tag:theconversation.com,2011:/us/topics/genus-18501/articlesGenus – The Conversation2022-10-27T14:41:14Ztag:theconversation.com,2011:article/1930272022-10-27T14:41:14Z2022-10-27T14:41:14ZA new way to name bacteria: 300-year-old system revised thanks to scientific advances<figure><img src="https://images.theconversation.com/files/491680/original/file-20221025-24-jcnb2p.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Prokaryotes are single-celled organisms without nuclei and are commonly known as bacteria.</span> <span class="attribution"><span class="source">Ichigomaru/Shutterstock</span></span></figcaption></figure><p>Nearly 300 years ago the Swedish botanist <a href="https://www.britannica.com/biography/Carolus-Linnaeus">Carl Linnaeus</a> secured his place in scientific history when he created what’s known as the <a href="https://byjus.com/biology/binomial-nomenclature/">binomial system</a>. The year was 1737 and, due to the large diversity of plants and animals collected by naturalist explorers in different parts of the world, Linnaeus saw the need to develop a logical system to classify and group this material in a systematic way. </p>
<p>It’s a system that’s stood the test of time – his basic formula is still in use.</p>
<p>The naming convention applies to all biological organisms: plants, animals and bacteria. Each species receives a name consisting of two parts. The genus name is similar to a surname; all species that share this name are closely related. The second name is unique for each species within the genus. This combination creates a unique name for any described organism. Well known examples include <em>Homo sapiens</em> (modern humans) and <em>Escherichia coli</em> (bacteria).</p>
<p>One of the main benefits of assigning universally accepted distinct names is that it helps people, and particularly scientists, to clearly communicate about a specific organism, regardless of language or geographic barriers. Another boon is that unique names link all the available information on a species together. It also helps scientists to understand shared characteristics and relationships between organisms.</p>
<p>Naming decisions are not made in a vacuum. Although ideas of what species are and how to recognise them have developed over the past 300 years, the naming system as proposed by Linnaeus remained unchanged. </p>
<p>There are “rule books” for the naming of organisms, generally referred to as “codes”. There are different codes for naming animals, plants, algae and fungi, viruses and bacteria. The <a href="https://www.iapt-taxon.org/nomen/main.php">Botanical Code</a>, which initially also dealt with bacteria, was first developed in 1867 and is revised every six years during the International Botanical Congress. The Bacterial Code was first published as a separate document in 1947 and was updated this year by the <a href="https://www.the-icsp.org/">International Committee on Systematics of Prokaryotes</a>.</p>
<p>But the existing code was not enough to deal with advances in technology that have changed how prokaryotes can be studied. So, a new, complementary code has been introduced.</p>
<h2>A stable system</h2>
<p>If the description of a new species meets all the requirements set out in the rules in the relevant code, the name will be validated – made permanent. </p>
<p>Each new species is also linked to type material: something concrete to compare other individuals against. The type <a href="https://www.sciencedirect.com/science/article/pii/S2052297522000439?via%3Dihub">can be represented</a> by museum or herbarium examples, living cultures or even drawings.</p>
<p>But this system doesn’t work well for prokaryotes. These single cell organisms, which don’t have nuclei, are commonly referred to as bacteria (though they also include the <em>Archaea</em>, a group of micro-organisms that are similar to but distinct from bacteria). Prokaryotes are named under the <a href="https://www.the-icsp.org/bacterial-code">International Code of Nomenclature of Prokaryotes</a>. </p>
<p>Unlike other disciplines’ naming rule books, this code is strict about type material: only a pure culture of the bacterium, available from collections in two different countries, counts as type material. But there’s a problem: most bacteria still can’t be grown in pure culture, on its own in a Petri dish in the laboratory.</p>
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<a href="https://theconversation.com/following-a-fungus-from-genes-to-tree-disease-a-journey-in-science-184978">Following a fungus from genes to tree disease: a journey in science</a>
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<p>This means that, under the code, they could not be named.</p>
<p>A new initiative, <a href="https://www.nature.com/articles/s41564-022-01214-9">SeqCode</a>, will change the game by allowing DNA sequencing data to serve as the type. I was one of several biologists around the world involved in creating the SeqCode and I believe it is a great achievement. </p>
<p>A formal and stable naming system for all bacteria will help science to unlock the hidden potential of the planet’s biodiversity and to understand their role in the functioning of ecosystems. It will also help scientists to communicate their findings to each other – a big step towards perhaps identifying the next generation of antibiotics or cancer treatment.</p>
<h2>Genome sequencing</h2>
<p>It’s not known how many prokaryotic species there are – there could be millions or trillions. But so far only around 18,000 have been given <a href="https://www.bacterio.net/">permanent (valid) names</a>. The increasing ubiquity of genome sequencing is an opportunity to change this. Rather than having to grow a prokaryotic species in a laboratory to then study and describe its characteristics, biologists can now sequence the organisms’ DNA directly from an environmental sample to obtain a complete or near complete genome. The genome is the DNA blueprint of the bacterium which encodes all the functions the organism will be able to perform.</p>
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<p>The sequence data is stable enough and adequate to be used to recognise other members belonging to the same species. </p>
<p>In 2018 an international group of bacterial taxonomists and ecologists attended a workshop in the US, funded by the US National Science Foundation, to discuss the future of bacterial taxonomy. The attendees recognised that genome sequencing was a good, scientifically sound way to give many prokaryotes permanent names. This idea was <a href="https://www.nature.com/articles/s41564-020-0733-x">supported</a> by many other microbiologists around the world. </p>
<p>However, a proposal to change the existing code to allow genome sequences as types was <a href="https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.004303">not accepted</a> by the International Committee on Systematics of Prokaryotes. With the support of the International Society for Microbial Ecology, some of the meeting attendees began <a href="https://www.isme-microbes.org/seqcode-initiative">discussing other possibilities</a>.</p>
<p>The idea of an entirely separate code for naming genomically described prokaryotes emerged. Wide consultation followed and, in September 2022, SeqCode – or, to give it its full name, the <a href="https://www.sciencedirect.com/science/article/pii/S0723202022000121?via%3Dihub;">Code of Nomenclature of Prokaryotes Described from Sequence Data</a>, was <a href="https://doi.org/10.1038/s41564-022-01214-9">launched</a>.</p>
<p>This doesn’t replace the existing code. Bacteria can still be named under the Bacterial Code when a pure culture is available. </p>
<p>It is possible that, in coming years, similar adjustments might be made to – or new codes created for – naming other genomically described micro-organisms such as yeasts and other fungi.</p><img src="https://counter.theconversation.com/content/193027/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Stephanus Nicolaas Venter receives funding from the National Research Foundation and the Water Research Commission.
He is currently a member of the organizing committee of the SeqCode Initiative and a member of the Committee on Systematics of Prokaryotes.</span></em></p>A new ‘rule book’ for naming genomically sequenced bacteria is a boon for science.Stephanus Nicolaas Venter, Professor in Microbiology and Deputy Director of the Forestry and Agricultural Biotechnology Institute (FABI), University of PretoriaLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1397542020-09-25T02:50:53Z2020-09-25T02:50:53ZWe accidentally found a whole new genus of Australian daisies. You’ve probably seen them on your bushwalks<figure><img src="https://images.theconversation.com/files/359924/original/file-20200925-16-1jdunxq.JPG?ixlib=rb-1.1.0&rect=3%2C27%2C2580%2C1909&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><span class="source">Alexander Schmidt-Lebuhn</span>, <span class="license">Author provided</span></span></figcaption></figure><p>When it comes to new botanical discoveries, one might imagine it’s done by trudging around a remote tropical rainforest. Certainly, that does <a href="https://theconversation.com/geosiris-is-an-early-contender-for-sexiest-plant-of-2019-109889">still happen</a>. But sometimes seemingly familiar plants close to home hold unexpected surprises. </p>
<p>We <a href="https://onlinelibrary.wiley.com/doi/10.1002/tax.12321">recently discovered</a> a new genus of Australian daisies, which we’ve named <em>Scapisenecio</em>. And we did so on the computer screen, during what was meant to be a routine analysis to test a biocontrol agent against <a href="https://research.csiro.au/cape-ivy/">a noxious weed</a> originally from South Africa. </p>
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<p>The term “genus” refers to groups of different, though closely related, species of flora and fauna. For example, there are more than 100 species of roses under the <em>Rosa</em> genus, and brushtail possums are members of the <em>Trichosurus</em> genus.</p>
<p>This accidental discovery shows how much is still to be learned about the natural history of Australia. <em>Scapisenecio</em> is a new genus, but thousands of visitors to the Australian Alps see one of its species flowering each summer. If this species was still misunderstood, surely similar surprises are still out there waiting for us.</p>
<h2>How it began</h2>
<p>It all started with a biocontrol researcher asking a plant systematist, who looks at the evolutionary history of plants, to help figure out the closest Australian native relatives of the weed, Cape ivy (<em>Delairea odorata</em>). </p>
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<a href="https://images.theconversation.com/files/359925/original/file-20200925-20-469wfd.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Cape ivy leaves covering a tree stump" src="https://images.theconversation.com/files/359925/original/file-20200925-20-469wfd.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/359925/original/file-20200925-20-469wfd.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/359925/original/file-20200925-20-469wfd.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/359925/original/file-20200925-20-469wfd.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/359925/original/file-20200925-20-469wfd.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/359925/original/file-20200925-20-469wfd.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/359925/original/file-20200925-20-469wfd.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>
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<span class="caption">Cape ivy is destructive to agriculture and native plants.</span>
<span class="attribution"><span class="source">Murray Fagg/Australian Plant Image Index</span>, <span class="license">Author provided</span></span>
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<p>Weeds like Cape ivy cause major damage to agriculture in Australia, displace native vegetation and require extensive management. <a href="https://theconversation.com/explainer-how-biocontrol-fights-invasive-species-31298">Biological control</a> (biocontrol) is one way to reduce their impact. This means taking advantage of insects or fungi that attack a weed, generally after introducing them from the weed’s home range. </p>
<p>A well-known Australian example is the introduction of the <em>Cactoblastis</em> moth in 1926 to control <a href="https://www.daf.qld.gov.au/__data/assets/pdf_file/0014/55301/IPA-Prickly-Pear-Story-PP62.pdf">prickly pear</a> in Queensland and New South Wales. Even today it continues to keep that weed in check.</p>
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<p>To minimise the risk of selecting a biocontrol agent that will damage native flora, ornamental plants or crops, it’s tested carefully against a list of species of varying degrees of relatedness to the target weed. </p>
<p>Authorities will approve the release of a biocontrol agent only if scientists can show it’s highly specific to the weed. Assembling a list of species to test therefore requires us to understand the evolutionary relationships of the target weed to other plant species. </p>
<p>If such relationships are poorly understood, we might fail to test groups of species that are closely related to the target. </p>
<h2>Missing data</h2>
<p>Our target weed Cape ivy is a climbing daisy that has <a href="https://weeds.dpi.nsw.gov.au/Weeds/CapeIvy">become invasive</a> in temperate forests and coastal woodlands throughout south-eastern Australia. One of us, Ben Gooden, is researching the potential use of <em>Digitivalva delaireae</em> — a stem-boring moth — for its biocontrol. </p>
<p>We tried to design a test list, but could not find up-to-date information on Cape ivy’s relatives. We already knew it is related to the large groundsel genus <em>Senecio</em>, but we didn’t know how closely. And no genetic data existed for many Australian native species of <em>Senecio</em>.</p>
<p>So, we set out to solve this problem together. </p>
<p>First, we assembled already-published DNA sequences for as many <em>Senecio</em> species and relatives as we could find, and then generated sequences for an additional 32 native Australian species. </p>
<p>We then united all these genetic data into a comprehensive <a href="https://www.nature.com/scitable/topicpage/reading-a-phylogenetic-tree-the-meaning-of-41956/">phylogenetic analysis</a>. “Phylogenetics” infers the evolutionary relatedness of organisms to each other.</p>
<h2>Hidden in the evolutionary tree</h2>
<p>The resulting “evolutionary tree” showed many of the native <em>Senecio</em> species where we expected them to be. More importantly, however, it showed us that Cape ivy is actually quite distantly related to <em>Senecio</em>. </p>
<p>To our surprise, the analysis also placed several Australian species traditionally belonging to the <em>Senecio</em> genus far outside of it, indicating they didn’t belong to <em>Senecio</em> at all and needed to be renamed.</p>
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<span class="caption">Simplified phylogenetic tree of the daisy tribe <em>Senecioneae</em> showing the evolutionary distance between Senecio, Cape ivy, and the new genus. Unlabelled branches indicate other lineages of the same tribe.</span>
<span class="attribution"><span class="source">Alexander Schmidt-Lebuhn</span>, <span class="license">Author provided</span></span>
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<p>The most interesting group of not-actually-<em>Senecio</em> are five species with leaf rosettes and one (or rarely, a few) flowerheads carried on distinctive stalks. </p>
<p>They’re all restricted to alpine or subalpine areas of south-eastern Australia, and all except one are found only in Tasmania. They turned out to be so unrelated, and so distinct from any other named plant genera, that they have to be recognised as a genus in its own right.</p>
<h2>Introducing <em>Scapisenecio</em></h2>
<p>We have now <a href="https://onlinelibrary.wiley.com/doi/10.1002/tax.12321">named</a> this new genus as <em>Scapisenecio</em>, after the long flower stalks (scapes) characterising the plants. </p>
<p>The most widespread and common species is <em><a href="https://bie.ala.org.au/species/https://id.biodiversity.org.au/node/apni/2920621">Scaposenecio pectinatus</a></em>, commonly known as the alpine groundsel, which is a familiar sight to hikers and bushwalkers in the Australian mainland alps and the central highlands of Tasmania. </p>
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<a href="https://images.theconversation.com/files/359927/original/file-20200925-18-d5xuyh.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Close-up of a single yellow daisy" src="https://images.theconversation.com/files/359927/original/file-20200925-18-d5xuyh.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/359927/original/file-20200925-18-d5xuyh.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/359927/original/file-20200925-18-d5xuyh.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/359927/original/file-20200925-18-d5xuyh.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/359927/original/file-20200925-18-d5xuyh.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/359927/original/file-20200925-18-d5xuyh.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/359927/original/file-20200925-18-d5xuyh.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>
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<span class="caption">Species belonging to this genus are a common sight to alpine hikers.</span>
<span class="attribution"><span class="source">Alexander Schmidt-Lebuhn</span>, <span class="license">Author provided</span></span>
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<p>Apart from the excitement of finding a previously undescribed, distinctive genus, these results were also directly relevant to the original purpose of our work: informing a plant list to test possible biocontrol agents. </p>
<p>The traditional misclassification of these species would have misled us about their true relationships. Our new genetic data now allow us to test biocontrol agents on an appropriate sample of species, to minimise risks to our native flora.</p>
<p>It is not often we find that a new, unexpected lineage of plants has existed all along, right in front of us.</p>
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<img src="https://counter.theconversation.com/content/139754/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Alexander Schmidt-Lebuhn receives funding from the Australian Department of Agriculture, Water, and the Environment. The project received grant funding from the Australian Government under the ‘Improving Your Local Parks and Environment’ program.</span></em></p><p class="fine-print"><em><span>Ben Gooden receives funding primarily from Commonwealth, state and local governments, and rural Research and Development Corporations.</span></em></p>This stroke of serendipity shows how much there is still to be learned about the natural history of Australia. Surely more surprises are out there waiting for us.Alexander Schmidt-Lebuhn, Research Scientist, CSIROBen Gooden, Plant ecologist, CSIROLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/730672017-02-26T16:58:55Z2017-02-26T16:58:55ZThe bushbaby family just got a new member. Here’s how we identified it<figure><img src="https://images.theconversation.com/files/157488/original/image-20170220-15931-7emet3.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><span class="source">hl_1001/Flickr</span></span></figcaption></figure><p>With their enormous eyes, impressive leaping skills and <a href="https://www.youtube.com/watch?v=SMgwBgQi_jk">strange cries</a>, galagids – more commonly known as bushbabies – are a familiar sight in sub-Saharan Africa. But there is still much we do not know about them. </p>
<p>The number of galagid species recognised today has more than tripled since the 1970s, from five to 18. The number of genera, or species groups, had risen from two to six. Now a seventh genus has been added, thanks to <a href="https://academic.oup.com/zoolinnean/article/2976136/A-new-genus-for-the-eastern-dwarf-galagos-Primates">research</a> conducted by my colleagues and I in the African Primate Initiative for Ecology and Speciation (<a href="http://www.ufh.ac.za/centres/apies/content/about-apies">APIES</a>) and our collaborators. </p>
<p>The detection of previously unknown diversity is always exciting. For starters, it has novelty value. It shows that we have, until now, underestimated the subtlety of natural variation. </p>
<p>But most importantly, newly recognised genetic populations carry their evolutionary history with them – and the history of their habitats. The detection of new species is important because it tells us about new populations with particular <a href="http://onlinelibrary.wiley.com/doi/10.1002/ajpa.23175/abstract">relationships to the environment</a>. A new genus provides more profound information about evolutionary history because it tells us about relationships among lineages that may reach deep into the past. </p>
<p>The emergence and extinction of species is closely linked to changes in earth’s environments and climates. So an accurate picture of the units of biodiversity is essential to understanding the nature of this interaction. This kind of information is crucial for forming conservation plans to defend vulnerable species against extinction – an increasingly urgent issue in the face of global climate change.</p>
<h2>Limited “clues” to true diversity</h2>
<p>Bushbabies (<a href="http://www.newworldencyclopedia.org/entry/Galago">Family Galagidae</a>) have only ever occurred in sub-Saharan Africa, where they have been evolving for at least 40 million years. They are nocturnal and relatively small; adult dwarf galagos weigh in at about 60g (the size of a large mouse) while the greater galagos can reach 1.5kg, the size of a cat.</p>
<p>Bushbabies are committed tree-dwellers although they may descend to the ground to feed or cross open areas. They have a number of adaptations that facilitate rapid and accurate movement through trees at night. These include their strong, grasping hands and feet, their elongated hind limbs and short forelimbs, and their large eyes fitted with mechanisms for accurate vision under low light intensities. </p>
<p>Understanding these animals’ true diversity is an ongoing task. This is because the bodies of different genera and species do not carry colourful flags or visual markers of identity, like many diurnal primates do. </p>
<p>For instance, most rain forest monkey species are distinguished by bright colour patterns on their faces and rumps that attract attention in gloomy forest. The lack of visually obvious markers in galagid species makes their recognition difficult to human observers – in the wild or even in museum collections. And true levels of genetic diversity may not be reflected in the animals’ external features. </p>
<p>The most reliable indicators of galagid species identity are the signals the animals use to communicate with one another at night. These include loud vocalisations and complex organic odours secreted by scent glands. The loud, repetitive call of the thick-tailed galago sounds like a baby crying, and has given rise to the common name “bushbaby”. Exploring these kinds of characteristics continues to inform us that our emphasis of visual differences has led us to underestimate biodiversity considerably.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/157497/original/image-20170220-15917-8x4s9c.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/157497/original/image-20170220-15917-8x4s9c.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/157497/original/image-20170220-15917-8x4s9c.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=397&fit=crop&dpr=1 600w, https://images.theconversation.com/files/157497/original/image-20170220-15917-8x4s9c.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=397&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/157497/original/image-20170220-15917-8x4s9c.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=397&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/157497/original/image-20170220-15917-8x4s9c.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=499&fit=crop&dpr=1 754w, https://images.theconversation.com/files/157497/original/image-20170220-15917-8x4s9c.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=499&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/157497/original/image-20170220-15917-8x4s9c.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=499&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">My, what big eyes you have!</span>
<span class="attribution"><span class="source">Reuters/Nikolay Doychinov</span></span>
</figcaption>
</figure>
<p>Seven “dwarf galago” species have been identified to date, distributed across western and eastern Africa. They’re found in rain forests, <a href="http://wwf.panda.org/what_we_do/where_we_work/borneo_forests/about_borneo_forests/ecosystems/montane_forests/">montane forests</a> or lowland forests. </p>
<p>Earlier models of bushbaby evolution viewed these small species as closely related and ancient, giving tacit credence to a commonly held view in mammal evolution: that members of a lineage start out small and get bigger over time. The discovery that these species are not ancient and closely related turns this idea on its head.</p>
<h2>What we uncovered</h2>
<p><a href="https://academic.oup.com/zoolinnean/article/2976136/A-new-genus-for-the-eastern-dwarf-galagos-Primates">Our study</a> used information from DNA sequences, field observations and recordings of vocal repertoires. We also studied hundreds of specimens in natural history museums around the world, taking detailed measurements of bushbaby skulls and teeth. </p>
<p>All of this work demonstrated unequivocally that the dwarf bushbabies of West and East Africa have not shared a common ancestor for at least 20 million years. That’s half of the evolutionary history of the family. The fact that the species resemble one another so closely is a testament to evolutionary conservatism: if the structure of the habitat does not change substantially, neither will the organisms inhabiting it. Evolution is as much about change as it is about stasis.</p>
<p>As part of our field research, we also identified eastern dwarf galagos within South Africa’s boundaries, although the this genus was previously thought to be restricted to the eastern tropics. We have named the new genus <em>Paragalago</em>; it is the close relative of the genus <em>Galago</em>, which includes the “nagapies” (literally “little night monkeys” in Afrikaans) that are found in South Africa’s northern woodland savannas, but is likely to have evolved much further north, in East Africa.</p>
<p>So what do the new studies tell us about the history of bushbabies and Africa? </p>
<p>First, we now know that small body size is not a sign of early evolution in bushbabies. Galago ancestors are unlikely to have been smaller than between 500g and 700g. Dwarfing is a common evolutionary response to unpredictable environmental conditions, reflecting Africa’s past climate change. </p>
<p>Using genetic dating techniques, we estimate that both the western and the eastern dwarf galago lineages emerged around 10 million years ago. This coincides with the beginning of the expansion of grassland savannas in Africa, long before the African Rift Valley sundered the continent. Grasslands replace forests when the climate becomes cooler and drier, causing the forests and their faunas to fragment into small, patchy populations unable to interbreed. </p>
<p>The divergence of the <em>Paragalago</em> lineage would have been a response to this habitat disruption. But many other organisms that did not adapt to the new circumstances would have gone extinct. Forests are the most vulnerable of African habitats to climate change. The crisis we are currently witnessing will be similarly destructive to those in the past, and the survivors are unlikely to be tree-dwelling animals.</p><img src="https://counter.theconversation.com/content/73067/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Judith Masters receives funding from the National Research Foundation of South Africa. She is a founder member of the Africa Earth Observatory Network at Nelson Mandela University.</span></em></p>Newly recognised genetic populations carry their evolutionary history with them, and the history of their habits. This is why detecting new species is so important.Judith Masters, Professor of Zoology at the University of Fort Hare, University of Fort HareLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/478402015-09-25T04:31:27Z2015-09-25T04:31:27ZHomo naledi: determining the age of fossils is not an exact science<figure><img src="https://images.theconversation.com/files/95463/original/image-20150920-11714-78ktva.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">The skull of Homo naledi is built like those of early Homo species but its brain was just more than half the size of the average ancestor from 2 million years ago. </span> <span class="attribution"><span class="source">SUPPLIED</span></span></figcaption></figure><p>Age is nothing but a number when it comes to unravelling the relationships of species from our past. We do not know the actual geological age of the <a href="http://www.wits.ac.za/homonaledi/">Dinaledi fossils</a>, the single largest fossil hominin find in Africa, but the discovery of <a href="http://voices.nationalgeographic.com/blog/rising-star-expedition/">Homo naledi</a> still provides insight into how our ancestors evolved. </p>
<p>The Dinaledi fossil collection is one of the most complete ever discovered, representing nearly the entire anatomy of a previously unknown species. Yet our team made no statement or conclusion about the fossils’ geological age. I reviewed with Ed Yong some of the <a href="http://www.theatlantic.com/science/archive/2015/09/why-dont-we-know-the-age-of-the-new-human-ancestor-homo-naledi/405148/">reasons</a> why it is difficult to determine the age of the fossils. </p>
<p>The bottom line is that, for now, we have little idea how old the fossils may be. </p>
<p>Most fossil hominins are found in association with extinct animals, which give us at least a general indication of their age. Famous fossil discoveries from more than a century ago, such as the Spy Neanderthal skeletons from Belgium and the first Homo erectus from Java, were found together with long-extinct creatures that indicated they were of great antiquity. This won’t work for Homo naledi because we have found no other animals in association with the hominin bones. </p>
<p>Even today, with methods that rely upon radioactive isotopes to determine the absolute ages of rock layers, geologists often have to revise their initial ideas of the ages of fossils. </p>
<p>Across the last 45 years, the age of the famous KNM-ER 1470 skull of Homo rudolfensis, from Koobi Fora, Kenya, has swung upward and down by more than a half million years as geologists revised age estimates of the famous KBS Tuff. The age of the Sterkfontein Member 4 fossils has been notoriously difficult to determine. Different teams have produced very different ages for the famous Little Foot skeleton from the Silberberg Grotto of Sterkfontein, ranging over more than a million years. </p>
<p>In other words, it pays to be cautious about geology. </p>
<h2>But how old is it?</h2>
<p>Our lack of a geological age for the fossils caught some other experts by surprise. Carol Ward, of the University of Missouri, <a href="http://www.theatlantic.com/science/archive/2015/09/homo-naledi-rising-star-cave-hominin/404362/">commented</a> to The Atlantic:</p>
<blockquote>
<p>“Without dates, the fossils reveal almost nothing about hominin evolution, beyond supporting the growing realisation that there was much more species diversity than previously thought.”</p>
</blockquote>
<p>William Jungers, from Stony Brook University, said in The <a href="http://www.theguardian.com/science/2015/sep/10/new-species-of-ancient-human-discovered-claim-scientist">Guardian</a>. </p>
<blockquote>
<p>“If they are as old as two million years, then they might be early South African versions of Homo erectus, a species already known from that region. If much more recent, they could be a relic species that persisted in isolation. In other words, they are more curiosities than game-changers for now.”</p>
</blockquote>
<p>Whether it turns out to be 20 000 years or 2 million years old, Homo naledi is equally distinct from Homo erectus either way. The age of the fossils is simply not relevant to their relationships with other hominins. In the study of anatomy, we focus on the shared features of different species, not their age. </p>
<p>Indeed, so-called relic species can be among the most important indicators of biological relationships, survivors that carry anatomical features from deep time. The coelacanth is much more than a curiosity: its anatomy provides vital clues that helped scientists understand how early land creatures could evolve from lobe-finned fish ancestors.</p>
<h2>How our ancestors evolved</h2>
<p>No matter its geological age, Homo naledi may provide vital clues about the way our ancestors stepped along a humanlike evolutionary path. This is where the real mystery comes in.</p>
<p>When we look across the skeleton of Homo naledi, we see some puzzling combinations of features. Homo naledi has a foot nearly the same as our own, much more humanlike than any early hominin we’ve discovered so far. Yet its hip and thighbone seem more primitive.</p>
<p>Likewise, Homo naledi had a hand and wrist that were largely humanlike, suitable for manipulating objects and possibly making tools. Yet powerful thumbs, curved finger bones and a shoulder canted upward like an ape’s shoulder suggest that its arms were used for climbing much more than any human today.</p>
<p>The skull of Homo naledi is built like those of early Homo species, especially Homo erectus, but its brain was just more than half the size of the average Homo erectus. Meanwhile, Homo naledi had teeth that were smaller than average for any early Homo species, a trait we have usually linked to eating better, more calorie-rich foods like meat or starchy tubers.</p>
<p>It’s almost as if Homo naledi evolved from the outside in. </p>
<figure class="align-right ">
<img alt="" src="https://images.theconversation.com/files/95560/original/image-20150921-31531-1530wz1.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/95560/original/image-20150921-31531-1530wz1.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=318&fit=crop&dpr=1 600w, https://images.theconversation.com/files/95560/original/image-20150921-31531-1530wz1.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=318&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/95560/original/image-20150921-31531-1530wz1.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=318&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/95560/original/image-20150921-31531-1530wz1.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=400&fit=crop&dpr=1 754w, https://images.theconversation.com/files/95560/original/image-20150921-31531-1530wz1.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=400&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/95560/original/image-20150921-31531-1530wz1.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=400&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Homo naledi skull DH3 compared with an example of Homo erectus from East Africa.</span>
<span class="attribution"><span class="source">SUPPLIED</span></span>
</figcaption>
</figure>
<p>The traits in direct contact with its environment, used for walking, handling things, and eating, are the most humanlike. The core of Homo naledi’s body, its brain, ribcage and hips, were more like our very distant relatives, the australopiths.</p>
<p>These combinations make it hard to be sure exactly where Homo naledi fits on our family tree. If we trust the humanlike foot and hand, and the Homo erectus-like cranial form, then Homo naledi looks like it may be closer to us than Homo habilis, the famous handy man. </p>
<p>Whether it is closer or not, Homo naledi’s features show that the key changes leading to our genus may have had nothing to do with a large brain. Testing this will bring us closer to understanding the causes that made us human. </p>
<p><em>John <a href="http://johnhawks.net">Hawks</a> is a core scientist on the Rising Star Expedition team and co-author on the papers describing Homo naledi.</em></p><img src="https://counter.theconversation.com/content/47840/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>John Hawks 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>Despite claims about its age, puzzling combinations of features from Homo naledi gives it an uncanny resemblance to human beings.John Hawks, Paleoanthropologist, University of Wisconsin-MadisonLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/443672015-07-08T04:21:12Z2015-07-08T04:21:12ZUnraveling the mystery of how dinosaurs get their names<figure><img src="https://images.theconversation.com/files/87667/original/image-20150707-1291-1jeh74b.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">What's in a name? Plenty, if it is a dinosaur such as the Changyuraptor, a genus of the 'four-winged' predatory dinosaur.</span> <span class="attribution"><span class="source">S. Abramowicz, Dinosaur Institute</span></span></figcaption></figure><p>Many kids can recite an A-Z list of dinosaur names. They take special delight in defeating tongue-twisters like <em>Carcharodontosaurus</em>, <em>Ekrixinatosaurus</em>, <em>Huehuecanauhtlus</em> and <em>Zuchengtyrannus</em>. </p>
<p><a href="http://www.nhm.ac.uk/nature-online/science-of-natural-history/biographies/richard-owen/">Sir Richard Owen</a> came up with the name <a href="http://wonderopolis.org/wonder/how-do-dinosaurs-get-their-names/">dinosaur</a> in 1841 to describe the fossils of extinct reptiles. He coined the word by combining the Greek words “deinos”, which means terrible, and “sauros”, which means lizard.</p>
<h2>What lies behind a name</h2>
<p>A dinosaur’s name says something about the dinosaur itself. Scientists often use Greek or Latin root words to give a name that describes the dinosaur in some way.</p>
<p>Dinosaurs, like all living organisms, are classified or grouped together according to similarities they share, which also indicates their ancestral relationships to one another. To do this objectively, scientists apply cladistics, a <a href="http://www.enchantedlearning.com/subjects/dinosaurs/dinoclassification/Classification.html">methodology</a> that enables the assessment of relationships of organisms to one another based on shared characteristics. </p>
<p>According to the classification system, there are always two parts to a dinosaur’s name – or any living organism for that matter – and they should both be italicised. The first part of the name is called the genus name and the second the species name. </p>
<p>There can be several different species (varieties) of a particular genus of an animal. For example, humans are <em>Homo sapiens</em>, but in the fossil record there are several other members of the genus <em>Homo</em> for example <em>Homo neanderthalensis,</em> and <em>Homo erectus</em> .</p>
<p>Before it can become official, and to prevent duplication, once palaeontologists have chosen a new name it has to be approved by the <a href="http://iczn.org/content/about-iczn">International Commission on Zoological Nomenclature</a>. Palaeontologists must also fully describe the anatomy of the dinosaur and explain the cladistic analyses and the derivation of the name in a peer-reviewed academic journal. </p>
<h2>Who gets to have a dinosaur named after them</h2>
<p>Only a few palaeontologists ever have the opportunity of naming a dinosaur, and even fewer have species named after them. Paleontologists get to name a dinosaur if they, or an expedition team, finds an animal that is distinct from any others known.</p>
<p>Occasionally the remains of a dinosaur may have been excavated a long time ago, but subsequent investigations reveal that it is in fact a new dinosaur. This is the case of <em>Sefapanosaurus zastronensis</em>, South Africa’s most recently named dinosaur which was excavated more than 80 years ago close to Zastron, a small town near South Africa’s border with Lesotho. At the time it was collected it was unnamed. Later scientists studied the bones cursorily and considered them to be like that of another early dinosaur called <em>Aardonyx</em> . </p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/87651/original/image-20150707-1311-1rtmt6z.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/87651/original/image-20150707-1311-1rtmt6z.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=231&fit=crop&dpr=1 600w, https://images.theconversation.com/files/87651/original/image-20150707-1311-1rtmt6z.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=231&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/87651/original/image-20150707-1311-1rtmt6z.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=231&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/87651/original/image-20150707-1311-1rtmt6z.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=291&fit=crop&dpr=1 754w, https://images.theconversation.com/files/87651/original/image-20150707-1311-1rtmt6z.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=291&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/87651/original/image-20150707-1311-1rtmt6z.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=291&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Meet South Africa’s most recently named dinosaur, Sefapanosaurus zastronensis, which was excavated more than 80 years ago close to Zastron.</span>
<span class="attribution"><span class="source">Alejandro Otera</span></span>
</figcaption>
</figure>
<p>But the material was recently re-examined and found to be quite unlike any of the known contemporary dinosaurs.</p>
<p>Given that its ankle bone had a very unusual cross shape we decided to <a href="http://onlinelibrary.wiley.com/doi/10.1111/zoj.12247/full">name</a> the dinosaur after this feature and to give it a Sesotho name, since this is the language prevalent in the area. Thus <em>Sefapanosaurus</em> is derived from “sefapano” which means “cross” in Sesotho and “saurus” which is Greek for “lizard”. The second part is derived from Zastron. </p>
<p>Like <em>Sefapnosaurus</em>, many dinosaurs are named for particular features in their skeletons. For example, last year, I was fortunate to be part of the team that <a href="http://mg.co.za/article/2014-07-15-winged-changyuraptor-adds-feather-to-sa-scientists-cap">named</a> a rare four-winged, long-tailed dinosaur from northeastern China, <em>Changuraptor</em>. “Changu” means “long feather” in Chinese, and “raptor” refers to its predatory habits. The second part of the name honours Yang Yandong, chairman of Bohai University, who provided funding to obtain the specimen.</p>
<p>There is a curious story about a Southern African predatory dinosaur called <em>Syntarsus</em>. Thirty-two years after it was named entomologist realised that the name was already given to a beetle in 1869 and they renamed the dinosaur, much to our dismay, <em>Megapnosaurus</em>, which means “big dead lizard”.</p>
<p>Another South African dinosaur, which we <a href="http://www.uct.ac.za/dailynews/?id=7177">named</a> in 2010, is <em>Aardonyx celestae</em>. This dinosaur’s name has its roots in Afrikaans (“aard” means earth) and Greek (“onyx” means claw), and refers to the fact that the animal had thick iron rich sediments, or hematite, surrounding many of its foot bones. The second part of the <em>Aardonyx</em> name pays tribute to Celeste Yates, who as a volunteer did the laborious, painstaking preparation of the fossils by removing the surrounding rock matrix in which they were embedded.</p>
<p>Ten years ago I was also part of the team that <a href="http://www.bioone.org/doi/abs/10.1671/0272-4634(2000">named</a> <em>Nqwebasaurus thwazi</em>, the first isi-Xhosa-named dinosaur. This dinosaur was discovered from the Kirkwood cliffs near Grahamstown in the Eastern Cape by my colleagues, Billy De Klerk from the Albany Museum and Callum Ross from the US. In isi-Xhosa, the Kirkwood region is known as “Nqweba”. “Thwazi” means fast-runner.</p>
<p>I have also had the privilege of being on the team that <a href="http://www.bioone.org/doi/abs/10.1080/02724634.2013.762708">named</a> <em>Zhouornis hani</em>, a large Mesozoic bird from China. In this case, the early bird is named after Zhou Zhonghe, a Chinese palaeontologist who has made a huge contribution to studies about the early evolution of birds. The species name honours the collector of the specimen, Lizhuo Han.</p>
<p>All dinosaur names have a particular meaning. It is fascinating to understand the derivation of their names, and to learn of the sometimes quirky stories behind them.</p><img src="https://counter.theconversation.com/content/44367/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Anusuya Chinsamy-Turan receives funding from the National Research Foundation.</span></em></p>A dinosaur’s name says something about the dinosaur itself. They are grouped together according to similarities they share, which also indicates their ancestral relationships to one another.Anusuya Chinsamy-Turan, Professor, Head, Biological Sciences Department, University of Cape TownLicensed as Creative Commons – attribution, no derivatives.