/file-20181116-194494-oitvwj.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=1250&fit=crop&dpr=1 754w, https://images.theconversation.com/files/246026/original/file-20181116-194494-oitvwj.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=1250&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/246026/original/file-20181116-194494-oitvwj.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=1250&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Seed advertising card, 1887.</span>
<span class="attribution"><a class="source" href="https://flic.kr/p/eDXbPN">Boston Public Library</a>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<p>Initially this program was informal, but in 1839 Commissioner of Patents Henry Ellsworth persuaded Congress to appropriate funds for it. Ellsworth owned large tracts of land in the Midwest, so his motives may not have been strictly public-minded. Soon his office was distributing 60,000 seed packages annually through the U.S. mail. By the turn of the 20th century, the Department of Agriculture was shipping a billion free packages of seed each year.</p>
<p>This was relatively uncontroversial until 1883, when a group of representatives from mostly vegetable seed trade firms formed the American Seed Trade Association. No business model can work if the government gives away for free what private merchants want to sell.</p>
<p>After decades of lobbying, the group convinced Congress to end the free seed program in 1924. Without granting ownership rights to plant breeders, members argued, there would be no incentive to “improve” seed for qualities such as yield, tolerance, germination length, root depth or aesthetics. As <a href="https://www.jstor.org/stable/301768?seq=1#metadata_info_tab_contents">two plant breeders put it in 1919</a>: </p>
<blockquote>
<p>“The man who originates a new plant which may be of incalculable benefit to the whole country gets nothing – not even fame – for his pains, as the plants can be propagated by anyone.” </p>
</blockquote>
<p>The 1930 <a href="https://www.princeton.edu/%7Eota/disk1/1989/8924/892407.PDF">Plant Patent Act</a> was a watershed. It initially applied only to nursery plants propagated through cuttings, such as roses and apple trees. Soon, however, breeders of agricultural commodities pressed to expand the law in recognition of their labor. As a result, the majority of commercial crops and garden plants in use today were developed by agricultural companies, to the point that <a href="https://theconversation.com/counter-crop-patents-by-freeing-seeds-to-feed-the-world-29858">three companies</a> – Bayer Monsanto, DuPont and Syngenta – account for roughly 50 percent of all global seed sales.</p>
<p>Today the seed industry is highly controlled. <a href="https://www.betterseed.org/the-issues/state/#resources">Every state</a> has laws that require suppliers to obtain licenses, test seeds to ensure they are the variety advertised and properly label them. And the federal government regulates seed sales across state lines. </p>
<p>These laws exist for good reason. If farmers buy seed that turns out to be the wrong variety, or doesn’t germinate, their livelihood is at risk. Seed laws hold providers accountable and protect buyers. Some laws apply even to those who offer seeds for barter, exchange or trade.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/246028/original/file-20181116-194497-1gzcao4.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/246028/original/file-20181116-194497-1gzcao4.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/246028/original/file-20181116-194497-1gzcao4.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=554&fit=crop&dpr=1 600w, https://images.theconversation.com/files/246028/original/file-20181116-194497-1gzcao4.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=554&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/246028/original/file-20181116-194497-1gzcao4.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=554&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/246028/original/file-20181116-194497-1gzcao4.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=697&fit=crop&dpr=1 754w, https://images.theconversation.com/files/246028/original/file-20181116-194497-1gzcao4.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=697&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/246028/original/file-20181116-194497-1gzcao4.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=697&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Benton County Nursery Co. seed catalogue, 1960.</span>
<span class="attribution"><a class="source" href="https://commons.wikimedia.org/wiki/File:Benton_County_Nursery_Co.,_Inc_(1960)_(20355889112).jpg">Internet Archive Book Images</a></span>
</figcaption>
</figure>
<h2>Seed sharing redux: Seed libraries</h2>
<p>But another community pillar is distributing seeds without charge: Libraries. The process works much the same as with books. Patrons receive seeds and plant them, then allow some of their plants to go to seed and return those seeds to the library for others’ use.</p>
<p>According to some proponents, there are <a href="http://www.richmondgrowsseeds.org/sister-libraries.html">more than 660 seed libraries in 48 states</a>. <a href="https://omahalibrary.org/browse_program/seed-library/">Public libraries</a>, <a href="https://new.library.arizona.edu/seed-library">universities</a> and <a href="https://sites.google.com/a/d64.org/lincoln-middle-school-lrc/seed-library">secondary schools</a> are getting involved. Their motives range from <a href="https://grist.org/food/seeds-on-seeds-on-seeds-why-more-biodiversity-means-more-food-security/">preserving plant diversity</a> and <a href="https://www.law.georgetown.edu/poverty-journal/wp-content/uploads/sites/25/2018/05/25-2-Seed-Libraries-and-Food-Justice.pdf">local history</a> to <a href="https://www.newlibs.org/article/5045-a-place-for-seed-libraries-in-higher-education-setting-the-stage-for-new-outreach-and-engagement-initiatives">enhancing food access</a> and building regional agricultural resiliency in the face of <a href="https://doi.org/10.1080/09614524.2017.1294653">climate change</a>. </p>
<p>One of the nation’s first seed libraries is the <a href="https://www.sfchronicle.com/homeandgarden/article/Seed-libraries-sow-more-than-good-will-6545823.php">Bay Area Seed Interchange Library</a>, or BASIL, which opened in 2000 at the Berkeley Ecology Center in Berkeley, California and is run by volunteers. Sascha DuBrul, its founder, is said to have came up with the idea after wanting to <a href="http://www.mapstotheotherside.net/history-of-seed-libraries/">find a home for seeds</a> that were left when the University of California, Berkeley closed its campus farm. </p>
<figure>
<iframe width="440" height="260" src="https://www.youtube.com/embed/GvnQjMXQre4?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">A librarian from the Tulsa City and County Community Library in Oklahoma explains their seed program.</span></figcaption>
</figure>
<p>People who I interviewed for my research say the seed library movement has grown exponentially, starting with a few pioneers but expanding rapidly in the past five years. The movement includes food and community activists, gardeners, lawyers and citizens who support the idea that everyone has a right to seed. </p>
<p>Libraries don’t test seeds or place expiration dates on packaged seed, so some states have moved to regulate seed libraries. For example, in 2014 the Pennsylvania Department of Agriculture informed the Joseph T. Simpson Public Library in Mechanicsburg that it was <a href="https://cumberlink.com/news/agriculture/pa-department-backs-seed-library-protocol-as-reaction-grows/article_d3acf6fc-1cf2-11e4-adf9-0019bb2963f4.html">violating the state’s Seed Act of 2004</a> and needed to follow the same stringent requirements as agricultural supply companies. </p>
<p>Labels had to be in English and clearly state the plant’s species name or commonly accepted name, and the library had to conduct germination and purity analyses. Failure to do so, one county commissioner asserted, could threaten local food supplies through what she called “<a href="https://cumberlink.com/news/local/communities/carlisle/department-of-agriculture-cracks-down-on-seed-libraries/article_8b0323f4-18f6-11e4-b4c1-0019bb2963f4.html">agri-terrorism</a>.”</p>
<p>The seed library eventually reopened after officials
agreed that patrons would not be required to bring seed back to the
library, and that seeds it provided would be commercially packaged. It now hosts seed swap events to encourage person-to-person sharing. </p>
<p><div data-react-class="Tweet" data-react-props="{"tweetId":"957296412777164801"}"></div></p>
<h2>Defending the right to share</h2>
<p>Seed sharing advocates believe, as one who I will call Barry told me, that “people ought to be able share seeds without being treated like they’re Monsanto.” Many are alarmed by government crackdowns on seed libraries. </p>
<p>I met Barry in Lincoln, Nebraska, where he was advising state officials on adding an exemption to the state’s seed law for seed libraries. “I’ve made the rounds”, he confessed when asked how many states’ revised seed laws have his fingerprints on them.</p>
<p>Since 2015, states ranging from <a href="http://seedstock.com/2015/05/03/the-little-library-that-could-advocates-change-seed-exchange-laws-in-minnesota/">Minnesota</a> to <a href="http://www.nda.nebraska.gov/regulations/plant/NebraskaSeedLawRelatedStatutes.pdf">Nebraska</a>, <a href="https://www.chicagotribune.com/suburbs/daily-southtown/opinion/ct-sta-slowik-seed-library-st-0125-20170124-story.html">Illinois</a> and, more recently, <a href="https://www.ktva.com/story/38928684/new-legislation-legalizes-seed-trading-in-alaska">Alaska</a> have adopted such exemptions. In <a href="https://caldwell.ces.ncsu.edu/2017/02/caldwell-seed-library/">North Carolina</a>, seed libraries are legal thanks to a blanket seed sharing exemption that applies to all nonprofit oganizations. <a href="http://alfafarmers.org/stories/news-detail/seed-library-cultivates-community-connections#.W9yu1npKigQ">Alabama</a> exempts any providers who sell up to US$3,000 worth of seed. </p>
<p>In September 2016, California Governor Jerry Brown signed <a href="https://leginfo.legislature.ca.gov/faces/billTextClient.xhtml?bill_id=201520160AB1810">Assembly Bill 1810</a>, known among activists as the Seed Exchange Democracy Act, into law. The measure amended state law to exempt seed libraries from burdensome testing and labeling requirements.</p>
<p>Despite these successes, a number of activists I spoke with fear that agribusinesses seeking to protect their intellectual property rights will push back if the seed library movement keeps expanding. The hard reality is that sharing is not a right, even in this age of the so-called <a href="https://www.investopedia.com/terms/s/sharing-economy.asp">sharing economy</a>, if the thing people want to share is a valuable commodity.</p><img src="https://counter.theconversation.com/content/106432/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Michael Carolan receives funding from the Ministry of Education of the Republic of Korea, the National Research Foundation of Korea, and the National Institute of Food and Agriculture . </span></em></p>Sharing seeds was common practice among farmers throughout history until the rise of agribusiness. Now seeds are trademarked and regulated, but there’s a new place to get them for free: the library.Michael Carolan, Professor of Sociology and Associate Dean for Research & Graduate Affairs, College of Liberal Arts, Colorado State UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/957852018-05-03T03:15:05Z2018-05-03T03:15:05ZA DNA test says you’ve got Indigenous Australian ancestry. Now what?<figure><img src="https://images.theconversation.com/files/216969/original/file-20180501-135837-1ocfg5o.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Families have secrets - and sometimes we don't know our complete genetic histories. </span> <span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/vintage-photos-family-archive-shot-beginning-46788088?src=NrskIcPo5iSekbL9okj_cw-1-33">from www.shutterstock.com </a></span></figcaption></figure><p><em>Technologies for amplifying, sequencing and matching DNA have created new opportunities in genomic science. In this series <a href="https://theconversation.com/au/topics/when-dna-talks-53134">When DNA Talks</a> we look at the ethical and social implications.</em> </p>
<hr>
<p>Getting your “DNA done” is all the rage in the United States.</p>
<p>The sensationalism started with celebrities such as <a href="https://www.youtube.com/watch?v=MsEZBSTc3a0">Jessica Alba</a> and <a href="https://www.youtube.com/watch?v=Exz0yNdvksg">Snoop Dog</a> – and has now spread to hundreds of video bloggers disclosing their ancestry to <a href="https://www.youtube.com/watch?v=_5-GwlAVS3w">drum rolls</a>, <a href="https://www.youtube.com/watch?v=pK7bLFfzLwo">exclamations</a>, <a href="https://www.youtube.com/watch?v=b0EDNX47S20">cheers</a> and <a href="https://www.youtube.com/watch?v=MdpuGIZfR90">tears</a>. </p>
<p>These tests claim to reveal deep ancestral origins, and many public users of this technology are black Americans seeking information about their African roots. </p>
<figure>
<iframe width="440" height="260" src="https://www.youtube.com/embed/Exz0yNdvksg?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">Snoop Dog sent his DNA to be tested – and did the maths faster than this TV host.</span></figcaption>
</figure>
<p>The uptake of direct-to-consumer genetic testing has been slower in Australia. Here it is <a href="https://theconversation.com/dna-nation-raises-tough-questions-for-indigenous-australians-59877">complicated by debates</a> both beyond and within the Indigenous community – with some leaders calling for greater scrutiny to prevent “<a href="http://www.theaustralian.com.au/national-affairs/indigenous/push-for-aboriginal-id-tests-by-indigenous-leaders/news-story/a0bd39a868ad44a22dab85cf76cb9dc7">fakes</a>” or “<a href="http://www.theaustralian.com.au/national-affairs/indigenous/brawl-over-wannabe-and-tickabox-aborigines/news-story/d4a8a3a47cf478d08a17b7c466d09e66">wannabes</a>” calling themselves Indigenous.</p>
<p>One of the authors of this article – Shaun Lehmann – was dropped into this debate inadvertently, after receiving the result of his own DNA test a few years ago. </p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/dna-nation-raises-tough-questions-for-indigenous-australians-59877">DNA Nation raises tough questions for Indigenous Australians</a>
</strong>
</em>
</p>
<hr>
<h2>Professional and personal</h2>
<p>Shaun had more professional reasons for doing the test than most: at the time he was lecturing in human genetic diversity at the Australian National University and wanted to use his own genetic data as teaching tool.</p>
<p>He also had personal questions about his maternal grandmother, who had died when he was a small child. She had grown up without her mother and said little about her background.</p>
<p>Because they are related through a direct maternal line, Shaun knew that it was his grandmother, and by extension mysterious great-grandmother, who gave him his <a href="https://www.sciencedirect.com/science/article/pii/S0005272898001613">mitochondrial genome</a>.</p>
<p>Mitochondria are the tiny organelles that make energy in our cells. While the genome in the nucleus of our cells – our 23 pairs of chromosomes – is made up of a mix of our biological mother’s and father’s DNA, the relatively small mitochondrial genome is passed down through the egg and so reflects a single line of maternal ancestors.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/explainer-what-are-mitochondria-and-how-did-we-come-to-have-them-83106">Explainer: what are mitochondria and how did we come to have them?</a>
</strong>
</em>
</p>
<hr>
<p>What Shaun didn’t know at the time, and what the test revealed, was that his particular mitochondrial genome fell into a haplogroup (a grouping of similar mitochondrial genomes) called “S2”, which has <a href="https://onlinelibrary.wiley.com/doi/full/10.1002/9780470015902.a0020815.pub2">only been observed in Aboriginal Australians</a>.</p>
<h2>Interpreting genetic results</h2>
<p>Being mitochondrial DNA, Shaun knew exactly where to look in his genealogy to find out more. Sure enough, he soon found records that his grandmother’s maternal family were Aboriginal people originally from the Albany area of Western Australia. With this information in hand, Shaun was able to trace his family tree to living <a href="https://www.noongarculture.org.au/">Noongar</a> relatives.</p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/217371/original/file-20180502-153873-lchl0i.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/217371/original/file-20180502-153873-lchl0i.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/217371/original/file-20180502-153873-lchl0i.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=511&fit=crop&dpr=1 600w, https://images.theconversation.com/files/217371/original/file-20180502-153873-lchl0i.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=511&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/217371/original/file-20180502-153873-lchl0i.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=511&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/217371/original/file-20180502-153873-lchl0i.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=642&fit=crop&dpr=1 754w, https://images.theconversation.com/files/217371/original/file-20180502-153873-lchl0i.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=642&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/217371/original/file-20180502-153873-lchl0i.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=642&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">How mitochondrial DNA and nuclear DNA are passed on.</span>
<span class="attribution"><a class="source" href="https://commons.wikimedia.org/wiki/File:Mitochondrial_DNA_versus_Nuclear_DNA.gif">Wikimedia Commons</a>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<p>Shaun’s discovery was certainly aided by the fact that he is a geneticist and could interpret his DNA test results. Most important, though, was that his Aboriginal ancestry happened to be in the direct maternal line. </p>
<p>Mitochondrial DNA is a reliable source of genetic information about Aboriginal ancestry, but it can’t help at all if your Aboriginal ancestors sit anywhere else in your family tree. That is, it’s only useful to track direct from mother to grandmother to great grandmother and so on.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/friday-essay-when-did-australias-human-history-begin-87251">Friday essay: when did Australia’s human history begin?</a>
</strong>
</em>
</p>
<hr>
<h2>Different kinds of DNA tests</h2>
<p>Most of the “ethnic breakdown” DNA results being shared publicly by bloggers come from testing companies that compare their nuclear DNA with material from various ethnic groups. The tests focus on variations in specific regions of genes – known as single nucleotide polymorphisms, or SNPs. </p>
<p>To our knowledge, DNA testing companies do not currently have reliable reference SNP data from Indigenous Australians. </p>
<p><a href="http://www.dnatribes.com/">One company</a> offering tests claiming to identify Indigenous Australians uses an approach that compares sequences in genes known as <a href="https://www.nature.com/scitable/topicpage/forensics-dna-fingerprinting-and-codis-736">Short Tandem Repeats, or STRs</a>. STR data from around the world are widely available in the forensic science literature because these are widely used in <a href="https://www.sciencedirect.com/science/article/pii/S1687157X12000194">criminal investigations and paternity testing</a>. </p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/is-your-genome-really-your-own-the-public-and-forensic-value-of-dna-95786">Is your genome really your own? The public and forensic value of DNA</a>
</strong>
</em>
</p>
<hr>
<p>Ethical and scientific concerns have been raised about the use of STR data for commercial ancestry testing. For example, it is difficult to know how companies get their <a href="https://theconversation.com/dna-nation-raises-tough-questions-for-indigenous-australians-59877">reference samples</a>. </p>
<p>The case of American blogger <a href="http://lisagarrigues.blogspot.com.au/2011/01/dna-tribes-and-all-my-relations.html">Lisa Garrigues</a> is illustrative. Garrigues did a test back in 2010 – it reportedly gave her second “Highest Resolution Global Population Match” as “European-Aboriginal”.</p>
<p>She was excited by this discovery, but also sceptical – her family has no known connections to the Southern Hemisphere. Lisa and her father subsequently did <a href="http://lisagarrigues.blogspot.com.au/2011/05/">more thorough DNA testing</a>, and it didn’t suggest Aboriginal ancestry. </p>
<p>In our personal correspondence with one of the genetic genealogists who assisted Lisa, <a href="http://isogg.org/wiki/McDonald's_BGA_project">Doug McDonald</a> suggests these kind of inconsistencies are extremely common – STR markers are not designed for ancestry tests, but for matching individual people.</p>
<h2>After the test: now what?</h2>
<p>We need to be on the lookout for misinformation and unethical practices around genealogy testing. But even where the science is reliable, such as Shaun’s mitochondrial DNA test, the implications of identifying genetic Indigenous ancestry are far from clear.</p>
<p>Shaun was proud to learn about his ancestry and has since got in contact with his relatives. He is also looking into his grandmother’s past to find out whether her separation from her mother was influenced by the policies that led to the Stolen Generations. </p>
<p>Existing research suggests there are many possible endings for journeys like Shaun’s. <a href="http://www.podsocs.com/podcast/finding-aboriginal-identity/">Bindi Bennett’s work</a> highlights how young, light-skinned people who had no previous ties to the Aboriginal community can develop a strong Indigenous identity, even in the face of resistance from that community. </p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/culture-not-colour-is-the-heart-of-aboriginal-identity-30102">Culture, not colour, is the heart of Aboriginal identity</a>
</strong>
</em>
</p>
<hr>
<p>But <a href="http://librarycatalogue.griffith.edu.au/record=b1357619">Fiona Noble’s 1996 research</a> with Queenslanders who discovered their Aboriginal ancestry late in life suggests many of this demographic see their heritage as extremely important, but not all-defining. </p>
<p>They are more comfortable describing themselves as being “of Aboriginal descent” rather than “Aboriginal”. </p>
<p>As <a href="http://www.borderlands.net.au/vol7no2_2008/ganter_turning.pdf">Regina Ganter notes</a>, the “in-between” status of these “half-steps” is not well-recognised contemporary policy and discourse – which tends to frame Aboriginality as an either/or identity.</p>
<p>Although Noble and Bennett’s research participants discovered their heritage through documents or family stories, not genetics, their work offers a window onto a future where more Australians discover Aboriginal ancestry through DNA tests.</p>
<p>Without a doubt, the inevitable collision of Aboriginal and Torres Strait Islander Australia with direct-to-consumer genetic testing will continue to raise challenging questions about ancestry and identity in the 21st century. </p>
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Read more:
<a href="https://theconversation.com/dna-facial-prediction-could-make-protecting-your-privacy-more-difficult-94740">DNA facial prediction could make protecting your privacy more difficult</a>
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<img src="https://counter.theconversation.com/content/95785/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Emma Kowal receives funding from the Australian Research Council and the National Health and Medical Research Council.</span></em></p><p class="fine-print"><em><span>Elizabeth Watt and Shaun Lehmann do not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and have disclosed no relevant affiliations beyond their academic appointment.</span></em></p>Ancestry and identity are not the same thing. A scientist tells the story of what happened when he sent his DNA to an ancestry company.Elizabeth Watt, Research Fellow, Deakin UniversityEmma Kowal, Professor of Anthropology, Deakin UniversityShaun Lehmann, UNSW SydneyLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/730672017-02-26T16:58:55Z2017-02-26T16:58:55ZThe bushbaby family just got a new member. Here’s how we identified it<figure><img src="https://images.theconversation.com/files/157488/original/image-20170220-15931-7emet3.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><span class="source">hl_1001/Flickr</span></span></figcaption></figure><p>With their enormous eyes, impressive leaping skills and <a href="https://www.youtube.com/watch?v=SMgwBgQi_jk">strange cries</a>, galagids – more commonly known as bushbabies – are a familiar sight in sub-Saharan Africa. But there is still much we do not know about them. </p>
<p>The number of galagid species recognised today has more than tripled since the 1970s, from five to 18. The number of genera, or species groups, had risen from two to six. Now a seventh genus has been added, thanks to <a href="https://academic.oup.com/zoolinnean/article/2976136/A-new-genus-for-the-eastern-dwarf-galagos-Primates">research</a> conducted by my colleagues and I in the African Primate Initiative for Ecology and Speciation (<a href="http://www.ufh.ac.za/centres/apies/content/about-apies">APIES</a>) and our collaborators. </p>
<p>The detection of previously unknown diversity is always exciting. For starters, it has novelty value. It shows that we have, until now, underestimated the subtlety of natural variation. </p>
<p>But most importantly, newly recognised genetic populations carry their evolutionary history with them – and the history of their habitats. The detection of new species is important because it tells us about new populations with particular <a href="http://onlinelibrary.wiley.com/doi/10.1002/ajpa.23175/abstract">relationships to the environment</a>. A new genus provides more profound information about evolutionary history because it tells us about relationships among lineages that may reach deep into the past. </p>
<p>The emergence and extinction of species is closely linked to changes in earth’s environments and climates. So an accurate picture of the units of biodiversity is essential to understanding the nature of this interaction. This kind of information is crucial for forming conservation plans to defend vulnerable species against extinction – an increasingly urgent issue in the face of global climate change.</p>
<h2>Limited “clues” to true diversity</h2>
<p>Bushbabies (<a href="http://www.newworldencyclopedia.org/entry/Galago">Family Galagidae</a>) have only ever occurred in sub-Saharan Africa, where they have been evolving for at least 40 million years. They are nocturnal and relatively small; adult dwarf galagos weigh in at about 60g (the size of a large mouse) while the greater galagos can reach 1.5kg, the size of a cat.</p>
<p>Bushbabies are committed tree-dwellers although they may descend to the ground to feed or cross open areas. They have a number of adaptations that facilitate rapid and accurate movement through trees at night. These include their strong, grasping hands and feet, their elongated hind limbs and short forelimbs, and their large eyes fitted with mechanisms for accurate vision under low light intensities. </p>
<p>Understanding these animals’ true diversity is an ongoing task. This is because the bodies of different genera and species do not carry colourful flags or visual markers of identity, like many diurnal primates do. </p>
<p>For instance, most rain forest monkey species are distinguished by bright colour patterns on their faces and rumps that attract attention in gloomy forest. The lack of visually obvious markers in galagid species makes their recognition difficult to human observers – in the wild or even in museum collections. And true levels of genetic diversity may not be reflected in the animals’ external features. </p>
<p>The most reliable indicators of galagid species identity are the signals the animals use to communicate with one another at night. These include loud vocalisations and complex organic odours secreted by scent glands. The loud, repetitive call of the thick-tailed galago sounds like a baby crying, and has given rise to the common name “bushbaby”. Exploring these kinds of characteristics continues to inform us that our emphasis of visual differences has led us to underestimate biodiversity considerably.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/157497/original/image-20170220-15917-8x4s9c.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/157497/original/image-20170220-15917-8x4s9c.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/157497/original/image-20170220-15917-8x4s9c.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=397&fit=crop&dpr=1 600w, https://images.theconversation.com/files/157497/original/image-20170220-15917-8x4s9c.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=397&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/157497/original/image-20170220-15917-8x4s9c.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=397&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/157497/original/image-20170220-15917-8x4s9c.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=499&fit=crop&dpr=1 754w, https://images.theconversation.com/files/157497/original/image-20170220-15917-8x4s9c.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=499&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/157497/original/image-20170220-15917-8x4s9c.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=499&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
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<span class="caption">My, what big eyes you have!</span>
<span class="attribution"><span class="source">Reuters/Nikolay Doychinov</span></span>
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<p>Seven “dwarf galago” species have been identified to date, distributed across western and eastern Africa. They’re found in rain forests, <a href="http://wwf.panda.org/what_we_do/where_we_work/borneo_forests/about_borneo_forests/ecosystems/montane_forests/">montane forests</a> or lowland forests. </p>
<p>Earlier models of bushbaby evolution viewed these small species as closely related and ancient, giving tacit credence to a commonly held view in mammal evolution: that members of a lineage start out small and get bigger over time. The discovery that these species are not ancient and closely related turns this idea on its head.</p>
<h2>What we uncovered</h2>
<p><a href="https://academic.oup.com/zoolinnean/article/2976136/A-new-genus-for-the-eastern-dwarf-galagos-Primates">Our study</a> used information from DNA sequences, field observations and recordings of vocal repertoires. We also studied hundreds of specimens in natural history museums around the world, taking detailed measurements of bushbaby skulls and teeth. </p>
<p>All of this work demonstrated unequivocally that the dwarf bushbabies of West and East Africa have not shared a common ancestor for at least 20 million years. That’s half of the evolutionary history of the family. The fact that the species resemble one another so closely is a testament to evolutionary conservatism: if the structure of the habitat does not change substantially, neither will the organisms inhabiting it. Evolution is as much about change as it is about stasis.</p>
<p>As part of our field research, we also identified eastern dwarf galagos within South Africa’s boundaries, although the this genus was previously thought to be restricted to the eastern tropics. We have named the new genus <em>Paragalago</em>; it is the close relative of the genus <em>Galago</em>, which includes the “nagapies” (literally “little night monkeys” in Afrikaans) that are found in South Africa’s northern woodland savannas, but is likely to have evolved much further north, in East Africa.</p>
<p>So what do the new studies tell us about the history of bushbabies and Africa? </p>
<p>First, we now know that small body size is not a sign of early evolution in bushbabies. Galago ancestors are unlikely to have been smaller than between 500g and 700g. Dwarfing is a common evolutionary response to unpredictable environmental conditions, reflecting Africa’s past climate change. </p>
<p>Using genetic dating techniques, we estimate that both the western and the eastern dwarf galago lineages emerged around 10 million years ago. This coincides with the beginning of the expansion of grassland savannas in Africa, long before the African Rift Valley sundered the continent. Grasslands replace forests when the climate becomes cooler and drier, causing the forests and their faunas to fragment into small, patchy populations unable to interbreed. </p>
<p>The divergence of the <em>Paragalago</em> lineage would have been a response to this habitat disruption. But many other organisms that did not adapt to the new circumstances would have gone extinct. Forests are the most vulnerable of African habitats to climate change. The crisis we are currently witnessing will be similarly destructive to those in the past, and the survivors are unlikely to be tree-dwelling animals.</p><img src="https://counter.theconversation.com/content/73067/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Judith Masters receives funding from the National Research Foundation of South Africa. She is a founder member of the Africa Earth Observatory Network at Nelson Mandela University.</span></em></p>Newly recognised genetic populations carry their evolutionary history with them, and the history of their habits. This is why detecting new species is so important.Judith Masters, Professor of Zoology at the University of Fort Hare, University of Fort HareLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/725802017-02-08T06:16:36Z2017-02-08T06:16:36ZThe tragic story of Soviet genetics shows the folly of political meddling in science<figure><img src="https://images.theconversation.com/files/156003/original/image-20170208-9107-zsfxyp.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">In Soviet Russia, the science tests you.</span> <span class="attribution"><a class="source" href="https://en.wikipedia.org/wiki/File:CominternIV.jpg">Wikimedia</a></span></figcaption></figure><p>A few years ago, one of us (Ian) was lucky enough to be invited to visit the <a href="http://www.vir.nw.ru/">N.I. Vavilov Institute of Plant Industry</a> in St Petersburg, Russia. Every plant breeder or geneticist knows of Nikolai Vavilov and his ceaseless energy in collecting important food crop varieties from all over the globe, and his application of genetics to plant improvement. </p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/155999/original/image-20170208-9117-taku51.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/155999/original/image-20170208-9117-taku51.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/155999/original/image-20170208-9117-taku51.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=742&fit=crop&dpr=1 600w, https://images.theconversation.com/files/155999/original/image-20170208-9117-taku51.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=742&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/155999/original/image-20170208-9117-taku51.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=742&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/155999/original/image-20170208-9117-taku51.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=932&fit=crop&dpr=1 754w, https://images.theconversation.com/files/155999/original/image-20170208-9117-taku51.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=932&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/155999/original/image-20170208-9117-taku51.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=932&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
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<span class="caption">Nikolai Vavilov was pilloried because he wasn’t a political favourite in Soviet Russia.</span>
<span class="attribution"><a class="source" href="https://commons.wikimedia.org/wiki/File:Nikolai_Vavilov_NYWTS.jpg">Library of Congress. New York World-Telegram & Sun Collection</a></span>
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<p>Vavilov championed the idea that there were <a href="http://www.biodiversidad.gob.mx/v_ingles/genes/centers_origin/centers_plants1a.html">Centres of Origin (or Diversity)</a> for all plant species, and that the greatest variation was to be found in the place where the species evolved: wheat from the Middle East; coffee from Ethiopia; maize from Central America, and so on. </p>
<p>Hence the Centres of Origin (commonly known as the Vavilov Centres) are where you should start looking to find genotypes – the set of genes responsible for a particular trait – with disease resistance, stress tolerance or any other trait you are looking for. This notion applies to any species, which is why you can find more human genetic variation in some African countries than in the rest of the world combined.</p>
<p>By the late 1920s, as director of the <a href="https://en.wikipedia.org/wiki/VASKhNIL">Lenin All-Union Academy of Agricultural Sciences</a>, Vavilov soon amassed the largest seed collection on the planet. He worked hard, he enjoyed himself, and drove other eager young scientists to work just as hard to make more food for the people of the Soviet Union. </p>
<p>However, things did not go well for Vavilov politically. How did this visionary geneticist, who aimed to find the means for food security, end up starving to death in a Soviet gulag in 1943?</p>
<h2>Heroic science?</h2>
<p>Enter the villain, <a href="https://www.britannica.com/biography/Trofim-Lysenko">Trofim Lysenko</a>, ironically a protégé of Vavilov’s. The notorious Vavilov-Lysenko antagonism became one of the saddest textbook examples of a futile effort to resolve scientific debate using a political approach. </p>
<figure class="align-left zoomable">
<a href="https://images.theconversation.com/files/156000/original/image-20170208-9113-1terg9.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/156000/original/image-20170208-9113-1terg9.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/156000/original/image-20170208-9113-1terg9.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=774&fit=crop&dpr=1 600w, https://images.theconversation.com/files/156000/original/image-20170208-9113-1terg9.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=774&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/156000/original/image-20170208-9113-1terg9.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=774&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/156000/original/image-20170208-9113-1terg9.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=973&fit=crop&dpr=1 754w, https://images.theconversation.com/files/156000/original/image-20170208-9113-1terg9.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=973&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/156000/original/image-20170208-9113-1terg9.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=973&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Lysenko’s theories went against the latest science, but prevailed due to politics.</span>
<span class="attribution"><a class="source" href="https://commons.wikimedia.org/wiki/File:Lysenko_in_field_with_wheat.jpg">Wikimedia</a></span>
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<p>Lysenko’s name leapt from the pages of history and into the news when Australia’s Chief Scientist, Alan Finkel, <a href="http://www.smh.com.au/technology/sci-tech/donald-trump-like-stalin-says-chief-scientist-alan-finkel-as-science--literally-under-attack-20170206-gu6f5w.html">mentioned him during a speech</a> at a meeting of chief scientists in Canberra this week.</p>
<p>Finkel was harking back to Lysenko in response to news that US President Donald Trump had acted in January to <a href="http://www.reuters.com/article/us-usa-trump-epa-climatechange-idUSKBN15906G">censor scientific data regarding climate change</a> from the Environmental Protection Agency. Lysenko’s story reminds us of the dangers of political interference in science, said Finkel:</p>
<blockquote>
<p>Lysenko believed that successive generations of crops could be improved by exposing them to the right environment, and so too could successive generations of Soviet citizens be improved by exposing them to the right ideology.</p>
<p>So while Western scientists embraced evolution and genetics, Russian scientists who thought the same were sent to the gulag. Western crops flourished. Russian crops failed.</p>
</blockquote>
<p>The emerging ideology of Lysenkoism was effectively a jumble of pseudoscience, based predominantly on his rejection of <a href="http://anthro.palomar.edu/mendel/mendel_1.htm">Mendelian genetics</a> and everything else that underpinned Vavilov’s science. He was a product of his time and political situation in the young USSR.</p>
<p>In reality, Lysenko was what we might today call a crackpot. Among other things, he denied the existence of DNA and genes, he claimed that plants selected their mates, and argued that they could acquire characteristics during their lifetime and pass them on. He also espoused the theory that some plants choose to sacrifice themselves for the good of the remaining plants – another notion that runs against the grain of evolutionary understanding. </p>
<p>Pravda – formerly the official newspaper of the Soviet Communist Party – celebrated him for finding a way to fertilise crops without applying anything to the field. </p>
<p>None of this could be backed up by solid evidence. His experiments were not repeatable, nor could his theories claim overwhelming consensus among other scientists. But Lysenko had the ear of the one man who counted most in the USSR: Joseph Stalin. </p>
<h2>Head to head</h2>
<p>The Lysenko vs Vavilov/Mendel/Darwin argument came to a head in 1936 at the <a href="https://www.marxists.org/subject/science/essays/speeches.htm">Conference of the Lenin Academy</a> when Lysenko presented his “-ism”. </p>
<p>In the face of scientific opinion, and the overwhelming majority of his peers, Pravda declared Lysenko the winner of the argument. By 1939, after quite a few scientists had been imprisoned, shot or “disappeared”, including the director of the Lenin Institute, there was a vacancy to be filled. And the most powerful man in the country filled it with Trofim Lysenko. Lysenko was now Vavilov’s boss.</p>
<p>Within a year, Vavilov was captured on one of his collection missions and interrogated for 11 months. He was accused of being a spy, having travelled to England and the United States, and been a regular correspondent with many geneticists outside the Soviet Union. </p>
<p>It did not help his cause that he came from a family of business people, whereas Lysenko was of peasant stock and a Soviet ideologue. Vavilov was sent to a gulag where, tragically, he died in 1943. </p>
<p>Meanwhile, his collection in Leningrad was in the middle of a 900-day siege. It only survived thanks to the sacrifice of his team who formed a militia to prevent the starving population (and rats) from eating the collection of more than 250,000 types of seeds, fruits and roots – even growing the potatoes in their stock near the front to ensure the tubers did not die before losing their viability.</p>
<p>In 1948, the Lenin Academy announced that Lysenkoism should be taught as the only correct theory, and that continued until the mid-1960s. </p>
<h2>Redemption and regrowth</h2>
<p>Thankfully, in the post-Stalin era, Lysenko was slowly sidelined along with his theory. Today it is Vavilov who is considered a Soviet hero. </p>
<p>In 1958, the Academy of Science began awarding <a href="https://en.wikipedia.org/wiki/Named_prizes_and_medals_of_the_Russian_Academy_of_Sciences">a medal in his honour</a>. The leading Russian plant science institute is <a href="http://www.vir.nw.ru/">named in his honour</a>, as is the <a href="http://en.sgau.ru/">Saratov State Vavilov Agrarian University</a>. In addition, <a href="https://en.wikipedia.org/wiki/2862_Vavilov">an asteroid</a>, a <a href="http://lunarnetworks.blogspot.com.au/2012/01/view-from-vavilov.html">crater on the Moon</a> and two <a href="http://www.tandfonline.com/doi/abs/10.1080/10889378409377213">glaciers</a> bear his name.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/156002/original/image-20170208-9139-1m5zj99.gif?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/156002/original/image-20170208-9139-1m5zj99.gif?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/156002/original/image-20170208-9139-1m5zj99.gif?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=340&fit=crop&dpr=1 600w, https://images.theconversation.com/files/156002/original/image-20170208-9139-1m5zj99.gif?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=340&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/156002/original/image-20170208-9139-1m5zj99.gif?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=340&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/156002/original/image-20170208-9139-1m5zj99.gif?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=427&fit=crop&dpr=1 754w, https://images.theconversation.com/files/156002/original/image-20170208-9139-1m5zj99.gif?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=427&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/156002/original/image-20170208-9139-1m5zj99.gif?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=427&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Trofim Lysenko speaking at the Kremlin in 1935, with Stalin on the far right.</span>
<span class="attribution"><a class="source" href="https://commons.wikimedia.org/wiki/File:Lysenko_with_Stalin.gif">Wikimedia</a></span>
</figcaption>
</figure>
<p>Since 1993, <a href="https://www.bioversityinternational.org/">Bioversity International</a> has awarded <a href="http://www.bioversityinternational.org/about-us/latest-news/news/tag-news/vavilov-frankel-fellowship/">Vavilov Frankel</a> (after Australian scientist <a href="https://www.science.org.au/fellowship/fellows/biographical-memoirs/otto-frankel-1900-1998">Otto Frankel</a>) fellowships to young scientists from developing countries to perform innovative research on plant genetic resources. </p>
<p>Meanwhile, research here in Australia, led by ARC Discovery Early Career Fellow <a href="https://qaafi.uq.edu.au/profile/108/lee-hickey">Lee Hickey</a>, we are continuing to find <a href="http://link.springer.com/article/10.1007/s10722-016-0380-5">new genetic diversity for disease resistance</a> in the Vavilov wheat collection.</p>
<p>In the post-Soviet era, students of genetics and agriculture in Russia are taught of the terrible outcomes of the applications of Lysenkoism to Soviet life and agricultural productivity. </p>
<p>Lysenkoism is a sad and terrible footnote in agricultural research, more important as a sadly misused “-ism” in the hands of powerful people who opt for ideology over fact. It’s also a timely reminder of the dangers of political meddling in science.</p><img src="https://counter.theconversation.com/content/72580/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Ian Godwin receives funding from the Australian Research Council, the Grains Research and Development Corporation, the Rural Industries Research and Development Corporation, the Australian Centre for International Research and the Queensland government.</span></em></p><p class="fine-print"><em><span>Yuri Trusov receives funding from the Australian Research Council. </span></em></p>When politics meddles with science, it can lead to tragedy, as was the case with Stalin’s favourite agricultural biologist Trofim Lysenko and his rival Nikolai Vavilov.Ian Godwin, Professor in Plant Molecular Genetics, The University of QueenslandYuri Trusov, Plant molecular biologist, The University of QueenslandLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/689902016-11-28T07:39:13Z2016-11-28T07:39:13ZThe end of coconut water? The world’s trendiest nut is under threat of species collapse<figure><img src="https://images.theconversation.com/files/147448/original/image-20161124-15344-1glvuux.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><span class="source">www.shutterstock.com</span></span></figcaption></figure><p>“Orange juice for breakfast is over,” an investor interested in creating large, fair trade coconut plantations recently joked to me. These days, coconut water is king.</p>
<p>For the trendy and the wealthy, including <a href="http://time.com/4488043/a-major-coconut-shortage-with-global-consequences-may-have-hit-the-caribbean/">celebrities</a> such as Rihanna, Madonna or Matthew McConaughey, <a href="http://www.dailymail.co.uk/money/markets/article-3804564/Avocado-coconut-water-prices-hit-high-set-rise-insatiable-demand-superfoods.html">rarest coconut water</a> extracted from the <a href="http://www.cogentnetwork.org/images/publications/catalog/countries/Thailand_271-273.pdf">aromatic varieties</a> of the nut, is the “it” drink and even a <a href="http://www.billboard.com/articles/news/471632/madonna-rihanna-team-up-for-coconut-water-campaign">source of income</a>. </p>
<p>Coconut water is <a href="http://www.wsj.com/articles/coconuts-go-upscale-boosting-price-of-conventional-coconut-oil-1460017362">being sold</a> by luxury brands, at up to US$7 for 33 cl, about the same price as basic champagne.</p>
<h2>A booming market</h2>
<p>There is no doubt that the coconut market is exploding. Coconut water currently represents an annual turnover of US$2 billion. It is expected to reach <a href="http://www.technavio.com/pressrelease/global-coconut-water-market-to-grow-at-a-high-cagr-of-more-than-25-by-2019-says">US$4 billion</a> in the next five years. </p>
<p>In 2007, a 25% stake in <a href="http://vitacoco.com/">Vitacoco</a>, the largest brand for coconut water, was sold for <a href="http://www.forbes.com/2009/06/04/vita-coco-zico-one-leadership-cmo-network-coconutwater.html">US$7 million</a> to <a href="http://verlinvest.be/portfolio/357-2/">Verlinvest</a> company. Seven years later, another 25% stake in Vitacoco was again sold to <a href="http://www.reignwood.com/red_bull.asp">Red Bull China</a> for about <a href="http://www.businesswire.com/news/home/20140714005327/en/Vita-Coco%C2%AE-Coconut-Water-Sells-25-Stake">US$166 million</a>.</p>
<p>Other large players in the coconut water business include <a href="http://www.coca-colacompany.com/press-center/press-releases/zico-8482-beverages-joins-the-coca-cola-family">Coca-Cola</a> and <a href="https://cu.pepsico.com/one/one-company-info">PepsiCo</a>, but more than <a href="http://www.businesswire.com/news/home/20160420005041/en/Technavio-Announces-Top-Vendors-Coconut-Water-Market">200 brands</a> are now marketing coconut water.</p>
<h2>An essential crop</h2>
<p>But there’s another side to the story. The coconut is one of 35 food crops listed in <a href="http://www.fao.org/fileadmin/templates/agphome/documents/PGR/PubPGR/ResourceBook/annex1.pdf">Annex 1</a> of the <a href="http://www.fao.org/plant-treaty/en/">International Treaty on Plant Genetic Resources for Food and Agriculture</a> and considered crucial to global food security. In 2014, <a href="http://faostat.fao.org/beta/en/#data/QC">the Food and Agriculture Organization</a> estimated global production to be 61.5 million tonnes. </p>
<p>It is an important livelihood crop for more than <a href="http://aciar.gov.au/files/node/748/pr125_pdf_50866.pdf">11 million farmers</a>, most of whom are smallholders, cultivating coconut palms on around 12 million hectares of land in at least 94 countries worldwide. The coconut palm is popularly known as the “<a href="http://aciar.gov.au/publication/pr125">Tree of Life</a>” – all its parts are useful. </p>
<p>The main products are copra – the dried inner meat of the nut, used for oil – and the husk, which provides a vital source of fibre. More recently, as we’ve seen, there is also high demand for tender coconut water and virgin coconut oil. </p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/147350/original/image-20161124-15359-1aiysgw.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/147350/original/image-20161124-15359-1aiysgw.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/147350/original/image-20161124-15359-1aiysgw.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/147350/original/image-20161124-15359-1aiysgw.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/147350/original/image-20161124-15359-1aiysgw.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/147350/original/image-20161124-15359-1aiysgw.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/147350/original/image-20161124-15359-1aiysgw.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Braiding ropes made from the husk of the <em>niu magi magi</em> variety on Taveuni Island, Fiji, 2012.</span>
<span class="attribution"><a class="source" href="https://www.flickr.com/photos/cogent-network/9422183592/in/photostream/">Cogent/Roland Bourdeix</a>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>Whole mature nuts are exported and sold to factories that produce desiccated coconut and coconut cream. At least half of the coconuts are <a href="http://diversiflora.blogspot.fr/2005/10/new-book-on-coconut-varieties-and.html">consumed locally</a>.</p>
<h2>Genetic diversity</h2>
<p>Over millennia, humans have slowly selected and maintained numerous coconut varieties, used for many purposes.</p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/146597/original/image-20161118-19348-1wijyq0.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/146597/original/image-20161118-19348-1wijyq0.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/146597/original/image-20161118-19348-1wijyq0.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=855&fit=crop&dpr=1 600w, https://images.theconversation.com/files/146597/original/image-20161118-19348-1wijyq0.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=855&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/146597/original/image-20161118-19348-1wijyq0.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=855&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/146597/original/image-20161118-19348-1wijyq0.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=1074&fit=crop&dpr=1 754w, https://images.theconversation.com/files/146597/original/image-20161118-19348-1wijyq0.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=1074&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/146597/original/image-20161118-19348-1wijyq0.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=1074&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Diversity of coconut fruits in <em>ex situ</em> genebanks.</span>
<span class="attribution"><span class="source">Roland Bourdeix</span></span>
</figcaption>
</figure>
<p>This has resulted in an extraordinary morphological diversity, which is expressed in the range of colours, shapes and sizes of the fruits. But the extent of this diversity is largely unknown at the global level. The <a href="http://link.springer.com/chapter/10.1007/978-0-387-71201-7_10#page-1">huge amount of work</a> that has gone into coconut breeding by farmers over millennia, and by scientists during the 20th century, remains greatly under-valued.</p>
<p>The rarest coconut varieties, for instance the <a href="http://cocotierpolynesie.blogspot.fr/2010/12/les-cocotiers-cornes.html">horned coconut</a>, grown and conserved on the <a href="http://polymotu.blogspot.fr/2010/10/premieres-plantations-du-conservatoire.html">Tetiaroa Atoll</a> and in <a href="http://www.indianjournals.com/ijor.aspx?target=ijor:ijpgr&volume=27&issue=1&article=024">India</a>, are not even recognised as coconuts by most people, especially Westerners.</p>
<h2>Coconut conservation</h2>
<p>The genetic diversity found in coconut populations and varieties, known by scientists as “germplasm”, is conserved by millions of small farmers.</p>
<figure class="align-left ">
<img alt="" src="https://images.theconversation.com/files/146730/original/image-20161121-4555-zzwqio.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/146730/original/image-20161121-4555-zzwqio.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=899&fit=crop&dpr=1 600w, https://images.theconversation.com/files/146730/original/image-20161121-4555-zzwqio.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=899&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/146730/original/image-20161121-4555-zzwqio.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=899&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/146730/original/image-20161121-4555-zzwqio.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=1129&fit=crop&dpr=1 754w, https://images.theconversation.com/files/146730/original/image-20161121-4555-zzwqio.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=1129&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/146730/original/image-20161121-4555-zzwqio.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=1129&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">A Samoan teen holds the famous <em>niu afa</em> coconut variety.</span>
<span class="attribution"><span class="source">Roland Bourdeix</span></span>
</figcaption>
</figure>
<p>A number of initiatives have been launched to recognise and support the role of these farmers, and to sustain them by promoting <a href="http://www.bioversityinternational.org/uploads/tx_news/Polymotu__a_new_concept_of_island-based_germplasm_bank_based_on_an_old_Polynesian_practice_1519.pdf">landscape management approaches</a>, such as the <a href="http://polymotu.blogspot.fr/2010/10/premieres-plantations-du-conservatoire.html">Polymotu concept</a> (“poly” meaning many, and “Motu” meaning island in Polynesian.)</p>
<p>The <a href="http://polymotu.blogspot.fr/">Polymotu concept</a> capitalises on the geographical or reproductive isolation of various species for the conservation and reproduction of individual varieties of plants, <a href="http://polymotu.blogspot.fr/2009/11/polymotu-precursors-pathi-maprao-kathi.html">trees</a> and even <a href="http://polymotu.blogspot.fr/2010/10/polymotu-precursors-bird-conservation.html">animals</a>. </p>
<p>In a project led by the <a href="https://lrd.spc.int/our-work/genetic-resources/centre-for-pacific-crops-and-trees/polymotu-conserves-special-coconut-varieties-in-the-pacific">Pacific Community</a> and funded by the <a href="https://www.croptrust.org/crop/coconut/">Global Crop Diversity Trust</a>, two small islands in <a href="http://coconutsamoa.blogspot.fr/2013/06/the-conservation-of-samoas-niu-afa.html">Samoa</a> have been recently replanted with the famous traditional <a href="http://coconutsamoa.blogspot.fr/2010/03/13.html"><em>niu afa</em></a> variety, which produces the largest coconut fruits in the world, reaching <a href="http://coconutsamoa.blogspot.fr/2010/03/19.html">more than 40 cm long</a>.</p>
<p>Sadly, the coconut is endangered. One of the main challenges of coconut cultivation is the existence of lethal diseases, which are <a href="https://www.youtube.com/watch?v=-rqb1-OITXI">rapidly expanding</a> and killing millions of palms. These pandemics are known as <a href="http://journal.frontiersin.org/article/10.3389/fpls.2016.01521/full">lethal yellowing diseases</a>. </p>
<p>The diseases ravage countries in Africa (in Tanzania, <a href="http://pub.epsilon.slu.se/13381/">Mozambique</a>, <a href="http://link.springer.com/chapter/10.1007/978-94-017-7294-5_3">Ghana</a>, <a href="http://search.proquest.com/openview/f10ab2ed27703a1f724d524301b93b2d/1?pq-origsite=gscholar&cbl=2032679">Nigeria</a>, <a href="http://agritrop.cirad.fr/439684/">Cameroon</a>, <a href="http://www.tandfonline.com/doi/abs/10.1080/07060661.2014.899275">Côte d’Ivoire</a>), and also in Asia (<a href="http://apsjournals.apsnet.org/doi/abs/10.1094/pdis-94-5-0636b">India</a>), North America (<a href="http://www.sciencedirect.com/science/article/pii/S088557651500003X">Mexico</a>, <a href="http://www.ndrs.org.uk/article.php?id=029012">the Caribbean</a>, <a href="http://onlinelibrary.wiley.com/doi/10.1111/j.1744-7348.2008.00240.x/full">Florida</a>) and the Pacific Region (<a href="https://www.youtube.com/watch?v=sivQAg_4yrQ&list=PLBZ3LrHoN5qxfSNYa129wwdhwKV6LuBq-">Papua New Guinea</a>, and probably <a href="http://link.springer.com/article/10.1007/s13314-015-0163-4">Solomon Islands</a>).</p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/147361/original/image-20161124-15325-166kfik.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/147361/original/image-20161124-15325-166kfik.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/147361/original/image-20161124-15325-166kfik.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/147361/original/image-20161124-15325-166kfik.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/147361/original/image-20161124-15325-166kfik.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/147361/original/image-20161124-15325-166kfik.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/147361/original/image-20161124-15325-166kfik.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">The genetic diversity of the flowers of coconut varieties on display at the Marc Delorme Research Centre, Côte d'Ivoire.</span>
<span class="attribution"><a class="source" href="https://www.flickr.com/photos/cogent-network/9416154688/">COGENT</a>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<h2>Diversity under threat</h2>
<p>Many coconut varieties that could be crucial for the future of agriculture are disappearing because of the loss of traditional knowledge, rapid transformations of agricultural landscapes, climate change and westernisation.</p>
<p>Due to the fragility of insular ecosystems, the <a href="http://www.cogentnetwork.org/images/publications/Scientific/Bourdeixetal_Biodiversity.pdf">Pacific Region</a> is probably the location where the losses are highest.</p>
<p>During <a href="http://coconutfreaks.blogspot.fr/2016/11/the-seven-in-one-coconut-palm-in.html">a recent survey in the Cook Islands</a>, we succeeded with considerable difficulty in locating a <a href="http://cocotierpolynesie.blogspot.fr/2010/10/14.html">sweet husk</a> palm, known as <em>niu mangaro</em> locally. This is a rare, highly threatened form of coconut. </p>
<p>The husk of its unripe fruit, which in other species is usually tough and astringent, is tender, edible and sweet. It can be chewed like sugarcane. Once the fruits are ripe, the husk fibres are white and thin. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/147331/original/image-20161124-15359-d2h0z6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/147331/original/image-20161124-15359-d2h0z6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/147331/original/image-20161124-15359-d2h0z6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/147331/original/image-20161124-15359-d2h0z6.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/147331/original/image-20161124-15359-d2h0z6.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/147331/original/image-20161124-15359-d2h0z6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/147331/original/image-20161124-15359-d2h0z6.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/147331/original/image-20161124-15359-d2h0z6.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">A comparison of the husk of a normal coconut (left) and a rare sweet husk coconut (right).</span>
<span class="attribution"><span class="source">Roland Bourdeix</span></span>
</figcaption>
</figure>
<p>Our survey was conducted together with a government agricultural officer. During the work, he took a tender coconut and started to chew the husk. Then he stopped, telling me, “I do not want people here to see me eating <em>niu mangaro</em>, because they will say I am a poor man.”</p>
<p>The consumption of traditional varieties being still perceived as socially stigmatising, not embracing a “modern” way of life. On the other hand, <a href="http://www.cookislandsnews.com/item/47171-fao-identifies-way-to-boost-cook-islands-agriculture/47171-fao-identifies-way-to-boost-cook-islands-agriculture">the consumption of imported food</a> is considered as a mark of modernity and richness. </p>
<p>During <a href="http://cocotierpolynesie.blogspot.fr/">another survey conducted in 2010</a> in Moorea Island, a Polynesian farmer interviewed about sweet husk varieties, known as <em>kaipoa</em> there, told me:</p>
<blockquote>
<p>I had one <em>kaipoa</em> coconut palm in my farm, but I cut it down two years ago … Over ten years, I was unable to harvest a single fruit: all were stolen and eaten by children from the neighbourhood. </p>
</blockquote>
<p>So, a traditional variety remains appreciated by the next generation of Polynesians, but the farmer is not aware of the rarity and of the cultural value of the resource.</p>
<figure>
<iframe width="440" height="260" src="https://www.youtube.com/embed/-rqb1-OITXI?wmode=transparent&start=18" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">Coconut lethal yellowing disease in Côte d'Ivoire: state of emergency. A video from Diversiflora International.</span></figcaption>
</figure>
<p>The social and economic factors affecting coconut conservation have been the subject of discussion at two international meetings organised in 2016 by the <a href="http://www.apccsec.org/apccsec/media.php?page=home">Asia and Pacific Coconut Community</a> in Indonesia and the <a href="http://www.cpcri.gov.in/">Central Plantation Crop Research Institute</a> in India. </p>
<p>Discussions included the constraints and advantages related to coconut biology; links with conservation in institutional field gene banks; <a href="http://reprocrop.blogspot.fr/">farmer’s knowledge</a> regarding the <a href="http://reprocrop.blogspot.fr/2015/02/biologie-reproductive-des-especes.html">reproductive biology</a> of their crop; socioeconomic dynamics; and policy measures. </p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/147060/original/image-20161122-10994-mivfte.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/147060/original/image-20161122-10994-mivfte.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=342&fit=crop&dpr=1 600w, https://images.theconversation.com/files/147060/original/image-20161122-10994-mivfte.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=342&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/147060/original/image-20161122-10994-mivfte.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=342&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/147060/original/image-20161122-10994-mivfte.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=430&fit=crop&dpr=1 754w, https://images.theconversation.com/files/147060/original/image-20161122-10994-mivfte.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=430&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/147060/original/image-20161122-10994-mivfte.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=430&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Nursery of coconut seedlings from the Green Dwarf variety for production of coconut water in Brazil.</span>
<span class="attribution"><a class="source" href="https://www.flickr.com/photos/cogent-network/9506087965/">Roland Bourdeix</a>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<h2>Big business, but little money for research</h2>
<p>The <a href="http://www.cogentnetwork.org/">International Coconut Genetic Resources Network</a> (COGENT) now comprises <a href="http://www.cogentnetwork.org/faq/131-countries">41 coconut-producing countries</a>, representing more than 98% of global production. Its activities are focused on conservation and breeding of coconut varieties. </p>
<p>Coconut germplasm is represented by <a href="http://www.cogentnetwork.org/faq/139-exsitu">about 400 varieties</a> and <a href="http://www.cogentnetwork.org/images/FAQ/2012_04_1680_accessions_ranked_per_name.pdf">1,600 accessions</a> in 24 genebanks. <a href="http://www.cogentnetwork.org/faq/141-faq-accession-cultivar">Accessions</a> are the basic units of genebanks. </p>
<p>In the case of the coconut palm, each accession is generally constituted of 45 to 150 palms, all collected at the same location. They are documented in a <a href="http://www.cogentnetwork.org/cgrd-version-6-0-test-version">Coconut Genetic Resources Database</a> and a <a href="http://www.cogentnetwork.org/conserved-germplasm-catalogue">global catalogue</a>. </p>
<p><a href="http://www.cogentnetwork.org/climbing-the-coconut-palm">COGENT</a> also works on sequencing the <a href="http://publications.cirad.fr/une_notice.php?dk=577727">coconut genome</a>, in the framework of a collaboration between research organisations in <a href="http://www.cnra.ci/">Côte d’Ivoire</a>, <a href="http://www.cirad.fr/en/home-page">France</a> and <a href="http://www.catas.cn/newDefault/search">China</a>.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/146615/original/image-20161118-19340-1kr20x2.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/146615/original/image-20161118-19340-1kr20x2.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/146615/original/image-20161118-19340-1kr20x2.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/146615/original/image-20161118-19340-1kr20x2.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/146615/original/image-20161118-19340-1kr20x2.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/146615/original/image-20161118-19340-1kr20x2.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/146615/original/image-20161118-19340-1kr20x2.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/146615/original/image-20161118-19340-1kr20x2.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Cultivating legumes in a coconut plantation devastated by the Lethal Yellowing Disease in Ghana.</span>
<span class="attribution"><span class="source">Roland Bourdeix</span></span>
</figcaption>
</figure>
<p>Despite the upturn in the global market, many coconut farmers remain insufficiently organised, and investment in coconut research is incredibly scarce.</p>
<p>A yearly investment of about US$3 to US$5 million in public international research would be enough to address most of the challenges of coconut agriculture. But private companies benefiting from the market boom are still scarcely involved in research funding. </p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/146614/original/image-20161118-19361-5odcvc.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/146614/original/image-20161118-19361-5odcvc.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/146614/original/image-20161118-19361-5odcvc.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=863&fit=crop&dpr=1 600w, https://images.theconversation.com/files/146614/original/image-20161118-19361-5odcvc.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=863&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/146614/original/image-20161118-19361-5odcvc.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=863&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/146614/original/image-20161118-19361-5odcvc.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=1085&fit=crop&dpr=1 754w, https://images.theconversation.com/files/146614/original/image-20161118-19361-5odcvc.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=1085&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/146614/original/image-20161118-19361-5odcvc.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=1085&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Coconut harvesters dance between trunks in Ghana.</span>
<span class="attribution"><span class="source">Roland Bourdeix</span></span>
</figcaption>
</figure>
<p>The coconut is a perennial crop, producing fruit year-round, but it takes a long time to grow. Investors, more interested in rapid profits, remain reluctant to fund the ten-year research programmes that are often needed to efficiently address the <a href="http://www.cogentnetwork.org/about-cogent/strategy">challenges of coconut research</a>.</p>
<p>In coconut-producing countries, <a href="http://www.cogentnetwork.org/network-projects/past-projects/upgrading-genebanks">under-resourced genebanks</a> and laboratories lack the necessary budget, labour, equipment and technical training to <a href="http://www.cogentnetwork.org/climbing-the-coconut-palm">conduct the controlled hand-pollinations</a> required for regenerating the germplasm, and to implement other activities such as <a href="http://www.cogentnetwork.org/images/publications/Coconut_genetic_resources.pdf">collecting, characterisation and breeding</a>.</p>
<p>Coconut water brands will only make billions as long as coconuts are plentiful and diverse. More importantly, people all over the world rely on the security of this vital crop. Securing its future must be a priority for everyone who farms, eats and profits from the coconut.</p><img src="https://counter.theconversation.com/content/68990/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Dr Roland Bourdeix is affiliated with the CIRAD, UMR AGAP, is President of Diversiflora International</span></em></p>Coconut water may be the ‘it’ drink, but its producers face multiple threats.Roland Bourdeix, Senior Researcher, CiradLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/685792016-11-10T19:14:29Z2016-11-10T19:14:29ZSwingers’ hookup program can find the right match for endangered species<figure><img src="https://images.theconversation.com/files/145383/original/image-20161110-26331-arizba.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">The program can work well for polygamous species such as gorillas.</span> <span class="attribution"><span class="source">Mary Ann McDonald/shutterstock.com</span></span></figcaption></figure><p>A quick look at the popularity of online dating services like <a href="https://www.okcupid.com/">OkCupid</a> and <a href="http://www.eharmony.com.au/">eHarmony</a> shows us that people are pretty comfortable with letting an algorithm choose them a mate. Now we at the <a href="http://www.molecularecology.flinders.edu.au/">Flinders Molecular Ecology Lab</a> want to do a similar thing for other animals.</p>
<p>With human-driven extinctions on the rise, many species are likely to be left relying on captive breeding for their survival. We hope that our algorithm will help ensure these breeding programs are successful, by pairing up matches who will have healthy, thriving offspring.</p>
<p>Unlike human dating services, we cannot ask a snake, fish or possum to answer questions. But we can look at their DNA. This allows us to breed individuals who are not closely related, avoiding the genetic problems that arise from inbreeding, and thus producing healthy populations with a diverse gene pool.</p>
<p>We have created <a href="http://www.molecularecology.flinders.edu.au/molecular-ecology-lab/software/swinger/swinger/">Swinger</a>, a computer program that uses DNA profiling to matchmake endangered animals for captive breeding - especially those that have multiple mates - and which we describe in a paper <a href="http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12609/full">published in the journal <em>Molecular Ecology Resources</em></a>. We envision it helping to conserve many endangered animals, with the first animals being native freshwater fishes in Australia.</p>
<h2>It’s all in the DNA</h2>
<p><a href="https://en.wikipedia.org/wiki/Genetic_diversity">Genetic diversity</a> is crucial, because it helps populations to adapt and evolve in response to environmental changes that they may encounter in the future. So maintaining a large gene pool is an important consideration for captive breeding programs, particularly in populations that have already dwindled to small numbers. This makes avoiding inbreeding vitally important. </p>
<p>Many species kept in zoos – such as pandas – have clear family relationships or are bred in pairs and so their parentage is certain. Armed with pedigree information, it is relatively easy for zoos to select unrelated breeding pairs, often by working in collaboration with other zoos.</p>
<p>But most animals in the world are polygamous, with each individual naturally having multiple partners, even around the same time. This is where it becomes harder to track family relationships, unless you can examine their DNA.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/145365/original/image-20161110-26334-d7urcw.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/145365/original/image-20161110-26334-d7urcw.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/145365/original/image-20161110-26334-d7urcw.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=398&fit=crop&dpr=1 600w, https://images.theconversation.com/files/145365/original/image-20161110-26334-d7urcw.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=398&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/145365/original/image-20161110-26334-d7urcw.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=398&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/145365/original/image-20161110-26334-d7urcw.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=501&fit=crop&dpr=1 754w, https://images.theconversation.com/files/145365/original/image-20161110-26334-d7urcw.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=501&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/145365/original/image-20161110-26334-d7urcw.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=501&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">It’s easier with pandas - well, the choosing part at least.</span>
<span class="attribution"><a class="source" href="https://commons.wikimedia.org/wiki/File%3ASichuan_Panda.jpg">Ritesh251123/Wikimedia Commons</a>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span>
</figcaption>
</figure>
<p>The matchmaking algorithm is also ideal for starting a captive breeding program from individuals newly brought into captivity. This is because we often have no idea about their relationships to each other, except through DNA, and they may be highly related individuals.</p>
<p>The very circumstances that brought about the need for captive breeding also often results in inbreeding in wild populations. This is because the population has reduced in size to the point that individuals may unavoidably breed with their close relatives. This makes it especially important to ensure breeding in captivity occurs between unrelated individuals.</p>
<h2>Captive breeding of swingers</h2>
<p>Even when dealing with such serious issues as extinction, we like to keep a sense of humour – hence the name Swinger, which we feel is pretty appropriate given that individuals of most species in the world are naturally polygamous. Indeed, our algorithm is just as suitable for setting up polygamous breeding groups as monogamous ones.</p>
<p>The algorithm is inspired by <a href="http://www.molecularecology.flinders.edu.au/uploads/54834/ufiles/pdf/166_WA.pdf">our efforts to save freshwater fishes in Australia</a>. Native freshwater fish lineages recently became at risk of extinction due to human activities during the Millennium Drought in the Murray-Darling Basin, in southeastern Australia. The fish needed to be saved by their removal from the wild before their habitat completely dried out.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/145359/original/image-20161110-26334-196bs2v.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/145359/original/image-20161110-26334-196bs2v.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/145359/original/image-20161110-26334-196bs2v.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=399&fit=crop&dpr=1 600w, https://images.theconversation.com/files/145359/original/image-20161110-26334-196bs2v.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=399&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/145359/original/image-20161110-26334-196bs2v.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=399&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/145359/original/image-20161110-26334-196bs2v.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=501&fit=crop&dpr=1 754w, https://images.theconversation.com/files/145359/original/image-20161110-26334-196bs2v.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=501&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/145359/original/image-20161110-26334-196bs2v.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=501&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Test species: Running River rainbowfish.</span>
<span class="attribution"><span class="source">Steven Hume</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>We created breeding groups of these rescued polygamous fish. This was done by using DNA information to create, by hand, “swinger” groups of unrelated individuals. <a href="http://www.abc.net.au/news/2016-03-04/pygmy-perch-population-in-lower-murray-darling-recover/7219228">The breeding was successful, with offspring reintroduced to the wild</a>. However, the breeding groups were unavoidably sub-optimal because at that time we had no algorithm to work out the best possible mates for individuals.</p>
<p>Swinger is now being used to <a href="http://www.lateralmag.com/articles/issue-16/watered-down">save native rainbowfish in northern Queensland</a>. Although it is still early days, the rainbowfish breeding has been very successful, producing thousands of fingerlings that our collaborators are releasing to the wild.</p>
<p>We are also using Swinger to inform the design of a breeding program of endangered species of Galápagos giant tortoises previously considered extinct. These tortoises <a href="https://theconversation.com/how-we-rediscovered-extinct-giant-tortoises-in-the-galapagos-islands-and-how-to-save-them-52073">were rediscovered in a remote volcano and moved to the captive breeding facility</a> of the Galápagos National Park. The aim is to reintroduce the captive-born offspring to the island where they evolved.</p>
<p>The brilliance of DNA is that it is in all living things. This means that Swinger could potentially be used to help breed all endangered species with sexual reproduction - especially, of course, the many polygamous species.</p>
<p>To borrow another concept from the world of human dating, there will hopefully soon be “<a href="http://www.pof.com/">Plenty of Fish</a>” as a result of our efforts.</p><img src="https://counter.theconversation.com/content/68579/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Catherine R. M. Attard has received funding from the Australian Government and other organisations.</span></em></p><p class="fine-print"><em><span>Luciano Beheregaray receives funding from the Australian Research Council.</span></em></p><p class="fine-print"><em><span>Jonathan Sandoval Castillo does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>Computer dating for animals? Finding the right matchup - using DNA rather than personality questionnaires - could help select the best partnerships for captive breeding programs.Jonathan Sandoval Castillo, Postdoctoral Fellow Molecular Ecology, Flinders UniversityCatherine R. M. Attard, Lecturer in Molecular Ecology, Flinders UniversityLuciano Beheregaray, Professor in Biodiversity Genetics and ARC Future Fellow, Flinders UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/565162016-03-23T10:30:24Z2016-03-23T10:30:24ZEthiopia’s vulnerable tropical forests are key to securing future of wild coffee<figure><img src="https://images.theconversation.com/files/115633/original/image-20160318-4417-gveub2.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Wild coffee grows here – and nowhere else.</span> <span class="attribution"><span class="source">Indrias Getachew</span>, <span class="license">Author provided</span></span></figcaption></figure><p>Coffee is the drink of choice for millions of us. But the world’s <a href="http://www.investorguide.com/article/11836/%20what-are-the-most-commonly-traded-commodities-igu/">second-most traded commodity</a> originates in Ethiopia – and its home is under threat.</p>
<p>Ethiopia isn’t all dusty deserts – far from it. The country also contains rugged highlands and lush, tropical forests. <em>Coffea arabica</em> grows here in its original, wild form. The forests of south-west Ethiopia are considered to be the birthplace of coffee and the centre of its genetic diversity. </p>
<p>But these forests and this gene pool are under pressure. It is already one of the last major woodlands remaining in Ethiopia, and deforestation over the past 40 years has resulted in <a href="http://wetlandsandforests.hud.ac.uk/ntfp-pfm/pdfs/Briefing%20Notes/Atlas%20of%20NTFP%20Project%20Area%20Land%20Cover%20Change.pdf">the loss of one-third of the south-west’s forest cover</a>. We risk losing the forests entirely in coming decades.</p>
<p>It is critical that these forests are protected. Commercially grown coffee has been bred over the years to ensure high yields and other useful characteristics. But it is descended from a small number of individual plants, and so relies on a relatively <a href="http://www.bbc.co.uk/news/magazine-32736366">narrow genetic range</a> – just 10% of the diversity <a href="http://www.kew.org/science-conservation/plants-fungi/environment/crops-and-their-wild-plant-relatives">found in the wild</a>. This makes it vulnerable to pests – and climate change is an additional threat. </p>
<p>Wild coffee on the other hand exhibits much greater genetic diversity, which increases its chances of adapting to new challenges and reduces the possibility of extinction. It represents an insurance policy for plantation coffee, in case commercial strains are ever badly damaged. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/115807/original/image-20160321-30926-1vcvxd.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/115807/original/image-20160321-30926-1vcvxd.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/115807/original/image-20160321-30926-1vcvxd.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/115807/original/image-20160321-30926-1vcvxd.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/115807/original/image-20160321-30926-1vcvxd.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/115807/original/image-20160321-30926-1vcvxd.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/115807/original/image-20160321-30926-1vcvxd.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/115807/original/image-20160321-30926-1vcvxd.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Tariku Mengesha, a local co-operative worker, harvests ripe wild coffee cherries.</span>
<span class="attribution"><span class="source">Indrias Getachew</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>These forests also play a <a href="http://wetlandsandforests.hud.ac.uk/ntfp-pfm/pdfs/Briefing%20Notes/Costs%20of%20Deforestation%20in%20SW%20Ethiopia.pdf">critical role</a> as a “water tower” for the river Nile – serving lowland Ethiopia, South Sudan and Egypt, storing carbon to stabilise the climate and enhancing rainfall upwind in the often drought-affected, northern highlands of Ethiopia.</p>
<p>But maintaining these forests is difficult. Rainfall in the south-west is good and the soil fertile and there is a long history of people moving here for farming, including from the drier and more densely settled north of the country. This, alongside investor interest in commercial coffee and tea plantations, has seen agricultural land encroach on the forest. Without adequate resources to police such a large area, the forest became “open access” – anyone could go in and take what they wanted and they rarely got apprehended.</p>
<p>In an effort to protect the country’s forest resources, the Ethiopian government adopted a nationwide policy of <a href="http://eprints.hud.ac.uk/24976/">Participatory Forest Management</a> (PFM), which bestows management responsibilities on communities that live near the forest and have had traditional rights to it.</p>
<p>Communities elect “forest management groups”, which include women, to administer their bit of forest for which they have secured tenured rights from the government. This helps them control access to the forest and stop deforestation. In return for the secure tenure and usage rights, the community has to ensure that the natural forest is maintained, which they do through regular monitoring.</p>
<p>This all takes time – a precious resource if you are a subsistence farmer. Rights to use coffee, honey, spices and other forest products provides an additional livelihood for people and compensation for looking after the forest. By making the forest pay it becomes a competitive land use, better able to compete with agriculture and motivating people to protect it and its valuable resources.</p>
<p>Over the past six years, the <a href="http://wetlandsandforests.hud.ac.uk/forests/wcc/wild_coffee_index.html">Wild Coffee Conservation Project</a> has worked with 55 forest management groups to secure more than 60,000 hectares of forest under these PFM agreements. Results to date look promising – deforestation in the project area has been reduced to <a href="http://wetlandsandforests.hud.ac.uk/pdf/wild-coffee-conservation.pdf">a twelfth</a> of that in non-project areas.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/115814/original/image-20160321-30917-1fklrpd.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/115814/original/image-20160321-30917-1fklrpd.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/115814/original/image-20160321-30917-1fklrpd.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/115814/original/image-20160321-30917-1fklrpd.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/115814/original/image-20160321-30917-1fklrpd.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/115814/original/image-20160321-30917-1fklrpd.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/115814/original/image-20160321-30917-1fklrpd.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/115814/original/image-20160321-30917-1fklrpd.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Members of the local community discuss forest management.</span>
<span class="attribution"><span class="source">Indrias Getachew</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>Furthermore, cooperatives set up to market forest products collected by locals have succeeded in producing a high-quality coffee from the wild strands in the forest. This has sold on the international market for the highest price ever for Ethiopian sun-dried coffee – three times the average non-wild price. </p>
<p>This is encouraging, but the project and communities need to do more to get a competitive edge over agriculture. We need carbon and other ecosystem payments (payment to landowners in exchange for managing their land in a way that conserves natural resouces), all of which help with the maintenance of biodiversity. And we need to develop market links for forest spices and honey.</p>
<p>Securing the future of wild coffee and the forests it lives in needs local people to maintain and use these forests, to earn a living from them so they can afford to protect them in the long term and want to do so. Such a system is sustainable – unlike many of the protectionist approaches such as <a href="http://www.unesco.org/new/en/natural-sciences/environment/ecological-sciences/biosphere-reserves/">Biosphere Reserves</a> which rely on fluctuating government funds and which exclude people from the forest. Forest people are the solution to this problem: we need to give them the responsibility for the forest, so that they can save it – and the wild coffee gene pool within it – if we want to continue to enjoy our lattes and cappuccinos in the future.</p>
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<p><em>Watch <a href="https://www.youtube.com/watch?v=tDJE4YP2JUs">this video</a> to learn more about the Wild Coffee Conservation project in Ethiopia.</em></p><img src="https://counter.theconversation.com/content/56516/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Fiona Hesselden receives funding for the WCC Project from the EU Delegation to Ethiopia, The Darwin Initiative (UK Government) and the Horn of Africa Regional Environment Centre. The authors are soley responsible for the views expressed in this article and they do not necessarily reflect those of the funders. </span></em></p><p class="fine-print"><em><span>Adrian Wood is receives funding from the EU and the Darwin Initiative (UK government) and HOAREC.</span></em></p>Protecting this ecosystem helps local people and secures coffee’s long-term genetic future.Fiona Hesselden, Researcher, Centre for Sustainable and Resilient Communities, University of HuddersfieldLicensed as Creative Commons – attribution, no derivatives.