tag:theconversation.com,2011:/us/topics/genomics-3639/articles
Genomics – The Conversation
2024-02-27T12:41:39Z
tag:theconversation.com,2011:article/219140
2024-02-27T12:41:39Z
2024-02-27T12:41:39Z
Could a couple of Thai otters have helped the UK’s otter population recover? Our study provides a hint
<p>Otter populations crashed in Britain around the 1960s from the lethal effects of chemical pollution in rivers and lakes – or so we thought. <a href="https://academic.oup.com/mbe/article/40/11/msad207/7275014">Our research</a> has looked more closely at what happened to otters in Britain over the last 800 years and has revealed a more complex picture. </p>
<p>Since Eurasian otters (<em>Lutra lutra</em>) are at the top of the aquatic food chain in Britain, any contamination consumed by their prey, and by the prey of their prey, <a href="https://pubs.acs.org/doi/10.1021/acs.est.1c05410">accumulates in otters</a>. So otters are particularly susceptible to any toxic chemicals in their environment. </p>
<p>Following the banning of many chemical pollutants, otter populations began to recover, and we now have otters in <a href="https://onlinelibrary.wiley.com/doi/10.1111/eva.13505">every county in Britain</a>. National otter surveys have been conducted in Wales, Scotland and England since 1977 and have helped to track population recovery. </p>
<p>However, we didn’t have a good grasp on what population sizes were like in the decades before this time. We only had anecdotal evidence that otter hunting was becoming less “successful” over time, and that both sightings and signs of otters were rarer. </p>
<h2>Otter population decline</h2>
<p>Our research shows that roughly between 1950 and 1970, an extreme population decline happened in the east of England, and a strong decline in south-west England. They were probably caused by chemical pollution. </p>
<p>In Scotland, otter populations showed a long-term, but smaller decline, which suggests less chemical pollution. There was a smaller population decline in Wales, which started around 1800, possibly linked to otter hunting and changes in how people shaped and used the landscape. </p>
<p>While both deal with DNA, genetics focuses on individual genes and their roles, while genomics examines the entire set of an organism’s DNA. Although there have been genetic studies of otters in Britain, our research was the first time genomics was used to study Eurasian otters anywhere in the world.</p>
<p>Working with scientists from the Smithsonian Conservation Biology Institute and the Wellcome Sanger’s Darwin Tree of Life project, we looked at the entire otter genome. The upgrade from genetics to genomics threw up a few surprises. </p>
<p>First, there was a mitochondrial DNA sequence found in the east of England, which was very different to the sequences in the rest of Britain. Mitochondrial DNA is a sequence of DNA found in a cell’s mitochondria, which is what generates the energy. Mitochondrial DNA is inherited only from the mother, while the rest of the DNA is a mix of both the mother’s and the father’s DNA.</p>
<p>Another <a href="https://www.tandfonline.com/doi/full/10.1080/19768354.2023.2283763">recent study</a> by our research group, in collaboration with colleagues in South Korea, suggested a divergence between these two lineages at least 80,000 years ago. Finding this mitochondrial lineage (that, based on our data, is otherwise restricted to Asia) in the UK was surprising. </p>
<p>Second, we found high levels of genetic diversity in the east of England. Normally, after an extreme population decline such as the one we identified in this area, genetic diversity decreases. Yet we saw much greater diversity here than in the population in Scotland, where there was no clear evidence for such a decline. </p>
<h2>Thai otters</h2>
<p>With a little detective work, we discovered that a pair of Eurasian otters (the same species that we have in the UK), were brought to Britain from Thailand in the 1960s. Populations of Eurasian otters range right across Europe and Asia. Although they are the same species, there are several genetically distinct subspecies, particularly in Asia. </p>
<p>It seems possible that these genetically different otters from Thailand bred with otters in the east of England. At the time of the population decline, when native UK populations were at their smallest, even a few individuals introduced into the population may have made a big difference. And they left unexpected marks on the genome. </p>
<p>We don’t know for sure if this is what happened, and we need to do more work to find out what effect this may have had on otters in the east of England. High genetic diversity is usually good for a population or species. But on the other hand, conservation often strives to maintain genetic differences between populations, rather than mixing distinct populations.</p>
<p>One way to find out more would be to compare the genome of a Eurasian otter from Thailand to the otters we see in the east of England. Unfortunately, it’s not that easy. Since the 1960s, otters in Thailand and across Asia have become increasingly rare. This is due to habitat loss, pollution and the illegal otter trade. So getting samples for genome sequencing is very difficult. It highlights the importance of conserving the species in Asia, despite population recoveries in Europe.</p>
<p>Our work shows the value of using modern genomic tools to look at the genetic diversity of a threatened species. The application of such tools can uncover surprising facts, even in supposedly well-studied species.</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>
</figcaption>
</figure>
<p><strong><em>Don’t have time to read about climate change as much as you’d like?</em></strong>
<br><em><a href="https://theconversation.com/uk/newsletters/imagine-57?utm_source=TCUK&utm_medium=linkback&utm_campaign=Imagine&utm_content=DontHaveTimeTop">Get a weekly roundup in your inbox instead.</a> Every Wednesday, The Conversation’s environment editor writes Imagine, a short email that goes a little deeper into just one climate issue. <a href="https://theconversation.com/uk/newsletters/imagine-57?utm_source=TCUK&utm_medium=linkback&utm_campaign=Imagine&utm_content=DontHaveTimeBottom">Join the 30,000+ readers who’ve subscribed so far.</a></em></p>
<hr><img src="https://counter.theconversation.com/content/219140/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Frank Hailer receives funding from NERC and Dŵr Cymru Welsh Water. </span></em></p><p class="fine-print"><em><span>Elizabeth Chadwick receives funding from the UK Natural Environment Research Council and from the Environment Agency</span></em></p><p class="fine-print"><em><span>Sarah du Plessis receives funding from the UK Natural Environment Research Council and the Global Wales International Mobility Fund.</span></em></p>
Research has revealed how British otters may have been able to recover from species loss in the 1950s with the help of otters from Asia.
Frank Hailer, Senior Lecturer in Evolutionary Biology, Cardiff University
Elizabeth Chadwick, Senior Lecturer at the School of Biosciences, Cardiff University
Sarah du Plessis, PhD Candidate, Cardiff University
Licensed as Creative Commons – attribution, no derivatives.
tag:theconversation.com,2011:article/221085
2024-02-22T20:50:27Z
2024-02-22T20:50:27Z
How advanced genetic testing can be used to combat the illegal timber trade
<p>According to <a href="https://www.interpol.int/Crimes/Environmental-crime/Forestry-crime">Interpol</a>, the organization dedicated to facilitating international police co-operation, between 15 per cent and 30 per cent of the world’s traded timber comes from illegal sources. This is an estimated annual value of US$51-152 billion dollars. </p>
<p>Illegal logging has serious consequences for the environment, the climate and the local livelihoods of the people who depend upon the affected forests. In turn, local governments are faced with losses in revenue, rising corruption and decreasing timber prices. These make it even more difficult for the legal forestry sector to remain competitive. </p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/illegal-logging-in-africa-is-a-threat-to-security-202291">Illegal logging in Africa is a threat to security</a>
</strong>
</em>
</p>
<hr>
<p>Even in Canada, customers are unwittingly supporting this theft by buying timber with false declarations. In the face of such issues, Canadian researchers are currently developing a <a href="https://publications.gc.ca/site/eng/9.891853/publication.html">traceability system</a> employing genomic identification technologies to help tackle the trade in illegal timber. </p>
<h2>Stemming the flow</h2>
<p>To help address poaching, the United States expanded the pre-existing <a href="https://www.fws.gov/law/lacey-act">Lacey Act in 2008</a>. Originally designed to control the illegal trade of <a href="https://www.ucsusa.org/resources/lacey-acts-effectiveness">wildlife</a>, it was adapted to help tackle the trade in illegally harvested wood. The 2008 amendments to the Lacey Act decreased the importation of illegally harvested wood into the U.S. by approximately 32 to 44 per cent. </p>
<p>In Canada, similar regulations have been put in place to avoid the exploitation of species at risk including the <a href="https://www.laws-lois.justice.gc.ca/eng/acts/W-8.5/index.html">Wild Animal and Plant Protection and Regulation of International and Interprovincial Trade Act</a>. But how do we know if the declarations of a wood product are accurate or correctly reported? </p>
<p>In general, identification methods can be categorized into three groups: anatomical, analytical or molecular biological techniques — each with its <a href="https://doi.org/10.13140/RG.2.2.21518.79689">own set of advantages and limitations</a>. </p>
<p>Identification methods which use the aid of <a href="https://doi.org/10.46830/wrirpt.21.00067">microscope technology</a> look for distinct characteristics of the wood anatomy including tissues and cells. It is also the group of methods most commonly used.</p>
<p>However, this method requires trained specialists, the appropriate equipment and can typically only provide meaningful conclusions at the <a href="https://www.biologyonline.com/dictionary/genus">genus level</a>. In addition, wood anatomy cannot tell us where a piece of wood comes from. </p>
<h2>Looking to genetics</h2>
<p>This is where genomics come into play. To determine the species identity and the geographic origin of a logged tree, <a href="https://www.nature.com/articles/35016000">researchers take advantage of evolution</a>. </p>
<p>A few key factors make genetic identification possible. </p>
<p>Firstly, there are clear genetic differences between distinct <em><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771874/#:%7E:text=We%20define%20a%20genetic%20species,from%20the%20Biological%20Species%20Concept.">species</a></em>. Secondly, the closer the relationship between individuals — in this case trees — the more genetically similar they are, while the more removed the individuals are the less genetic information is shared.</p>
<p>Therefore, it is possible to assign an individual to a “local population” based on its genetic fingerprint, sharing parts of its genetic makeup with that population and, consequently, <a href="https://pubs.cif-ifc.org/doi/abs/10.5558/tfc2018-010">also the specific region where it originates from</a>. This method is called population genetics. </p>
<p>The power of population genetics lies in its ability to identify groups of individuals that share a certain amount of genetic information that can be used to assign individuals to a species or a geographic region. The same methods can be used for humans to find unknown relatives or trace back the ethnic origin of your ancestors. </p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/weakening-australias-illegal-logging-laws-would-undermine-the-global-push-to-halt-forest-loss-172770">Weakening Australia's illegal logging laws would undermine the global push to halt forest loss</a>
</strong>
</em>
</p>
<hr>
<p>To reliably assign individuals, a variety of genetic markers is needed, varying between species and local populations. </p>
<p>In Canada, the first successful use of genetic material to conduct forensic testing on trees was pioneered by geneticist Eleanor White who succeeded in <a href="https://cfs.nrcan.gc.ca/pubwarehouse/pdfs/5177.pdf">tracing a wood log directly to the specific stump of an 800-year-old cedar tree in Western Canada</a> left behind after its illegal felling.</p>
<p>White’s success demonstrates the power of genomic identification in regulating the timber trade.</p>
<h2>Developing new systems</h2>
<p>Genomic sequencing in combination with genetic data analyses gained public traction during the COVID-19 pandemic, as these were used to <a href="https://doi.org/10.1038/s41467-020-18314-x">identify an outbreak of a new virus variant and trace its origin</a>.</p>
<p>Current research in wood forensics is using similar tools to assign an individual to a source population with high accuracy. Since genetic analyses can be costly, genetic databases of <a href="https://doi.org/10.1002/ppp3.10297">previously studied species</a> are compiled and used as test data to determine the best and most reliable analytical method.</p>
<p>The aim is to create a simple traceability system for timber products that border officials can implement quickly and easily. This should help stop the sale of illegally harvested timber and hold those responsible to account. </p>
<p>The long-term goal is to make it more difficult to sell illegally harvested timber in Canada and thus contribute to the protection of valuable forests. In addition, traceability can certify areas in Canada which are sustainably managed, making it easier for consumers to support sustainable forest management practices.</p><img src="https://counter.theconversation.com/content/221085/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Melanie Zacharias receives funding from Génome Québec. </span></em></p>
Effective use of genomic identification could revolutionize the control of the illegal timber trade.
Melanie Zacharias, Postdoctoral researcher in forest genetics, Université Laval
Licensed as Creative Commons – attribution, no derivatives.
tag:theconversation.com,2011:article/219620
2024-01-18T16:38:26Z
2024-01-18T16:38:26Z
DNA from stone age chewing gum sheds light on diet and disease in Scandinavia’s ancient hunter-gatherers
<figure><img src="https://images.theconversation.com/files/570142/original/file-20240118-27-aehxwa.jpg?ixlib=rb-1.1.0&rect=0%2C0%2C464%2C352&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">A mold cast of one of the chewed pitch pieces.</span> <span class="attribution"><span class="source">Verner Alexandersen</span>, <span class="license">Author provided</span></span></figcaption></figure><p>Some 9,700 years ago on an autumn day, a group of people were camping on the west coast of Scandinavia. They were hunter-gatherers that had been fishing, hunting and collecting resources in the area. </p>
<p>Some teenagers, both boys and girls, were chewing resin to produce glue, just after eating trout, deer and hazelnuts. Due to a severe gum infection (periodontitis), one of the teenagers had problems eating the chewy deer-meat, as well as preparing the resin by chewing it.</p>
<p>This snapshot of the Mesolithic period, just before Europeans started farming, comes from analysis of DNA left in the chewed resin that we have conducted, now <a href="https://www.nature.com/articles/s41598-023-48762-6">published in Scientific Reports</a>. </p>
<p>The location is now known as <a href="https://lup.lub.lu.se/search/publication/3c1fd58a-9495-4403-ab7d-d22104f2fafb">Huseby Klev</a>, situated north of Gothenburg (Göteborg), Sweden. <a href="https://www.cambridge.org/core/journals/antiquity/article/abs/wet-and-the-wild-followed-by-the-dry-and-the-tame-or-did-they-occur-at-the-same-time-diet-in-mesolithic-neolithic-southern-sweden/D91F7830FE704FD24DFAFB55E551039B">It was excavated</a> by archaeologists in the early 1990s, and yielded some 1,849 flint artefacts and 115 pieces of resin (mastic). The site has been radiocarbon dated to between 10,200 and 9,400 years ago, with one of the pieces of resin dated to 9,700 years ago.</p>
<p>Some of the resin has teeth imprints, indicating that children, actually teenagers, had been chewing them. Masticated lumps, often with imprints of teeth, fingerprints or both, are not uncommon to find in Mesolithic sites. </p>
<p>The pieces of resin we have analysed were made of <a href="https://www.nature.com/articles/s41467-019-13549-9">birch bark pitch</a>, which is known to have been used as an <a href="https://phys.org/news/2019-08-neanderthal-tool-making-simpler-previously-thought.html">adhesive substance in stone tool technology</a> from the Middle Palaeolithic onward. However, they were also chewed for recreational or medicinal purposes in traditional societies.</p>
<p>A variety of substances with similar properties, such as resins from coniferous trees, natural bitumen, and other plant gums, are known to have been used in analogous ways in many parts of the world.</p>
<h2>The power of DNA</h2>
<p>In some of the resin, half the <a href="https://www.nature.com/articles/s42003-019-0399-1">DNA extracted</a> was of human origin. This is a lot compared to what we often find in ancient bones and teeth. </p>
<p>It represents some of the oldest human genomes from Scandinavia. It has a particular ancestry profile common among Mesolithic hunter gatherers who once lived there. </p>
<p>Some of the resin contains male human DNA while others have female DNA. We think that teenagers of both sexes were preparing glue for use in tool making, such as attaching a stone axe to a wooden handle.</p>
<p>But what of the other half of the DNA that was of non-human origin? Most of this DNA is from organisms such as bacteria and fungi that have lived in the mastic since it was discarded 9,700 years ago. But some of it was from bacteria living in the human that chewed it, along with material the human had been chewing on before they put the birch bark pitch in their mouths.</p>
<p>Analysing all this DNA is a demanding task and treads new ground. We had to both adapt existing computing tools and also develop some new analytical strategies. As such, this work has become the starting point for developing a new workflow for this kind of analysis. </p>
<p>This includes mining the DNA using different strategies to characterise it, trying to piece together short DNA fragments into longer ones and using machine learning techniques to work out which DNA fragments belong to pathogens (harmful microorganisms). It also involves comparing the data to what we see in the mouths of modern people with <a href="https://www.ncbi.nlm.nih.gov/books/NBK551699/">tooth decay (caries)</a> and periodontitis.</p>
<h2>Higher organisms</h2>
<p>Naturally, we found the kind of bacteria that would be expected in an oral microbiome, the range of naturally occurring microorganisms found in the mouth. We also found traces of bacteria implicated in conditions such as tooth decay or caries (<em>Streptococcus mutans</em>), and systemic diseases such as Hib disease and endocarditis. There were also bacteria that can cause abscesses. </p>
<p>Although these pathogenic microorganisms were present at an elevated frequency, they were not clearly above the level expected for a healthy oral microbiome. There is thus no conclusive evidence that members of the group suffered from diseases these microorganisms are associated with. </p>
<p>What we did find, however, was an abundance of bacteria associated with serious gum disease – <a href="https://www.mayoclinic.org/diseases-conditions/periodontitis/symptoms-causes/syc-20354473">periodontitis</a>. When we applied a <a href="https://www.ibm.com/topics/machine-learning">machine learning</a> strategy (in this case, a technique called <a href="https://www.ibm.com/topics/random-forest">Random Forest modelling</a>) we reached the conclusion that the girl who chewed one of the pieces of resin had probably suffered from periodontitis – with more than a 75% probability.</p>
<p>We also found DNA from larger organisms than just bacteria. We found DNA for red deer, brown trout and hazelnuts. This DNA probably came from material the teenagers had been chewing before they put the birch pitch in their mouths. </p>
<p>However, we need to be a little bit cautious because exactly what we find is also dependent on the comparison data that we have. As genomes from eukaryotic organisms – the group that includes plants and animals – <a href="https://www.ncbi.nlm.nih.gov/books/NBK9846/">are larger and more complex</a> than those from microorganisms, it is more complicated to assemble a eukaryotic genome of high quality. </p>
<p>There are fewer eukaryotic genomes in the samples of resin, and they are of lower quality. This means that our brown trout, for example, may not actually be a brown trout, but we at least feel certain it is from the salmon family.</p>
<p>We also found a lot of fox DNA, but this is harder to interpret. Fox meat may have been a part of the diet, but these teenagers could also have chewed on tendons and fur from foxes for use in textiles. Alternatively, the fox DNA could even be from territorial marking and got into the resin after it was spat out.</p>
<p>However, what we have learned for sure represents a big step in understanding these fascinating records of human culture from the Stone Age. As we analyse more of these, even more surprises could emerge.</p><img src="https://counter.theconversation.com/content/219620/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Anders Götherström receives funding from: the Swedish Research Council (2019-00849_VR), Riksbankens Jubileumsfond (P16-0553:1)</span></em></p><p class="fine-print"><em><span>Emrah Kırdök 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>
Genetic analysis reveals one of the teenagers probably had advanced gum disease.
Anders Götherström, Professor in Molecular Archaeology, Department of Archaeology and Classical Studies, Stockholm University
Emrah Kırdök, Assistant Professor, Department of Biotechnology, Mersin University
Licensed as Creative Commons – attribution, no derivatives.
tag:theconversation.com,2011:article/217025
2023-11-13T21:44:00Z
2023-11-13T21:44:00Z
Gulf of St. Lawrence: Analyzing fish blood can show us how healthy they are
<figure><img src="https://images.theconversation.com/files/557461/original/file-20231003-21-bibw4p.jpeg?ixlib=rb-1.1.0&rect=30%2C12%2C3995%2C3005&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">The industrialization of the fishing industry and changes in the environment have raised many issues about the management of our fisheries.</span> <span class="attribution"><span class="source">(Fanny Fronton)</span>, <span class="license">Fourni par l'auteur</span></span></figcaption></figure><p>The Gulf of St. Lawrence is an invaluable resource for Canada. Fish and shellfish fisheries that date to the 16th century have remained an essential source of income for many communities, including those on the North Shore and Gaspésie or the Îles-de-la-Madeleine.</p>
<p>For example, in <a href="https://publications.gc.ca/collections/collection_2019/mpo-dfo/Fs124-10-2018-eng.pdf">Îles-de-la-Madeleine</a>, nearly 1,800 jobs (for a total of 12,500 inhabitants) were linked to fishing in 2015.</p>
<p>But the industrialization of fishing, and changes in the environment, have brought about many new problems in the management of our fisheries. The abundance of different fish species in the Gulf has fluctuated greatly over the last 20 years.</p>
<hr>
<figure class="align-right ">
<img alt="" src="https://images.theconversation.com/files/469058/original/file-20220615-9549-jj1phn.png?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/469058/original/file-20220615-9549-jj1phn.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=398&fit=crop&dpr=1 600w, https://images.theconversation.com/files/469058/original/file-20220615-9549-jj1phn.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=398&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/469058/original/file-20220615-9549-jj1phn.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=398&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/469058/original/file-20220615-9549-jj1phn.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=500&fit=crop&dpr=1 754w, https://images.theconversation.com/files/469058/original/file-20220615-9549-jj1phn.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=500&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/469058/original/file-20220615-9549-jj1phn.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=500&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption"></span>
</figcaption>
</figure>
<p><em>This article is part of our series, <a href="https://theconversation.com/ca-fr/topics/fleuve-saint-laurent-116908">The St. Lawrence River: In depth</a>.
Don’t miss new articles on this mythical river of remarkable beauty. Our experts look at its fauna, flora and history, and the issues it faces. This series is brought to you by <a href="https://theconversation.com/ca-fr">La Conversation</a>.</em></p>
<hr>
<p>A case in point: the number of Greenland halibut has declined drastically. This year, <a href="https://www.hi.no/hi/nettrapporter/imr-pinro-en-2023-6">landings</a> are six times lower for fishermen compared to last year.</p>
<p>But other species are benefiting from the situation. This is the case for the population of Atlantic halibut, which is at record levels today.</p>
<p>What is causing these changes? And can we predict further changes?</p>
<p>As a doctoral student in biology at the Institut national de la recherche scientifique (INRS), I am trying to find possible answers to these questions as part of my research work.</p>
<h2>A new health monitoring technique</h2>
<p>The means available for studying the health of fish at the individual level are limited. On the one hand, we can calculate indicators from the weight and height of individual fish. But these measurements are too vague and don’t tell us much.</p>
<p>The logistics of performing biopsies on the tissue of fish — which requires taking samples from their muscle or organs — are complex. To carry them out, researchers must have to travel to the ocean, physically collect samples and bring them back to a laboratory. And then there are ethical considerations, since obviously fish must be sacrificed to achieve this.</p>
<p>Even so, these methods are not very effective for detecting stress induced by environmental changes, and are not effective for detecting stress at early stages, before the physical effects can become manifest.</p>
<p>Yet in a context where the abundance of certain fish species is in rapid decline, an analysis of their overall health is necessary. Fortunately, a new tool is being developed: the <a href="https://www.nature.com/articles/s41598-023-32690-6">circulating microbiome</a>.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/551779/original/file-20231003-15-6ou9xh.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="viruses in the blood" src="https://images.theconversation.com/files/551779/original/file-20231003-15-6ou9xh.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/551779/original/file-20231003-15-6ou9xh.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=343&fit=crop&dpr=1 600w, https://images.theconversation.com/files/551779/original/file-20231003-15-6ou9xh.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=343&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/551779/original/file-20231003-15-6ou9xh.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=343&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/551779/original/file-20231003-15-6ou9xh.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=431&fit=crop&dpr=1 754w, https://images.theconversation.com/files/551779/original/file-20231003-15-6ou9xh.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=431&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/551779/original/file-20231003-15-6ou9xh.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=431&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 is often wrongly believed that blood is sterile.</span>
<span class="attribution"><span class="source">(Shutterstock)</span></span>
</figcaption>
</figure>
<h2>A little-known practice</h2>
<p>The circulating microbiome is a biomarker, an alarm signal that can be detected in fish even before their health begins to deteriorate. A good biomarker is sensitive, easy to sample, and inexpensive.</p>
<p>The analysis of the circulating microbiome, made up of the DNA of bacteria found in the blood, is directly inspired by <a href="https://theconversation.com/ladn-%20circulating-a-new-simple-and-rapid-weapon-in-the-diagnosis-and-monitoring-of-cancers-206786">similar analyses performed on humans</a>, which provide a great deal of information.</p>
<p>In particular, these analyses make it possible to detect anomalies resulting from the effect of a stress factor on the body, or the development of a disease.</p>
<p>Changes in the environment can also be detected from studying the circulating microbiome. But a major problem emerges here: a fish is not a human. Humans are studied in such detail that knowledge about their health can then be used for an infinite amount of further research. However, sampling fish blood is not a common practice. So there is a great deal that needs to be done before we can properly evaluate the health of fish.</p>
<p>Since the analysis of the circulating microbiome in fish has never been studied before, a lot of work needs to be done to develop the technique.</p>
<h2>Traces of bacteria in the blood?</h2>
<p>As blood circulates throughout the body, it comes into contact specifically with bacteria that make up the other microbiomes (intestinal, oral, dermal). Both in fish and humans, these bacteria are essential for good health.</p>
<p>When we analyze bacterial DNA in the blood, it is therefore possible to find bacteria from the intestine, mouth, or skin. But the hypothesis that these are bacteria specific to the blood cannot be completely ruled out either.</p>
<p>While some continue to believe that blood is sterile, and therefore does not contain any bacteria, we have known since the 1970s that this hypothesis is false — it was confirmed <a href="https://doi.org/10.1128/jcm.39.5.1956-1959.2001">in the 2000s by genomic studies</a>. It’s possible that in 1674, the Dutch microbiologist Antonie Van Leeuwenhoek may even have observed bacteria in salmon blood <a href="https://doi.org/10.3389/fcimb.2019.00148">under a microscope</a>.</p>
<p>Today, we can analyze these bacteria in detail by targeting a very specific bacterial gene, the 16S ribosomal RNA gene. Present in all bacteria around the world, this gene varies slightly from one species to another. That makes it possible to identify and analyze the biodiversity of the microbiome.</p>
<h2>I eat, therefore I am</h2>
<p>Our recent work has made it possible to characterize, for the first time, the <a href="https://www.nature.com/articles/s41598-023-32690-6">circulating microbiomes of turbot and halibut</a>. We have demonstrated that the two fish species have circulating microbiomes dominated by the presence of the species <em>Pseudoalteromonas</em> and <em>Psychrobacter</em>. These bacteria are known to colonize cold environments, for example the bottom of the Gulf of St. Lawrence, which is around 5°C. They are also known to produce bioactive compounds (antibacterials and antifungals). They are more tenacious than other bacteria.</p>
<figure class="align-left zoomable">
<a href="https://images.theconversation.com/files/551768/original/file-20231003-29-qhulgz.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="person with blue gloves holds a fish" src="https://images.theconversation.com/files/551768/original/file-20231003-29-qhulgz.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/551768/original/file-20231003-29-qhulgz.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=800&fit=crop&dpr=1 600w, https://images.theconversation.com/files/551768/original/file-20231003-29-qhulgz.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=800&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/551768/original/file-20231003-29-qhulgz.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=800&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/551768/original/file-20231003-29-qhulgz.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=1005&fit=crop&dpr=1 754w, https://images.theconversation.com/files/551768/original/file-20231003-29-qhulgz.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=1005&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/551768/original/file-20231003-29-qhulgz.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">Greenland halibut.</span>
<span class="attribution"><span class="source">(Fanny Fronton)</span>, <span class="license">Fourni par l'auteur</span></span>
</figcaption>
</figure>
<p>However, differences can be observed between the two species. Turbot has more bacteria called <em>Vibrio</em>, some of which metabolize chitin, a molecule that makes up the shells of the invertebrates on which it feeds. Atlantic halibut, for its part, presents more <em>Acinetobacter</em> bacteria, typical of piscivorous (fish-eating) diets in the intestinal microbiomes. The circulating microbiome in these two fish species therefore seems to be influenced by intestinal bacteria, as is the case in humans. We could therefore potentially link a blood microbiome to the fish’s diet, which is often difficult to estimate.</p>
<h2>An embryonic, but promising technique</h2>
<p>So this first bacterial mapping of the blood of these two species probably reflects their respective intestinal microbiome. From this characterization, detection of a variation in the composition of bacteria could be linked to stress, a change in the environment or a physiological change in the animal.</p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/540859/original/file-20230802-23891-ctgz3u.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="comic strip" src="https://images.theconversation.com/files/540859/original/file-20230802-23891-ctgz3u.png?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/540859/original/file-20230802-23891-ctgz3u.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=907&fit=crop&dpr=1 600w, https://images.theconversation.com/files/540859/original/file-20230802-23891-ctgz3u.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=907&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/540859/original/file-20230802-23891-ctgz3u.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=907&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/540859/original/file-20230802-23891-ctgz3u.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=1140&fit=crop&dpr=1 754w, https://images.theconversation.com/files/540859/original/file-20230802-23891-ctgz3u.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=1140&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/540859/original/file-20230802-23891-ctgz3u.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=1140&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Comic strip illustrating the principle of analyzing the circulating microbiome.</span>
<span class="attribution"><span class="source">(Fanny Fronton)</span>, <span class="license">Fourni par l'auteur</span></span>
</figcaption>
</figure>
<p>For example, we know that in humans, the loss of <em>Actinobacteria</em> in the circulating microbiome is associated with severe acute <a href="https://doi.org/10.3389/fcimb.2018.00005">pancreatitis</a>. And there are dozens of examples like this in humans.</p>
<p>This study, the result of a collaboration between university researchers from INRS, the University of Québec at Rimouski and the Department of Fisheries and Oceans Canada, provides a small overview of the informative potential offered by the blood microbiomes of fish from the Gulf of St. Lawrence.</p>
<p>Further research will make it possible to estimate their health and better predict the evolution of their population. The dramatic collapse of the cod stock in the late 1980s had a major impact on fishermen. Several of them even fear that this situation will happen again with another species. As turbot remains a species at risk, it is essential to ensure better management of St. Lawrence species.</p>
<p>Only by refining our analysis techniques and deepening our scientific knowledge can we prevent this type of collapse from happening again in the future.</p><img src="https://counter.theconversation.com/content/217025/count.gif" alt="La Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Fanny Fronton received a grant from the Fondation Armand Frappier.</span></em></p>
Blood isn’t sterile, and analyzing the bacteria in it could help assess the health of fish and prevent the collapse of their populations.
Fanny Fronton, Doctorante en Écologie halieutique et biologie moléculaire, Institut national de la recherche scientifique (INRS)
Licensed as Creative Commons – attribution, no derivatives.
tag:theconversation.com,2011:article/216326
2023-11-09T13:32:30Z
2023-11-09T13:32:30Z
Cranberries can bounce, float and pollinate themselves: The saucy science of a Thanksgiving classic
<figure><img src="https://images.theconversation.com/files/558166/original/file-20231107-21-cmo43c.jpg?ixlib=rb-1.1.0&rect=15%2C9%2C2029%2C1140&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Cranberries grow on vines in sandy bogs and marshes.</span> <span class="attribution"><a class="source" href="https://flic.kr/p/Mm6QhN">Lance Cheung, USDA/Flickr</a></span></figcaption></figure><p>Cranberries are a staple in U.S. households at Thanksgiving – but how did this bog dweller end up on holiday tables? </p>
<p>Compared to many valuable plant species that were domesticated over thousands of years, cultivated cranberry (<em>Vaccinium macrocarpon</em>) is a young agricultural crop, just as the U.S. is a young country and Thanksgiving is <a href="https://theconversation.com/how-advertising-shaped-thanksgiving-as-we-know-it-86819">a relatively new holiday</a>. But <a href="https://soilcrop.tamu.edu/people/desalvio-serina/">as a plant scientist</a>, I’ve learned much about cranberries’ ancestry from their botany and genomics.</p>
<h2>New on the plant breeding scene</h2>
<p>Humans have cultivated <a href="https://doi.org/10.1007/s10437-018-9314-2">sorghum for some 5,500 years</a>, <a href="https://www.nsf.gov/news/news_summ.jsp?cntn_id=114445">corn for around 8,700 years</a> and <a href="https://doi.org/10.1534/g3.120.401362">cotton for about 5,000 years</a>. In contrast, cranberries were domesticated around 200 years ago – but people were eating the berries before that.</p>
<p>Wild cranberries are native to North America. They were an important food source for Native Americans, who used them in puddings, sauces, breads and a <a href="https://www.cranberries.org/exploringcranberries/into/maki_back.html">high-protein portable food called pemmican</a> – a carnivore’s version of an energy bar, made from a mixture of dried meat and rendered animal fat and sometimes studded with dried fruits. Some tribes <a href="https://lakotarednations.com/2017/11/wo-lakota-making-wasna/">still make pemmican today</a>, and even <a href="https://tankabar.com/">market a commercial version</a>. </p>
<p>Cranberry cultivation began in 1816 in Massachusetts, where Revolutionary War veteran Henry Hall found that <a href="https://www.youtube.com/watch?v=nt7NA7G808Y&t=5s">covering cranberry bogs with sand</a> fertilized the vines and retained water around their roots. From there, the fruit spread throughout the U.S. Northeast and Upper Midwest. </p>
<p>Today, <a href="https://www.ers.usda.gov/data-products/chart-gallery/gallery/chart-detail/?chartId=102649">Wisconsin produces roughly 60%</a> of the U.S. cranberry harvest, followed by Massachusetts, Oregon and New Jersey. Cranberries also are grown in Canada, where they are <a href="https://canadianfoodfocus.org/in-season/whats-in-season-cranberries/">a major fruit crop</a>.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/558168/original/file-20231107-29-f3xdq7.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Four men in waders, holding long rakes, thigh-deep in a flooded bog, its surface covered with floating cranberries." src="https://images.theconversation.com/files/558168/original/file-20231107-29-f3xdq7.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/558168/original/file-20231107-29-f3xdq7.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=305&fit=crop&dpr=1 600w, https://images.theconversation.com/files/558168/original/file-20231107-29-f3xdq7.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=305&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/558168/original/file-20231107-29-f3xdq7.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=305&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/558168/original/file-20231107-29-f3xdq7.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=383&fit=crop&dpr=1 754w, https://images.theconversation.com/files/558168/original/file-20231107-29-f3xdq7.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=383&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/558168/original/file-20231107-29-f3xdq7.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=383&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Farmers often flood cranberry bogs to harvest the fruit, which they rake loose from the vines.</span>
<span class="attribution"><a class="source" href="https://flic.kr/p/bBmqts">Michael Galvin, Massachusetts Office of Travel and Tourism/Flickr</a>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<h2>A flexible and adaptable plant</h2>
<p>Cranberries have many interesting botanical features. Like roses, lilies and daffodils, cranberry flowers are hermaphroditic, which means they <a href="https://www.gardeningknowhow.com/garden-how-to/info/hermaphroditic-plant-information.htm">contain both male and female parts</a>. This allows them to self-pollinate instead of relying on birds, insects or other pollinators. </p>
<p>A cranberry blossom has four petals that peel back when the flower blooms. This exposes the anthers, which contain the plant’s pollen. The flower’s resemblance to the beak of a bird earned the cranberry its original name, <a href="https://gobotany.nativeplanttrust.org/species/vaccinium/macrocarpon/">the “craneberry</a>.” </p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/558169/original/file-20231107-23-zvban6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="A flower with four curved white petals tinged with pink." src="https://images.theconversation.com/files/558169/original/file-20231107-23-zvban6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/558169/original/file-20231107-23-zvban6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=742&fit=crop&dpr=1 600w, https://images.theconversation.com/files/558169/original/file-20231107-23-zvban6.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=742&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/558169/original/file-20231107-23-zvban6.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=742&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/558169/original/file-20231107-23-zvban6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=932&fit=crop&dpr=1 754w, https://images.theconversation.com/files/558169/original/file-20231107-23-zvban6.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=932&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/558169/original/file-20231107-23-zvban6.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>
<figcaption>
<span class="caption">A blossom on a cranberry bush in Wisconsin.</span>
<span class="attribution"><a class="source" href="https://commons.wikimedia.org/wiki/File:Cranberry_Blossom_%289180939392%29.jpg">Aaron Carlson/Wikimedia</a>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span>
</figcaption>
</figure>
<p>When cranberries don’t self-pollinate, they rely on bumblebees and honeybees to transport their pollen from flower to flower. They can also be propagated sexually, by planting seeds, or asexually, through rooting vine cuttings. This is important for growers because seed-based propagation allows for higher genetic diversity, which can translate to things like increased disease resistance or more pest tolerance. </p>
<p>Asexual reproduction is equally important, however. This method allows growers to create clones of varieties that perform very well in their bogs and grow even more of those high-performing types.</p>
<p>Every cranberry <a href="https://www.wisfarmer.com/story/news/2018/07/13/farm-technology-days-five-fun-cranberry-facts/784392002/">contains four air pockets</a>, which is why they float when farmers flood bogs to harvest them. The air pockets also make raw cranberries bounce when they are dropped on a hard surface – a good indicator of whether they are fresh.</p>
<p>These pockets serve a biological role: They enable the berries to float down rivers and streams to disperse their seeds. Many other plants disperse their seeds via animals and birds that eat their fruits and excrete the seeds as they move around. But as anyone who has tasted them raw knows, cranberries are ultra-tart, so they have <a href="https://plants.usda.gov/DocumentLibrary/plantguide/pdf/pg_viopa2.pdf">limited appeal for wildlife</a>. </p>
<h2>Reading cranberry DNA</h2>
<p>For cranberries being such a young crop, scientists already know <a href="https://doi.org/10.1002/9781119616801.ch8">a lot about their genetics</a>. The cranberry <a href="https://www.genome.gov/genetics-glossary/Diploid">is a diploid</a>, which means that each cell contains one set of chromosomes from the maternal parent and one set from the paternal parent. It has 24 chromosomes, and its genome size is less than one-tenth that of the human genome. </p>
<p>Insights like these help scientists better understand where potentially valuable genes might be located in the cranberry genome. And diploid crops tend to have fewer genes associated with a single trait, which makes breeding them to emphasize that trait much simpler. </p>
<p>Researchers have also described the genetics of the cultivated cranberry’s wild relative, which is known as the “<a href="https://plants.usda.gov/DocumentLibrary/plantguide/pdf/cs_vaox.pdf">small cranberry” (<em>Vaccinium oxycoccos</em>)</a>. Comparing the two can help scientists determine where the cultivated cranberry’s agronomically valuable traits reside in its genome, and where some of the small cranberry’s cold hardiness might come from. </p>
<p><div data-react-class="InstagramEmbed" data-react-props="{"url":"https://www.instagram.com/p/CxGCZq0xv16/?utm_source=ig_web_copy_link","accessToken":"127105130696839|b4b75090c9688d81dfd245afe6052f20"}"></div></p>
<p>Researchers are <a href="https://www.vacciniumcap.org/">developing molecular markers</a> – tools to determine where certain genes or sequences of interest reside within a genome – to help determine the best combinations of genes from different varieties of cranberry that can enhance desired traits. For example, a breeder might want to make the fruits larger, more firm or redder in color.</p>
<p>While cranberries have only been grown by humans for a short period of time, they have been evolving for much longer. They entered agriculture with a long genetic history, including things like <a href="https://doi.org/10.1371/journal.pone.0264966">whole genome duplication events and genetic bottlenecks</a>, which collectively change which genes are gained or lost over time in a population. </p>
<p>Whole genome duplication events occur when two species’ genomes collide to form a new, larger genome, encompassing all the traits of the two parental species. Genetic bottlenecks occur when a population is greatly reduced in size, which limits the amount of genetic diversity in that species. These events are extremely common in the plant world and can lead to both gains and losses of different genes. </p>
<p>Analyzing the cranberry’s genome can indicate when it diverged evolutionarily from some of its relatives, such as the blueberry, lingonberry and huckleberry. Understanding <a href="https://theconversation.com/modern-tomatoes-are-very-different-from-their-wild-ancestors-and-we-found-missing-links-in-their-evolution-130041">how modern species evolved</a> can teach plant scientists about how different traits are inherited, and how to effectively breed for them in the future.</p>
<h2>Ripe at the right time</h2>
<p>Cranberries’ close association with Thanksgiving was simply a practical matter at first. Fresh cranberries are ready to harvest from mid-September through mid-November, so Thanksgiving falls within that perfect window for eating them. </p>
<p>Cranberry sauce was first loosely described in accounts from the American colonies in the 1600s, and appeared in a <a href="https://www.smithsonianmag.com/history/what-americas-first-cookbook-says-about-our-country-its-cuisine-180967809/">cookbook for the first time in 1796</a>. The berries’ tart flavor, which comes from <a href="https://rucore.libraries.rutgers.edu/rutgers-lib/60677/">high levels of several types of acids</a>, makes them more than twice as acidic as most other edible fruits, so they add a welcome zing to a meal full of blander foods like turkey and potatoes.</p>
<p>In recent decades, the cranberry industry has branched out into <a href="https://theconversation.com/can-cranberries-conquer-the-world-a-us-industry-depends-on-it-87912">juices, snacks and other products</a> in pursuit of year-round markets. But for many people, Thanksgiving is still the time when they’re most likely to see cranberries in some form on the menu.</p><img src="https://counter.theconversation.com/content/216326/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Serina DeSalvio does not work for, consult, own shares in or receive funding from any company or organization that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>
Cranberries add color and acidity to Thanksgiving menus, but they also have many interesting botanical and genetic features.
Serina DeSalvio, Ph.D. Candidate in Genetics and Genomics, Texas A&M University
Licensed as Creative Commons – attribution, no derivatives.
tag:theconversation.com,2011:article/209312
2023-09-15T12:31:41Z
2023-09-15T12:31:41Z
Can at-home DNA tests predict how you’ll respond to your medications? Pharmacists explain the risks and benefits of pharmacogenetic testing
<figure><img src="https://images.theconversation.com/files/545852/original/file-20230831-15-xftd5k.jpg?ixlib=rb-1.1.0&rect=0%2C0%2C2070%2C1449&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Pharmacogenetic testing is a form of precision medicine, using your genes to personalize your care.</span> <span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/photo/medicine-concept-royalty-free-image/815702424">D3Damon/E+ via Getty Images</a></span></figcaption></figure><p>Have you ever wondered why certain medications <a href="https://theconversation.com/why-prescription-drugs-can-work-differently-for-different-people-168645">don’t seem to work as well</a> for you as they do for others? This variability in drug response is what pharmacogenomic testing hopes to explain by looking at the genes within your DNA. </p>
<p><a href="https://www.cdc.gov/genomics/disease/pharma.htm">Pharmacogenomics, or PGx</a>, is the study of how genes affect your response to medications. <a href="https://www.genome.gov/genetics-glossary/Gene">Genes are segments of DNA</a> that serve as an instruction manual for cells to make proteins. Some of these proteins break down or transport certain medications through the body. Others are proteins that medications target to generate a desired effect.</p>
<p><a href="https://www.pharmacy.pitt.edu/people/kayla-rowe">As pharmacists</a> <a href="https://scholar.google.com/citations?user=9Np7_DYAAAAJ&hl=en">who see</a> <a href="https://scholar.google.com/citations?user=LKG31OkAAAAJ&hl=en">patients who</a> have stopped multiple medications because of side effects or ineffectiveness, we believe pharmacogenomic testing has the potential to help guide health care professionals to more precise dosing and prescribing.</p>
<h2>How do PGx tests work?</h2>
<p><a href="https://medlineplus.gov/lab-tests/pharmacogenetic-tests/">PGx tests</a> look for variations within the genes of your DNA to predict drug response. For instance, the presence of one genetic variant might predict that the specific protein it codes for is unable to break down a particular medication. This could potentially lead to increased drug levels in your body and an increased risk of side effects. The presence of another genetic variant might predict the opposite: It might predict that the protein it codes for is breaking down a medication more rapidly than expected, which may decrease the drug’s effectiveness.</p>
<p>For example, <a href="https://doi.org/10.1002/cpt.2903">citalopram is an antidepressant</a> broken down by a protein called CYP2C19. Patients with genetic variants that code for a version of this protein with a reduced ability to break down the drug may have an increased risk of side effects.</p>
<figure>
<iframe width="440" height="260" src="https://www.youtube.com/embed/dGMIyzCRl-A?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">PGx is a form of personalized or precision medicine.</span></figcaption>
</figure>
<p>Currently, there are over 80 medications with <a href="https://cpicpgx.org/">prescribing recommendations</a> based on PGx results, including treatments for depression, cancer and heart disease. There are commercially available PGx tests that patients can have sent directly to their doorstep with or without the involvement of a health care professional. These direct-to-consumer PGx tests collect DNA from either a saliva sample or cheek swab that is then sent to the laboratory. Results can take anywhere from a few days to a few weeks depending on the company. </p>
<p>Some companies <a href="https://doi.org/10.1038%2Fnature15817">require a consultation</a> with a health care provider, often a pharmacist or genetic counselor, who can facilitate a test order and discuss any medication changes once the results come back. </p>
<h2>Limitations of PGx testing</h2>
<p>PGx testing will not be able to predict how you will respond to all medications for several reasons.</p>
<p>First, most PGx tests <a href="https://doi.org/10.3390/genes11121456">do not look for every possible variant</a> of every gene in the human genome. Instead, they look only at a limited number of genes and variants strongly linked to specific drugs. PGx tests can predict how you will respond only to medications associated with the genes it tests for. </p>
<p>Some drugs are broken down in very complicated pathways entailing multiple proteins and byproducts, and the usefulness of PGx testing for them remains unclear. For example, the <a href="https://www.pharmgkb.org/pathway/PA166170276">antidepressant bupropion</a> has three major pathways involved in its breakdown and forms three active byproducts that can interact with other drugs or body processes. This makes predicting how you will respond to the drug much more challenging because there is more than one variable involved. In many cases, there also isn’t conclusive data to confidently predict the general function of a protein and how it would affect your response to a drug.</p>
<p>The applicability of PGx test results is additionally limited by a <a href="https://theconversation.com/uncovering-the-genetic-basis-of-mental-illness-requires-data-and-tools-that-arent-just-based-on-white-people-this-international-team-is-collecting-dna-samples-around-the-globe-185997">lack of diversity of study participants</a>. Typically, populations of European ancestry are overrepresented in clinical trials. An ongoing research initiative by the National Institutes of Health called the <a href="https://allofus.nih.gov/">All of Us Research Program</a> aims to address this issue by collecting genetic samples from people of diverse backgrounds. </p>
<figure>
<iframe width="440" height="260" src="https://www.youtube.com/embed/ti50nS7B5vI?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">The All of Us research program seeks to conduct research that is more representative of a diverse population.</span></figcaption>
</figure>
<p>Another limitation of direct-to-consumer PGx tests is that they can predict drug response based only on your genetics. <a href="https://my.clevelandclinic.org/health/diagnostics/21093-pharmacogenomics">Lifestyle and environmental factors</a> such as your age, liver or kidney function, tobacco use, drug interactions and other diseases can heavily influence how you may respond to medication. For example, leafy greens with high amounts of vitamin K can <a href="https://www.pennmedicine.org/updates/blogs/heart-and-vascular-blog/2015/june/consistency-not-avoidance-the-truth-about-blood-thinners-leafy-greens-and-vitamin-k">lower the effectiveness</a> of the blood thinner warfarin. But PGx tests don’t take these factors into account.</p>
<p>Finally, your PGx results may predict that you may respond to medications differently, but this does not guarantee that the medication won’t have its intended effect. In other words, PGx testing is predictive rather than deterministic.</p>
<h2>Risks of PGx testing</h2>
<p>PGx testing carries the risk of not telling the whole story of drug response. If variations within the gene are not found, the testing company often assumes the proteins those genes code for function normally. Because of this assumption, someone carrying a rare or unknown variant may receive inaccurate results.</p>
<p>It may be tempting for some people to see their results and want to change their dose or discontinue their medications. However, this can be dangerous. Abruptly stopping some medications may cause withdrawal effects. Never change the way you take your medications without consulting your pharmacist and physician first.</p>
<p>Sharing your PGx test results with all the clinicians involved in your care can help prevent medication failure and improve safety. Pharmacists are increasingly trained in pharmacogenomics and can serve as a resource to address medication-related questions or concerns.</p>
<p>PGx tests that are not authorized by the Food and Drug Administration cannot be clinically interpreted and therefore cannot be used to inform prescribing. Results from these tests should not be added to your medical record.</p>
<h2>Benefits of PGx testing</h2>
<p>Direct-to-consumer PGx testing can empower patients to advocate for themselves and be an active participant in their health care by increasing access to and knowledge of their genetic information.</p>
<p>Patients’ knowledge of their PGx genetic profile has the potential to improve treatment safety. For example, a 2023 study of over 6,000 patients in Europe found that those who used their PGx results to guide medication therapy were <a href="https://doi.org/10.1016/s0140-6736(22)01841-4">30% less likely</a> to experience adverse drug reactions.</p>
<p>Most PGx test results stay valid throughout a patient’s life, and <a href="https://mhealthfairview.org/services/pharmacogenomics">retesting is not needed</a> unless additional genes or variants need to be evaluated. As more research on gene variants is conducted, prescribing recommendations may be updated. </p>
<p>Overall, genetic information from direct-to-consumer PGx tests can help you collaborate with health care professionals to select more effective medications with a lower risk of side effects.</p><img src="https://counter.theconversation.com/content/209312/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>
Genetic testing can help take the guesswork out of finding the right treatment. For certain diseases. To an extent.
Kayla B. Rowe, Fellow in Clinical Pharmacogenomics, University of Pittsburgh
Lucas A. Berenbrok, Associate Professor of Pharmacy and Therapeutics, University of Pittsburgh
Philip Empey, Associate Professor of Pharmacogenomics, University of Pittsburgh
Licensed as Creative Commons – attribution, no derivatives.
tag:theconversation.com,2011:article/210056
2023-07-19T20:00:03Z
2023-07-19T20:00:03Z
Ancient DNA reveals the earliest evidence of the last massive human migration to Western Europe
<p>Nomadic animal-herders from the Eurasian steppe mingled with Copper Age farmers in southeastern Europe centuries earlier than previously thought. </p>
<p>In a new study <a href="https://www.nature.com/articles/s41586-023-06334-8">published in Nature</a>, we used ancient DNA to gain new insights into the spread of culture, technologies and ancestry at a crucial juncture in European history.</p>
<h2>How ancient DNA can help us understand change</h2>
<p>Humanity’s archaeological record reveals massive changes in cultural practices and <a href="https://theconversation.com/how-a-handful-of-prehistoric-geniuses-launched-humanitys-technological-revolution-171511">technologies</a>. </p>
<p>However, it is not always clear how these changes moved between different groups of people. It can happen either by a spread of ideas (such as through trade), or through the migration of people.</p>
<p>In Europe, there have been <a href="https://theconversation.com/european-invasion-dna-reveals-the-origins-of-modern-europeans-38096">two major migrations</a> in the past 10,000 years. </p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/european-invasion-dna-reveals-the-origins-of-modern-europeans-38096">European invasion: DNA reveals the origins of modern Europeans</a>
</strong>
</em>
</p>
<hr>
<p>First, there was an expansion of early farming groups from Anatolia around 9,000 years ago. This was associated with the introduction of farming practices and animal husbandry, a more sedentary lifestyle (permanent housing) and the wide use of pottery and new types of polished stone tools.</p>
<p>Second was the expansion of steppe herders from the <a href="https://www.oneearth.org/ecoregions/pontic-steppe/">Eurasian Pontic Steppes</a> around 5,000 years ago. This is associated with the spread of pastoralism and dairying technologies, a different type of ancestry and possibly some of the Indo-European languages.</p>
<p>In our <a href="https://www.nature.com/articles/s41586-023-06334-8">new research</a>, we studied the interaction between farming and pastoralist groups from the steppe from a new angle by analysing the genomes of 135 individuals from southeastern Europe and the northwestern Black Sea region, who lived between 4,000 and 7,000 years ago. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/538000/original/file-20230718-21-739xyt.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="A map showing the Black Sea and surrounding areas." src="https://images.theconversation.com/files/538000/original/file-20230718-21-739xyt.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/538000/original/file-20230718-21-739xyt.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=380&fit=crop&dpr=1 600w, https://images.theconversation.com/files/538000/original/file-20230718-21-739xyt.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=380&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/538000/original/file-20230718-21-739xyt.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=380&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/538000/original/file-20230718-21-739xyt.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=477&fit=crop&dpr=1 754w, https://images.theconversation.com/files/538000/original/file-20230718-21-739xyt.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=477&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/538000/original/file-20230718-21-739xyt.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=477&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 area around Odesa was a ‘melting pot’ of cultures and ancestries.</span>
<span class="attribution"><span class="source">Modified from Penske et al. (2023)</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>We uncovered previously unknown and significant genetic changes in the people living in these regions. We also found the presence of steppe ancestry in the contact zone in the northwestern Black Sea region around 5,500 years ago, some 500 years earlier than previously assumed. </p>
<h2>The Copper Age in southeastern Europe</h2>
<p>Southeastern Europe played an important role in the spread of farming across Europe after early farmers from Anatolia arrived around 9,000-8,000 years ago. Approximately 1,000 years later, easy access to copper, gold and salt led to the development of <a href="https://doi.org/10.1177/1461957107086121">many flourishing settlements</a> in parts of today’s Bulgaria and Romania. </p>
<p>Settlements on the Black Sea and major rivers such as the Danube thrived through contact and trade with surrounding areas. Similarity in material culture visible in the archaeological record across a wider region indicates a period of social and political stability of approximately 500 years, between around 6,200 and 6,700 years ago.</p>
<p>Ninety-five of the ancient genomes we analysed were from this period and region, and this cultural similarity and stability is reflected in the absence of major genetic differences. </p>
<h2>A new era and a melting pot of human interaction</h2>
<p>Following this period of stability, many Copper Age settlements were abruptly abandoned around 6,000 years ago. For almost the next 1,000 years so few people lived in southeastern Europe that the period is often referred to as “the dark millennium”. The reason for this is not fully understood, but it is likely due to the depletion of resources due to unfavourable climatic conditions. </p>
<p>Instead, large settlements of several thousand houses emerged further north in parts of what are now Moldova and Ukraine. Located on the western end of the forest steppe zone, these mega-sites were associated with the <a href="https://doi.org/10.1007/s10963-017-9105-8">Cucuteni-Trypillia culture</a>. </p>
<p>Here, during a period called the Eneolithic spanning from 5,200 to 6,500 years ago, the region around today’s Odesa became a “melting pot” of human interaction. Numerous cultural influences appear in the archaeological record, including the waning Copper Age cultures and the Cucuteni-Trypillia culture. </p>
<p>Interestingly, the resulting style of pottery and other artefacts at the mega-sites showed influences from two additional groups. First, from nearby groups that could be traced to the steppe region east of Odesa. Second, from the distant Maykop culture of the North Caucasus, a mountain range east of the Black Sea. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/537927/original/file-20230718-20840-oyfm8y.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Many photos of jewellery, weapons, tools and pots shown on a white background." src="https://images.theconversation.com/files/537927/original/file-20230718-20840-oyfm8y.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/537927/original/file-20230718-20840-oyfm8y.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=931&fit=crop&dpr=1 600w, https://images.theconversation.com/files/537927/original/file-20230718-20840-oyfm8y.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=931&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/537927/original/file-20230718-20840-oyfm8y.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=931&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/537927/original/file-20230718-20840-oyfm8y.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=1170&fit=crop&dpr=1 754w, https://images.theconversation.com/files/537927/original/file-20230718-20840-oyfm8y.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=1170&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/537927/original/file-20230718-20840-oyfm8y.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=1170&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Characteristic jewellery, weapons, tools and pottery from the melting pot area around today’s Odesa. The pottery combines characteristics from numerous cultures of the area.</span>
<span class="attribution"><span class="source">I. Manzura (2020), History Carved by the Dagger: the Society of the Usatovo Culture in the 4th Millennium BC</span></span>
</figcaption>
</figure>
<p>The steppe groups practised a different way of life, called nomadic pastoralism. Where farmers lived on and worked the same piece of land, nomadic pastoralists kept moving to find fresh pastures for their large herds of animals.</p>
<p>On top of this very different lifestyle, they also carried a distinct genetic profile called “steppe ancestry”.</p>
<h2>A surprising discovery</h2>
<p>By analysing the genomes of 18 ancient individuals from the Odesa region from this period, we could see genetic evidence of the many cultural influences observed by archaeologists. </p>
<p>In addition to the previously observed Copper Age ancestry, we detected new genetic contributions from individuals from the forest steppe regions, and the North Caucasus. This new ancestry and its appearance in western Europe had been uniquely associated with the spread of a later cultural group known as the Yamnaya. </p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/how-a-handful-of-prehistoric-geniuses-launched-humanitys-technological-revolution-171511">How a handful of prehistoric geniuses launched humanity's technological revolution</a>
</strong>
</em>
</p>
<hr>
<p>This was a huge surprise. We didn’t expect to see signs of this ancestry until at least 500 years later, when the Yamnaya arrived.</p>
<p>These findings show there was not only a cultural exchange between the different groups. There must have also been biological interactions of many genetically distinct people coming together in this contact zone as early as 5,400 to 6,500 years ago. </p>
<p>Due to this “melting pot” the Eneolithic was characterised by a number of innovations. Technologies such as wheels, wagon transportation and improved metal-working spread quickly into western Europe and Central Asia.</p>
<h2>A mosaic of ancestries</h2>
<p>We also analysed 21 individuals from the Early Bronze Age, approximately 4,000–5,300 years ago. In eight of these individuals we observed the expected westward expansion of steppe pastoralists, this time associated with <a href="https://doi.org/10.1038/nature14317">the Yamnaya culture</a>. </p>
<p>This final migration brought with it the last part of the modern Western European gene pool, likely emerging from the preceding period of contact and exchange that we identified. However, the remaining 13 individuals retained the genetic signature from the preceding Copper Age. These findings indicated a coexistence of these genetically distinct peoples. </p>
<p>Our study of genetic data over time reveals a highly dynamic picture of human prehistory in southeastern Europe. As more ancient DNA data becomes available, so too will more chapters of this story.</p><img src="https://counter.theconversation.com/content/210056/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 organisation that would benefit from this article, and have disclosed no relevant affiliations beyond their academic appointment.</span></em></p>
Ancient DNA from Ukraine uncovers the earliest evidence of the arrival of the ‘steppe ancestry’ – the last piece of the modern Western European genetic puzzle.
Adam "Ben" Rohrlach, Mathematics Lecturer and Ancient DNA Researcher, University of Adelaide
Sandra Penske, PhD Student, Max Planck Institute for Evolutionary Anthropology
Licensed as Creative Commons – attribution, no derivatives.
tag:theconversation.com,2011:article/208279
2023-07-10T20:10:00Z
2023-07-10T20:10:00Z
The true origins of the world’s smallest and weirdest whale
<figure><img src="https://images.theconversation.com/files/535994/original/file-20230706-23-9x5f7i.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Skull of Caperea marginata.</span> <span class="attribution"><span class="license">Author provided</span></span></figcaption></figure><p>The <a href="https://www.marinebio.org/species/pygmy-right-whales/caperea-marginata/">pygmy right whale</a>, <em>Caperea marginata</em>, is the weirdest whale you’ve probably never heard of. </p>
<p>It is the smallest of the living <a href="https://coastalstudies.org/connect-learn/stellwagen-bank-national-marine-sanctuary/marine-mammals/cetaceans/baleen-whales/">baleen whales</a> and restricted to the Southern Hemisphere. </p>
<p>Its tank-like skeleton is unique among whales, and its ecology and behaviour remain virtually unknown. Even its mitochondria – the power plants of the cell – seem to be ticking differently. </p>
<p>Because <em>Caperea</em> is so unusual, its evolutionary relationships have long been a bone of contention. </p>
<p>Our <a href="https://onlinelibrary.wiley.com/doi/10.1111/mms.13047">new study</a> in the international Marine Mammal Science journal finally solves this enduring mystery.</p>
<p><div data-react-class="Tweet" data-react-props="{"tweetId":"1606213583238488064"}"></div></p>
<h2>You are what you eat?</h2>
<p>For 150 years, anatomists considered <em>Caperea</em> a relative of <a href="https://www.fisheries.noaa.gov/species/north-atlantic-right-whale">right whales</a>. </p>
<p>Then came the age of DNA, and <em>Caperea</em> was reinterpreted as a distant cousin of <a href="https://www.scientificamerican.com/article/why-are-blue-whales-so-gigantic/">rorquals</a>, which include the mighty blue whale, humpback and minke whale. </p>
<p>Many scientists remained unconvinced, however, leading to decades of acrimonious debates over bones, fossils and molecules.</p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/535686/original/file-20230705-3397-htklq2.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/535686/original/file-20230705-3397-htklq2.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=342&fit=crop&dpr=1 600w, https://images.theconversation.com/files/535686/original/file-20230705-3397-htklq2.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=342&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/535686/original/file-20230705-3397-htklq2.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=342&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/535686/original/file-20230705-3397-htklq2.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=430&fit=crop&dpr=1 754w, https://images.theconversation.com/files/535686/original/file-20230705-3397-htklq2.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=430&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/535686/original/file-20230705-3397-htklq2.jpeg?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">The smallest baleen whale, <em>Caperea marginata</em>, compared to the largest: the blue whale, <em>Balaenoptera musculus</em>.</span>
<span class="attribution"><span class="source">Carl Buell</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>For more than a century, the case for <em>Caperea</em> being a right whale seemed sound. Sure, it looked weird and small, but its feeding strategy was a dead ringer. </p>
<p>Like right whales, <em>Caperea</em> uses long, finely-fringed baleen plates to skim tiny crustaceans from seawater. Also like right whales, it has a hugely arched snout to accommodate its long baleen, which water and prey stream past continuously during feeding.</p>
<p>Now compare this to rorquals. Unlike <em>Caperea</em>, they feed in short bouts during which they engulf enormous amounts of water and prey in expandable throat pouches. They then expel the water through their short, coarsely-fringed baleen and trap any prey inside the mouth. </p>
<p>The implications of this brief comparison are obvious: <em>Caperea</em> resembles right whales far more than it does rorquals, and so must have the same evolutionary origin.</p>
<figure>
<iframe width="440" height="260" src="https://www.youtube.com/embed/1R73eqslR0I?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
</figure>
<h2>Morphology versus molecules</h2>
<p>Molecular data for <em>Caperea</em> first became available in the 1990s and immediately challenged the traditional view. Time and again, genes allied <em>Caperea</em> with rorquals, rather than right whales. </p>
<p>Such disagreements are normal in science and do not diminish the importance of anatomy, which, after all, remains the only way to study the 99% of species that are already extinct. But anatomical family trees have a nemesis: convergence.</p>
<p>Convergent evolution happens when unrelated species evolve similar traits. Just think of the streamlined bodies of sharks, whales and the extinct ichthyosaurs. Could this be what happened to <em>Caperea</em>?</p>
<p>As molecular evidence mounted, geneticists began to accept <em>Caperea</em> as a distant rorqual relative. Anatomists, however, disagreed.</p>
<p>Fuelling the debate was the fact that only some of the DNA of <em>Caperea</em> had actually been sequenced. Interpreting such a subset is risky, as each gene can have its own unique evolutionary history.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/northern-exposure-fossils-of-a-southern-whale-found-for-the-first-time-in-the-north-85254">Northern exposure: fossils of a southern whale found for the first time in the north</a>
</strong>
</em>
</p>
<hr>
<p>Also unhelpful was the deplorable <a href="https://theconversation.com/northern-exposure-fossils-of-a-southern-whale-found-for-the-first-time-in-the-north-85254">fossil record</a> of pygmy right whales. Sometimes, key fossils can settle evolutionary debates, as happened in 2001 when two pivotal finds confirmed the <a href="https://evolution-outreach.biomedcentral.com/articles/10.1007/s12052-009-0135-2">origin of whales from hoofed mammals</a>. </p>
<p><em>Caperea</em>, however, remains largely alone. Even though its lineage is undoubtedly ancient, we only know of six related fossils worldwide.</p>
<p>With both traditional genetic and fossil approaches at a loss, where else was there to turn? Enter genomics.</p>
<h2>What our DNA testing revealed</h2>
<p>Genomics studies all of an organism’s DNA – its entire molecular blueprint. DNA ultimately determines body shape, so comparing genomes should either corroborate anatomical family trees or expose the effects of convergence. </p>
<p>Sequencing genomes is costly and took a long time to achieve at scale. Even so, recent years have seen huge advances and produced genomes for most baleen whales. Except, you guessed it, the elusive <em>Caperea</em>.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/genome-and-satellite-technology-reveal-recovery-rates-and-impacts-of-climate-change-on-southern-right-whales-147168">Genome and satellite technology reveal recovery rates and impacts of climate change on southern right whales</a>
</strong>
</em>
</p>
<hr>
<p>Here is where our study comes in. Using a sample from a stranded individual from South Australia, we finally sequenced the genome of the pygmy right whale.</p>
<p>Unbeknown to us, a separate research group in Europe had <a href="https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-023-01579-1">had the same idea</a>. Both teams published their results within a few weeks of each other. </p>
<p>Crucially, their conclusions were the same: <em>Caperea</em> is indeed related to rorquals like the blue whale. Its similarities with right whales are the result of similar feeding strategies, rather than genetics.</p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/535985/original/file-20230706-21-jrjl5b.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/535985/original/file-20230706-21-jrjl5b.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=666&fit=crop&dpr=1 600w, https://images.theconversation.com/files/535985/original/file-20230706-21-jrjl5b.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=666&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/535985/original/file-20230706-21-jrjl5b.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=666&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/535985/original/file-20230706-21-jrjl5b.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=837&fit=crop&dpr=1 754w, https://images.theconversation.com/files/535985/original/file-20230706-21-jrjl5b.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=837&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/535985/original/file-20230706-21-jrjl5b.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=837&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">The skull of <em>Caperea</em> resembles that of right whales because both need to accommodate long baleen plates for skim feeding. Their similarities are the result of convergent evolution.</span>
</figcaption>
</figure>
<h2>So what is <em>Caperea</em> really?</h2>
<p>Proving that <em>Caperea</em> is not a right whale raises another question: why is it so unlike its rorqual cousins?</p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/536389/original/file-20230709-19-64vtgj.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/536389/original/file-20230709-19-64vtgj.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/536389/original/file-20230709-19-64vtgj.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=1509&fit=crop&dpr=1 600w, https://images.theconversation.com/files/536389/original/file-20230709-19-64vtgj.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=1509&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/536389/original/file-20230709-19-64vtgj.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=1509&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/536389/original/file-20230709-19-64vtgj.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=1897&fit=crop&dpr=1 754w, https://images.theconversation.com/files/536389/original/file-20230709-19-64vtgj.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=1897&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/536389/original/file-20230709-19-64vtgj.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=1897&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 fossil skull of the Late Miocene cetotheriid <em>Piscobalaena nana</em> from the Muséum National d'Histoire Naturelle.</span>
<span class="attribution"><span class="source">Felix Marx</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>To start answering this, we need to consider the great antiquity of <em>Caperea</em>‘s ancestry. Molecular dating suggests it diverged from other whales at least 14 million years ago, and perhaps much earlier. The oldest recognisable fossils, however, are just 10 million years old. </p>
<p>What, then, fills the gap? One possibility is that <em>Caperea</em> <a href="https://www.nationalgeographic.com/science/article/theres-something-about-caperea-marginata">sprang from the cetotheriids</a>, an ancient family of whales once thought to be extinct. </p>
<p>Many palaeontologists remain sceptical about this idea and instead have clung to the traditional grouping of <em>Caperea</em> with right whales. But anatomical data sets will now need to be re-examined to weed out the effects of convergence. </p>
<p>What this process might reveal remains unclear, of course, but cetotheriids are certainly back in the running.</p>
<p>New insights might also come from new fossils or <a href="https://www.nature.com/articles/d41586-019-01986-x">ancient proteins</a>. Whereas DNA completely breaks down after about a million years, proteins can persist far longer - maybe just long enough to test ideas like <em>Caperea</em>’s cetotheriid origin more rigorously. </p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/empty-mollusc-shells-hold-the-story-of-evolution-even-for-extinct-species-now-we-can-decode-it-187927">Empty mollusc shells hold the story of evolution, even for extinct species. Now we can decode it</a>
</strong>
</em>
</p>
<hr>
<img src="https://counter.theconversation.com/content/208279/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Nic Rawlence receives funding from the Royal Society of New Zealand Marsden Fund. </span></em></p><p class="fine-print"><em><span>Felix Georg Marx received funding from an EU Marie Skłodowska-Curie Global Postdoctoral fellowship.</span></em></p><p class="fine-print"><em><span>Ludovic Dutoit 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>
Our new genomic research finally solves a 150 years of scientific mystery about the unusual and ancient pygmy right whale.
Nic Rawlence, Senior Lecturer in Ancient DNA, University of Otago
Felix Georg Marx, Curator Vertebrates, Te Papa Tongarewa
Ludovic Dutoit, University of Otago
Licensed as Creative Commons – attribution, no derivatives.
tag:theconversation.com,2011:article/206200
2023-05-24T03:15:20Z
2023-05-24T03:15:20Z
Ancient humans may have paused in Arabia for 30,000 years on their way out of Africa
<figure><img src="https://images.theconversation.com/files/527894/original/file-20230524-20-w6g0dp.jpg?ixlib=rb-1.1.0&rect=0%2C0%2C6000%2C3997&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>Most scientists agree modern humans developed in Africa, more than 200,000 years ago, and that a great human diaspora across much of the rest of the world occurred between perhaps 60,000 and 50,000 years ago. </p>
<p>In new research <a href="https://www.pnas.org/doi/10.1073/pnas.2213061120">published</a> in Proceedings of the National Academies of Sciences, we have uncovered dozens of distinctive historical changes in the human genome to reveal a new chapter in this story. </p>
<p>Our work suggests there may have been a previously unknown phase of humanity’s great migration: an “Arabian standstill” of up to 30,000 years in which humans settled in and around the Arabian Peninsula. These humans slowly adapted to life in the region’s colder climate before venturing to Eurasia and beyond. </p>
<p>The legacy of these adaptations still lingers. Under modern conditions, many genetic changes from this period are linked to diseases including obesity, diabetes, and cardiovascular disorders. </p>
<h2>History in our genomes</h2>
<p>Since the first human genome was published in 2000, the amount of human genomic data available has grown exponentially. These rapidly growing datasets contain traces of key events in human history. Researchers have been actively developing new techniques to find those traces.</p>
<p>When ancient humans left Africa and moved around the globe, they likely met new environments and challenges. New pressures would have led to adaptation and genetic changes. These changes would subsequently have been inherited by modern humans.</p>
<p><a href="https://www.nature.com/articles/s41586-021-03244-5">Previous research</a> on genomic data shows ancient humans most likely left Africa and spread across the planet between 60,000 and 50,000 years ago. </p>
<p>However, we still don’t know much about genetic adaptations during this crucial time period. </p>
<h2>Ancient adaptation events</h2>
<p>Our team of evolutionary and medical researchers has shed new light on this period. By studying both ancient and modern genomes, we have shown genetic selection was probably an important facilitator of this ancient human diaspora.</p>
<p>Using ancient human genomes makes it possible to recover <a href="https://theconversation.com/ancient-dna-reveals-a-hidden-history-of-human-adaptation-193251">evidence of past events</a> in which specific genetic variants were strongly favoured over others and swept through a population. These “hard sweep” events are surprisingly rare in modern human genomes, most likely because their traces have been erased or distorted by subsequent mixing between populations.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/ancient-dna-reveals-a-hidden-history-of-human-adaptation-193251">Ancient DNA reveals a hidden history of human adaptation</a>
</strong>
</em>
</p>
<hr>
<p>However, in <a href="https://www.nature.com/articles/s41559-022-01914-9">earlier work</a> we identified 57 regions in the human genome where an initially rare beneficial genetic variant effectively replaced an older variant in ancient Eurasian groups. </p>
<p>In our <a href="https://www.pnas.org/doi/10.1073/pnas.2213061120">new study</a>, we reconstructed the historical spread of these genetic variants. We also estimated the temporal and geographical origins of the underlying selection pressures. </p>
<p>Further, we identified the gene in each hard sweep region most likely to have been selected for. Knowing these genes helped us understand the ancient pressures that may have led to their selection.</p>
<h2>Coping with cold</h2>
<p>Our findings suggest early humans went through a period of extensive adaptation, lasting up to 30,000 years, before the big diaspora between 60,000 and 50,000 years ago. This period of adaptation was followed by rapid dispersal across Eurasia and as far as Australia. </p>
<p>We call this period the “Arabian standstill”. Genetic, archaeological and climatic evidence all suggest these ancient humans were most likely living in and around the Arabian Peninsula.</p>
<p><iframe id="8yMnX" class="tc-infographic-datawrapper" src="https://datawrapper.dwcdn.net/8yMnX/1/" height="400px" width="100%" style="border: none" frameborder="0"></iframe></p>
<p>The genetic adaptations involved parts of the genome related to fat storage, nerve development, skin physiology, and tiny hair-like fibres in our airways called cilia. These adaptations share striking functional similarities with those found in humans and other mammals living in the Arctic today. </p>
<p>We also detected similar functional similarities with previously identified human adaptive genes derived from historical mixing events with Neanderthals and Denisovans. These distant relatives of humans are also thought to have adapted to cold Eurasian climates. </p>
<p>Overall, these changes seem likely to have been driven by adaptation to the cool and dry climates in and around prehistoric Arabia between 80,000 and 50,000 years ago. The changes would also have prepared the ancient humans for the cold Eurasian climates they would eventually encounter.</p>
<h2>Old adaptations, modern diseases</h2>
<p>Many of these adaptive genes have links to modern diseases, including obesity, diabetes, and cardiovascular disorders. The adaptations around the human expansion from Africa may have established genetic variations that, under modern conditions, are associated with common diseases. </p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/we-found-traces-of-humanitys-age-old-arms-race-with-coronaviruses-written-in-our-dna-163254">We found traces of humanity's age-old arms race with coronaviruses written in our DNA</a>
</strong>
</em>
</p>
<hr>
<p>As we have suggested in <a href="https://theconversation.com/we-found-traces-of-humanitys-age-old-arms-race-with-coronaviruses-written-in-our-dna-163254">another study</a>, genes that were adaptive in the past might contribute to modern human susceptibility to various diseases. Identifying the genetic targets of historical adaptation events could help the development of therapeutic approaches and preventive measures for contemporary populations.</p>
<p>Our findings contribute to a new but growing literature highlighting the importance of adaptation in shaping human history. They also show the growing potential of evolutionary genetics for medical research.</p><img src="https://counter.theconversation.com/content/206200/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Ray Tobler receives funding from Australian Research Council.</span></em></p><p class="fine-print"><em><span>Shane T Grey receives funding from NHMRC, ARC, MRFF, JDRF and NIH. </span></em></p><p class="fine-print"><em><span>Yassine Souilmi is supported by funding from the ARC and NHMRC.</span></em></p>
Genetic evidence reveals a long, previously unknown period of adaptation to cold climates in the history of ancient human migrations across the globe.
Ray Tobler, Postdoctoral fellow, Australian National University
Shane T Grey, Chair professor, Garvan Institute
Yassine Souilmi, Group Leader, Genomics and Bioinformatics, Australian Centre for Ancient DNA, University of Adelaide
Licensed as Creative Commons – attribution, no derivatives.
tag:theconversation.com,2011:article/204284
2023-05-11T05:28:46Z
2023-05-11T05:28:46Z
African scientists are working to pool data that decodes diseases – a giant step
<figure><img src="https://images.theconversation.com/files/525336/original/file-20230510-19-rgkrh3.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">African scientists need a central repository where the genomic data they capture can be uploaded and shared.</span> <span class="attribution"><span class="source">iStock/Getty Images Plus</span></span></figcaption></figure><p>Infectious disease outbreaks in African countries are, unfortunately, all too common. <a href="https://theconversation.com/ebola-what-are-the-symptoms-how-does-it-spread-and-where-did-it-come-from-191518">Ebola</a> in the Democratic Republic of the Congo or Uganda; Marburg virus in <a href="https://theconversation.com/the-first-human-case-of-marburg-virus-in-west-africa-is-no-surprise-heres-why-166694">Guinea</a> or <a href="https://theconversation.com/what-is-marburg-virus-and-should-we-be-worried-200082">Equatorial Guinea</a>; cholera in <a href="https://theconversation.com/why-cholera-continues-to-threaten-many-african-countries-197799">Malawi</a>; malaria and tuberculosis are among them. </p>
<p>These diseases do not respect <a href="https://theconversation.com/how-africas-porous-borders-make-it-difficult-to-contain-ebola-118719">human-made or porous borders</a>. So it’s essential that scientists in Africa are able to generate and share critical data on the pathogens in time to inform public-health decisions.</p>
<p>Genomic sequencing technologies are powerful tools in this kind of work. They enable scientists to decode the genetic material of diseases and create biological “fingerprints” to investigate and track the pathogens that cause those diseases. This information aids in developing diagnostics, treatments and vaccines. It also helps public health authorities to guide and prepare their public health systems for effective outbreak detection and response.</p>
<p>Tackling infectious diseases across countries and continents requires many complex, overlapping and broad interventions. One of those is a common repository where countries, public health authorities and their scientists can share information about diseases and the pathogens that cause them. They can then collaborate around the shared data. These <a href="https://www.insdc.org/">kinds of platforms</a> exist in many high-income countries. But the African region lags behind.</p>
<p>This is set to change. In a <a href="https://www.nature.com/articles/s41591-023-02266-y">new publication</a> in Nature Medicine we outline the work that’s being done to create such a repository for the African continent. </p>
<h2>Human and economic costs</h2>
<p>Africa accounts for <a href="https://www.sciencedirect.com/science/article/pii/S0092867420312381#cebib0010">most of the estimated 10 million deaths</a> caused globally every year by infectious diseases. </p>
<p>Those diseases also stomp the brakes on the continent’s development ambitions: according to a World Health Organisation (WHO) report they account for an <a href="https://www.afro.who.int/publications/heavy-burden-productivity-cost-illness-africa">annual estimated productivity loss</a> of US$800 billion. </p>
<p>These figures highlight the urgency of improving the scientific response to infectious diseases. </p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/investing-in-health-systems-is-the-only-way-to-stop-the-next-ebola-outbreak-124957">Investing in health systems is the only way to stop the next Ebola outbreak</a>
</strong>
</em>
</p>
<hr>
<p>There are some green shoots. The COVID pandemic showed what African institutions are capable of. The Africa Centres for Disease Control (Africa CDC), through the <a href="https://ipg.africacdc.org/initiatives/africa-pathogen-genomics-initiative-africa-pgi">Africa Pathogen Genomics Initiative</a>, oversaw the <a href="https://africacdc.org/news-item/africa-cdc-ramps-up-training-on-sars-cov-2-genomics-and-bioinformatics/">training</a> of hundreds of laboratory staff.</p>
<p>DNA sequencing machines and essential laboratory consumables – like reagents, the chemical cocktails that make testing possible – have been <a href="https://www.sciencedirect.com/science/article/pii/S1473309920309397">put in place</a>. Today, public health laboratories in many African countries, with varying levels of capacity, can generate their own genomic sequences of pathogens. </p>
<p>So, the data is not the problem. The questions are: what is going to happen to and with it? How and where is it going to be secured, and by whom? Will it be, as has been the <a href="https://theconversation.com/global-health-still-mimics-colonial-ways-heres-how-to-break-the-pattern-121951">custom up to now</a>, “exported” and the intellectual property moved offshore?</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/how-biobanks-can-help-improve-the-integrity-of-scientific-research-100035">How biobanks can help improve the integrity of scientific research</a>
</strong>
</em>
</p>
<hr>
<p>Global data sharing platforms have played a significant role in sharing of data. However, <a href="https://www.science.org/content/article/invented-persona-behind-key-pandemic-database">transparency and governance issues</a> are currently being raised by the global community.</p>
<p>Since 2020, the Africa CDC in collaboration with the <a href="https://aslm.org/">African Society for Laboratory Medicine</a>, the <a href="https://www.uwc.ac.za/study/all-areas-of-study/institutes/south-african-national-bioinformatics-institute/overview">South African National Bioinformatics Institute</a> and several public health institutions across Africa are working to develop a continental platform for pathogen genomic data management and sharing. The technology innovation and development involves <a href="https://hominum.global/">industry</a> and other <a href="http://nzconline.co.za">partners</a>.</p>
<p>The development of such a platform is not merely a technical exercise, though. An ecosystem must be created for its adoption. So it is being built in parallel with a consultation led by the Africa CDC with its member states, to refine data sharing agreements between countries and support national data governance frameworks.</p>
<p>The platform rests on six pillars.</p>
<h2>Collaboration and consistency</h2>
<p>The first pillar is adoption and change management. Regional organisations – those that drove training and infrastructure investment during the COVID-19 pandemic – must drive the development of the necessary policies, processes and system changes across the continent.</p>
<p>Second, the platform must offer a good user experience that will allow for seamless, cost-effective data collection and the timely sharing and use of data across Africa.</p>
<p>Third, we need data services and products to facilitate the sharing of data and information with decision-makers who are not scientists or geneticists. </p>
<p>Fourth, standardised and consistent data management processes, practices, tools and controls for how data is processed, stored, shared and deployed are needed across countries and contexts. </p>
<p>Core infrastructure is the fifth pillar: the technical side of the platform must be composed of application and infrastructure components that can be rapidly reconfigured for contexts and diseases. </p>
<p>And, finally, good programme management and sustainable resources will be key.</p>
<h2>A global imperative</h2>
<p>As we argue in <a href="https://www.nature.com/articles/s41591-023-02266-y">our journal article</a>, data management and analytics to support data-driven decision making in public health is a global imperative. It requires continuous engagement with international disease surveillance stakeholders and technology platform developers.</p>
<p>The human and resource costs of unchecked diseases in Africa have been pointed out. If there is going to be a collective response to Africa’s burden of diseases – and it is a massive task – a shared pathogen genomics data platform would be a crucial step in underpinning those efforts.</p>
<p>An African owned and African led data sharing platform will be critical for timely sharing of locally produced data to inform rapid response to outbreaks. It will also be a critical step towards an equitable mechanism to maximise the value and utility of pathogen genetic data for national, regional and global health security.</p><img src="https://counter.theconversation.com/content/204284/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Alan Christoffels receives funding from the South African Medical Research Council, The South African National Research Foundation and the Bill & Melinda Gates Foundation. The partners in this repository development project are the Public Health Alliance for Genomic Epidemiology, the Overture.bio team at the Ontario institute for Cancer Research in Canada, the Centre for High Performance Computing at the CSIR, South Africa, and Hominum Global.</span></em></p><p class="fine-print"><em><span>Sofonias Kifle Tessema 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>
Time and information is of the essence when tackling infectious diseases across countries and continents.
Alan Christoffels, Director South African National Bioinformatics Institute, University of the Western Cape
Sofonias Kifle Tessema, Program Lead for Pathogen Genomics at the Africa CDC
Licensed as Creative Commons – attribution, no derivatives.
tag:theconversation.com,2011:article/200048
2023-05-08T12:19:31Z
2023-05-08T12:19:31Z
Clothes moths: Why I admire these persistent, destructive, difficult-to-eradicate and dull-looking pests
<figure><img src="https://images.theconversation.com/files/524520/original/file-20230504-1338-tnizp0.jpg?ixlib=rb-1.1.0&rect=78%2C103%2C1284%2C860&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">*Tineola bisselliella* can survive on as little as a hairball and some vitamin B.</span> <span class="attribution"><a class="source" href="https://commons.wikimedia.org/wiki/File:Tineola.bisselliella.7218.jpg">Olaf Leillinger/Wikimedia Commons</a>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span></figcaption></figure><p>Every day, I come into the lab to check the moth jar. The jar, which previously housed a liter of honey, now contains a multitude of small golden moths and their wriggly caterpillar offspring.</p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/524198/original/file-20230503-19-qkt3kv.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="smiling woman holds a liter-size jar with scrunched up knitting in it" src="https://images.theconversation.com/files/524198/original/file-20230503-19-qkt3kv.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/524198/original/file-20230503-19-qkt3kv.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=749&fit=crop&dpr=1 600w, https://images.theconversation.com/files/524198/original/file-20230503-19-qkt3kv.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=749&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/524198/original/file-20230503-19-qkt3kv.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=749&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/524198/original/file-20230503-19-qkt3kv.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=941&fit=crop&dpr=1 754w, https://images.theconversation.com/files/524198/original/file-20230503-19-qkt3kv.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=941&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/524198/original/file-20230503-19-qkt3kv.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=941&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 author in the lab with her prized moth jar.</span>
<span class="attribution"><span class="source">Isabel Novick</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>The founding population came from within my house – pests that fervently fed on my sweaters, rugs and horsehair plaster. When they emerge from my walls in the evenings, I chase them with zeal and catch them in jam jars. “Moth!” I shout, jumping up from the couch, knocking over whatever is in front of me. In the lab, I feed them clippings of a mohair sweater that shrank in the wash, which I soak in brewer’s yeast.</p>
<p><a href="https://scholar.google.com/citations?hl=en&user=Cog3A6IAAAAJ&view_op=list_works&gmla=AHoSzlX3j284dvhFbLwvsoW_JOhIs5qvImnVBOhC7QrqXwX53uEoVh9osKUVd9oBWd7foWeY7X0W3TJBE-pg97Ik">I’m a doctoral candidate</a> <a href="https://www.bu.edu/biology/people/profiles/isabel-novick/">studying the evolutionary relationships</a> within the moth family Tineidae. I’m interested in how webbing clothes moths, <em>Tineola bisselliella</em>, have dispersed so widely and colonized our homes so readily. I am using a population genetics approach, examining the DNA of isolated populations of moths from all over the world. They eat crazy stuff. They live mostly indoors. How did this happen?</p>
<h2>Resourceful, vigorous, tanklike eating machines</h2>
<p>Webbing clothes moths are part of a distinctive, primordial lineage called the <a href="https://doi.org/10.1007/978-1-4020-6359-6_3921">fungus moth family</a>. These guys emerged long before more well-known species like silk moths. If you’re unlucky, you are already aware of the destruction they can wreak on sweaters, rugs and upholstery. But you many not realize how fascinating Tineidae are.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/524201/original/file-20230503-22-bkppfb.PNG?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="little worms on the surface of a knitted material" src="https://images.theconversation.com/files/524201/original/file-20230503-22-bkppfb.PNG?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/524201/original/file-20230503-22-bkppfb.PNG?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=437&fit=crop&dpr=1 600w, https://images.theconversation.com/files/524201/original/file-20230503-22-bkppfb.PNG?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=437&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/524201/original/file-20230503-22-bkppfb.PNG?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=437&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/524201/original/file-20230503-22-bkppfb.PNG?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=549&fit=crop&dpr=1 754w, https://images.theconversation.com/files/524201/original/file-20230503-22-bkppfb.PNG?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=549&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/524201/original/file-20230503-22-bkppfb.PNG?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=549&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption"><em>Tineola bisselliella</em> larvae living it up on a scrap of sweater in the lab.</span>
<span class="attribution"><span class="source">Isabel Novick</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>These moths can eat hair, skin and feathers, all of which comprise a protein called keratin. Keratin – the main ingredient in nails, hoofs and horns – is <a href="https://doi.org/10.1371/journal.pone.0202608">notoriously tough to digest</a>. Biologists still aren’t sure how clothes moths can metabolize keratin, and this is something I aim to address in my research. One study posits that they harbor a <a href="https://doi.org/10.3390/microorganisms8091415">microorganism in their gut</a> that uses digestive enzymes to break down keratin for them.</p>
<p>However mysterious the process may be, their nutritional needs can be met with as little as a hairball and <a href="http://publichealth.lacounty.gov/eh/docs/safety/managing-clothes-moth-infestations.pdf">some vitamin B</a>, which they can glean from sweat, pee and food stains. Not only that, but research suggests these moths somehow <a href="https://agris.fao.org/agris-search/search.do?recordID=US201301122326">produce water as a byproduct of digesting keratin</a>, so they can happily survive within the dry recesses of your home.</p>
<p>Incredibly, webbing clothes moths can safely digest poisonous heavy metals like <a href="https://doi.org/10.1071/BI9510049">arsenic, mercury and lead</a>. They can easily <a href="https://doi.org/10.1016/j.jspr.2005.08.004">chew through soft plastics and metabolize synthetic fabrics</a>. They have been known to feast on <a href="https://www.researchgate.net/publication/292321410_Forensic_entomology_applied_to_a_mummified_corpse">mummified human remains</a> and have even been a recognizable pest long enough to be <a href="https://bible.knowing-jesus.com/topics/Moths">mentioned in the Bible</a>. They are so economically destructive that by the 1990s they were causing up to <a href="https://www.wiley.com/en-us/Introduction+to+Insect+Pest+Management%2C+3rd+Edition-p-9780471589570">US$1 billion in damage per year in the U.S. alone</a>.</p>
<p>This pest insect, over time, has hitchhiked all over the world. It can now be found from Australia to Chile, from Nigeria to Canada. The current hypothesis is that these moths originated in Africa and expanded their range by <a href="https://doi.org/10.1016/j.jspr.2005.08.004">hitchhiking on 19th-century ships</a>. </p>
<p>Scientists consider webbing clothes moths synanthropes: organisms that benefit from, and <a href="https://davidrousefaicp.com/synanthropic-species-why-are-they-important-to-our-future/">have adapted to, human spaces</a>, much like pigeons or bedbugs. They have taken this to an extreme and are now <a href="https://doi.org/10.4081/jear.2011.83">mostly found indoors</a>.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/524673/original/file-20230505-27-dokyrv.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="color drawing of an insect with long antennae and folded wings" src="https://images.theconversation.com/files/524673/original/file-20230505-27-dokyrv.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/524673/original/file-20230505-27-dokyrv.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=456&fit=crop&dpr=1 600w, https://images.theconversation.com/files/524673/original/file-20230505-27-dokyrv.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=456&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/524673/original/file-20230505-27-dokyrv.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=456&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/524673/original/file-20230505-27-dokyrv.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=572&fit=crop&dpr=1 754w, https://images.theconversation.com/files/524673/original/file-20230505-27-dokyrv.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=572&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/524673/original/file-20230505-27-dokyrv.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=572&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 moths aren’t particularly pleasing to the human eye.</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/news-photo/carpet-moth-tineidae-artwork-by-steve-roberts-news-photo/492779087">Steve Roberts/De Agostini Picture Library via Getty Images</a></span>
</figcaption>
</figure>
<p>Researchers are still not sure what evolutionary adaptations have allowed these moths to colonize, and ultimately depend upon, human environments. However, it seems likely to me that their global domination is associated with their diet. Webbing clothes moths are known as <a href="https://doi.org/10.4081/jear.2011.83">facultative keratinophages</a>, which means they can choose to eat and digest keratin, but it’s not a required part of their diet. This kind of nutritional flexibility is common to other well-known synanthropic species – is there anything a raccoon won’t eat? – and may be fundamental to the moths’ successful global dispersal.</p>
<h2>Moth genes from around the world</h2>
<p>To study the differences between populations of webbing clothes moths around the world, I am analyzing a type of genomic data made from sequencing “<a href="https://doi.org/10.1093/sysbio/sys004">ultraconserved elements</a>.” This technique targets specific genes that all moth species share, called orthologs, and compares the variable genetic regions on both sides of the conserved sequence. This data tells researchers like me how distantly related the clothes moths in, say, Australia are to clothes moths in Hawaii.</p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/524647/original/file-20230505-25-gz6i5l.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="about a dozen small dead moths stuck to sticky cardboard" src="https://images.theconversation.com/files/524647/original/file-20230505-25-gz6i5l.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/524647/original/file-20230505-25-gz6i5l.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=619&fit=crop&dpr=1 600w, https://images.theconversation.com/files/524647/original/file-20230505-25-gz6i5l.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=619&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/524647/original/file-20230505-25-gz6i5l.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=619&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/524647/original/file-20230505-25-gz6i5l.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=778&fit=crop&dpr=1 754w, https://images.theconversation.com/files/524647/original/file-20230505-25-gz6i5l.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=778&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/524647/original/file-20230505-25-gz6i5l.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=778&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">This trap came back with plenty of moths that unwittingly donated themselves to science.</span>
<span class="attribution"><span class="source">Isabel Novick</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>To that end, I’ve spent the past two years internationally shipping pheromone-baited moth traps to interested volunteers. They set up the traps in their closets or storage rooms. After two months, I ask whether they’ve caught anything, request a photo of the trap and have them ship it back to me.</p>
<p>People generally want to help because they hope my research will yield better <a href="https://ipm.ucanr.edu/PMG/PESTNOTES/pn7435.html">methods of moth eradication</a>. Ultimately, it may, but I’m primarily interested in appreciating these organisms from an evolutionary perspective.</p>
<p>So far, I have received over 600 moths. But many of my correspondents don’t catch anything, or catch the wrong thing. Sometimes the trap gets thrown out with the trash. Sometimes I send a trap and never hear from the recipient again. It can be a frustrating process. I end up spending hundreds of dollars and sifting through hundreds of moths, most of them other tineids or pantry moths, looking for the flash of dusty golden wings. </p>
<p>I spend a lot of my time in the lab extracting moth DNA and a lot of time on my computer analyzing it. Ideally, this research will yield a more comprehensive picture of how moths in this family are related to one another, and clarify whether clothes moths from around the world are actually the species we think they are. If these moths are experiencing sexual isolation, we might be using the wrong methods to control them depending on their location. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/524202/original/file-20230503-1364-y4rm31.PNG?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="pale moth with dark eye" src="https://images.theconversation.com/files/524202/original/file-20230503-1364-y4rm31.PNG?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/524202/original/file-20230503-1364-y4rm31.PNG?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=277&fit=crop&dpr=1 600w, https://images.theconversation.com/files/524202/original/file-20230503-1364-y4rm31.PNG?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=277&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/524202/original/file-20230503-1364-y4rm31.PNG?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=277&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/524202/original/file-20230503-1364-y4rm31.PNG?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=348&fit=crop&dpr=1 754w, https://images.theconversation.com/files/524202/original/file-20230503-1364-y4rm31.PNG?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=348&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/524202/original/file-20230503-1364-y4rm31.PNG?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=348&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption"><em>Tineola bisselliella</em> moth, ready for its close-up through the microscope.</span>
<span class="attribution"><span class="source">Isabel Novick</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<h2>Appreciation for a pest</h2>
<p>Even though clothes moths can destroy your wardrobe or devour priceless objects like taxidermy, oriental carpets and upholstered furniture <a href="https://www.latimes.com/entertainment-arts/story/2021-04-22/getty-museum-covid-closure-moth-remediation">in museum collections</a>, I can’t help but admire them.</p>
<p>They are not intentionally pests; they are innovative, cunning and endlessly capable. Their ability to capitalize on unfilled niches has allowed them to spread far and wide throughout homes everywhere. They’re not chomping through your drapes with malicious intent; they’re operating exactly as they evolved to, in a way that has worked to their advantage for thousands of years. The reasons people dislike them – being persistent, destructive and difficult to eradicate, not to mention dull-colored – are the reasons they’ve been able to survive and thrive so successfully for so long.</p>
<p>I gently urge you to consider their efficiency and determination as a sort of evolutionary elegance. How incredible is it for something to have evolved to eat the inedible, to occupy the uninhabitable and to overcome every evolutionary obstacle in its way? Of course, that doesn’t mean their damage can’t be devastating, or that battling these moths doesn’t stink. But, from an evolutionary standpoint, the webbing clothes moth should inspire wonder instead of disgust, awe instead of frustration, and instead of exasperation, admiration.</p><img src="https://counter.theconversation.com/content/200048/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>I used to work at the Museum of Science, Boston</span></em></p>
An appreciation for the moths that chomp holes in your clothes. They eat the inedible, occupy the uninhabitable and overcome every evolutionary obstacle in their way.
Isabel Novick, Doctoral Candidate in Ecology, Behavior and Evolution, Boston University
Licensed as Creative Commons – attribution, no derivatives.
tag:theconversation.com,2011:article/199978
2023-05-08T06:47:10Z
2023-05-08T06:47:10Z
Our tropical fruits are vulnerable to climate change. Can we make them resilient in time?
<figure><img src="https://images.theconversation.com/files/524839/original/file-20230508-94623-cet8aw.jpeg?ixlib=rb-1.1.0&rect=0%2C0%2C1421%2C1255&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><span class="source">Emily Rames</span>, <span class="license">Author provided</span></span></figcaption></figure><p>Plants provide almost every calorie of food we eat. Grains like rice, wheat and corn make civilisation possible. For millennia, farmers have bred grains, fruit and vegetable varieties to get larger harvests and plants better able to tolerate different climates. </p>
<p>But climate change is going to bring enormous disruption to the plants we rely on. A hotter world. Drier in some places. Wetter in others. Intensified droughts. More fire. Sudden torrential rain. </p>
<p>We’re going to need plants with even greater resilience. But can it be done? </p>
<p>We believe so. Our team has been working to climate-proof five popular fruits – banana, the single most commonly bought item in supermarkets, as well as pineapple, passionfruit, custard apples and paw paw. We’ve already done this with chickpeas to produce new, more resilient varieties. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/524837/original/file-20230508-171112-qeacvz.jpg?ixlib=rb-1.1.0&rect=57%2C26%2C3441%2C2302&q=45&auto=format&w=1000&fit=clip"><img alt="pineapple farm" src="https://images.theconversation.com/files/524837/original/file-20230508-171112-qeacvz.jpg?ixlib=rb-1.1.0&rect=57%2C26%2C3441%2C2302&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/524837/original/file-20230508-171112-qeacvz.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/524837/original/file-20230508-171112-qeacvz.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/524837/original/file-20230508-171112-qeacvz.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/524837/original/file-20230508-171112-qeacvz.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/524837/original/file-20230508-171112-qeacvz.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/524837/original/file-20230508-171112-qeacvz.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">Pineapple plants like tropical conditions. Their genomes may hold the secrets of climate resilience.</span>
<span class="attribution"><span class="source">Garth Sanewski, Queensland Department of Agriculture and Fisheries</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<h2>What does climate change mean for horticulture?</h2>
<p>Australia, the driest inhabited continent, has already seen weather patterns shift. Droughts have become more severe, heatwaves and fire have intensified, and intense rainfall and floods are more common. In some areas, there’s less winter rainfall, and the ocean temperature is rising. </p>
<p>Fruit and vegetable growing is one of Australia’s most important agricultural sectors, with an annual production value (excluding wine grapes) <a href="https://www.agriculture.gov.au/agriculture-land/farm-food-drought/hort-policy#production">exceeding</a> A$11 billion in 2021–2022. </p>
<p>But this could change. The warping climate and heightened instability make it harder for fruit farmers to plan. </p>
<p>Already, the Australian fruit industry has seen large-scale losses of young fruit trees, or seasons where fruit <a href="https://www.abc.net.au/news/2022-11-01/four-seasons-in-one-day-for-queensland-farmers/101601094">develops poorly</a>. </p>
<p>As winters get warmer, we could see lower apple, pear, cherry and nut yields. That’s because these trees usually go dormant during cold periods. If the weather isn’t cold enough, they don’t grow and develop normally. </p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/farms-are-adapting-well-to-climate-change-but-theres-work-ahead-164860">Farms are adapting well to climate change, but there's work ahead</a>
</strong>
</em>
</p>
<hr>
<h2>What can we do?</h2>
<p>Fruit farmers have to play a long game. It takes years for apple tree saplings planted today to begin bearing saleable fruit. </p>
<p>These long times to a payoff can make it hard to respond quickly to climate challenges. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/524843/original/file-20230508-40482-po496w.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/524843/original/file-20230508-40482-po496w.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/524843/original/file-20230508-40482-po496w.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/524843/original/file-20230508-40482-po496w.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/524843/original/file-20230508-40482-po496w.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/524843/original/file-20230508-40482-po496w.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/524843/original/file-20230508-40482-po496w.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/524843/original/file-20230508-40482-po496w.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">Custard apples are a popular tropical fruit. But they have limits.</span>
<span class="attribution"><span class="source">Grant Bignell, Queensland Department of Agriculture and Fisheries</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>But there are new methods we are trying. Modern tools such as whole genome sequencing and allele mining are letting us get better at finding how vital traits are coded on a tree’s genome. This, in turn, can help us target traits like drought and heat tolerance which will be valuable in the future. With this knowledge, we can manipulate these genes to get stronger effects, or transfer them to other plants using modern breeding techniques. </p>
<p>We have already used these techniques to <a href="https://phys.org/news/2019-04-breakthrough-high-yield-drought-resilient-chickpeas.html">find genes</a> in chickpeas that code for better drought resistance. Plants with these genes can survive temperatures of up to 38°C and produce better yields to boot. After we isolated these genes, breeders in India and African nations <a href="https://timesofindia.indiatimes.com/city/hyderabad/icrisat-develops-3-new-drought-resistant-chickpeas/articleshow/86792826.cms">used this knowledge</a> to produce new, more drought tolerant varieties.</p>
<p>You might think drought tolerance is about retaining water better. Not necessarily. In these new and improved varieties, we see deeper roots, more vigorous growth and better leaf growth. This vigour safeguards their yields under drought stress. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/525000/original/file-20230509-213756-i2uj9s.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="chickpea drought resistant" src="https://images.theconversation.com/files/525000/original/file-20230509-213756-i2uj9s.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/525000/original/file-20230509-213756-i2uj9s.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=600&fit=crop&dpr=1 600w, https://images.theconversation.com/files/525000/original/file-20230509-213756-i2uj9s.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=600&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/525000/original/file-20230509-213756-i2uj9s.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=600&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/525000/original/file-20230509-213756-i2uj9s.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=753&fit=crop&dpr=1 754w, https://images.theconversation.com/files/525000/original/file-20230509-213756-i2uj9s.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=753&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/525000/original/file-20230509-213756-i2uj9s.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=753&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 worked for chickpeas. This image shows lead author Rajeev Varshney with a drought tolerant chickpea variety in Patancheru, India.</span>
<span class="attribution"><span class="source">Rajeev Varshney</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>Now we are using these techniques to mine the genomes of popular tropical fruit such as bananas and pineapples. We want to do the same as for chickpeas: create climate resilient cultivars. </p>
<p>What worked for chickpeas may not work for pawpaw and other fruit species. What we want is to find any characteristics which will boost survival rates in extreme conditions. </p>
<p>What would make these fruit trees and plants resilient to climate change? High tolerance to stress is vital. If you’re a gardener, you’ll know some plants can take a lot of punishment – while others are finicky and can die easily. Finding genes to promote robustness will help. </p>
<p>But there are other genes we’re looking for – those which code for improved yields and better fruit quality. </p>
<p>We are also working on accurate forecasting of climate resilience traits against the predicted changes to climates in our fruit growing regions. We can map the usefulness of these traits for specific regions by statistically testing correlations between different genes and measurements of plant traits. </p>
<p>Once we have greater ability to reliably forecast crop performance, we’ll avoid the long time needed to repeatedly grow and test new cultivars in field conditions and wait for the intense conditions needed to test how they respond. </p>
<p>The climate is changing, rapidly. We need to adapt our food sources just as quickly. </p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/from-field-to-store-to-plate-farmers-are-worried-about-climate-change-178885">From field to store to plate, farmers are worried about climate change</a>
</strong>
</em>
</p>
<hr>
<p><em>We are grateful to Vanika Garg, Anu Chitikineni, Robert Henry, Natalie Dillon, David Innes, Rebecca Ford, Parwinder Kaur and Ben Callaghan for their collaboration and support</em></p><img src="https://counter.theconversation.com/content/199978/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Rajeev Varshney receives funding from Hort Innovation Australia for establishing the Advanced Genomics Platform mentioned in this article</span></em></p><p class="fine-print"><em><span>Abhishek Bohra receives funding from Hort Innovation Australia </span></em></p>
Climate change is bringing heightened droughts, heat stress and floods. For our fruit trees, that means tougher conditions. To prepare means mining their genomes to hunt for resilience.
Rajeev Varshney, Professor, Murdoch University
Abhishek Bohra, Senior research fellow, Murdoch University
Licensed as Creative Commons – attribution, no derivatives.
tag:theconversation.com,2011:article/204507
2023-05-02T11:20:35Z
2023-05-02T11:20:35Z
DNA study sheds light on Scotland’s Picts, and resolves some myths about them
<figure><img src="https://images.theconversation.com/files/523315/original/file-20230427-20-enm6fg.jpg?ixlib=rb-1.1.0&rect=14%2C21%2C4716%2C3137&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Pictish stones feature distinctive symbols.</span> <span class="attribution"><span class="source">© Cathy MacIver</span>, <span class="license">Author provided</span></span></figcaption></figure><p>The people known as <a href="https://en.wikipedia.org/wiki/Picts">the Picts</a> have puzzled archaeologists and historians for centuries. They lived in Scotland during the early medieval period, from around AD300 to AD900, but many aspects of their society remain mysterious.</p>
<p>The Picts’ unique cultural characteristics, such as large stones decorated with distinct symbols, and lack of written records, have led to numerous theories about their origins, way of life, and culture. </p>
<p>This is commonly referred to in archaeology as the “Pictish problem”, a term popularised by the <a href="https://books.google.co.uk/books/about/The_Problem_of_the_Picts_Edited_by_F_T_W.html?id=EWZEtwAACAAJ&redir_esc=y">title of a 1955 edited book</a> by the archaeologist Frederick Threlfall Wainwright.</p>
<p>Our genetic study of human remains from this period challenges several myths about the Picts. These include a proposed origin in eastern Europe, as well as a longstanding idea that the inheritance of wealth passed down the female side of the family.</p>
<p>We attempted to shed light on the Picts’ origins and legacy by sequencing whole genomes – the full complement of DNA in human cells – from skeletons excavated at two cemeteries. </p>
<h2>Stone monuments</h2>
<p>These cemeteries, at Balintore in Easter Ross and Lundin Links in Fife, date to between the 5th and 7th centuries AD. The results of our research have been <a href="https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1010360">published in PLOS Genetics</a>.</p>
<p>The Balintore burials are not well understood, but Lundin Links is characterised by <a href="https://www.tandfonline.com/doi/full/10.1080/00766097.2017.1296031">exceptional stone monuments</a>. The burials take the form of round or rectangular cairns – where numerous stones are piled up as markers – and long cists. Cists are stone-built “boxes” that hold the remains of the dead. </p>
<p>The cemetery probably housed people of a high-status, but this is still hypothetical due to the limited knowledge of these burials and society more generally during this period. Human remains in general from the Pictish era are relatively scarce and often poorly preserved.</p>
<p>There is no known settlement associated with Lundin Links. This is a common issue in Pictish archaeology, as the extent of their settlements is still largely unknown. Recently, however, excavations led by Professor Gordon Noble at the University of Aberdeen have <a href="https://www.google.co.uk/books/edition/Picts/J1iZEAAAQBAJ?hl=en&gbpv=0">discovered several new Pictish sites</a>, frequently hillforts, around Scotland.</p>
<h2>Origin myths</h2>
<p>In our study, we looked at how genetically similar the Pictish genomes were to other ancient genomes from Britain and Ireland, Scandinavia and mainland Europe dating to the Iron Age, Roman, Anglo-Saxon and Viking periods. Our findings support a prevailing view that the Picts descended from Iron Age groups in Britain and Ireland. </p>
<p>This contrasts with older, often elaborate, myths of exotic origins, such as the one recounted in the <a href="https://en.wikipedia.org/wiki/Ecclesiastical_History_of_the_English_People#:%7E:text=The%20Ecclesiastical%20History%20of%20the,Roman%20Rite%20and%20Celtic%20Christianity.">Ecclesiastical History of the English People</a>, written by the <a href="https://www.britannica.com/biography/Saint-Bede-the-Venerable">Anglo-Saxon scholar Bede</a> in AD731. This claimed that the Picts migrated from Scythia (a historical region around the northern coast of the Black Sea) to northern Britain.</p>
<figure class="align-center ">
<img alt="DNA double helix" src="https://images.theconversation.com/files/523394/original/file-20230428-16-hmppm9.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/523394/original/file-20230428-16-hmppm9.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=337&fit=crop&dpr=1 600w, https://images.theconversation.com/files/523394/original/file-20230428-16-hmppm9.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=337&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/523394/original/file-20230428-16-hmppm9.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=337&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/523394/original/file-20230428-16-hmppm9.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=424&fit=crop&dpr=1 754w, https://images.theconversation.com/files/523394/original/file-20230428-16-hmppm9.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=424&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/523394/original/file-20230428-16-hmppm9.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">The researchers used a method that involves looking at long stretches of DNA.</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/blue-helix-human-dna-structure-1669326868">Billion Photos / Shutterstock</a></span>
</figcaption>
</figure>
<p>Other theories include an origin in <a href="https://en.wikipedia.org/wiki/Thrace">Thrace</a> (a historical region in south-east Europe) and islands to the north of Britain.</p>
<p>We sequenced two genomes to medium or high coverage, meaning that we determined the order of the “letters” in the DNA code multiple times while piecing together the highly fragmented genetic sequence. This allowed us to “zoom in” on the genetic diversity – or variation – in the ancient and modern people from our study, gaining greater analytical resolution.</p>
<p>We were able to look at fine-scale differences among ancient and modern groups across Britain and Ireland. We applied a method that investigates something called <a href="https://en.wikipedia.org/wiki/Identity_by_descent">identity-by-descent (IBD)</a>. This involves looking at relatively long stretches of DNA (“chunks” of chromosomes) that are shared by different individuals. </p>
<p>IBD is an indicator of relatedness via shared genetic ancestors. While we all share ancestors, sometimes we share more recent genetic ancestors with some individuals than with others. In this scenario, we would also share more IBD segments of DNA. </p>
<h2>Female inheritance</h2>
<p>The Pictish genomes share more long DNA chunks with present-day people from western Scotland, Wales and Northern Ireland. We interpreted this as a sign of genetic continuity from the Pictish period to the present-day. </p>
<p>But present-day populations in Britain and Ireland also share relatively high amounts of IBD segments with Anglo-Saxon genomes from southern regions, suggesting mixture between populations in a south-to-north direction.</p>
<p>This fascinating insight provides a glimpse into the demographic processes that have shaped genetic diversity and population structure in present-day populations. However, there were also small but significant differences in the genetic similarity between Pictish genomes and other ancient groups, such as Iron Age genomes we compared them with. </p>
<p>This suggests that “Pictish genetic ancestry” was not static or homogenous. Instead, the genetic variation among ancient people reflects dynamic and complex communities.</p>
<p>Lastly, we managed to address an intriguing question. Bede stated that when the Picts stopped off in Ireland before settling in Britain, they were allowed to marry local women on the condition that Pictish succession passed down the female line. </p>
<p>This led to the notion that the Picts followed a tradition of “matrilineal succession”, where the sister’s son inherits the wealth instead of sons on the male line – a system often associated with women marrying locally. Scholars now believe this idea was probably fabricated to boost Pictish identity and validate specific rulers.</p>
<p>We sequenced complete genomes of mitochondria – structures in cells, often described as biological “batteries” – in seven samples from Lundin Links. They all carried unique mutations, meaning that none of the individuals were closely related on the maternal line. </p>
<p>This is more consistent with female exogamy, where women marry outside their social group. This is just one population sample from one location, though, so more research is required to test whether this holds elsewhere.</p>
<p>The study fills gaps in our understanding of the genetic landscape of Britain and Ireland during the early medieval period. It provides a baseline for future studies to investigate the complex genetic ancestry of present-day populations.</p><img src="https://counter.theconversation.com/content/204507/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Linus Girdland Link was supported by the school of geoscience, University of Aberdeen. Kate Britton was supported by the Leverhulme Trust during production of this manuscript. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</span></em></p><p class="fine-print"><em><span>Adeline Morez was supported by ECR strategic support of early career researchers in the faculty of science at LJMU, awarded to Linus Girdland-Flink.</span></em></p>
The genetic study challenges previous theories about the origins and culture of the Picts.
Linus Girdland Flink, Visiting lecturer at Liverpool John Moores University, lecturer in biomolecular archaeology, University of Aberdeen
Adeline Morez, Post-doctorate researcher, Université Toulouse III - Paul Sabatier, visiting lecturer, Liverpool John Moores University
Licensed as Creative Commons – attribution, no derivatives.
tag:theconversation.com,2011:article/204340
2023-04-24T21:42:07Z
2023-04-24T21:42:07Z
Canadian science pioneers’ role in the Human Genome Project shows why it’s crucial to fund research
<figure><img src="https://images.theconversation.com/files/522693/original/file-20230424-1269-xtr2u1.jpg?ixlib=rb-1.1.0&rect=149%2C17%2C1623%2C991&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">The research and vision of Canadian scientists were key foundations of the Human Genome Project. Today, lack of funding threatens discovery research in Canada.</span> <span class="attribution"><span class="source">(Pixabay)</span></span></figcaption></figure><p>On April 25, the world will celebrate <a href="https://www.genome.gov/dna-day">DNA Day</a>, marking two events: the 70th anniversary of the <a href="https://www.cam.ac.uk/stories/DNA-structure-discovery-cambridge-70th-anniversary">discovery of the double helix</a> and the 20th anniversary of the <a href="https://www.genome.gov/human-genome-project">Human Genome Project</a>, which sequenced humans’ genetic blueprint for the first time.</p>
<p>For the Human Genome Project, Canadians were at the forefront. </p>
<p>The distinguished Canadian medical geneticist Charles Scriver of McGill University, <a href="https://healthenews.mcgill.ca/in-memoriam-charles-r-scriver/">who recently passed away</a>, convinced the Howard Hughes Medical Institute in the United States in 1986 to bring together the parties who could fund and execute the Human Genome project. This objective has been acknowledged as prescient. </p>
<p>The meeting was attended by Nobel Prize winners <a href="https://www.nobelprize.org/prizes/chemistry/1980/gilbert/biographical/">Walter Gilbert</a> and <a href="https://www.nobelprize.org/prizes/medicine/1962/watson/biographical/">James Watson</a>, and is described as a major catalyst for the Human Genome Project in <em><a href="https://books.google.ca/books/about/The_Book_of_Man.html?id=ys5qAAAAMAAJ&redir_esc=y">The Book of Man: The Human Genome Project and the Quest to Discover Our Genetic Heritage</a></em>.</p>
<h2>From inspiration to sequencing the genome</h2>
<p>Scriver was well aware of the <a href="https://www.ncbi.nlm.nih.gov/books/NBK234203/">significance sequencing the human genome</a> would have on clinical genetics and the impact it would have on the health of patients, including identifying genetic causes of diseases.</p>
<figure>
<iframe width="440" height="260" src="https://www.youtube.com/embed/-hryHoTIHak?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">The Human Genome Project.</span></figcaption>
</figure>
<p>To move forward from Scriver’s inspiration, a proof of principle project was needed. This was provided by the discovery of the gene for cystic fibrosis (CF) by Lap-Chee Tsui and Jack Riordan, who were then at the University of Toronto, and Francis Collins, then at the University of Michigan. In 1990 they indicated: </p>
<blockquote>
<p>“<a href="https://doi.org/10.1080/21548331.1990.11704019">More broadly, the cloning of the CF gene provides a fast start in the international effort to clone and map the entire human genome</a>”</p>
</blockquote>
<p>These pioneers performed the very challenging task of <a href="https://doi.org/10.1126/science.2475911">identifying the gene mutation in unaffected people (those with a single mutated gene)</a>. CF is a recessive genetic condition, meaning a person must inherit two mutated genes — one from each parent — to develop the disease. Today as a result of Canadian discovery science, <a href="https://www.cysticfibrosis.ca/registry/2021AnnualDataReport.pdf">patients with cystic fibrosis have a median age of survival of 57 years</a>, compared to 35.9 years in 2001.</p>
<p>One of these pioneers went on to lead the even more challenging Human Genome Project. Collins received Canada’s Gairdner International Award in 2002 for “<a href="https://www.gairdner.org/winner/francis-s-collins">his outstanding leadership in the Human Genome Project and particularly for the international effort to map and sequence human and other genomes</a>.”</p>
<p>This was a rare occurrence of a scientist winning a second Gairdner International Award, with Collins receiving his first Gairdner for the CF gene discovery, along with Tsui and Riordan, in 1990.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/solving-the-puzzle-of-cystic-fibrosis-and-its-treatments-is-a-nobel-prize-worthy-breakthrough-175335">Solving the puzzle of cystic fibrosis and its treatments is a Nobel Prize-worthy breakthrough</a>
</strong>
</em>
</p>
<hr>
<p>Another Gairdner International award winner recognized for leadership in the Human Genome Project is <a href="https://www.gairdner.org/winner/james-d-watson">Watson</a>. This year’s DNA Day will celebrate the 70th anniversary of the double helix, for which Watson was later recognized with a <a href="https://www.nobelprize.org/prizes/medicine/1962/summary/">Nobel prize in 1962</a>.</p>
<p>It was belatedly recognized that the experimental data for the double helix was actually an <a href="https://www.nobelprize.org/prizes/medicine/1962/speedread/">X-ray of a crystal of DNA by the late Rosalind Franklin</a>.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/closing-the-gender-gap-in-the-life-sciences-is-an-uphill-struggle-112920">Closing the gender gap in the life sciences is an uphill struggle</a>
</strong>
</em>
</p>
<hr>
<p>The consequences of the discovery of DNA and the sequencing of the Human Genome have been monumental for health research globally. As <a href="https://doi.org/10.1056/NEJMp2030694">summarized in 2021 by Collins</a>, the genes for over 5,000 rare diseases were discovered as well as insight into Alzheimer’s disease, schizophrenia, heart disease and cancer.</p>
<figure>
<iframe width="440" height="260" src="https://www.youtube.com/embed/HkRqgeLE_fs?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">Charles Scriver, Canadian Medical Hall of Fame laureate 2001.</span></figcaption>
</figure>
<p>Astonishingly, it is through DNA that all of us can follow the trajectory of our families through genetic genealogy. Remarkably, the Nobel Prize in 2022 was awarded to Svante Pääbo of the Max Planck Institute in Leipzig, Germany for the <a href="https://www.nobelprize.org/prizes/medicine/2022/press-release/">new field of paleogenomics</a>. His discoveries involving the intricate sequencing of genomic DNA from our extinct human ancestors led to the discovery of a new branch of human ancestors now known as the Denisovans.</p>
<p>Today, the genetic genealogy of modern and ancient humans has been extended through the analysis of the DNA of over 7,000 different genomes. This new study has defined the <a href="https://doi.org/10.1126%2Fscience.abi8264">geographic location of the trajectory of our ancestors</a> extending to over 800,000 years ago! DNA Day is a worthy celebration.</p>
<h2>Can DNA Day be of significance in Canada?</h2>
<p>The dedication of our accomplished discovery researchers Tsui, Riordan and Scriver inspired and led to the Human Genome Project. However, the project did not involve Canada. The major reason for this was funding. </p>
<p>The Human Genome Project was largely funded by the U.S. National Institutes of Health to the labs of <a href="https://doi.org/10.1073/pnas.042692499">Robert Waterston at Washington University and Eric Lander at MIT</a>. In addition, John Sulston was funded in the United Kingdom as part of the trio who actually sequenced the human genome.</p>
<p>Journalist and political commentator Paul Wells recently lamented the <a href="https://paulwells.substack.com/p/building-pyramids-from-the-top-down">decades of deteriorating funding for Canadian discovery research</a>. In 2019, Canada was ranked 18th globally in researchers per 1,000 population down from its 8th rank in 2011. </p>
<p>Without funding improvements, Canada will continue to lose the talent it was once proud to have. This loss is unsustainable for meeting the challenges of future pandemics, climate change and the continuing ravages of disease.</p>
<p>Scriver, Tsui and Riordan should inspire pride for the value of discovery research in Canada that globally saves human lives. Canada should remember their legacy on DNA day.</p>
<p><em>John Bergeron gratefully acknowledges Kathleen Dickson as co-author.</em></p><img src="https://counter.theconversation.com/content/204340/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>John Bergeron 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>
On DNA Day, Canada should be inspired by the lifesaving discoveries of its researchers. However, lack of funding threatens Canadian researchers’ ability to meet the challenges of the future.
John Bergeron, Emeritus Robert Reford Professor and Professor of Medicine, McGill University
Licensed as Creative Commons – attribution, no derivatives.
tag:theconversation.com,2011:article/202490
2023-04-14T12:31:04Z
2023-04-14T12:31:04Z
DNA study opens a window into African civilisations that left a lasting legacy
<figure><img src="https://images.theconversation.com/files/519034/original/file-20230403-14-m699gl.jpg?ixlib=rb-1.1.0&rect=9%2C0%2C6473%2C4325&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Stone obelisks stand tall in Aksum, Ethiopia. This city was once the capital of a kingdom spanning northeast Africa and the Arabian peninsula.</span> <span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/ancient-monolith-stone-obelisk-symbol-old-1831447870">Shutterstock / Artist</a></span></figcaption></figure><p>Pre-colonial African history is alive with tales of civilisations rising and falling and of different cultures intermingling across the continent. We have now shed more light on some of these societies using the science of genetics. </p>
<p>In a study <a href="https://www.science.org/doi/10.1126/sciadv.abq2616">published in Science Advances</a>, my co-authors and I used DNA information from people from the present-day continent to shed light on important civilisations that existed before colonialism. Genetic information from cheek swabs was extracted by machines. Once the sequence of “letters” in the DNA code had been read, or sequenced, we could use computers to compare genetic differences and similarities between the populations in the study.</p>
<p>One striking result concerned two ethnic groups in the north of present-day Cameroon, in west-central Africa, the Kanuri and Kotoko peoples. We found that these two groups were descended from three ancestral populations. </p>
<p>These ancestral groups most resembled people now living in coastal regions of west Africa as well as in parts of east Africa such as Ethiopia and populations living today in north Africa and the Levant. The populations intermixed – had children together – roughly 600 years ago. But what caused them to migrate thousands of kilometres across a desert into northern Cameroon? </p>
<figure class="align-left ">
<img alt="Map of the Kanem-Bornu empire" src="https://images.theconversation.com/files/519336/original/file-20230404-28-zarx0t.png?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/519336/original/file-20230404-28-zarx0t.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=615&fit=crop&dpr=1 600w, https://images.theconversation.com/files/519336/original/file-20230404-28-zarx0t.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=615&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/519336/original/file-20230404-28-zarx0t.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=615&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/519336/original/file-20230404-28-zarx0t.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=773&fit=crop&dpr=1 754w, https://images.theconversation.com/files/519336/original/file-20230404-28-zarx0t.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=773&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/519336/original/file-20230404-28-zarx0t.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=773&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">The Kanem-Bornu empire at its greatest extent.</span>
<span class="attribution"><a class="source" href="https://commons.wikimedia.org/wiki/File:Afrika-Kanem-Bornu.png">Tourbillon / Wikipedia Project</a></span>
</figcaption>
</figure>
<p>We think the answer is the <a href="https://www.vincenthiribarren.com/pdf/Hiribarren_-_2016_-_Kanem-Bornu.pdf">Kanem-Bornu empire</a>, a civilisation that existed for over 1,000 years – beginning around 700 AD. At its height, the empire spanned what is now northern Cameroon, northern Nigeria, Chad, Niger and southern Libya. It operated vast trade networks across the Sahara and attracted populations from every direction.</p>
<p>This example highlights how our genomes hold information about major events of the past. Merchants travelling along trade routes or the formation of empires from smaller political units can leave footprints in our DNA. <a href="https://www.science.org/doi/full/10.1126/science.1243518">Previous work</a> <a href="https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1001373">shows</a> that <a href="https://www.science.org/doi/10.1126/science.aay6826">the Roman empire</a>, the <a href="https://www.frontiersin.org/articles/10.3389/fgene.2021.735786/full">Mongol empire</a>, and <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4267745/">Silk Road trade</a> probably all left lasting legacies in the genomes of modern-day people across Eurasia.</p>
<h2>Hidden in the genome</h2>
<p>We analysed 1,300 newly collected genomes of people from across Africa. They came from 150 ethnic groups within five countries. We collaborated with anthropologists, archaeologists and linguists from Africa and elsewhere. They helped us understand the historical context of these events.</p>
<figure class="align-center ">
<img alt="Mandara mountains" src="https://images.theconversation.com/files/519315/original/file-20230404-982-x059iv.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/519315/original/file-20230404-982-x059iv.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=360&fit=crop&dpr=1 600w, https://images.theconversation.com/files/519315/original/file-20230404-982-x059iv.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=360&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/519315/original/file-20230404-982-x059iv.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=360&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/519315/original/file-20230404-982-x059iv.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=452&fit=crop&dpr=1 754w, https://images.theconversation.com/files/519315/original/file-20230404-982-x059iv.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=452&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/519315/original/file-20230404-982-x059iv.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=452&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">The Kotoko and Kanuri people live in northern Cameroon and Nigeria. The photo shows a landscape in the Mandara mountains, near the border of the two countries.</span>
<span class="attribution"><span class="source">Scott MacEachern</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>African genome data <a href="https://www.annualreviews.org/doi/10.1146/annurev-biodatasci-102920-%20112550?url_ver=Z39.88-2003&rfr_id=ori%3Arid%3Acrossref.org&rfr_dat=cr_pub++0pubmed">is underrepresented</a> compared with that from other world regions. This means that lots of genetic diversity – or variety – in the DNA of populations is probably being missed by scientists. </p>
<p>Studying genetic diversity has many potential uses – such as understanding risks to health and developing new treatments for disease. Our group was concerned with genetic diversity as a window into the past.</p>
<h2>Dating events</h2>
<p>We modelled a person’s genome as a mixture of segments of DNA inherited from their ancestors. If a person had DNA segments closely matching two groups of people – for example, Europeans and west Africans – it suggested that this person descended from mixing between those two groups. </p>
<figure class="align-center ">
<img alt="Great Zimbabwe" src="https://images.theconversation.com/files/519299/original/file-20230404-20-1aikqn.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/519299/original/file-20230404-20-1aikqn.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/519299/original/file-20230404-20-1aikqn.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/519299/original/file-20230404-20-1aikqn.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/519299/original/file-20230404-20-1aikqn.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/519299/original/file-20230404-20-1aikqn.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/519299/original/file-20230404-20-1aikqn.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">Mysteries remain about other civilisations not studied in the latest work. These are buildings from Great Zimbabwe, a medieval city in Southern Africa.</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/great-zimbabwe-medieval-city-southeastern-hills-1048631507">evenfh / Shutterstock</a></span>
</figcaption>
</figure>
<p>Present-day human groups that were formed from a recent mixture of Europeans and west Africans should have long sections of DNA from both populations. Those ancestral DNA segments get shorter as the genetic material of their descendants is shuffled with each new generation. </p>
<p>This provides a way of dating when mixture events took place. The longer the DNA segments matching, for example, west Africans or Europeans, the more recent the mixture event was.</p>
<h2>Peace treaty</h2>
<p>Another historical event we found evidence for was the Arab expansion in Africa. This began in the seventh century, when separate Arab armies travelling south along the Levantine coast and north from Medina in today’s Saudi Arabia crossed the Sinai desert and conquered Egypt.</p>
<figure class="align-left ">
<img alt="The kingdom of Makuria at its peak around 960 AD." src="https://images.theconversation.com/files/519342/original/file-20230404-20-2sx8ay.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/519342/original/file-20230404-20-2sx8ay.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=1255&fit=crop&dpr=1 600w, https://images.theconversation.com/files/519342/original/file-20230404-20-2sx8ay.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=1255&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/519342/original/file-20230404-20-2sx8ay.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=1255&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/519342/original/file-20230404-20-2sx8ay.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=1577&fit=crop&dpr=1 754w, https://images.theconversation.com/files/519342/original/file-20230404-20-2sx8ay.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=1577&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/519342/original/file-20230404-20-2sx8ay.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=1577&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">The kingdom of Makuria at its peak around 960 AD.</span>
<span class="attribution"><a class="source" href="https://commons.wikimedia.org/wiki/File:The_Kingdom_of_Makuria_at_its_peak.jpg">Le Gabrie</a>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span>
</figcaption>
</figure>
<p>In Sudan at this time, the Kingdom of Makuria <a href="http://nubianmonasteries.uw.edu.pl/about/">ruled along the Nile river</a>. Makuria signed a peace treaty with the Egyptian Arabs in the <a href="https://bmcr.brynmawr.edu/2003/2003.01.16/">middle of the seventh century</a> that lasted almost 700 years.</p>
<p>The majority of mixing between these two ancestral groups, one closely related to Arabs and the other to Sudanese, dates to after the peace treaty began breaking down. This in turn coincided with the decline and eventual collapse of Makuria itself, which would have allowed Arab groups to continue down the Nile into Sudan. </p>
<p>But we also found evidence of earlier migrations into Africa from the Arabian peninsula, which occurred by sea. This intermixing coincided in time with the <a href="https://education.nationalgeographic.org/resource/kingdom-aksum/">Kingdom of Aksum</a>, located in northeast Africa and southern Arabia, during the first millennium AD.</p>
<figure class="align-center ">
<img alt="The throne hall of Old Dongola in Sudan, capital of the Makuria kingdom" src="https://images.theconversation.com/files/519067/original/file-20230403-20-eo26qk.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/519067/original/file-20230403-20-eo26qk.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=900&fit=crop&dpr=1 600w, https://images.theconversation.com/files/519067/original/file-20230403-20-eo26qk.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=900&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/519067/original/file-20230403-20-eo26qk.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=900&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/519067/original/file-20230403-20-eo26qk.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=1131&fit=crop&dpr=1 754w, https://images.theconversation.com/files/519067/original/file-20230403-20-eo26qk.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=1131&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/519067/original/file-20230403-20-eo26qk.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=1131&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">The throne hall of Old Dongola in Sudan, capital of the Makuria kingdom.</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/throne-hall-building-old-dongola-deserted-2118567158">Matyas Rehak / Shutterstock</a></span>
</figcaption>
</figure>
<p>Aksum was once considered <a href="https://link.springer.com/chapter/10.1007/978-1-137-11786-%201_2#:%7E:text=The%20Persian%20prophet%20Mani%2C%20who,the%20kingdom%20of%20the%20Chi%20nese.">one of the world’s four great powers</a>, alongside contemporary empires in China, Persia and Rome.</p>
<figure class="align-center ">
<img alt="Map of the Kingdom of Aksum." src="https://images.theconversation.com/files/519565/original/file-20230405-26-hndwxk.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/519565/original/file-20230405-26-hndwxk.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=540&fit=crop&dpr=1 600w, https://images.theconversation.com/files/519565/original/file-20230405-26-hndwxk.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=540&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/519565/original/file-20230405-26-hndwxk.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=540&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/519565/original/file-20230405-26-hndwxk.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=679&fit=crop&dpr=1 754w, https://images.theconversation.com/files/519565/original/file-20230405-26-hndwxk.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=679&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/519565/original/file-20230405-26-hndwxk.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=679&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Map of the Kingdom of Aksum.</span>
<span class="attribution"><a class="source" href="https://commons.wikimedia.org/wiki/File:Kingdom_of_Aksum_Map.png">Newslea Staff / Wikipedia</a>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span>
</figcaption>
</figure>
<h2>The expansion of Bantu-speaking peoples</h2>
<p>Genetic studies have also found evidence of a continent-wide migration known as the expansion of Bantu-speaking peoples. “Bantu” is a language group, now spoken by around <a href="https://www.britannica.com/art/Bantu-languages">one-quarter of Africans</a>.</p>
<p>There has been debate about whether the Bantu languages spread largely as a transmission of culture, or whether large-scale migration was involved. The latest research shows that the latter explanation is the likeliest. This migration started in a small area of western Cameroon roughly 4,000 years ago, before rapidly spreading south and east. It covered more than 4,000 kilometres in less than 2,000 years. </p>
<p>Bantu speakers mixed with local groups, <a href="https://www.science.org/doi/full/10.1126/science.aal1988">changing patterns of genetic diversity in Africa</a> forever. We showed that migrations not only occurred to the south and east of Cameroon, but also to the west. Why so much movement took place at this time is unknown, but climate change may have played a role.</p>
<p>It’s vital that scientists analyse more DNA from genomes of African people. As we do so, it will undoubtedly reveal an intricate picture of the continent’s rich past.</p><img src="https://counter.theconversation.com/content/202490/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Nancy Bird receives funding from NERC. </span></em></p>
DNA analysis sheds light on important societies within Africa that existed before colonialism.
Nancy Bird, Postdoctoral research associate, UCL
Licensed as Creative Commons – attribution, no derivatives.
tag:theconversation.com,2011:article/202440
2023-03-23T11:27:11Z
2023-03-23T11:27:11Z
We used DNA from Beethoven’s hair to shed light on his poor health – and stumbled upon a family secret
<figure><img src="https://images.theconversation.com/files/517132/original/file-20230323-28-r65l6y.jpeg?ixlib=rb-1.1.0&rect=54%2C0%2C4582%2C3717&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><span class="source">Kevin Brown</span>, <span class="license">Author provided</span></span></figcaption></figure><p>Many astonishingly creative people have lived lives cut tragically short by illness. Johannes Vermeer, Wolfgang Amadeus Mozart, Jane Austen, Franz Schubert and Emily Brontë are some famous examples. </p>
<p>Ludwig van Beethoven’s life was not quite as short; he was 56 when he died in 1827. Yet it was short enough to tantalise us as to what more he might have achieved, had he had better health.</p>
<p>For much of his adult life, Beethoven was frequently tormented by pain and poor health – not to mention hearing loss. He gave anguished thought to these afflictions, especially his hearing loss, and <a href="https://www.labonline.com.au/content/life-scientist/article/beethoven-s-genome-sheds-light-on-health-and-history-248507668">hoped they would</a> one day be understood and the explanation made public.</p>
<p>At times he despaired and <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1071597/">contemplated suicide</a>; at times he stopped composing altogether.</p>
<p>Entire books have been written on Beethoven’s health, based on records from the time. However, my colleagues and I approached the topic from a different perspective. We asked what clues Beethoven’s genome – his DNA – might provide.</p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/517133/original/file-20230323-22-smm40f.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/517133/original/file-20230323-22-smm40f.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/517133/original/file-20230323-22-smm40f.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=722&fit=crop&dpr=1 600w, https://images.theconversation.com/files/517133/original/file-20230323-22-smm40f.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=722&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/517133/original/file-20230323-22-smm40f.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=722&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/517133/original/file-20230323-22-smm40f.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=907&fit=crop&dpr=1 754w, https://images.theconversation.com/files/517133/original/file-20230323-22-smm40f.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=907&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/517133/original/file-20230323-22-smm40f.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=907&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Beethoven lived from 1770 to 1827.</span>
<span class="attribution"><span class="source">Wikimedia</span></span>
</figcaption>
</figure>
<p>We found some answers, and some surprises, as we explain in new research published in <a href="https://doi.org/10.1016/j.cub.2023.02.041">Current Biology</a>.</p>
<h2>Planting the seed</h2>
<p>Our multinational collaboration began with <a href="https://www.clarehall.cam.ac.uk/news/beethovengenome23/">Tristan Begg</a> – a Beethoven enthusiast and student of biological anthropology, then at the University of California Santa Cruz. </p>
<p>While volunteering at the Ira F. Brilliant Center for Beethoven Studies at San José State University, Begg encountered the centre’s director at the time, historical musicologist William Meredith.</p>
<p>The seed of the project was sown then, but it took eight years and the input of several other specialists to develop it to the point of being published. All the complex multidisciplinary collaborations notwithstanding, the only person who has worked full-time on the project is Begg himself, now in his final PhD year at the University of Cambridge.</p>
<h2>Where did the DNA come from?</h2>
<p>It’s very challenging to extract and analyse DNA from the remains of a dead person (or other animal) – much more so than from living tissues. Nonetheless, huge technical advances have transformed the field of ancient DNA studies. </p>
<p>Generally, the best DNA sources from human remains include teeth and the <a href="https://en.wikipedia.org/wiki/Petrous_part_of_the_temporal_bone">petrous bone</a> in the skull, but none of Beethoven’s bones or teeth were available to us. </p>
<p>What was available was hair. In Beethoven’s day, it was common to collect locks from famous people or loved ones. Dozens of locks attributed to Beethoven are held in public and private collections.</p>
<p>However, hair without roots is a less tractable source of DNA. This DNA tends to exist in short and sometimes degraded sequences. These have to be painstakingly pieced together, using specialised computer software, to construct as much of a complete genome sequence as possible.</p>
<h2>How do we know the locks are Beethoven’s?</h2>
<p>Our project used samples from eight independently sourced locks attributed to Beethoven. Of these, five yielded DNA from the same male individual, with degrees of damage consistent with origins in the early 19th century. </p>
<p>Working with the ancestry firm FamilyTreeDNA, we traced the ancestry for this person to western-central Europe. We are confident it is Beethoven, since two of the locks exist alongside uninterrupted provenance records going as far back as the 1820s.</p>
<p>Three more locks, genetically identical with the other two, also had good (although not completely uninterrupted) provenance records.</p>
<p>The combination of excellently documented provenances with perfect genetic agreement between five independently sourced samples made it very difficult to doubt these hair samples came from Beethoven.</p>
<p>That left three locks of hair. Two of these were clearly genetically different from the other five: one is a woman’s. We don’t know how these came to be attributed to Beethoven.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/517134/original/file-20230323-16-doyl0m.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/517134/original/file-20230323-16-doyl0m.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/517134/original/file-20230323-16-doyl0m.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=356&fit=crop&dpr=1 600w, https://images.theconversation.com/files/517134/original/file-20230323-16-doyl0m.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=356&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/517134/original/file-20230323-16-doyl0m.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=356&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/517134/original/file-20230323-16-doyl0m.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=447&fit=crop&dpr=1 754w, https://images.theconversation.com/files/517134/original/file-20230323-16-doyl0m.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=447&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/517134/original/file-20230323-16-doyl0m.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=447&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Our results showed the Hiller lock, previously attributed to Beethoven, actually came from a woman.</span>
<span class="attribution"><span class="source">Ira F. Brilliant Center for Beethoven Studies, San Jose State University / William Meredith</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>One of the misattributions is significant in itself, because it was the basis of <a href="https://www.science.org/content/article/beethoven-dead-lead#">earlier research</a> that concluded Beethoven had been subject to lead poisoning. Our findings show this conclusion no longer stands. </p>
<p>The eighth lock yielded too little DNA to be declared authentic or otherwise.</p>
<h2>What we learnt about Beethoven’s health</h2>
<p>We didn’t expect to find a genetic basis for Beethoven’s most widely known health problem – his hearing loss – and this was borne out. Beethoven had <a href="https://www.pennmedicine.org/for-patients-and-visitors/find-a-program-or-service/ear-nose-and-throat/general-audiology/center-for-adult-onset-hearing-loss#:%7E:text=Adult%2Donset%20hearing%20loss%20is%20a%20form%20of%20progressive%20deafness,educational%20success%2C%20and%20cognitive%20decline.">adult-onset hearing loss</a>, which is only rarely attributable to primarily genetic causes.</p>
<p>He was, however, beset for many years by other health problems – particularly gastrointestinal problems (pain and diarrhoea) and liver disease. </p>
<p>Working with the Bonn University medical genetics team, we didn’t find Beethoven to be especially genetically susceptible to any particular gastrointestinal condition, such as inflammatory bowel disease, irritable bowel syndrome, coeliac disease or lactose intolerance (as some <a href="https://pubmed.ncbi.nlm.nih.gov/16015189/#">have hypothesised</a>). Our main discoveries related to liver disease.</p>
<p>We already knew through documentation that Beethoven had attacks of jaundice. Begg’s work has now shown Beethoven had two copies of a particular variant of the <a href="https://www.journal-of-hepatology.eu/article/S0168-8278(16)30084-8/pdf">PNPLA3 gene</a>, which is linked to liver cirrhosis. He also had single copies of two variants of a gene that causes haemochromatosis, a condition that damages the liver.</p>
<p>Quite remarkably, the analyses also revealed Beethoven was infected with the hepatitis B virus in the final months of his life (and perhaps before). Hepatitis B infection <a href="https://onlinelibrary.wiley.com/doi/full/10.1111/liv.12409">may have been</a> common in Europe at the time, but details on this are scant.</p>
<p>What’s more, alcohol consumption may have exacerbated Beethoven’s liver disease risk. There has been controversy regarding the extent and nature of his alcohol consumption, which is referred to – but not quantified – in surviving records. </p>
<p>Begg reviewed the records carefully and concluded Beethoven’s alcohol consumption was likely unexceptional <a href="https://www.ncbi.nlm.nih.gov/books/NBK524980/">for the time and place</a>, but may have still been at levels now considered harmful.</p>
<h2>Revelations from the Beethoven family</h2>
<p>There was one more surprise in store for us. As part of our work, we sought to link Beethoven’s genome with those of living members of the Beethoven lineage. To do this we focused on the Y chromosome, which is inherited in the male line only (following a similar pattern to surnames in most European traditions). </p>
<p>Five men with the surname Beethoven contributed their DNA samples. They were not closely related to each other, and were living in present-day Belgium where the surname originates. They all essentially shared the same Y chromosome, which could be put down to descent from a common male ancestor: Aert van Beethoven (1535-1609).</p>
<p>The surprise was that Ludwig van Beethoven’s locks had a different Y chromosome. Having considered other explanations, we inferred that at some point in the seven generations between Aert and Ludwig, someone’s father for social and legal purposes was not their biological father. </p>
<p>But we couldn’t decipher, based on the evidence available, which generation this might have been.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/beethoven-250-analysis-of-the-composers-letters-proves-that-creativity-does-spring-forth-from-misery-149771">Beethoven 250: analysis of the composer's letters proves that creativity does spring forth from misery</a>
</strong>
</em>
</p>
<hr>
<h2>What’s next?</h2>
<p>We will be making the genome we sequenced publicly available, as there may be more to discover from further analyses.</p>
<p>Beyond Beethoven, our project is an example of wider possibilities opening up in the field of DNA analysis. It shows meaningful results can be obtained even from such unpromising DNA sources as historical hair locks.</p>
<p>To date, population genetics has seldom taken its analyses down to the level of a single individual. This is hard to do, but we show it’s not impossible.</p>
<p>Who might be next? Perhaps someone else about whom there is a distinct question to answer – or even someone who may themselves have wanted that question answered.</p>
<hr>
<p><em>Acknowledgments: In addition to lead author Tristan Begg (University of Cambridge), I would like to acknowledge all other co-authors including Johannes Krause and Arthur Kocher (Max Planck Institute for Evolutionary Anthropology, Leipzig), Toomas Kivisild and Maarten Larmuseau (KU Leuven), Markus Nöthen and Axel Schmidt (University of Bonn), and all sample donors including philanthropist Kevin Brown.</em></p><img src="https://counter.theconversation.com/content/202440/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>I have been a student (50 years ago) at the University of Cambridge, and more recently a staff member at the University of Cambridge, a departmental colleague of Toomas Kivisild, and a PhD supervisor of Tristan Begg.</span></em></p>
Beethoven was afflicted with health conditions for much of his adult life, and wished for their cause to be discovered and made public.
Robert Attenborough, Honorary Senior Lecturer in Bioanthropology, Australian National University
Licensed as Creative Commons – attribution, no derivatives.
tag:theconversation.com,2011:article/200899
2023-03-01T19:06:23Z
2023-03-01T19:06:23Z
We thought the first hunter-gatherers in Europe went missing during the last ice age. Now, ancient DNA analysis says otherwise
<figure><img src="https://images.theconversation.com/files/512788/original/file-20230301-22-56r83n.jpeg?ixlib=rb-1.1.0&rect=5%2C0%2C3964%2C2179&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Reconstruction of a hunter-gatherer associated with the Gravettian culture.</span> <span class="attribution"><span class="source">Tom Bjoerklund</span></span></figcaption></figure><p>Hunter-gatherers took shelter from the ice age in Southwestern Europe, but were replaced on the Italian Peninsula according to two new studies, published in <a href="https://www.mpg.de/19941740/0223-evan-ice-age-survivors-150495-x">Nature</a> and <a href="https://www.nature.com/articles/s41559-023-01987-0">Nature Ecology & Evolution</a> today.</p>
<p>Modern humans first began to spread across Eurasia approximately 45,000 years ago, arriving from the near east. <a href="https://doi.org/10.1093/gbe/evac045">Previous research</a> claimed these people disappeared when massive ice sheets covered much of Europe around 25,000–19,000 years ago. By comparing the DNA of various ancient humans, we show this was not the case for all hunter-gatherer groups.</p>
<p>Our new results show the hunter-gatherers of Central and Southern Europe did disappear during the last ice age. However, their cousins in what is now France and Spain survived, leaving genetic traces still visible in the DNA of Western European peoples nearly 30,000 years later.</p>
<h2>Two studies with one intertwining story</h2>
<p>In our first study in Nature, we analysed the genomes – the complete set of DNA a person carries – of 356 prehistoric hunter-gatherers. In fact, our study compared every available ancient hunter-gatherer genome.</p>
<p>In our second study in Nature Ecology & Evolution, we analysed the oldest hunter-gatherer genome recovered from the southern tip of Spain, belonging to someone who lived approximately 23,000 years ago. We also analysed three early farmers who lived roughly 6,000 years ago in southern Spain. This allowed us to fill an important sampling gap for this region.</p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/512790/original/file-20230301-23-w9p7rl.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="A photo of dark bones on a sandy beach" src="https://images.theconversation.com/files/512790/original/file-20230301-23-w9p7rl.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/512790/original/file-20230301-23-w9p7rl.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=795&fit=crop&dpr=1 600w, https://images.theconversation.com/files/512790/original/file-20230301-23-w9p7rl.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=795&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/512790/original/file-20230301-23-w9p7rl.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=795&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/512790/original/file-20230301-23-w9p7rl.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=999&fit=crop&dpr=1 754w, https://images.theconversation.com/files/512790/original/file-20230301-23-w9p7rl.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=999&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/512790/original/file-20230301-23-w9p7rl.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=999&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Human fossils that were genetically analysed in this study were found on the Dutch coast and dated from around 11,000 to 8,000 years ago. They originally came from Doggerland, a now submerged land under the North Sea, where European hunter-gatherers lived.</span>
<span class="attribution"><span class="source">National Museum of Antiquities (RMO), modified by Michelle O‘Reilly</span></span>
</figcaption>
</figure>
<p>By combining results from these two studies, we can now describe the most complete story of human history in Europe to date. This story includes migration events, human retreat from the effects of the ice age, long-lasting genetic lineages and lost populations.</p>
<h2>Post-ice-age genetic replacement</h2>
<p>Between 32,000 and 24,000 years ago, hunter-gatherer individuals (associated with what’s known as <a href="https://doi.org/10.1016/j.quaint.2014.03.025">Gravettian culture</a>) were widespread across the European continent. This critical time period ends at the Last Glacial Maximum. This was the coldest period of the last ice age in Europe, and took place 24,000 to 19,000 years ago. </p>
<p>Our data show that populations from Southwestern Europe (today’s France and Iberia), and Central and Southern Europe (today’s Italy and Czechia), were not closely genetically related. These two distinct groups were instead linked by similar weapons and art.</p>
<p>We could see that Central and Southern European Gravettian populations left no genetic signal after the Last Glacial Maximum – in other words, they simply disappeared. The individuals associated with a later culture (known as the Epigravettian) were not descendants of the Gravettian. According to one of my Nature co-authors, He Yu, they were</p>
<blockquote>
<p>genetically distinct from the area’s previous inhabitants. Presumably, these people came from the Balkans, arrived first in northern Italy around the time of the Last Glacial Maximum, and spread all the way south to Sicily.</p>
</blockquote>
<p>In Central and Southern Europe, our data indicate people associated with the Epigravettian populations of the Italian peninsula later spread across Europe. This occurred approximately 14,000 years ago, following the end of the ice age.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/512793/original/file-20230301-22-fh6yle.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Fragments of bones and a skull on a dark background" src="https://images.theconversation.com/files/512793/original/file-20230301-22-fh6yle.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/512793/original/file-20230301-22-fh6yle.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=431&fit=crop&dpr=1 600w, https://images.theconversation.com/files/512793/original/file-20230301-22-fh6yle.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=431&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/512793/original/file-20230301-22-fh6yle.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=431&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/512793/original/file-20230301-22-fh6yle.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=542&fit=crop&dpr=1 754w, https://images.theconversation.com/files/512793/original/file-20230301-22-fh6yle.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=542&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/512793/original/file-20230301-22-fh6yle.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=542&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Male skull and stone tools from Groß Fredenwalde (Germany), dated to 7,000 years ago. This individual’s population lived side-by-side with the first European farmers without mixing. (Cooperation with Brandenburgisches Landesamt für Denkmalpflege)</span>
<span class="attribution"><span class="source">Volker Minkus</span></span>
</figcaption>
</figure>
<h2>Climate refuge</h2>
<p>While the Gravettian populations of Central and Southern Europe disappeared, the fate of the Southwestern populations was not the same.</p>
<p>We detected the genetic profile of Southwestern Gravettian populations again and again for the next 20,000 years in Western Europe. We saw this first in their direct descendants (known as <a href="https://www.jstor.org/stable/24931600">Solutrean</a> and <a href="https://doi.org/10.1016/j.quaint.2012.02.056">Magdalenian</a> cultures). These were the people who took refuge and flourished in Southwestern Europe during the ice age. Once the ice age ended, the Magdalenians spread northeastward, back into Europe.</p>
<p>Remarkably, the 23,000-year-old remains of a Solutrean individual from Cueva de Malalmuerzo in Spain allowed us to make a direct link to the first modern humans that settled Europe. We could connect them to a 35,000-year-old individual from Belgium, and then to hunter-gatherers who lived in Western Europe long after the Last Glacial Maximum.</p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/512813/original/file-20230301-22-xdhza.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/512813/original/file-20230301-22-xdhza.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/512813/original/file-20230301-22-xdhza.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/512813/original/file-20230301-22-xdhza.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/512813/original/file-20230301-22-xdhza.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/512813/original/file-20230301-22-xdhza.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/512813/original/file-20230301-22-xdhza.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">Archaeological cave site of Cueva del Malalmuerzo from the southern tip of Spain where the 23,000 year old Solutrean individual was discovered.</span>
<span class="attribution"><span class="source">Pedro Cantalejo</span></span>
</figcaption>
</figure>
<p>Sea levels during the ice age were lower, making it only 13 kilometres from the tip of Spain to Northern Africa. However, we observed no genetic links between individuals in southern Spain and northern Morocco from 14,000 years ago. This showed that while European populations retreated south during the ice age, they surprisingly stopped before reaching Northern Africa.</p>
<p>Our results show the special role the Iberian peninsula played as a safe haven for humans during the ice age. The genetic legacy of hunter-gatherers would survive in the region after more than 30,000 years, unlike their distant relatives further east.</p>
<h2>Post ice-age interaction</h2>
<p>Some 2,000 years after the end of the ice age, there were again two genetically distinct hunter-gatherer groups. There was the “old” group in Western and Central Europe, and the “more recent” group in Eastern Europe.</p>
<p>These groups showed no evidence of genetic exchange with southwestern hunter-gatherer populations for approximately 6,000 years, until roughly 8,000 years ago.</p>
<p>At this time, agriculture and a sedentary lifestyle had begun to spread with new peoples from Anatolia into Europe, forcing hunter-gatherers to retreat to the northern fringes of Europe.</p><img src="https://counter.theconversation.com/content/200899/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Adam "Ben" Rohrlach was a postdoctoral researcher at the Max Planck Institute for Evolutionary Anthropology until January 2023, and still holds an affiliation there.</span></em></p>
45,000 years ago, people first started arriving in what’s known as Europe today. We thought a worsening ice age made them disappear – but it seems some lineages survived.
Adam "Ben" Rohrlach, Mathematics Lecturer and Archaeogeneticist, University of Adelaide
Licensed as Creative Commons – attribution, no derivatives.
tag:theconversation.com,2011:article/200815
2023-02-28T05:53:22Z
2023-02-28T05:53:22Z
Genomics has helped identify a new strep A strain in Australia – and what has made it dangerous
<figure><img src="https://images.theconversation.com/files/512584/original/file-20230228-1747-a7sbvw.jpg?ixlib=rb-1.1.0&rect=10%2C26%2C3486%2C2157&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/abnormal-neutrophil-pleural-fluid-smear-septicaemia-412363624">Shutterstock</a></span></figcaption></figure><p>Group A streptococci, also known as “strep A”, has been on the rise around the world with a new strain <a href="https://www.theguardian.com/society/2022/dec/15/strep-a-kills-three-more-children-as-uk-activates-new-medicines-plan">reported</a> in the United Kingdom and Europe. This variant has been linked with surges of scarlet fever and a marked increase in life-threatening invasive strep A infections. </p>
<p>Now genomic <a href="https://www.nature.com/articles/s41467-023-36717-4">research</a> by our team of scientists has identified this new strain in the Australian community for the first time. In parallel, we have seen an increase in invasive strep A cases across New South Wales, Queensland, Western Australia and <a href="https://www.health.vic.gov.au/health-advisories/health-warning-on-invasive-group-a-streptococcal-disease">Victoria</a>. </p>
<p>Strep A is a common bacteria carried by people primarily in their throat. It can cause <a href="https://www.cdc.gov/groupastrep/diseases-public/index.html">mild illness</a> including sore throat, scarlet fever (named for the red rash it causes) and impetigo (“school sores”). But it can also cause “invasive” disease, such as sepsis. Repeated strep A infections can lead to other serious conditions including acute rheumatic fever and rheumatic heart disease. </p>
<p>We investigated the genetic composition of the new strep A strain called “M1UK” and zeroed in on what makes it different to the previous strain.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/strep-a-three-doctors-explain-what-you-need-to-look-out-for-195972">Strep A: three doctors explain what you need to look out for</a>
</strong>
</em>
</p>
<hr>
<h2>What we know about strep A</h2>
<p>Strep A only infects humans, with around <a href="https://doi.org/10.1542/peds.2009-2648">10% of school-aged children</a> carrying it. It causes more than <a href="https://pubmed.ncbi.nlm.nih.gov/16253886/">half a million deaths</a> worldwide per year. </p>
<p>We’ve known about the bacteria for over 100 years and it was a <a href="https://pubmed.ncbi.nlm.nih.gov/1571445/">major cause of childhood death</a> in the 19th and early 20th centuries. But it’s been less of a public health threat since antibiotic medications were developed to treat it. In the 1980s, one type of strep A strain called “M1” emerged as the major cause of invasive strep A infections in high-income settings.</p>
<p>Over the last decade, resurgence of scarlet fever strep A infections has been reported in the <a href="https://www.eurosurveillance.org/content/10.2807/1560-7917.ES2014.19.12.20749">United Kingdom</a> and <a href="https://www.thelancet.com/journals/ebiom/article/PIIS2352-3964(18)30014-8/fulltext">China</a>. </p>
<p>Invasive infection is <a href="https://www.who.int/emergencies/disease-outbreak-news/item/2022-DON429">rare</a>. But when it occurs, the death rate can be <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6474463/">as high as 20%</a> of those infected.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/512564/original/file-20230228-24-obo37h.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="woman getting throat checked by health worker using tongue depressor" src="https://images.theconversation.com/files/512564/original/file-20230228-24-obo37h.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/512564/original/file-20230228-24-obo37h.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=383&fit=crop&dpr=1 600w, https://images.theconversation.com/files/512564/original/file-20230228-24-obo37h.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=383&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/512564/original/file-20230228-24-obo37h.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=383&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/512564/original/file-20230228-24-obo37h.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=481&fit=crop&dpr=1 754w, https://images.theconversation.com/files/512564/original/file-20230228-24-obo37h.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=481&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/512564/original/file-20230228-24-obo37h.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=481&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Strep A can cause a sore throat or be much more serious.</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/doctor-checking-woman-throat-medical-stick-339999557">Shutterstock</a></span>
</figcaption>
</figure>
<h2>What’s different about this strain?</h2>
<p>The M1UK variant of strep A was first reported in the UK in <a href="https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(19)30446-3/fulltext">2019</a> and identified using <a href="https://www.who.int/news-room/questions-and-answers/item/genomics">genomics</a> – the study of the DNA sequence to identify changes in the genetic makeup of an organism.</p>
<p>UK scientists identified that the M1UK variant expressed up to five times more of a specific strep A toxin than the previous M1 <a href="https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(19)30446-3/fulltext">strain</a>, but they weren’t sure how. This toxin, originally termed the “scarlet fever toxin”, is associated with the development of invasive strep A by short-circuiting the host’s immune system.</p>
<p>Our laboratory team went about trying to understand which changes in the bacteria led to this increased expression. </p>
<p>We <a href="https://www.nature.com/articles/s41467-023-36717-4">looked at the genetic code</a> of the strep A M1UK variant and compared it to previous ones. We found a number of mutations, one of which was located near the toxin gene.</p>
<p>Then we worked backwards to repair that change and see how it affected the amount of toxin expressed. In this way, we identified the mechanism of how M1UK strep A became toxin supercharged. </p>
<h2>Will we see more dangerous strep A strains?</h2>
<p>Genomics helps us identify and track bacterial variants. Then scientists need to use that knowledge within a biological context to figure out how a strain is gaining competitive advantage to become dominant over a previous strain – as M1UK <a href="https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(20)30279-6/fulltext">has in the UK</a>. </p>
<p>It’s possible this new strain of strep A is better at transmitting from person to person, but we’ll need more research to know if this is the case. </p>
<p><div data-react-class="Tweet" data-react-props="{"tweetId":"1603414373355044864"}"></div></p>
<h2>Invasive strep A is now a notifiable disease</h2>
<p>Invasive strep A infection was added to Australia’s National Notifiable Diseases List in <a href="https://www.legislation.gov.au/Details/F2021L00778">July 2021</a>, paving the way for it to be formally recorded across states and territories. This means that detected invasive strep A cases get reported to a central registry so authorities can keep track of outbreaks and case numbers.</p>
<p>Our researchers will have access to a repository of national strep A strains. We will be piloting a national strep A genomic surveillance program within the <a href="https://www.auspathogen.org.au/">AusPathoGen</a> program, which will speed up our ability to identify and track emerging strep A variants. </p>
<p>We’ve seen how this type of genomic research has helped <a href="https://theconversation.com/as-new-zealands-omicron-infections-rise-rapidly-genome-surveillance-is-shifting-gears-177441">track COVID changes</a> and guide public health response. By undertaking this pilot program with public health partners, we aim to build a national invasive strep A surveillance framework. </p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/strep-a-cases-are-rising-we-must-remember-our-earliest-hygiene-lessons-as-vaccine-trials-continue-197617">Strep A cases are rising. We must remember our earliest hygiene lessons as vaccine trials continue</a>
</strong>
</em>
</p>
<hr>
<h2>How can people protect themselves?</h2>
<p>Invasive strep A is still extremely rare, so there’s no need to panic – but we shouldn’t be complacent either.</p>
<p>Basic hygiene practices and staying away from other people when sick remain <a href="https://www.healthdirect.gov.au/group-a-streptococcal">important</a> for preventing spread. </p>
<p>Kids or the elderly are <a href="https://www.ncbi.nlm.nih.gov/books/NBK333415/">more likely</a> to get invasive disease, so if you note <a href="https://www.health.vic.gov.au/health-advisories/health-warning-on-invasive-group-a-streptococcal-disease">symptoms</a> such as high fever (especially with a skin rash), severe pain from an infected skin sore, and any difficulties with breathing then you should go to your local hospital’s emergency department or consult a GP immediately. </p>
<p>Antibiotics are highly effective at treating infection, provided they are <a href="https://www.cdc.gov/groupastrep/igas-infections-investigation.html">available</a>. </p>
<p>We also need to think about alternative ways of controlling infection. Australian scientists are at the <a href="https://imb.uq.edu.au/article/2023/02/funding-injection-strep-vaccine-research">forefront</a> of efforts to develop a global strep A vaccine. </p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/antibiotics-shortages-whats-causing-them-and-how-countries-can-minimise-the-impact-196540">Antibiotics shortages: what's causing them and how countries can minimise the impact</a>
</strong>
</em>
</p>
<hr>
<img src="https://counter.theconversation.com/content/200815/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Mark Davies receives funding from the National Health and Medical Research Council of Australia. </span></em></p>
The new M1UK strain of strep A has a dangerous ability to make the disease trigger more toxin release in the body.
Mark Davies, Laboratory Head, Doherty Institute, The University of Melbourne
Licensed as Creative Commons – attribution, no derivatives.
tag:theconversation.com,2011:article/197221
2023-01-05T20:33:11Z
2023-01-05T20:33:11Z
DNA reveals large migration into Scandinavia during the Viking age
<figure><img src="https://images.theconversation.com/files/503216/original/file-20230105-20-c8gnzd.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">More people moved into Scandinavia in Viking times than at any other time period analysed in the study.</span> <span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/old-wooden-viking-snekkja-longship-type-2044280747">Shutterstock</a></span></figcaption></figure><p>We often think of the Vikings as ultimate explorers, taking their culture with them to far-off lands. But we may not typically think of Viking age Scandinavia as a hub for migration from all over Europe.</p>
<p><a href="https://www.cell.com/cell/fulltext/S0092-8674(22)01468-4">In a study published in Cell</a>, we show this is exactly what happened. The Viking period (late 8th century to mid 11th century) was the catalyst for an exceptional inflow of people into Scandinavia. These movements were greater than for any other period we analysed.</p>
<p>What’s also striking is that later Scandinavians don’t show the same high levels of non-local ancestry present in their Viking-era counterparts. We don’t completely understand why the migrants’ genetic impact was reduced in later Scandinavians, but there are some possibilities.</p>
<p>We analysed genomes (the full complement of DNA contained in human cells) from around 17,000 Scandinavian individuals, including nearly 300 from ancient burials. We combined <a href="https://www.sciencedirect.com/science/article/pii/S0960982218308443">existing datasets</a> with new samples. These were analysed together in a dataset spanning 2,000 years.</p>
<p>We used these genomes to explore when people arrived in the region from outside and where they came from. New DNA samples were collected from several iconic Swedish archaeological sites. </p>
<p>These included Sandby borg, which is a “ring fortress” <a href="https://www.cambridge.org/core/journals/antiquity/article/moment-frozen-in-time-evidence-of-a-late-fifthcentury-massacre-at-sandby-borg/5C803B7E77A41439BC3B50D4BF96560E">where a massacre occurred just before 500 AD</a>, and the Vendel cemetery, which features several burials contained in large boats and dating to between the 6th and 8th centuries AD. We also used samples from Viking chamber burials and remains from Kronan, a <a href="https://www.tandfonline.com/doi/abs/10.1111/j.1095-9270.1990.tb00276.x">warship that capsized with more than 800 men</a> in 1676.</p>
<p>Two previous studies <a href="https://www.sciencedirect.com/science/article/pii/S0960982218308443">noted extensive migration</a> into Scandinavia <a href="https://www.nature.com/articles/s41586-020-2688-8">during the Viking age</a>. But in our latest study, we have clarified some of the details about this flow of genes into the region.</p>
<p>We found that movements of people from western Europe impacted all of Scandinavia, while migration from the east was more localised, with peaks in the Lake Mälaren Valley and Gotland. Finally, gene flow from southern Europe largely affected the south of Scandinavia. </p>
<p>Since the study was based on a 2,000-year chronology, it was not only possible to see there was an increase in migration during the Viking era, but also that it starts to fall with the onset of the medieval period.</p>
<p>The non-local ancestry that arrives in the region at this time falls away in later periods. Much of the genetic influence from eastern Europe disappears and the western and southern influence becomes significantly diluted. The best way to explain this is that people who arrived in Scandinavia during Viking times did not have as many children as the people who were already living there.</p>
<p>There are different possible reasons for this. The migrants could have belonged to groups that did not intend to settle down in Scandinavia, instead aiming to return to where they came from. Tradespeople and diplomats are examples in this category. Additionally, the migrants could also have belonged to groups that were not allowed to have families or children, such as slaves and priests.</p>
<p>We also looked at influences that began at earlier periods in time. For example, the DNA of modern Scandinavians <a href="https://www.nature.com/articles/s41431-021-00899-6">changes gradually as you travel from north to south</a>. This genetic “cline”, or gradient, is due to migrations into the region of people carrying shared genetic similarities known as the Uralic component.</p>
<p>Modern examples of where the Uralic genetic component can be found are among Sami people, people in modern Finland, some Native Americans and some central Asian groups. </p>
<p>In our dataset, we found occasional instances of people with Uralic ancestry – mainly in northern Scandinavia – during the Viking period and medieval times. But the Uralic influence seems to increase after this time, since individuals from our 17th century sample have similar levels of this ancestry to people living today.</p>
<p>There were many other fascinating stories from our study. For example, at the Viking age burial site of Sala, by the river Sagån, we find a woman that seems to be fully British or Irish in her genomic composition. This woman was buried in a prestigious Viking period boat burial. We don’t know exactly what position she held in society, but she would not have been a slave or a priest. </p>
<p>Among the individuals found on the wreck of the Kronan, there were two people who came from what is now Finland and another who has a genetic affinity with people from the Baltic states, such as Lithuania and Latvia (though this identification is not conclusive). At the time of the Kronan incident in 1676, these areas were part of the Swedish Empire, though they are independent today.</p>
<p>The work sheds more light on the historical events that shaped the populations of Scandinavia over time. The Viking age was marked by Scandinavians’ curiosity of the world outside their home region. But, from our results, it also appears that the world outside this region was curious enough about the Vikings to travel to Scandinavia.</p><img src="https://counter.theconversation.com/content/197221/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Anders Götherström receives funding from VR, KVA, and EU. </span></em></p><p class="fine-print"><em><span>Ricardo Rodriguez Varela 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>
DNA analysis reveals a large migration of people into Scandinavia during Viking times.
Anders Götherström, Professor in Molecular Archaeology, Department of Archaeology and Classical Studies, Stockholm University
Ricardo Rodriguez Varela, Research in Molecular Archaeology, Department of Archaeology and Classical Studies, Stockholm University, Stockholm University
Licensed as Creative Commons – attribution, no derivatives.
tag:theconversation.com,2011:article/194319
2022-11-23T22:07:46Z
2022-11-23T22:07:46Z
Back from the brink: how genome research is helping the recovery of the Chatham Island black robin
<figure><img src="https://images.theconversation.com/files/496698/original/file-20221122-14-osonqr.jpeg?ixlib=rb-1.1.0&rect=9%2C73%2C2035%2C1149&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><span class="source">Wikimedia/Leon Berard</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span></figcaption></figure><p>The story of Old Blue and Old Yellow, two Chatham Island black robins that went on to save their species, is one of New Zealand’s best known conservation stories. </p>
<p>Once abundant on Rēkohu/Chatham Islands before European arrival, the black robin population crashed when rats invaded the archipelago. In the early 1900s, 35 black robins remained on a small island (Tapuaenuku/Little Mangere), but by 1976, only seven birds had survived. </p>
<p>They were moved to an adjacent, predator-free island (Maung’ Rē/Mangere) and Old Blue and Old Yellow, the only remaining breeding pair, became “Adam and Eve” for the species. </p>
<p>Conservation biologists worried such an extreme genetic bottleneck would lessen the species’ chances of recovery by leading to an accumulation of genetic defects. But our new <a href="https://pubmed.ncbi.nlm.nih.gov/36357860/">genome study</a> shows that, contrary to our expectations, harmful genetic mutations have not increased since the severe decline.</p>
<h2>Genetic threats to small populations</h2>
<p>When we think about species extinction, human-associated threats such as habitat degradation, overhunting or introduced predators come to mind. We intuitively understand that small populations are at greater risk of extinction than large ones.</p>
<p>But even when major threats are removed, more subtle problems like inbreeding can push wild species to the brink of extinction. The Chatham Island black robin (karure, <em>Petroica traversi</em>) illustrates these issues perfectly. </p>
<figure class="align-right ">
<img alt="A Chatham Island black robin sitting on a small branch" src="https://images.theconversation.com/files/496859/original/file-20221122-24-cqnhs3.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/496859/original/file-20221122-24-cqnhs3.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=781&fit=crop&dpr=1 600w, https://images.theconversation.com/files/496859/original/file-20221122-24-cqnhs3.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=781&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/496859/original/file-20221122-24-cqnhs3.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=781&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/496859/original/file-20221122-24-cqnhs3.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=982&fit=crop&dpr=1 754w, https://images.theconversation.com/files/496859/original/file-20221122-24-cqnhs3.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=982&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/496859/original/file-20221122-24-cqnhs3.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=982&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Black robins were once common throughout Rēkohu/Chatham Islands.</span>
<span class="attribution"><span class="source">Wikimedia/Peter de Lange</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>At the start of the species’ recovery, the extreme level of inbreeding, with all birds descending from one pair, is not ideal. A previous <a href="https://onlinelibrary.wiley.com/doi/full/10.1111/evo.12315">study</a> suggested inbreeding and harmful mutations, which often accumulate in extremely inbred populations, had a severe effect on individual survival and reproduction and even slowed down the recovery of the species. </p>
<p>Even to non-biologists, this is not surprising. Everyone familiar with the fate of European dynasties like the Habsburgs knows that <a href="https://www.livescience.com/habsburg-jaw-inbreeding.html">relatedness between parents can cause major issues</a>. Charles II, for example, the last Habsburg ruler of Spain and descendent of generations of closely related ancestors, died childless at the age of 39 after lifelong health struggles. </p>
<p>For now, black robins appear to have escaped this fate. As of 2022, there are about 290 birds, split between two different islands. </p>
<h2>Are black robins out of the woods?</h2>
<p>To answer this question, we compared the genomes from birds that died in the 1800s to the genomes of birds from 2014-2019. Curiously, even though inbreeding had increased severely, we did not see an increase in the number of harmful mutations over the past 200 years. </p>
<p>It is possible the species has been “pre-adapted” to surviving in small populations. Living on a few small islands, inbreeding might have always been a problem. There would have always been a percentage of the population with reduced health due to damaging mutations. </p>
<figure class="align-center ">
<img alt="A landscape image of Rēkohu/Chatham Islands, across a wide bay." src="https://images.theconversation.com/files/496860/original/file-20221122-12-tsjijp.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/496860/original/file-20221122-12-tsjijp.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=229&fit=crop&dpr=1 600w, https://images.theconversation.com/files/496860/original/file-20221122-12-tsjijp.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=229&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/496860/original/file-20221122-12-tsjijp.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=229&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/496860/original/file-20221122-12-tsjijp.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=287&fit=crop&dpr=1 754w, https://images.theconversation.com/files/496860/original/file-20221122-12-tsjijp.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=287&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/496860/original/file-20221122-12-tsjijp.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=287&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">With populations on several small islands in the Rēkohu archipelago, inbreeding may have always been an issue for black robins.</span>
<span class="attribution"><span class="source">Shutterstock/Steve Todd</span></span>
</figcaption>
</figure>
<p>Natural selection might have eliminated those individuals and their harmful mutations from the gene pool without major impacts on the overall population. With few harmful mutations left in the population when the species dwindled to only two breeding birds, the negative effects of extreme inbreeding might have been reduced. </p>
<p>In other words, their evolution on a small archipelago may have prepared the black robins better than large mainland species for fending off the negative effects of inbreeding. </p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/a-new-3d-koala-genome-will-aid-efforts-to-defend-the-threatened-species-153873">A new 3D koala genome will aid efforts to defend the threatened species</a>
</strong>
</em>
</p>
<hr>
<h2>The relevance of genomics in conservation</h2>
<p>The Chatham Island robin is not the only species to benefit from recent advances in genomics. Similar <a href="https://www.nature.com/articles/s41467-020-14803-1">genomic</a> <a href="https://www.sciencedirect.com/science/article/pii/S2666979X21000021">studies</a> have shown that some highly inbred species seem to have lost a large proportion of genetically harmful defects. While genetic threats remain, these species may be doing better than we once thought. </p>
<p>These results are also important from a management perspective as better estimates of inbreeding and harmful mutations can help identify the most genetically healthy individuals for translocations and breeding programmes (such as for <a href="https://www.biorxiv.org/content/10.1101/2022.10.22.513130v1.abstract">kākāpō</a> and <a href="https://onlinelibrary.wiley.com/doi/full/10.1111/mec.15943">Swedish Arctic foxes</a>). Genomic data can also improve or verify the <a href="https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.13575">accuracy of pedigrees</a>. </p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/a-huge-project-is-underway-to-sequence-the-genome-of-every-complex-species-on-earth-175033">A huge project is underway to sequence the genome of every complex species on Earth</a>
</strong>
</em>
</p>
<hr>
<p>The main concern for conservation managers will be to determine whether and when a recovering species like black robins or kākāpō will be able to fend for themselves. How long will they require intensive management in the form of nest surveys, supplementary feeding or even artificial rearing of chicks? </p>
<p>At which point can we consider a species healthy enough and resilient to diseases or other external threats? And what if the recovery stops, slows down or even reverses as new harmful mutations accumulate in the population? </p>
<p>We do not have answers to these questions yet. Genomics can help address some of them, but it is just one tool in the conservation toolbox. Conservation successes will come from an integration of all available sources of information, including often underused sources such as traditional ecological knowledge. </p>
<p>If we want to know more about how black robins behaved and lived before European predators were introduced, we also need to look for – and listen to – the stories from that time. For the black robin, as well as for other highly endangered species, it is the combination of all available information that will eventually make the difference between success and failure.</p><img src="https://counter.theconversation.com/content/194319/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Nicolas Dussex receives funding from the Swiss National Science Foundation, the Carl Tryggers Foundation and University of Otago.</span></em></p><p class="fine-print"><em><span>Michael Knapp has received funding from the Royal Society of New Zealand (Rutherford Discovery Fellowship (14-UOO-007) and the University of Otago. </span></em></p>
Inbreeding usually leads to an accumulation of genetic defects, but evolution on a small archipelago may have helped the severely inbred Chatham Island black robin to avoid this fate.
Nicolas Dussex, Postdoctoral researcher, Centre for Palaeogenetics, Stockholm University
Michael Knapp, Associate Professor in Biological Anthropology, Coastal People: Southern Skies Centre of Resarch Excellence, University of Otago
Licensed as Creative Commons – attribution, no derivatives.
tag:theconversation.com,2011:article/193251
2022-10-31T19:01:36Z
2022-10-31T19:01:36Z
Ancient DNA reveals a hidden history of human adaptation
<figure><img src="https://images.theconversation.com/files/492472/original/file-20221031-25-pdhdyt.jpg?ixlib=rb-1.1.0&rect=53%2C26%2C5937%2C3961&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><span class="source"> Chelms Varthoumlien / Unsplash</span></span></figcaption></figure><p>Humans may be just as vulnerable to environmental change as other animals, according to <a href="https://www.nature.com/articles/s41559-022-01914-9">our new research</a> analysing genetic data from more than a thousand people who lived across Europe and Asia over the past 45,000 years. </p>
<p>We found traces of more than 50 “hard sweeps” in which a rare genetic variant rapidly swept through a population – most likely after a change in conditions in which those lacking the variant died out. The most striking sweep occurred among early Anatolian farming people, in a genetic region associated with the immune system called MHC-III.</p>
<p>Hard sweeps have often been seen in other species, but until now there has been little sign of them in humans. The traces of the hard sweeps had been hidden by frequent mixing between populations over the past 8,000 years.</p>
<p>Our results show humans’ famed ability to adapt our behaviour and develop new tools and techniques has not always been enough to survive when times have grown tough. </p>
<h2>How natural selection works</h2>
<p>Modern humans live in a huge variety of natural environments, from the frozen Arctic to sweltering tropical rainforest. </p>
<p>Unlike most animals, humans can draw on cultural innovations – such as fire and clothing – to overcome the challenges these environments present. </p>
<p>However, these innovations may not always have been enough to cope with new environmental conditions. This is when genetic variability among individuals comes into play.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/we-found-traces-of-humanitys-age-old-arms-race-with-coronaviruses-written-in-our-dna-163254">We found traces of humanity's age-old arms race with coronaviruses written in our DNA</a>
</strong>
</em>
</p>
<hr>
<p>Individuals with genetic variations that make them better equipped to deal with the new conditions will tend to leave more offspring. As a result, these beneficial variants become more common in future generations. </p>
<p>This process of genetic adaptation was dubbed “natural selection” by Charles Darwin nearly 200 years ago. </p>
<h2>How humans adapt</h2>
<p>Using statistical tools to search for evidence of hard sweeps, researchers have found ample evidence for past adaptive events in many animals and plants, but little in human genomes. More specifically, hard sweeps are conspicuously rare in humans. </p>
<p>As a result, <a href="https://www.science.org/doi/abs/10.1126/science.1198878">some have speculated</a> that genetic adaptation in humans is rare, perhaps because cultural innovations have made it largely unnecessary. Others have suggested selection has occurred across many moderately beneficial genetic variants, leading to subtle and hard-to-detect signals.</p>
<h2>Hidden signals</h2>
<p>Almost 40 years ago, new technologies to extract tiny amounts of DNA from archaeological skeletal remains were developed. This has made it possible to <a href="https://theconversation.com/ancient-dna-is-a-powerful-tool-for-studying-the-past-when-archaeologists-and-geneticists-work-together-111127">study the genomes of ancient populations</a>, and changed our view of how ancient human groups and civilisations are related to each other.</p>
<p>Ancient DNA research revealed that over the past 10,000 years in Eurasia, intermixing between genetically divergent populations has been particularly frequent. </p>
<p>We thought these events might have erased historical sweep signals from modern human genomes – but that ancient genomes predating these intermixing events may still retain traces of the signals.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/the-origin-of-us-what-we-know-so-far-about-where-we-humans-come-from-54385">The origin of 'us': what we know so far about where we humans come from</a>
</strong>
</em>
</p>
<hr>
<p>Around 10,000 years ago, after the end of the last ice age, there was <a href="https://theconversation.com/there-was-a-decline-of-male-diversity-when-humans-took-to-agriculture-38725">much more genetic variety</a> among the the hunter-gatherers living in Europe than there is among the humans living there today.</p>
<p>In fact, the genetic differences between groups of ancient European hunter-gatherers were as large as the differences now observed between contemporary populations in western Europe and east Asia. </p>
<p>This extreme genetic differentiation collapsed over the past 8,000 years due to several migrations and mixing events, making modern Europeans much more genetically homogeneous.</p>
<h2>‘Hard sweeps’ in human history</h2>
<p>In our new research, <a href="https://www.nature.com/articles/s41559-022-01914-9">published today in Nature Ecology & Evolution</a>, we revisited this question by scanning more than a thousand ancient human genomes sourced from across Eurasia.</p>
<p>We wondered: could these relatively recent mixing events have masked historical selective sweeps, so they were invisible in modern human genomes? </p>
<p>To test this idea, we first carried out some computer simulations based on estimates of genetic mixing from studies of ancient Eurasian genomes. The simulation results suggested ancient selection signals could indeed be strongly diluted in modern genomes. </p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/nobel-prize-svante-paabos-ancient-dna-discoveries-offer-clues-as-to-what-makes-us-human-191805">Nobel prize: Svante Pääbo's ancient DNA discoveries offer clues as to what makes us human</a>
</strong>
</em>
</p>
<hr>
<p>Next, we compiled and analysed genetic information from more than 1,000 ancient human remains, with the oldest sample being around 45,000 years old. </p>
<p>We compared selection signals in ancient genomes with those from modern genomes. The ancient data contained many more hard sweep signals than the modern samples.
More recent sweeps were particularly prone to erasure, due to being rare or absent in at least one of the mixing populations. </p>
<p>Our results confirm hard sweeps were indeed part of the repertoire of human genetic adaptation. This suggests we may not be so different from other animal species after all.</p>
<h2>The genetic basis of adaptation</h2>
<p>Genetic evidence for historical mixing events between different populations is growing. This is not only in humans but also in other species, suggesting such mixing may be reasonably common in nature. </p>
<p>If these mixing events are widespread, our study suggests hard sweeps may also have been more common than we currently think. Overall, we may have a biased view of how species have genetically adapted to environmental pressures. </p>
<p>To more fully understand how adaptation works at a genetic level, we will need to develop new statistical methods to disentangle signals of hard sweeps and other selection events.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/whats-next-for-ancient-dna-studies-after-nobel-prize-honors-groundbreaking-field-of-paleogenomics-191899">What’s next for ancient DNA studies after Nobel Prize honors groundbreaking field of paleogenomics</a>
</strong>
</em>
</p>
<hr>
<img src="https://counter.theconversation.com/content/193251/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 organisation that would benefit from this article, and have disclosed no relevant affiliations beyond their academic appointment.</span></em></p>
New genetic research shows humans’ famed ability to adapt our behaviour and develop new tools and techniques has not always been enough to survive when times have grown tough.
Yassine Souilmi, Group Leader, Genomics and Bioinformatics, Australian Centre for Ancient DNA, University of Adelaide
Christian Huber, Assistant Professor of Biology, Penn State
Ray Tobler, Postdoctoral fellow, Australian National University
Licensed as Creative Commons – attribution, no derivatives.
tag:theconversation.com,2011:article/185997
2022-09-12T12:15:12Z
2022-09-12T12:15:12Z
Uncovering 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>
<p><div data-react-class="Tweet" data-react-props="{"tweetId":"1492867130622193664"}"></div></p>
<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>
<figure>
<iframe width="440" height="260" src="https://www.youtube.com/embed/eFVmhyyWgzw?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">Ethically and equitably expanding the diversity of genomics data can help improve care and reduce disparities.</span></figcaption>
</figure>
<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>
<figcaption>
<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>
</figcaption>
</figure>
<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>
<figure>
<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>
</figure>
<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 University
Licensed as Creative Commons – attribution, no derivatives.
tag:theconversation.com,2011:article/189629
2022-09-01T01:21:51Z
2022-09-01T01:21:51Z
Scientists release world-first DNA map of an endangered Australian mouse, and it will help to save it
<figure><img src="https://images.theconversation.com/files/481972/original/file-20220831-29-gjvrzk.jpeg?ixlib=rb-1.1.0&rect=0%2C25%2C1914%2C1138&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><span class="source">David Paul, Museums Victoria</span>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span></figcaption></figure><p>The native Australian rodent <em>Pseudomys fumeus</em>, named smoky mouse for its colour, was already fighting off extinction when the 2019–20 bushfire season hit.</p>
<p>The Black Summer bushfires, <a href="https://theconversation.com/australias-black-summer-of-fire-was-not-normal-and-we-can-prove-it-172506">which torched more than 24 million hectares</a>, may have killed an estimated 1 billion animals and put more than 100 threatened species at risk. The fires also destroyed more than 90% of the smoky mouse’s habitat, with nine mice even dying at a captive breeding facility near Canberra from bushfire smoke inhalation.</p>
<p>But all is not lost – a newly sequenced reference genome will now help the ongoing conservation efforts of this native Australian species.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/death-by-irony-the-mystery-of-the-mouse-that-died-of-smoke-inhalation-but-went-nowhere-near-a-fire-139906">'Death by irony': The mystery of the mouse that died of smoke inhalation, but went nowhere near a fire</a>
</strong>
</em>
</p>
<hr>
<h2>Precious pockets of mice</h2>
<p>We haven’t seen wild smoky mice in the Australian Capital Territory <a href="https://www.environment.act.gov.au/__data/assets/pdf_file/0010/576487/The_Smoky_Mouse_factsheet.pdf">since 1987</a>. In Victoria, the species is only around in the Grampians, Central Highlands and alpine regions, and in New South Wales in the alpine regions of Kosciuszko National Park and southeastern forests near Nullica.</p>
<p>An active recovery plan was established for the mouse in 2006. As part of this, conservationists started two captive populations, with <a href="https://www.abc.net.au/news/2022-08-16/endangered-smoky-mouse-released-wild-south-east-nsw/101338246">releases taking place</a> into southeastern forests near Nullica, and a predator-proof reserve in the ACT.</p>
<p>These <a href="https://www.environment.nsw.gov.au/threatenedspeciesapp/profile.aspx?id=10686">little native mice</a> are beyond cute, roughly double the size of the introduced house mouse (<em>Mus musculus</em>). Their charcoal fur is soft and silky, and they smell really nice, too. Males especially smell kind of like smoky burnt vanilla; these animals have lovely, calm temperaments.</p>
<p>In the past 12 months, a Museums Victoria Research Institute team has been undertaking surveys to search for surviving pockets of the endangered mouse’s population with an eye towards future reintroduction efforts of captive bred mice.</p>
<p>To support these ongoing conservation efforts, <a href="https://www.dnazoo.org/">DNA Zoo</a> at The University of Western Australia teamed up with <a href="https://collections.museumsvictoria.com.au/species/8434">Museums Victoria</a> Senior Curator of Mammals Kevin Rowe to sequence a world-first full chromosome-length reference genome for the animal.</p>
<figure class="align-center ">
<img alt="A small, grey rodent with round ears looking towards the camera, sitting on a rock" src="https://images.theconversation.com/files/481797/original/file-20220830-19040-tvzu0l.jpg?ixlib=rb-1.1.0&rect=212%2C135%2C1408%2C1376&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/481797/original/file-20220830-19040-tvzu0l.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=473&fit=crop&dpr=1 600w, https://images.theconversation.com/files/481797/original/file-20220830-19040-tvzu0l.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=473&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/481797/original/file-20220830-19040-tvzu0l.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=473&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/481797/original/file-20220830-19040-tvzu0l.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=595&fit=crop&dpr=1 754w, https://images.theconversation.com/files/481797/original/file-20220830-19040-tvzu0l.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=595&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/481797/original/file-20220830-19040-tvzu0l.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=595&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Conservationists have been working to save the smoky mouse with an active recovery plan since 2006.</span>
<span class="attribution"><span class="source">David Paul, Museums Victoria</span>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<h2>Protecting what we have</h2>
<p>We can now use this reference genome to inform conservation strategy. Researchers will map 70 individual smoky mouse DNA sequences from across the animal’s habitat range – in the Grampians in western Victoria to southeastern New South Whales.</p>
<p>Increasing our understanding of living wildlife and responsibly stewarding available resources are among the most crucial scientific and social challenges we face today.</p>
<p>Despite great technological advances, there’s much we don’t know about <a href="https://www.dcceew.gov.au/environment/biodiversity">Australia’s native biodiversity</a>. At the same time, it’s increasingly threatened by wildfires, climate change, habitat destruction, species exploitation and other human-related activities.</p>
<p>Thankfully, we can use genomics to help formulate an informed conservation strategy. That’s because sampling genomic diversity can give us a baseline understanding of how well the species is faring (what biologists call “population fitness”). With that knowledge in hand, we can better design conservation programs.</p>
<p>For example, in endangered species with severely reduced populations, we can avoid inbreeding if we use genomic data to help design breeding programs. That way, the animals will have fewer genes that lead to premature death, and have increased disease resistance.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/weve-decoded-the-numbat-genome-and-it-could-bring-the-thylacines-resurrection-a-step-closer-176528">We've decoded the numbat genome – and it could bring the thylacine's resurrection a step closer</a>
</strong>
</em>
</p>
<hr>
<h2>Consulting the genetic blueprints</h2>
<p>Obtaining the genetic blueprints for Australian wildlife will create a powerful source of discovery for improving and increasing ecosystem services. A well-designed monitoring framework is crucial to the on-ground success of conservation programs.</p>
<p>As part of the recovery plan for the smoky mouse, we have DNA sequences from individuals in the Grampians, as well as historical samples dating back to 1934 from extinct populations in the Otways and Far East Gippsland. </p>
<p>The Grampians samples are of particular interest. That’s because this population is the most isolated, removed by about 350 kilometres from the nearest known population in the Yarra Ranges of the Central Highlands.</p>
<p>Since 2012, Museums Victoria and partners have trapped, marked and collected samples – ear biopsies and poo pellets, neither of which are harmful to the animals – from more than 200 smoky mice in the Grampians. Thanks to this work, we now have the most numerous and continuous record of the species in Victoria.</p>
<figure class="align-center ">
<img alt="An adorable, rat-like animal with a soft grey coat and cute pink nose" src="https://images.theconversation.com/files/481796/original/file-20220830-22-2eix1i.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/481796/original/file-20220830-22-2eix1i.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=417&fit=crop&dpr=1 600w, https://images.theconversation.com/files/481796/original/file-20220830-22-2eix1i.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=417&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/481796/original/file-20220830-22-2eix1i.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=417&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/481796/original/file-20220830-22-2eix1i.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=524&fit=crop&dpr=1 754w, https://images.theconversation.com/files/481796/original/file-20220830-22-2eix1i.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=524&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/481796/original/file-20220830-22-2eix1i.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=524&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Some smoky mice have been discovered in the Grampians, far removed from others of their kind.</span>
<span class="attribution"><span class="source">David Paul, Museums Victoria</span>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<p>In addition, <a href="https://www.researchgate.net/publication/295403229_The_status_of_Smoky_Mouse_populations_at_some_historic_sites_in_Victoria_and_survey_methods_for_their_detection">trapping and wildlife camera surveys</a> at more than 100 sites have revealed smoky mouse populations localised to two areas less than 10km from the Victoria Range and Mt William Range, respectively. </p>
<p>Researchers will now be looking for genetic clues on how these animals persisted despite drought, invasive predators and significant fire.</p>
<p>What’s encouraging is how powerful technology – such as genome sequencing, bioinformatics, and more combined together – is now helping us to understand and preserve biodiversity. For the first time in history, we can fast-track and efficiently sequence the genomes of our unique native Australian species.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/its-not-too-late-to-save-them-5-ways-to-improve-the-governments-plan-to-protect-threatened-wildlife-147669">It's not too late to save them: 5 ways to improve the government's plan to protect threatened wildlife</a>
</strong>
</em>
</p>
<hr>
<img src="https://counter.theconversation.com/content/189629/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Parwinder Kaur 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>
The smoky mouse was already fighting extinction when a devastating bushfire season decimated 90% of its habitat. Thankfully, all is not lost.
Parwinder Kaur, Associate Professor | Director, DNA Zoo Australia, The University of Western Australia
Licensed as Creative Commons – attribution, no derivatives.
tag:theconversation.com,2011:article/184482
2022-07-06T13:35:37Z
2022-07-06T13:35:37Z
Africans make up a tiny portion of genomics data: why there’s an urgent need for change
<figure><img src="https://images.theconversation.com/files/471412/original/file-20220628-22-v51h6c.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Nigeria provides an excellent lens to look at the genetic diversity of African people.</span> <span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/photo/sample-being-pipetted-into-a-eppendorf-tube-for-royalty-free-image/1140201417?adppopup=true">Getty Images </a></span></figcaption></figure><p><em>A group of Nigerian scientists, in conjunction with the London School of Hygiene and Tropical Medicine, <a href="https://www.nature.com/articles/s41588-022-01071-6">established</a> the Noncommunicable Diseases Genetic Heritage Study consortium in February 2020. The aim is to produce a comprehensive catalogue of human genetic variation in Nigeria and assess the burden of noncommunicable diseases in 100,000 adults in the country. The Conversation Africa asked genetic epidemiologist <a href="https://www.lshtm.ac.uk/aboutus/people/fatumo.segun">Segun Fatumo</a>, one of the leaders of the consortium, to explain what they are doing and why.</em> </p>
<hr>
<h2>How does Africa feature in global genomics?</h2>
<p>Until recently, only about <a href="https://www.nature.com/articles/538161a">3% of genomic data</a> being used for genome-wide association studies came from people of African descent. Unfortunately, this proportion has fallen even further, <a href="https://www.nature.com/articles/s41591-021-01672-4">to 1.1% in 2021</a>. This means people of African descent may miss out on the potential benefits of genomic research, including early detection of disease and rational drug design. </p>
<p>The current lack of genomic diversity has led to major scientific opportunities being missed. <a href="https://www.nature.com/articles/ng1509">One study</a> which included people of African descent discovered a gene called <em>PCSK9</em> which helps in lowering bad cholesterol. This study led to new drugs that help prevent heart disease. This benefits everyone irrespective of their ancestry populations. It wouldn’t have been possible without including people of African descent. </p>
<p>Africans have the most diverse genomes of all the human populations because modern <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2953791/">humans originated in Africa</a> and then spread across the globe over the past 80,000 years. Therefore, studying the genome of Africans could uncover genetic variants not found in other populations. Such genes could yield new ways to diagnose, prevent and treat diseases for everyone. </p>
<h2>What does the consortium plan to do?</h2>
<p>We teamed up with <a href="https://54gene.com/">54gene</a>, a health technology platform company that’s building diverse datasets to unlock scientific discoveries. Together we established the <a href="https://www.nature.com/articles/s41588-022-01071-6">NonCommunicable Diseases Genetic Heritage Study consortium</a>. One aim is to develop a catalogue of human genetic variation in 100,000 adults in Nigeria. This will be the largest genomic data resource ever to come from continental Africa. It will be of great value to genomics researchers globally and may help in the prevention and control of noncommunicable diseases in sub-Saharan Africa.</p>
<p>The other aim is to assess Nigeria’s burden of disease. We’re looking at things like haematological cancers and cardiovascular, neurodegenerative, metabolic, kidney function and sickle cell disorders.</p>
<p>Our consortium could serve as a template for large-scale genomics across the continent. We hope it will advance precision medicine and offer insights that will improve the health and well-being of African and global populations. </p>
<p>The consortium has five points on its agenda:</p>
<ul>
<li><p>address health issues of concern for Africans and other populations</p></li>
<li><p>ensure projects meet the highest ethical, legal and socially appropriate standards for research</p></li>
<li><p>generate, process, store and use large genomic datasets</p></li>
<li><p>build research capacity</p></li>
<li><p>develop leaders for genomics in Africa.</p></li>
</ul>
<p>The first step is to collect samples. A minimum of 100,000 research participants have been recruited and samples of biological material like blood and urine have been stored for further genomic studies. </p>
<p>Next is to design a small chip that is able to capture a picture of somebody’s DNA sequence. There are three billion base pairs in any human genome. The chip will capture at least one million genetic variants that are important for different diseases. We are also developing other studies using the whole-genome DNA sequence of all three billion base pairs.</p>
<p>We will also be fostering a scientific community that will empower African genomics scientists to be leaders in the genomic world. We want more people in Africa to be in a position to write the continent’s own genomics agenda.</p>
<h2>Why focus on Nigeria?</h2>
<p>First, Nigeria has one of the most diverse ethnolinguistic concentrations in the world, with more than <a href="http://rogerblench.info/Language/Africa/Nigeria/Atlas%20of%20Nigerian%20Languages%202020.pdf">300 ethnic groups and 500 languages</a>. This diversity is taken as a proxy for potential genetic diversity, as seen in other populations. Data from the Nigerian population provides an excellent lens to look at the genetic diversity of African people. This will ensure that most genetic variations are captured.</p>
<p>Second, with <a href="https://www.statista.com/statistics/1122838/population-of-nigeria/#:%7E:text=As%20of%202022%2C%20Nigeria's%20population%20was%20estimated%20at%20around%20216.7%20million.">over 200 million people</a>, Nigeria represents a quarter of the African population. We are recruiting people from across the six geopolitical zones in Nigeria.</p>
<p>With 100,000 research participants, we will be able to estimate the prevalence of noncommunicable diseases in the population, and understand the associated risk factors. </p>
<p>We are poised to provide information that could be used to develop tools for the <a href="https://pubmed.ncbi.nlm.nih.gov/31537347/">early detection of diseases</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/31537368/">disease prevention strategies</a> and <a href="https://www.healthaffairs.org/doi/10.1377/hlthaff.2017.1595">treatment options</a>. </p>
<h2>What other initiatives are there on the continent?</h2>
<p>Our effort will complement other initiatives like <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4138491/">H3Africa</a>, <a href="https://www.sciencedirect.com/science/article/pii/S0092867419311201">Uganda Genome Resource</a> and a few others.</p>
<p>H3Africa was launched in 2012. It has recruited close to 100,000 research participants for genomic research in the last decade and trained over 1,000 African scientists, including me. </p>
<p>The <a href="https://acegid.org/">African Centre of Excellence for Genomics of Infectious Diseases</a> is another successful Nigerian-based initiative. It is making an impact through training, discovery and surveillance of infectious pathogens.</p>
<p>The <a href="http://www.nbgnetwork.org/">Nigerian Bioinformatics and Genomics Network</a> is another. It is fostering genetic research collaboration and provides opportunities for career development in genomics and bioinformatics.</p>
<p>The Uganda Genome Resource is currently <a href="https://theconversation.com/what-weve-learnt-from-building-africas-biggest-genome-library-126293">one of the largest</a> and most successful genomic initiatives in Africa. In 2019, a rich, diverse resource was <a href="https://www.sciencedirect.com/science/article/pii/S0092867419311201">published</a> using data from 6,400 Ugandans. It includes whole genome sequencing of nearly 2,000 people.</p>
<p><em>Aminu Yakubu and Babatunde Olusola helped research this article.</em></p><img src="https://counter.theconversation.com/content/184482/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Segun Fatumo received consultancy fees from 54gene Nigeria Ltd.</span></em></p>
A new study hopes to produce a catalogue of human genetic variation and assess the burden of noncommunicable diseases in 100,000 adults in Nigeria.
Segun Fatumo, Associate Professor of Genetic epidemiology & Bioinformatics, London School of Hygiene & Tropical Medicine
Licensed as Creative Commons – attribution, no derivatives.
tag:theconversation.com,2011:article/185140
2022-06-27T19:51:15Z
2022-06-27T19:51:15Z
Drones and DNA tracking: we show how these high-tech tools are helping nature heal
<figure><img src="https://images.theconversation.com/files/470487/original/file-20220623-52178-4g1i30.jpg?ixlib=rb-1.1.0&rect=82%2C14%2C4910%2C3974&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><span class="source">Gontran Isnard/Unsplash</span>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span></figcaption></figure><p>Technology has undoubtedly contributed to global biodiversity loss and ecosystem degradation.</p>
<p>Where forests once stood, artificial lights now illuminate vast urban jungles. Where animals once roamed, huge factories now churn out microchips, computers, and cars. But now, we can also leverage technology to help repair our precious ecosystems.</p>
<p>Here, we discuss our two new research papers published today. They show how <a href="https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.13912">drones</a> and <a href="https://royalsocietypublishing.org/doi/10.1098/rstb.2021.0381">genomics</a> (the same technology used to identify COVID strains) can help protect and restore nature. </p>
<p>One paper demonstrates that drones can help safeguard biodiversity and monitor ecosystem restoration activities. They can also help us understand how impacts in one ecosystem may affect another. </p>
<p>Genomics can help identify populations that may be vulnerable to future climate change, and monitor elusive animals such as platypuses, lynx, and newts. Yet, our other paper found ecologists without genomics expertise thought the technology still needed to be tried and tested.</p>
<h2>Remote sensing with drones</h2>
<p>Drones are an increasingly common sight in, for instance, urban parks and weddings. Farmers also use them to <a href="https://www.sciencedirect.com/science/article/pii/S2214317322000087">assess crop health</a>, and engineers use them to detect damage to bridges and wind turbines. </p>
<p>Drone technology has rapidly advanced over the last decade. Advancements include obstacle avoidance, enhanced flight times, high-definition cameras, and the ability to carry heavier payloads. </p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/five-of-the-worlds-tiniest-robots-184790">Five of the world's tiniest robots</a>
</strong>
</em>
</p>
<hr>
<p>But can drones help repair damaged ecosystems? We <a href="https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.13912">reviewed the scientific literature</a> from various environmental sectors to explore the existing and emerging uses of drones in restoring degraded ecosystems. The answer, we found, is a resounding “yes”. </p>
<p>We found drones can help map vegetation and collect water, soil, and grassland samples. They can also monitor plant health and wildlife population dynamics. This is essential for understanding whether a restoration intervention is working. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/470489/original/file-20220623-52151-q7h3i2.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Large grass fire burning" src="https://images.theconversation.com/files/470489/original/file-20220623-52151-q7h3i2.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/470489/original/file-20220623-52151-q7h3i2.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=338&fit=crop&dpr=1 600w, https://images.theconversation.com/files/470489/original/file-20220623-52151-q7h3i2.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=338&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/470489/original/file-20220623-52151-q7h3i2.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=338&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/470489/original/file-20220623-52151-q7h3i2.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=424&fit=crop&dpr=1 754w, https://images.theconversation.com/files/470489/original/file-20220623-52151-q7h3i2.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=424&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/470489/original/file-20220623-52151-q7h3i2.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">Some drones can help extinguish fires in the wild.</span>
<span class="attribution"><span class="source">Shutterstock</span></span>
</figcaption>
</figure>
<p>In Australia, for instance, drones have helped <a href="https://doi.org/10.1111/emr.12505">researchers identify</a> the habitat requirements for marsupials such as the spotted-tailed quoll and the eastern bettong. Thanks to having the drone’s birds-eye view, researchers and practitioners are gaining a better understanding of what vegetation to restore as well as new approaches to monitor the return of critical habitat.</p>
<p>Famously, drones have recently been used to plant trees by dropping “seed bombs” <a href="https://www.abc.net.au/news/2022-06-19/giant-drones-dropping-tree-seeds/101150496">to help restore forests</a>. While drone-based tree planting has potential, it still requires more research as the survival rate of seedlings is currently poor. </p>
<p>Some researchers have even developed <a href="https://www.mdpi.com/2504-446X/3/1/17">bushfire-fighting drones</a> to protect sensitive ecosystems. This is where one drone detects fire using thermal technology, and another puts it out by dropping fire-extinguishing balls. But controlled wildfires can sometimes be vital to ecosystem restoration, so we can also use drones to drop tiny fireballs, too.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/heat-detecting-drones-are-a-cheaper-more-efficient-way-to-find-koalas-140332">Heat-detecting drones are a cheaper, more efficient way to find koalas</a>
</strong>
</em>
</p>
<hr>
<p>However, there are many pitfalls to consider when using drones. In the wrong hands, drones can be a nuisance and harm wildlife. </p>
<p>Studies have shown flying too close to animals, such as birds and bears can <a href="https://www.sciencedirect.com/science/article/pii/S0960982215008271">impact their physiology</a>. For example, a 2015 study showed drones flying too close to American black bears caused their heart rates to rise – even for one bear deep in hibernation. </p>
<p>Drone pilots should acquire appropriate licences and follow strict protocols when flying them in sensitive habitats.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/470488/original/file-20220623-51187-a658u1.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Black bear at edge of river" src="https://images.theconversation.com/files/470488/original/file-20220623-51187-a658u1.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/470488/original/file-20220623-51187-a658u1.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=399&fit=crop&dpr=1 600w, https://images.theconversation.com/files/470488/original/file-20220623-51187-a658u1.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=399&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/470488/original/file-20220623-51187-a658u1.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=399&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/470488/original/file-20220623-51187-a658u1.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=502&fit=crop&dpr=1 754w, https://images.theconversation.com/files/470488/original/file-20220623-51187-a658u1.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=502&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/470488/original/file-20220623-51187-a658u1.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"></a>
<figcaption>
<span class="caption">A study found black bears became stressed when drones flew too close.</span>
<span class="attribution"><span class="source">Shutterstock</span></span>
</figcaption>
</figure>
<h2>Genomics: valuable, yet misunderstood</h2>
<p>Genomics is a toolkit jam-packed full of innovative ways of looking at DNA, the blueprint of life on Earth. When scientists talk about genomics, they usually refer to modern <a href="https://en.wikipedia.org/wiki/Massive_parallel_sequencing">DNA sequencing technologies</a> or the analysis of vast collections of DNA. </p>
<p>But despite the potential for <a href="https://www.nature.com/articles/s41576-019-0152-0">genomics to improve ecosystem restoration</a>, our <a href="https://royalsocietypublishing.org/doi/10.1098/rstb.2021.0381">recent study</a> showed restoration scholars without genomics experience were concerned genomics was over-hyped.</p>
<p>We interviewed leading experts in different ecology disciplines and found many called for case studies to demonstrate the benefits of genomics in restoration. </p>
<p>But surprisingly, we found restoration genomics literature included over 70 restoration genomics studies, many of which used environmental DNA to monitor ecosystem health. So, plenty of case studies already exist. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/470491/original/file-20220623-51718-fzzg0b.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/470491/original/file-20220623-51718-fzzg0b.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/470491/original/file-20220623-51718-fzzg0b.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/470491/original/file-20220623-51718-fzzg0b.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/470491/original/file-20220623-51718-fzzg0b.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/470491/original/file-20220623-51718-fzzg0b.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/470491/original/file-20220623-51718-fzzg0b.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/470491/original/file-20220623-51718-fzzg0b.jpeg?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">Genomics can help choose which seeds of red ironbark trees can withstand the changing climate.</span>
<span class="attribution"><span class="source">John Tann/Wikimedia</span>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span>
</figcaption>
</figure>
<p>In ecosystem restoration, the two most common genomics applications are population genomics and environmental DNA. </p>
<p>Population genomics studies small differences in an organism’s genome to answer questions such as how much genetic variation exists in a population, how related individuals are, or how landscapes change migration patterns. </p>
<p>Linking changes in DNA sequences to historical climates has become central to modern-day nature conservation and restoration. It allows us to understand how resilient animals, plants and <a href="https://www.sciencedirect.com/science/article/pii/S0301479722003218">microbes are to future climates</a>. </p>
<p>For example, we have used this approach to select robust tree seeds, such as red ironbark (<em>Eucalyptus tricarpa</em>), for woodland restoration <a href="https://www.nature.com/articles/s41576-019-0152-0">plantings across southeast Australia</a>. Using genomics to select the most resilient seeds gives the trees the best chance of surviving in a changing climate.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/weve-unveiled-the-waratahs-genetic-secrets-helping-preserve-this-australian-icon-for-the-future-174772">We've unveiled the waratah's genetic secrets, helping preserve this Australian icon for the future</a>
</strong>
</em>
</p>
<hr>
<p>Scientists can also gain insights into ecosystems and monitor elusive species using the DNA organisms leave behind in environments, such as soil or water. </p>
<p>This environmental DNA data can help track the presence of species — invasive, endangered, or cryptic — and help measure community health and diversity. This includes <a href="https://onlinelibrary.wiley.com/doi/full/10.1111/mec.14350">pollinators such as bees</a>, other animals and plants and our invisible friends, <a href="https://www.nature.com/articles/s41598-021-89065-y">the microbes</a>. </p>
<p>For instance, in the United Kingdom, ecologists currently use environmental DNA to detect the presence of vulnerable amphibians, such as great crested newts. </p>
<figure class="align-center ">
<img alt="A water dragon with orange background" src="https://images.theconversation.com/files/470495/original/file-20220623-51812-bk7tlm.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/470495/original/file-20220623-51812-bk7tlm.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/470495/original/file-20220623-51812-bk7tlm.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/470495/original/file-20220623-51812-bk7tlm.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/470495/original/file-20220623-51812-bk7tlm.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/470495/original/file-20220623-51812-bk7tlm.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/470495/original/file-20220623-51812-bk7tlm.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">Great crested newt populations are declining.</span>
<span class="attribution"><span class="source">Shutterstock</span></span>
</figcaption>
</figure>
<h2>Where to from here?</h2>
<p>Greater uptake of remote sensing and genomics in restoration has clear potential to help improve the monumental task of restoring our degraded ecosystems. Our papers outline ways for restoration ecologists to integrate drones and genomics into their toolboxes. </p>
<p>Given humans have caused substantial degradation to global ecosystems, it makes sense to use the technologies now available to restore wildlife and prevent additional biodiversity loss.</p><img src="https://counter.theconversation.com/content/185140/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Jake M Robinson is affiliated with Flinders University in South Australia and the University of Sheffield in the UK. </span></em></p><p class="fine-print"><em><span>Jakki Mohr receives funding from the U.S. National Science Foundation. </span></em></p><p class="fine-print"><em><span>Martin Breed receives funding from the Australian Research Council. </span></em></p><p class="fine-print"><em><span>Peter Harrison receives funding from the Tasmanian Government. </span></em></p><p class="fine-print"><em><span><a href="mailto:suzanne.mavoa@unimelb.edu.au">suzanne.mavoa@unimelb.edu.au</a> previously received funding from University of Melbourne and the Australian National Health and Medical Research Council. </span></em></p>
From discovering hidden populations of vulnerable newts to dropping “seed bombs”, two new research papers show how genomics and drones help restore threatened ecosystems.
Jake M Robinson, Ecologist and Researcher, Flinders University
Jakki Mohr, Professor of Marketing & Innovation, University of Montana
Martin Breed, Senior Lecturer in Biology, Flinders University
Peter Harrison, Lecturer in Forest Adaptation and Restoration Genetics, University of Tasmania
Suzanne Mavoa, The University of Melbourne
Licensed as Creative Commons – attribution, no derivatives.