tag:theconversation.com,2011:/id/topics/phylogenetic-analysis-8006/articlesPhylogenetic analysis – The Conversation2023-06-05T20:03:48Ztag:theconversation.com,2011:article/2069882023-06-05T20:03:48Z2023-06-05T20:03:48ZThe world’s first flowers were pollinated by insects<figure><img src="https://images.theconversation.com/files/529932/original/file-20230604-129052-ofkmgy.jpeg?ixlib=rb-1.1.0&rect=850%2C1047%2C2161%2C1706&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><span class="source">Ruby E Stephens</span>, <span class="license">Author provided</span></span></figcaption></figure><p>Plants existed on Earth for hundreds of millions of years before the first flowers bloomed. But when flowering plants did evolve, more than 140 million years ago, they were a huge evolutionary success.</p>
<p>What pollinated these first flowering plants, the ancestor of all the flowers we see today? Was it insects carrying pollen between those early flowers, fertilising them in the process? Or perhaps other animals, or even wind or water?</p>
<p>The question has been a tricky one to answer. However, in <a href="https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.18993">new research</a> published in New Phytologist, we show the first pollinators were most likely insects. </p>
<p>What’s more, despite some evolutionary detours, around 86% of all flowering plant species throughout history have also relied on insects for pollination.</p>
<h2>How to move pollen</h2>
<p>The timing of the evolution of the first flowering plants is still <a href="https://doi.org/10.1093/jxb/erac130">a matter of debate</a>. However, their success is inarguable.</p>
<p>Around 90% of modern plants – some 300,000-400,000 species – are flowering plants, or what scientists call angiosperms. To reproduce, these plants make pollen in their flowers, which needs to be transferred to another flower to fertilise an ovule and produce a viable seed. </p>
<p>Small and highly mobile, insects can be highly effective pollen transporters. Indeed, recent <a href="http://doi.org/10.1016/j.tree.2023.03.008">research on fossil insects</a> shows some insects may have been pollinating plants even before the first flowers evolved.</p>
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<img alt="" src="https://images.theconversation.com/files/529933/original/file-20230604-25-bz6uu0.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/529933/original/file-20230604-25-bz6uu0.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=196&fit=crop&dpr=1 600w, https://images.theconversation.com/files/529933/original/file-20230604-25-bz6uu0.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=196&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/529933/original/file-20230604-25-bz6uu0.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=196&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/529933/original/file-20230604-25-bz6uu0.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=246&fit=crop&dpr=1 754w, https://images.theconversation.com/files/529933/original/file-20230604-25-bz6uu0.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=246&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/529933/original/file-20230604-25-bz6uu0.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=246&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Flowers have evolved every sort of shape and colour to get themselves pollinated.</span>
<span class="attribution"><span class="source">Ruby E Stephens</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>Most of today’s flowering plants rely on insects for pollination. The plant’s flowers have evolved to attract insects via colour, scent and even sexual mimicry, and most reward them with nectar, pollen, oils or other types of food, making the relationship beneficial to both parties.</p>
<p>Some flowers, however, rely on other means to transport their pollen, such as vertebrate animals, wind or even water. </p>
<p>Which kind of pollination evolved first? Were insects there at the beginning, or were they a later “discovery”? </p>
<p>While <a href="https://doi.org/10.1073/pnas.0707989105">early evidence</a> suggests it was probably insects, until now this has never been tested across the full diversity of flowering plants – their full evolutionary tree.</p>
<h2>A family tree</h2>
<p>To find an answer, we used a “<a href="https://doi.org/10.1038/s41559-020-1241-3">family tree</a>” of all families of flowering plants, sampling more than 1,160 species and reaching back more than 145 million years.</p>
<p>This tree shows us when different plant families evolved. We used it to map backwards from what pollinates a plant in the present to what might have pollinated the ancestor of that plant in the past.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/529930/original/file-20230604-80115-8wjczk.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/529930/original/file-20230604-80115-8wjczk.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/529930/original/file-20230604-80115-8wjczk.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=597&fit=crop&dpr=1 600w, https://images.theconversation.com/files/529930/original/file-20230604-80115-8wjczk.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=597&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/529930/original/file-20230604-80115-8wjczk.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=597&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/529930/original/file-20230604-80115-8wjczk.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=750&fit=crop&dpr=1 754w, https://images.theconversation.com/files/529930/original/file-20230604-80115-8wjczk.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=750&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/529930/original/file-20230604-80115-8wjczk.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=750&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 evolutionary tree for all flowering plant families shows when wind, water and vertebrate pollination evolved from insect pollination.</span>
<span class="attribution"><span class="source">Ruby E Stephens</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>We found insect pollination has been overwhelmingly the most common method over the history of flowering plants, occurring around 86% of the time. And our models suggest the first flowers were most likely pollinated by insects. </p>
<h2>Birds, bats and wind</h2>
<p>We also learned about the evolution of other forms of pollination. Pollination by vertebrate animals, such as birds and bats, small mammals and <a href="https://doi.org/10.1086/593050">even lizards</a>, has evolved at least 39 times – and reverted back to insect pollination at least 26 of those times.</p>
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<a href="https://images.theconversation.com/files/529929/original/file-20230604-15-o6v4bp.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="A microscope photo showing tiny grass flowers." src="https://images.theconversation.com/files/529929/original/file-20230604-15-o6v4bp.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/529929/original/file-20230604-15-o6v4bp.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=563&fit=crop&dpr=1 600w, https://images.theconversation.com/files/529929/original/file-20230604-15-o6v4bp.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=563&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/529929/original/file-20230604-15-o6v4bp.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=563&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/529929/original/file-20230604-15-o6v4bp.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=708&fit=crop&dpr=1 754w, https://images.theconversation.com/files/529929/original/file-20230604-15-o6v4bp.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=708&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/529929/original/file-20230604-15-o6v4bp.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=708&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Wind pollinated flowers are often very small and plain, like these grass flowers which can only be seen clearly under a microscope.</span>
<span class="attribution"><span class="source">Ruby E Stephens</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>Wind pollination has evolved even more often: we found 42 instances. These plants rarely go back to insect pollination.</p>
<p>We also found wind pollination evolved more often in open habitats, at higher latitudes. Animal pollination is more common in closed-canopy rainforests, near the equator.</p>
<h2>What kind of insects were the first pollinators?</h2>
<p>If you think of a pollinating insect, you probably imagine a bee. But while we don’t know exactly what insects pollinated the first flowering plants, we can be confident they weren’t bees.</p>
<p>Why not? Because most evidence we have indicates bees didn’t evolve until <a href="https://doi.org/10.1016/j.tplants.2022.04.004">after the first flowers</a>.</p>
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Read more:
<a href="https://theconversation.com/flies-like-yellow-bees-like-blue-how-flower-colours-cater-to-the-taste-of-pollinating-insects-167111">Flies like yellow, bees like blue: how flower colours cater to the taste of pollinating insects</a>
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<p>So what do we know about the pollinators of the first flowering plants? Well, some early flowers have been preserved as fossils – and most of these are very small.</p>
<p>The first flower pollinators must have been quite small, too, to poke around in these flowers. The most likely culprits are some kind of small fly or beetle, maybe even a midge, or some extinct types of insects that have long disappeared.</p>
<p>If only we had a time machine we could go back and see these pollinators in action - but that will require a lot more research!</p><img src="https://counter.theconversation.com/content/206988/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Ruby E. Stephens receives funding from the Australian Government's Research Training Program. </span></em></p><p class="fine-print"><em><span>Hervé Sauquet receives funding from the Australian Research Council and Australian Research Data Commons. </span></em></p><p class="fine-print"><em><span>Lily Dun received funding from Australian Research Data Commons. </span></em></p><p class="fine-print"><em><span>Rachael Gallagher receives funding from The Australian Research Council. </span></em></p><p class="fine-print"><em><span>Will Cornwell 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>New research suggests insects have pollinated flowers since the pollen-bearing blooms first evolved more than 140 million years ago.Ruby E. Stephens, PhD Candidate, School of Natural Sciences, Macquarie UniversityHervé Sauquet, Senior Research Scientist, Royal Botanic Gardens Sydney and Adjunct Associate Professor, UNSW SydneyLily Dun, Research Assistant, UNSW SydneyRachael Gallagher, Associate Professor, Hawkesbury Institute for the Environment, Western Sydney UniversityWill Cornwell, Associate Professor in Ecology and Evolution, UNSW SydneyLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1123622019-02-28T16:01:08Z2019-02-28T16:01:08Z‘Micro snails’ we scraped from sidewalk cracks help unlock details of ancient earth’s biological evolution<figure><img src="https://images.theconversation.com/files/261353/original/file-20190228-150705-1y0ui0k.jpg?ixlib=rb-1.1.0&rect=0%2C12%2C1357%2C905&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">A live _Padaungiella lageniformis_ wiggles its pseudopods.</span> <span class="attribution"><span class="source">Daniel J. G. Lahr</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span></figcaption></figure><p>Every step you take, you’re likely walking on a world of unseen and undescribed microbial diversity. And you don’t need to head out into nature to find these usually unnoticed microscopic organisms.</p>
<p><a href="https://scholar.google.com/citations?user=UvN4AQsdfygC&hl=en&oi=sra">As</a> <a href="https://scholar.google.com/citations?user=rBfI91QAAAAJ&hl=en&oi=ao">biologists</a>, we know this firsthand. A meetup for coffee several years ago ended with our using makeshift sampling tools – actually a coffee stirrer and a coffee cup lid – to collect some of the black gunk from between the sidewalk’s concrete slabs. In this mundane space on the Mississippi State University campus, we discovered microbes that have lived on Earth for millions of years.</p>
<p>Finding these charismatic organisms in the environment, while exciting, is just the first step. Our mutual interest is to better understand how organisms are related to one another. We’re using DNA to reveal their relationships in the very distant past.</p>
<p>By sampling organisms that are alive today, we can <a href="https://doi.org/10.1016/j.cub.2019.01.078">ask deeper questions</a> about the evolution that happened millions of years ago in now extinct ancestors.</p>
<h2>Piecing together the tree of life</h2>
<p>Our simple act of collection after our 2015 coffee date started a fruitful collaboration <a href="http://mwb250.biology.msstate.edu">between</a> <a href="http://www.ib.usp.br/zoologia/lahr/index.php">our labs</a> in the field of molecular protistology. Our focus is on the microscopic single-celled organisms called protists, particularly ones that move around using tiny tentacles called pseudopodia. </p>
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<a href="https://images.theconversation.com/files/261251/original/file-20190227-150708-1noh5wh.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/261251/original/file-20190227-150708-1noh5wh.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/261251/original/file-20190227-150708-1noh5wh.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=508&fit=crop&dpr=1 600w, https://images.theconversation.com/files/261251/original/file-20190227-150708-1noh5wh.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=508&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/261251/original/file-20190227-150708-1noh5wh.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=508&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/261251/original/file-20190227-150708-1noh5wh.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=638&fit=crop&dpr=1 754w, https://images.theconversation.com/files/261251/original/file-20190227-150708-1noh5wh.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=638&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/261251/original/file-20190227-150708-1noh5wh.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=638&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>Amphizonella</em> – identified in the authors’ sidewalk sample – has a soft protective layer.</span>
<span class="attribution"><span class="source">Matthew W. Brown</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>One elusive critter we identified in our sidewalk sample is an amoeba named <em>Amphizonella</em>; we joke that it makes its own “leather jacket” in the form of a soft, protective outer layer.</p>
<p>Despite what other scientists had previously thought, we had a hunch that this organism <a href="https://doi.org/10.1093/molbev/msx162">wasn’t closely related to other amoebae</a> that have tougher outer coverings. This other much larger group, called testate amoebae, have shells – imagine microscopic snails – instead of leather jackets.</p>
<p><iframe id="tc-infographic-375" class="tc-infographic" height="400px" src="https://cdn.theconversation.com/infographics/375/92aaf90fccdec0dd5fd69fddaabd8e0fd99de6ae/site/index.html" width="100%" style="border: none" frameborder="0"></iframe></p>
<p>Because testate amoebae make a hard shell, they have the potential to fossilize. In fact, their vivid fossil record represents <a href="https://doi.org/10.1017/S1089332600002321">some of the oldest unequivocal fossils of eukaryotes</a> – the category of life whose members hold their DNA within their cells’ nuclei. Why is this important? Human beings are also eukaryotes, as are <a href="https://doi.org/10.1111/jeu.12691">plants, fungi, other animals, kelps and protists</a>. Because these amoebae are some of the oldest eukaryotic fossils, they can in turn tell researchers like us something about our own species’ origins. </p>
<p>Since the advent of DNA sequencing in the early 2000s, biologists have used a small piece of the genome, even a single gene, to examine the relationships between organisms, though with limited success. Through similarity of DNA sequences between living organisms, one can infer relationships using complex computational approaches that model evolution change over time from empirically derived data. Simply put, scientists try to piece together who’s related to whom in order to reconstruct the evolutionary tree of life, or what we call a phylogenetic tree.</p>
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<iframe width="440" height="260" src="https://www.youtube.com/embed/pBSJMwIUVcg?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">The first step of single-cell transcriptomics is isolating a single organism. Here, a micropipette picks up one <em>Amphizonella</em> cell. Credit: Matthew W. Brown.</span></figcaption>
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<p>In most cases the testate amoebae are quite difficult to cultivate in the laboratory, making it very hard to obtain enough material to sequence their DNA with the usual methods.</p>
<p>To overcome these challenges, we’re using a cutting-edge technique that allows us to take an organism directly from the environment and sequence its entire transcriptome – that’s the blueprint of all the proteins that it makes. This way, we’re able to bypass sequencing the whole genome (with its extraneous information) and sequence only the protein-coding regions. We end up with high-quality data of billions of base pairs of DNA that we can directly compare with similar data from other organisms.</p>
<p>This method provides better resolution by sampling hundreds of genes, rather than a single one. Then we use the data to build a phylogenetic tree of life that organizes our amoebae by how closely related they are to each other based on the similarity of their DNA. With these data, we can go further and compare our testate amoebae to other eukaryotes and identify what makes them unique and similar at a genomic level.</p>
<h2>Connecting today’s life to ancient ancestors</h2>
<p>Because life evolved over billions of years <a href="https://doi.org/10.1038/nature09014">from a last universal common ancestor</a>, all organisms, both living and extinct, must be related to each other in a single family tree.</p>
<p>But fossils don’t preserve DNA information. While it’s true that some ancient DNA sequencing is possible, in general it’s only been done with frozen samples like the <a href="https://www.bbc.com/news/science-environment-32432693">woolly mammoth</a> or ancient human beings like <a href="https://www.nytimes.com/2010/12/23/science/23ancestor.html">mummified remains</a>. These ancient DNA samples have not really fossilized, and in comparison to fossils, they’re significantly more recent – for instance, the oldest human-related DNA to have been sequenced was from a <a href="https://www.nytimes.com/2010/12/23/science/23ancestor.html">Denisovan person’s tooth</a>, which is about 110,000 years old.</p>
<p>In contrast, the fossil of <em>Archaeopteryx</em>, one of the most ancient <a href="https://www.washingtonpost.com/news/speaking-of-science/wp/2018/03/13/this-feathery-dinosaur-probably-flew-but-not-like-any-bird-you-know/?noredirect=on&utm_term=.6e348130bf40">relatives of birds</a>, is about 150 million years old. That means that, today, we are about 100,000 times more distant to <em>Archaeopteryx</em> than we are to the Denisovan remains. That’s an immense amount of time.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/261328/original/file-20190227-150721-5afk32.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/261328/original/file-20190227-150721-5afk32.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/261328/original/file-20190227-150721-5afk32.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/261328/original/file-20190227-150721-5afk32.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/261328/original/file-20190227-150721-5afk32.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/261328/original/file-20190227-150721-5afk32.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/261328/original/file-20190227-150721-5afk32.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/261328/original/file-20190227-150721-5afk32.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">A scanning electron micrograph of a fossilized <em>Ciclocyrillium torquata</em>, sampled from the Urucum formation in central Brazil.</span>
<span class="attribution"><span class="source">Luana Morais</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>The <a href="https://doi.org/10.1016/j.cub.2019.01.078">fossils that seem to relate to today’s testate amoebae</a> are about 750 million years old, from a time period called the <a href="https://en.wikipedia.org/wiki/Neoproterozoic">Neoproterozoic</a>. Scientists know very little about what was happening on Earth in that very distant past. Researchers have identified these tiny fossils in rocks collected in the Grand Canyon and central Brazil.</p>
<p>In order to compare the tree we created based on DNA from living species with the fossilized shells of the Neoproterozoic, we had to somehow extrapolate our data. Using the rates of evolution calculated in our tree, we were able to apply these rates using how the shells look today, to estimate what they might have looked in the past. This way, we can create a hypothetical ancestor that we can then compare to the actual fossils.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/261048/original/file-20190226-150728-ay7r0a.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/261048/original/file-20190226-150728-ay7r0a.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/261048/original/file-20190226-150728-ay7r0a.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=542&fit=crop&dpr=1 600w, https://images.theconversation.com/files/261048/original/file-20190226-150728-ay7r0a.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=542&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/261048/original/file-20190226-150728-ay7r0a.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=542&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/261048/original/file-20190226-150728-ay7r0a.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=681&fit=crop&dpr=1 754w, https://images.theconversation.com/files/261048/original/file-20190226-150728-ay7r0a.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=681&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/261048/original/file-20190226-150728-ay7r0a.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=681&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 family tree of testate amoebae linking the fossil record (left) to present day testate amoebae (right).</span>
<span class="attribution"><span class="source">Lahr et al. 2019, Current Biology https://doi.org/10.1016/j.cub.2019.01.078.</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>Our results were impressive. We calculated seven hypothetical ancestors based on a few million possibilities. When we compared them to the fossil record, previously described in the literature, we found five fossil species that were <a href="https://doi.org/10.1016/j.cub.2019.01.078">incredibly similar to our predictions</a>. This allowed us to confidently determine that those Neoproterozoic fossils are indeed very ancient testate amoebae, and that this group has been around since before 750 million years ago. And even by then, they had already considerably diversified. </p>
<p>Showing that these creatures were around and diverse at such deep time scales is important because they’re complex organisms, with complex ecologies and behaviors. They provide an inside look into what life might have been like in those ancient eras. The amoebae can be predators, but they can also be grazers, or even harbor symbiotic algae that produce their food, making them primary producers. </p>
<p>The fact that many diverse types of testate amoebae were around by this stage implies that complex food webs had already developed, which in turn has implications for what the environment might have been like. Now, geochemists will compare their notes to our biological insights, and our understanding of ancient earth will continue to improve.</p><img src="https://counter.theconversation.com/content/112362/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Matthew Brown receives funding from National Science Foundation (Division of Environmental Biology: Award #1456054) and Texas EcoLab. </span></em></p><p class="fine-print"><em><span>Daniel Lahr receives funding from Fundação de Amparo a Pesquisa do Estado de São Paulo, FAPESP grant #2013/04585-3. </span></em></p>Using the family relationships between single-celled protists alive today, researchers hypothesized what their evolutionary ancestors looked like – and then looked in the fossil record for matches.Matthew Brown, Assistant Professor of Biological Sciences, Mississippi State UniversityDaniel Lahr, Assistant Professor of Zoology, Universidade de São Paulo (USP)Licensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/889472017-12-11T19:13:38Z2017-12-11T19:13:38ZTasmanian tigers were going extinct before we pushed them over the edge<figure><img src="https://images.theconversation.com/files/198462/original/file-20171211-27686-lrmoci.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Gone since 1936, and ailing since long before that.</span> <span class="attribution"><span class="source">Tasmanian Museum and Art Gallery</span>, <span class="license">Author provided</span></span></figcaption></figure><p>There’s no doubt that humans killed off the <a href="https://australianmuseum.net.au/the-thylacine">Tasmanian tiger</a>. But a new genetic analysis suggests this species had been on the decline for millennia before humans arrived to drive them to extinction.</p>
<p>The Tasmanian tiger, also known as the thylacine, was unique. It was the largest marsupial predator that survived into recent times. Sadly it was hunted to extinction in the wild, and the last known Tasmanian tiger died in captivity in 1936.</p>
<p>In a <a href="http://nature.com/articles/doi:10.1038/s41559-017-0417-y">paper published in Nature Ecology and Evolution today</a>, my colleagues and I piece together its entire genetic sequence for the first time. It tells us that thylacines’ genetic health had been declining for many millennia before they first encountered human hunters.</p>
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<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/will-we-hunt-dingoes-to-the-brink-like-the-tasmanian-tiger-19982">Will we hunt dingoes to the brink like the Tasmanian tiger?</a>
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</em>
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<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/198466/original/file-20171211-27693-1jgss5o.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/198466/original/file-20171211-27693-1jgss5o.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/198466/original/file-20171211-27693-1jgss5o.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=738&fit=crop&dpr=1 600w, https://images.theconversation.com/files/198466/original/file-20171211-27693-1jgss5o.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=738&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/198466/original/file-20171211-27693-1jgss5o.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=738&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/198466/original/file-20171211-27693-1jgss5o.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=927&fit=crop&dpr=1 754w, https://images.theconversation.com/files/198466/original/file-20171211-27693-1jgss5o.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=927&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/198466/original/file-20171211-27693-1jgss5o.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=927&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Hounded by hunters.</span>
<span class="attribution"><span class="source">Tasmanian Museum and Art Gallery</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>Our research also offered the chance to study the origins of the similarity in body shape between the thylacine and dogs. The two are almost identical, despite having last shared a common ancestor more than 160 million years ago – a remarkable example of so-called “convergent evolution”. </p>
<p>Decoding the thylacine genome allowed us to ask the question: if two animals develop an identical body shape, do they also show identical changes in their DNA?</p>
<h2>Thylacine secrets</h2>
<p>These questions were previously difficult to answer. The age and storage conditions of existing specimens meant that most thylacine specimens have DNA that is highly fragmented into very short segments, which are not suitable for piecing together the entire genome.</p>
<p>We identified a 109-year-old specimen of a young pouch thylacine in the Museums Victoria collection, which had much more intact DNA than other specimens. This gave us enough pieces to put together the entire jigsaw of its genetic makeup.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/198463/original/file-20171211-27708-kte384.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/198463/original/file-20171211-27708-kte384.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/198463/original/file-20171211-27708-kte384.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=747&fit=crop&dpr=1 600w, https://images.theconversation.com/files/198463/original/file-20171211-27708-kte384.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=747&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/198463/original/file-20171211-27708-kte384.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=747&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/198463/original/file-20171211-27708-kte384.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=939&fit=crop&dpr=1 754w, https://images.theconversation.com/files/198463/original/file-20171211-27708-kte384.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=939&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/198463/original/file-20171211-27708-kte384.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=939&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 preserved young, thylacine with enough DNA to reveal its whole genome.</span>
<span class="attribution"><span class="source">Museums Victoria</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>Next, we made a detailed comparison of thylacines and dogs to see just how similar they really are. We used digital imaging to compare the thylacine’s skull shape to many other mammals, and found that the thylacine was indeed very similar to various types of dog (especially the wolf and red fox), and quite different from its closest living marsupial relatives such as the numbat, Tasmanian devil, and kangaroos. </p>
<p>Our results confirmed that thylacines and dogs really are the best example of convergent evolution between two distantly related mammal species ever described.</p>
<p>We next asked whether this similarity in body form is reflected by similarity in the genes. To do this, we compared the DNA sequences of thylacine genes with those of dogs and other animals too. </p>
<p>While we found many similarities between thylacines’ and dogs’ genes, they were not significantly more similar than the same genes from other animals with different body shapes, such as Tasmanian devils and cows.</p>
<p>We therefore concluded that whatever the reason why thylacines and dogs’ skulls are so similarly shaped, it is not because evolution is driving their gene sequences to be the same. </p>
<h2>Family ties</h2>
<p>The thylacine genome also allowed us to deduce its precise position in the marsupial family tree, which has been a controversial topic.</p>
<p>Our analyses showed that the thylacine was at the root of a group called the Dasyuromorphia, which also includes the <a href="http://www.environment.gov.au/cgi-bin/sprat/public/publicspecies.pl?taxon_id=294">numbat</a> and <a href="http://www.parks.tas.gov.au/?base=387">Tasmanian devil</a>. </p>
<p>By examining the amount of diversity present in the single thylacine genome, we were able to estimate its effective population size during past millennia. This demographic analysis revealed extremely low genetic diversity, suggesting that if we hadn’t hunted them into extinction the population would be in very poor genetic health, just like today’s Tasmanian devils.</p>
<p>The less diversity you have in your genome, the more susceptible you are to disease, which might be why devils have contracted the facial tumour virus, and certainly why it has been so easily spread. The thylacine would have been at a similar risk of contracting devastating diseases.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/198465/original/file-20171211-27698-1sg40zd.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/198465/original/file-20171211-27698-1sg40zd.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/198465/original/file-20171211-27698-1sg40zd.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=375&fit=crop&dpr=1 600w, https://images.theconversation.com/files/198465/original/file-20171211-27698-1sg40zd.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=375&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/198465/original/file-20171211-27698-1sg40zd.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=375&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/198465/original/file-20171211-27698-1sg40zd.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=471&fit=crop&dpr=1 754w, https://images.theconversation.com/files/198465/original/file-20171211-27698-1sg40zd.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=471&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/198465/original/file-20171211-27698-1sg40zd.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=471&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">The last thylacine alive.</span>
<span class="attribution"><span class="source">Tasmanian Museum and Art Gallery</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>This loss in population diversity was previously thought to have occurred as a population of thylacines (and devils) became isolated on Tasmania some 15,000 years ago, when the land bridge closed between it and the mainland. </p>
<p>But our analysis suggests that the process actually began much earlier – between 70,000 and 120,000 years ago. This suggests that both the devil and thylacine populations already had very poor genetic health long before the land bridge closed.</p>
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<em>
<strong>
Read more:
<a href="https://theconversation.com/how-curiosity-can-save-species-from-extinction-52006">How curiosity can save species from extinction</a>
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</em>
</p>
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<p>Now that we know the whole genome of the Tasmanian tiger, we know much more about this extinct animal and the unique place it held in Australia’s marsupial family tree. We are expanding our analyses of the genome to determine how it came to look so similar to the dog, and to continue to learn more about the genetics of this unique marsupial apex predator.</p><img src="https://counter.theconversation.com/content/88947/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Andrew Pask receives funding from Australian Research Council (ARC), National Health and Medical Research Council (NHMRC), The University of Melbourne. </span></em></p>The new Tasmanian tiger genome reveals some fascinating facts about this extinct marsupial, including why they were so similar to dogs, and how they were growing more vulnerable to genetic disease.Andrew Pask, Associate Professor, The University of MelbourneLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/756612017-04-06T18:01:54Z2017-04-06T18:01:54ZAre viruses alive? Giant discovery suggests they’re more like zombies<figure><img src="https://images.theconversation.com/files/164285/original/image-20170406-16660-7dyfvt.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption"></span> <span class="attribution"><span class="source">Shutterstock</span></span></figcaption></figure><p>What the hell is that? Scientists ask this question every day when trying to work out how different living things are related to each other. The answers aren’t easy or trivial. Biological affiliations are used not just to build a catalogue of life but also to understand how life has evolved into its many forms.</p>
<p><a href="https://theconversation.com/explainer-what-is-a-virus-22902">Viruses are</a> an excellent example. They pose a problem for biologists because they don’t have cells and so don’t fall into any of the main three groups or “domains” of life that all other organisms do – bacteria, archaea (a different form of microbe) and eukaryota (plants, animals and fungi, among others). Some scientists argue that viruses don’t count as living organisms and are better seen as rogue genetic material that can’t reproduce on their own and need to hijack host cells. Others believe viruses evolved from cellular organisms and so count as a fourth domain of life. </p>
<p>The latter theory was boosted by the <a href="http://science.sciencemag.org/content/306/5700/1344.long">discovery a decade ago</a> of giant viruses that are more similar to cellular lifeforms. But a new study, <a href="http://science.sciencemag.org/cgi/doi/10.1126/science.aal4657">published in the journal Science</a>, on the genomes of these giant viruses calls this idea into question. So will scientists have to start their search for the origins of viruses all over again?</p>
<p>Viruses are tiny, minimalistic beings that get away from the nuances of cellular life. They are usually <a href="https://micro.magnet.fsu.edu/cells/virus.html">composed of</a> genetic material (DNA or its molecular cousin RNA), often surrounded by a protein coat called a capsid, sometimes with additional layers borrowed from a host cell. Viruses can only replicate within a host cell by hacking its metabolism, and each domain of life is infected by different versions of these cellular squatters.</p>
<p>This tremendous dependence on host cells push them to the <a href="https://www.scientificamerican.com/article/are-viruses-alive-2004/">limits of the definition</a> of life, with some considering them alive and others dead. It is no wonder that most zombie stories involve a virus. Maybe it would be just easier to consider viruses undead. The big question is: where do they come from?</p>
<p><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4609113/">Competing theories</a> try to explain how viruses evolved. One portrays viruses as descendants of an ancient lineage of cellular organisms that lived within other cells and simplified their structure over time. This would make them the only survivors of a long-lost fourth domain of life that left the cell organisation behind. If viruses evolved from living organisms, it would make sense to think of them as alive now.</p>
<h2>Rogue agents</h2>
<p>Another theory proposes that viruses started as rogue genetic agents, vagrants in the genome that escaped their cellular confinement. They could be related to <a href="http://www.nature.com/scitable/topicpage/transposons-or-jumping-genes-not-junk-dna-1211">jumping genes</a> that can copy or cut themselves from a genome and then paste themselves into other parts of the DNA. In that case, viruses would be the result of molecular accidents that became evolutionary stable. This would mean they have never been complete living organisms, just as a computer virus is not a complete computer.</p>
<p>Both these proposals have their flaws. The first fails to explain how simple viruses are. There are no other known organisms with that extreme degree of simplification. On the other hand, the second theory doesn’t explain why viruses are so much more complex than other mobile genetic elements, none of which have anything comparable to a capsid coat.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/164283/original/image-20170406-16669-ds8v2z.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/164283/original/image-20170406-16669-ds8v2z.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/164283/original/image-20170406-16669-ds8v2z.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=424&fit=crop&dpr=1 600w, https://images.theconversation.com/files/164283/original/image-20170406-16669-ds8v2z.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=424&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/164283/original/image-20170406-16669-ds8v2z.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=424&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/164283/original/image-20170406-16669-ds8v2z.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=533&fit=crop&dpr=1 754w, https://images.theconversation.com/files/164283/original/image-20170406-16669-ds8v2z.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=533&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/164283/original/image-20170406-16669-ds8v2z.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=533&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Virus attack.</span>
<span class="attribution"><a class="source" href="https://commons.wikimedia.org/wiki/File:Figure_21_02_01.png">CNX OpenStax</a>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
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</figure>
<p>Then, in 2004, scientists <a href="http://science.sciencemag.org/content/306/5700/1344">discovered a kind of giant virus</a> (or “girus”) that seemed to tip the balance in favour of viruses having cellular origins. They are called giant for good reason. Some are ten times larger in both size and genome length than our beloved flu virus, and have <a href="http://news.nationalgeographic.com/news/2013/07/130718-viruses-pandoraviruses-science-biology-evolution/">as many 2,500 genes</a> compared to influenza’s meagre 11.</p>
<p>This additional genetic material includes instructions for making proteins, something sorely lacking in other viruses but present in all other lifeforms. The molecular system is not complete and giruses still need to invade cells to make more giruses. But <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3291303/">some researchers suggested</a> that these genes could be leftovers of a cellular past, backing up the existence of a fourth domain of life. </p>
<p>On the other hand, the jumpy genetic nature of viruses makes them prone to take genes from other organisms. This has prompted <a href="http://rstb.royalsocietypublishing.org/content/370/1678/20140327.long">others to argue</a> that all these additional genes in giruses are products of evolutionary thievery.</p>
<h2>Giant problem</h2>
<p>Now a <a href="http://science.sciencemag.org/cgi/doi/10.1126/science.aal4657">new study</a> has confirmed the “borrowed” nature of all these genes in viruses. The research uses the most advanced methods, named Next Generation Sequencing (NGS), to map out DNA extracted from a wastewater treatment plant in Klosterneuburg, Austria. In the last few years, NGS-based studies <a href="http://www.nature.com/nature/journal/v541/n7637/full/nature21031.html">have uncovered myriad</a> <a href="http://www.nature.com/articles/nmicrobiol201648">new types of lifeform</a>, and in this instance NGS has revealed a completely new lineage of giant viruses, the Klosneuviruses.</p>
<p>Among all giruses, Klosneuviruses have the largest set of genes involved in making proteins. By comparing the genomes of different giant viruses and carefully reconstructing their evolution, the researchers persuasively show that the protein-making machinery in these giruses is a relatively recent genetic addition – not the scraps of a larger ancestral genome.</p>
<p>The study argues that the host cells these viruses tried to hijack may have evolved a defence strategy based on hiding proteins from the invaders. Then the viruses adapted by incorporating some of these genes into their genome. The researchers conclude that the giant viruses analysed in this study have evolved multiple times from smaller viruses, rejecting the idea they evolved from cellular lifeforms.</p>
<p>However, the new evidence doesn’t kill viruses completely. New gnarls in the tree of life are discovered every day, and a new finding could still provide a link between cellular and acellular life – or prove the opposite. Until then, we will keep thinking about the nature of life, the relationship between zombies and viruses, and wondering “what the hell is that?”</p><img src="https://counter.theconversation.com/content/75661/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Jordi Paps 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 latest research dismisses the idea that viruses form a fourth type of life.Jordi Paps, Lecturer, School of Biological Sciences, University of EssexLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/750182017-03-22T18:14:32Z2017-03-22T18:14:32ZWe might have to completely redraw the dinosaur family tree<figure><img src="https://images.theconversation.com/files/162080/original/image-20170322-31213-p8lz9a.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><span class="source">Shutterstock</span></span></figcaption></figure><p>Normally the dinosaurian world is rocked by a new fossil – the biggest, fastest, or toothiest. But the latest dinosaur research threatens to change our understanding of how dinosaurs evolved at a much deeper level, and blow aside 130 years of agreement on the topic.</p>
<p>A new paper <a href="http://nature.com/articles/doi:10.1038/nature21700">published in the journal Nature</a> suggests that scientists need to reorganise the major groups used to classify dinosaurs. This means we may have to revisit what we think we know about the first dinosaurs, what features they evolved first, and where in the world they came from. </p>
<p>The way we classify dinosaurs goes back to the 19th century. In 1887, Harry Govier Seeley, a classic, hard-working Victorian palaeontologist, divided dinosaurs into <a href="http://www.ucmp.berkeley.edu/diapsids/dinomm.html">two major suborders</a> based primarily on their hip structure. Saurischia comprises the flesh-eating theropods such as <em>Tyrannosaurus</em> and the ponderous, long-necked sauropodomorphs such as <em>Diplodocus</em>. Ornithischia comprises all the rest, including the two-legged <em>Iguanodon</em>, and the armoured, four-legged <em>Stegosaurus</em>, <em>Triceratops</em>, and <em>Ankylosaurus</em>.</p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/162046/original/image-20170322-31180-dg5gp.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/162046/original/image-20170322-31180-dg5gp.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=401&fit=crop&dpr=1 600w, https://images.theconversation.com/files/162046/original/image-20170322-31180-dg5gp.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=401&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/162046/original/image-20170322-31180-dg5gp.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=401&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/162046/original/image-20170322-31180-dg5gp.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=504&fit=crop&dpr=1 754w, https://images.theconversation.com/files/162046/original/image-20170322-31180-dg5gp.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=504&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/162046/original/image-20170322-31180-dg5gp.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=504&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
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<span class="caption">The old family tree.</span>
<span class="attribution"><a class="source" href="https://commons.wikimedia.org/wiki/File:Evolution_of_dinosaurs_EN.svg">Zureks/Wikimedia</a>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span>
</figcaption>
</figure>
<p>This ordering of dinosaurs has stood the test of time for 130 years, weathering the onslaught of cladistics in the 1980s, when palaeontologists began using computers to <a href="http://www.ucmp.berkeley.edu/clad/clad1.html">analyse and categorise groups</a> of animals based on features that pointed to a common ancestor. There are now thousands of diagrams (cladograms) of dinosaur subgroups, and ever-growing data matrices, that closely document the anatomical features of each species.</p>
<p><a href="http://nature.com/articles/doi:10.1038/nature21700">The new paper</a> completely disrupts the consensus over Seeley’s categories. The researchers ran a cladistic analysis of 457 characteristics across 74 species (that is a data matrix of 33,818 bits of information recorded from skeletons). They concluded that, based on 21 unique characteristics of the fossils, the theropods were more closely related to the Ornithischia group and should be moved into that category. This would create a new group named Ornithoscelida and leave behind the Sauropodomorpha.</p>
<p>The trick in cladistics is to find a unique anatomical feature that evolved at a specific time and can indicate a particular subgroup. For example, <a href="http://www.ucmp.berkeley.edu/diapsids/dinomm.html">Seeley noted</a> that the hip bones of ornithischians were arranged with pubis and ischium running backwards (superficially, like modern-day birds). Meanwhile, the hip bones of saurischians (including theropods) matched other reptiles, with pubis forwards and ischium back.</p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/162078/original/image-20170322-31180-1aevdi0.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/162078/original/image-20170322-31180-1aevdi0.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=469&fit=crop&dpr=1 600w, https://images.theconversation.com/files/162078/original/image-20170322-31180-1aevdi0.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=469&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/162078/original/image-20170322-31180-1aevdi0.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=469&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/162078/original/image-20170322-31180-1aevdi0.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=589&fit=crop&dpr=1 754w, https://images.theconversation.com/files/162078/original/image-20170322-31180-1aevdi0.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=589&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/162078/original/image-20170322-31180-1aevdi0.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=589&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">The new tree.</span>
<span class="attribution"><span class="source">Matthew Baron/Nature</span></span>
</figcaption>
</figure>
<p>This suggests the two groups split from a common ancestor and evolved different hip shapes. This was a massive anatomical change or novelty, and palaeontologists until now have assumed that it happened only once in evolutionary history. Grouping the theropods with the ornithischians suggests that the hip change occurred later and raises the question of whether some early theropods had this feature.</p>
<p>The researchers also suggest that the new analysis can reset our understanding of where dinosaurs originated and what their diet was. The classic view was that the first dinosaur was a carnivore living in what is now South America. The new analysis makes this more of an open question and suggests they might have evolved as omnivores in the northern hemisphere.</p>
<h2>Tree of life</h2>
<p>None of this changes what we know for sure about what dinosaurs evolved which traits and when. But the key point is that accurately depicting the <a href="http://www.nature.com/scitable/topicpage/trait-evolution-on-a-phylogenetic-tree-relatedness-41936">tree of life matters</a>. If you care about modern biodiversity, it’s important that all species are not equal. Some are more distinctive than others, possessing more unique features, and having a longer independent history. Working this out requires an accurate tree.</p>
<p>On a broader scale, getting the tree right affects our calculations of rates of trait evolution, extinction and post-extinction recoveries. We will never find the very first dinosaur but we can establish some things about it by estimating the ancestral states of different species from a correct tree.</p>
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<p>We invest enormous efforts into constructing testable systems for categorising different species, and their size is increasing as computing power grows. When I ran my first cladogram in 1982, I had to use punch cards on a mainframe computer, and I could include only ten or 12 species and 50 or so characteristics.</p>
<p>Today, I was able to run all the data for this new paper through my desktop computer and get an answer in 33.21 seconds, while writing this article at the same time. Recent publications have sported trees of all <a href="http://www.nature.com/nature/journal/v491/n7424/abs/nature11631.html">10,000 species of birds</a>, and even summary <a href="http://www.pnas.org/content/112/41/12764.short">trees of all life</a>. The dream is to run such trees with all 1.5m named species, using data about both genes and physical shape.</p>
<p>Is this new paper the true answer for the evolutionary origins of dinosaurs? The data we have is riddled with question marks, and so the algorithms still struggle to calculate the one true tree. This is no criticism of the researchers, just a statement of the practicalities. We don’t know yet whether we can see the wood for the trees.</p><img src="https://counter.theconversation.com/content/75018/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Michael J. Benton 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>A new fossil study challenges 130 years of thinking about how dinosaurs evolved.Michael J. Benton, Professor of Vertebrate Palaeontology, University of BristolLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/726292017-02-27T13:41:56Z2017-02-27T13:41:56ZThe evidence that shows dinosaurs were in decline for 40 million years before the asteroid hit<figure><img src="https://images.theconversation.com/files/158136/original/image-20170223-32729-rf681f.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">The end was nigh.</span> <span class="attribution"><a class="source" href="https://www.shutterstock.com/image-illustration/3d-illustration-brontosaurs-looking-upon-meteors-408550594?src=nBYOFRL9VULXHjReGGp5sg-1-6">Shutterstock</a></span></figcaption></figure><p>When the dinosaurs were wiped off the face of the planet, how did they leave? Was it a slow, plodding decline or a short sharp bang? Back in the 1960s and 1970s, debate about this question was mainly taking place on the ground, at <a href="https://yalealumnimagazine.com/articles/3921-the-man-who-saved-the-dinosaurs">fossil sites in places like Montana</a>. Paleontologist <a href="http://www.nytimes.com/1985/10/29/science/dinosaur-experts-resist-meteor-extinction-idea.html?pagewanted=all">Robert Sloan</a> and his colleagues documented evidence for the long-term decline of dinosaurs over a 10m to 20m-year period. Dinosaurs had been losing out, ever so slowly, to the rising mammals, mainly as a result of cooling climates.</p>
<p>Indeed, climates at this time were cooling. And because dinosaurs relied on the external environment to maintain their body temperatures, this would have hurt them. </p>
<p>But two revelations dramatically switched the consensus against gradual decline. First, the geological field evidence <a href="http://geology.geoscienceworld.org/content/23/10/881">suggested no gradual decline</a> in dinosaur fossils in the rocks. Plus the overlap of declining dinosaurs and rising mammals noted by Sloan turned out to be based on faulty fieldwork and fossil dating. Fossils can be moved from one type of rock to another by being “reworked” or eroded, moved along and then deposited for a second time in younger rocks, providing misleading information about their true age.</p>
<p>The other revelation was the <a href="https://theconversation.com/how-does-an-invisible-underwater-crater-prove-an-asteroid-killed-the-dinosaurs-57711">1980 discovery by Luis Alvarez</a>, which showed that the Earth had been <a href="https://theconversation.com/revealed-asteroid-that-killed-the-dinosaurs-boiled-earths-atmosphere-36606">struck by a huge meteorite</a> 66m years ago. It was a collision that threw up vast tonnages of black dust into the atmosphere, which blacked out the sun, leading to freezing and darkness for some months. This was accepted reluctantly at first by geologists, but then enthusiastically as the <a href="http://www.livescience.com/26933-chicxulub-cosmic-impact-dinosaurs.html">evidence accumulated</a>. </p>
<p>Impact and sudden death of the dinosaurs made complete sense. The last dinosaurs, such as <em>Triceratops</em> and <em>Tyrannosaurus rex</em>, were imagined as dumbfounded by the asteroid streaking through the sky, and killed wholesale by a consequent fireball and then freezing darkness.</p>
<p>But did the dinosaurs really disappear with a bang? <a href="http://research-information.bristol.ac.uk/files/70584653/Sakamoto_et_al._2016._PNAS_final_submitted_ver.pdf">New evidence</a> now suggests instead a very, very, long decline, perhaps as long as 40m years. Part of this comes from <a href="http://research-information.bristol.ac.uk/files/70584653/Sakamoto_et_al._2016._PNAS_final_submitted_ver.pdf">our application</a> of a modelling technique to the data. The key here is to have an evolutionary tree, what is known as a “phylogeny”, which is dated accurately against geological time. Although the fossil record of dinosaurs is incomplete and patchy, we do have high quality phylogenies, tested over <a href="http://www.nature.com/subjects/phylogenetics">30 years of research</a>, that provide solid information on dinosaurian relationships. </p>
<p>Once you have a phylogeny, and date it against a geological time scale, you can read off a great deal of new information. It helps to joins the dots, linking isolated finds, and bridging gaps. It also provides a framework from which rich data on rates of evolution can be calculated.</p>
<p>We wanted to explore a hint of decline that had been noted in the first such comparative <a href="https://issuu.com/felipeelias/docs/lloyd-et-al--2008">phylogenetic analysis</a>.<a href="http://www.pnas.org/content/113/18/5036">Our new work</a> focused on exploring the diversity dynamics of dinosaurs through their entire evolution. We confirmed first that they did most of their evolving in the first half of their reign on Earth, during the late <a href="http://www.bbc.co.uk/nature/history_of_the_earth/Triassic">Triassic</a> and early to middle <a href="http://www.bbc.co.uk/nature/history_of_the_earth/Jurassic">Jurassic</a> periods, some 230m to 150m years ago. </p>
<h2>Decline and fall</h2>
<p>Most importantly, we found clear evidence for a long-term decline from 40m years before the end of the <a href="http://www.bbc.co.uk/nature/history_of_the_earth/Cretaceous">Cretaceous</a> period. We looked at all dinosaurs, and then each of the main subgroups. The only exceptions were the duck-billed dinosaurs (hadrosaurs) and the horned ceratopsians, both of which showed renewed bursts of evolving into new distinct species later on.</p>
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<p>So after so much recent disagreement, can our <a href="http://research-information.bristol.ac.uk/files/70584653/Sakamoto_et_al._2016._PNAS_final_submitted_ver.pdf">new theory</a> be believed? We believe so. It is based on the most detailed data ever assembled, a complete evolutionary tree of more than 600 species of dinosaurs, with better control on the time scale than ever before. </p>
<p>The result was obtained through modelling of the data using an approach which allowed us to repeat the calculations millions of time, using different assumptions about uncertainties each time, to see whether the analysis converged on a single result. In this case, we modelled uncertainties in the phylogeny, in geological dating, and in sampling, and tried every variant of the data, and the result was robust. We can now say categorically: for their final 40m years on Earth, the dinosaurs were in decline - their rate of species extinction was on average consistently higher than their rate of forming new and distinct species (speciation).</p>
<p>But what we cannot yet explain is why this was so. We <a href="http://research-information.bristol.ac.uk/files/70584653/Sakamoto_et_al._2016._PNAS_final_submitted_ver.pdf">found correlation</a> of our speciation dynamics data with sea level, but a more detailed exploration is needed of the impact of cooling climates and their interactions with other species such as mammals. Whatever the driver, dinosaurs were declining. They went out with a long, protracted whimper … followed by that almighty meteoric bang.</p><img src="https://counter.theconversation.com/content/72629/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Michael J. Benton 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>Their days were numbered for quite some time …Michael J. Benton, Professor of Vertebrate Palaeontology, University of BristolLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/686412016-11-16T13:26:50Z2016-11-16T13:26:50ZRed, yellow, pink and green: How the world’s languages name the rainbow<figure><img src="https://images.theconversation.com/files/146234/original/image-20161116-13506-10ayrig.jpg?ixlib=rb-1.1.0&rect=307%2C71%2C3877%2C2628&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">How many colors in your language's rainbow?</span> <span class="attribution"><a class="source" href="http://www.shutterstock.com/pic-130215719.html">Eye image via www.shutterstock.com.</a></span></figcaption></figure><p>It is striking that English color words come from many sources. Some of the more exotic ones, like “vermilion” and “chartreuse,” were borrowed from French, and are named after the color of a particular item (a type of mercury and a liquor, respectively). But even our words “black” and “white” didn’t originate as color terms. “Black” comes from a word meaning “burnt,” and “white” comes from a word meaning “shining.” </p>
<p>Color words vary a lot across the world. Most languages have between two and 11 basic color words. English, for example, has the full set of 11 basic colors: black, white, red, green, yellow, blue, pink, gray, brown, orange and purple. In a 1999 survey by linguists <a href="http://www1.icsi.berkeley.edu/%7Ekay/">Paul Kay</a> and <a href="http://terralingua.org/">Luisa Maffi</a>, languages were <a href="http://wals.info/feature/133A#2/22.3/153.7">roughly equally distributed</a> between the basic color categories that they tracked.</p>
<p>In languages with fewer terms than this – such as the Alaskan language Yup'ik with its five terms – the range of a word expands. For example, for languages without a separate word for “orange,” hues that we’d call “orange” in English might be named by the same color that English speakers would call “red” or “yellow.” We can think of these terms as a system that together cover the visible spectrum, but where individual terms are centered on various parts of that spectrum.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/146097/original/image-20161115-31138-1hotkg5.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/146097/original/image-20161115-31138-1hotkg5.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/146097/original/image-20161115-31138-1hotkg5.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=600&fit=crop&dpr=1 600w, https://images.theconversation.com/files/146097/original/image-20161115-31138-1hotkg5.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=600&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/146097/original/image-20161115-31138-1hotkg5.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=600&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/146097/original/image-20161115-31138-1hotkg5.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=754&fit=crop&dpr=1 754w, https://images.theconversation.com/files/146097/original/image-20161115-31138-1hotkg5.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=754&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/146097/original/image-20161115-31138-1hotkg5.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"></a>
<figcaption>
<span class="caption">Illustration of a color system with 20 hues.</span>
<span class="attribution"><a class="source" href="https://commons.wikimedia.org/wiki/File:MunsellColorWheel.svg">Thenoizz</a>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<p>Does that mean that speakers of languages with fewer words for colors see less color? No, just as English speakers can see the difference between the “blue” of the sky and the “blue” of an M&M. Moreover, if language words limited our perception of color, words wouldn’t be able to change; speakers would not be able to add new distinctions. </p>
<p>My colleague <a href="http://hannahhaynie.com/">Hannah Haynie</a> and <a href="http://campuspress.yale.edu/clairebowern">I</a> were interested in how color terms might change over time, and in particular, in how color terms might change as a system. That is, do the words change independently, or does change in one word trigger a change in others? <a href="http://doi.org/10.1073/pnas.1613666113">In our research, recently published in the journal PNAS</a>, we used a computer modeling technique more common in biology than linguistics to investigate typical patterns and rates of color term change. Contrary to previous assumptions, what we found suggests that color words aren’t unique in how they evolve in language.</p>
<h2>Questioning common conceptions on colors</h2>
<p>Previous work (such as by anthropological linguists <a href="http://www.ucpress.edu/op.php?isbn=9780520076358">Brent Berlin and Paul Kay</a>) has suggested that the order in which new color terms are added to a language is largely fixed. Speakers begin with two terms – one covering “black” and dark hues, the other covering “white” and light hues. There are plenty of languages with only two color terms, but in all cases, one of the color terms is centered on “black” and the other on “white.”</p>
<p>When a language has three terms, the third is one is almost always centered on hues that English speakers would call “red.” There are no languages with three color terms where the named colors are centered on black, white and light green, for example. If a language has four color terms, they will be black, white, red and either yellow or green. In the next stage, both yellow and green are present, while the next color terms to be added are blue and brown (in that order). Cognitive scientists and linguists such as <a href="http://lclab.berkeley.edu/papers/tics2-published.pdf">Terry Regier</a> have argued that these particular parts of the color spectrum are most noticeable for people.</p>
<p>Berlin and Kay also hypothesized that language speakers don’t lose color terms. For example, once a language has a distinction between “red-like” hues (such as blood) and “yellow-like” ones (such as bananas), they wouldn’t collapse the distinction and go back to calling them all by the same color name again.</p>
<p>This would make color words quite different from other areas of language change, where words come and go. For example, words can <a href="http://dx.doi.org/10.1016/B0-08-044854-2/01105-6">change their meaning</a> when they are used metaphorically, but over time the metaphoric meaning becomes basic. They can broaden or narrow their meanings; for example, English “starve” used to mean “die” (generally), not “die of hunger,” as it primarily means now. “Starve” has also acquired metaphorical meanings.</p>
<p>That there’s something unique about the stability of color concepts is an assumption we wanted to investigate. We were also interested in patterns of color naming and where color terms come from. And we wanted to look at the rates of change – that is, if color terms are added, do speakers tend to add lots of them? Or are the additions more independent, with color terms added one at a time?</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/146236/original/image-20161116-13506-15zf4h7.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/146236/original/image-20161116-13506-15zf4h7.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/146236/original/image-20161116-13506-15zf4h7.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/146236/original/image-20161116-13506-15zf4h7.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/146236/original/image-20161116-13506-15zf4h7.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/146236/original/image-20161116-13506-15zf4h7.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/146236/original/image-20161116-13506-15zf4h7.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/146236/original/image-20161116-13506-15zf4h7.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">Everyone sees them all, but languages divide them into different color terms.</span>
<span class="attribution"><a class="source" href="http://www.shutterstock.com/pic.mhtml?id=300363659&src=lb-29877982">Colors image via www.shutterstock.com.</a></span>
</figcaption>
</figure>
<h2>Modeling how a language tree grew</h2>
<p>We tested these ideas using color words in Australian Aboriginal languages. We worked with Australian languages (rather than European or other languages) for several reasons. Color demarcations vary in Indo-European, but the number of colors in each language is pretty similar; the ranges differ but the number of colors don’t vary very much. Russian has two terms that cover the hues that English speakers call “blue,” but Indo-European languages have many terms.</p>
<p>In contrast, Australian languages are a lot more variable, ranging from systems like Darkinyung’s, with just two terms (<em>mining</em> for “black” and <em>barag</em> for “white”), to languages like Kaytetye, where there are at least eight colors, or Bidyara with six. That variation gave us more points of data. Also, there are simply a lot of languages in Australia: Of the more than 400 spoken at the time of European settlement, we had color data for 189 languages of the Pama-Nyungan family, from the <a href="http://pamanyungan.net/chirila">Chirila</a> <a href="https://scholarspace.manoa.hawaii.edu/bitstream/handle/10125/24685/bowern.pdf">database</a> of Australian languages.</p>
<p>In order to answer these questions, we used techniques originally developed in biology. Phylogenetic methods use computers to study the remote past. In brief, we use probability theory, combined with a family tree of languages, to make a model of what the history of the color words might have been.</p>
<p>First, we construct a tree that shows how languages are related to one another. The <a href="https://en.wikipedia.org/wiki/Pama_nyungan">contemporary Pama-Nyungan languages</a> are all descended from a single ancestor language. Over 6,000 years, Proto-Pama-Nyungan split into different dialects, and those dialects turned into different languages: about 300 of them at the time of the European settlement of Australia. Linguists usually show those splits on a family tree diagram. </p>
<figure class="align-left zoomable">
<a href="https://images.theconversation.com/files/145959/original/image-20161115-30749-1mlxf6a.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/145959/original/image-20161115-30749-1mlxf6a.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/145959/original/image-20161115-30749-1mlxf6a.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=842&fit=crop&dpr=1 600w, https://images.theconversation.com/files/145959/original/image-20161115-30749-1mlxf6a.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=842&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/145959/original/image-20161115-30749-1mlxf6a.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=842&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/145959/original/image-20161115-30749-1mlxf6a.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=1059&fit=crop&dpr=1 754w, https://images.theconversation.com/files/145959/original/image-20161115-30749-1mlxf6a.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=1059&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/145959/original/image-20161115-30749-1mlxf6a.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=1059&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Family tree of Australian languages with their color terms and reconstructions of color systems for major subgroups.</span>
<span class="attribution"><span class="source">Haynie and Bowern (2016): Figure 3</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>Then, we build a model for that tree of how different features (in this case, color terms) are gained or lost, and how quickly those features might change. This is a complicated problem; we estimate likely reconstructions, evaluate that model for how well it fits our hypotheses, tweak the model parameters a bit to produce a different set of results, score that model, and so on. We repeat this many times (millions of times, usually) and then take a random sample of our estimates. This method is due originally to evolutionary biologists <a href="http://www.evolution.reading.ac.uk/">Mark Pagel and Andrew Meade</a>.</p>
<p>Estimates that are very consistent (like reconstructing terms for “black,” “white” and “red”) are highly likely to be good reconstructions. Other forms were consistently reconstructed as absent (for instance, “blue” from many parts of the tree). A third set of forms were more variable, such as “yellow” and “green” in some parts of the tree; in that case, we have some evidence they were present, but it’s unclear. </p>
<p>Our results supported some of the previous findings, but questioned others. In general, our findings backed up Berlin and Kay’s ideas about the sequential adding of terms, in the order they proposed. For the most part, our color data showed that Australian languages also show the patterns of color term naming that have been proposed elsewhere in the world; if there are three named colors, they will be black, white and red (not, for example, black, white and purple). But we show that it is most likely that Australian languages have lost color terms, as well as gained them. This contradicts 40 years of assumptions of how color terms change – and makes color words look a lot more like other words. </p>
<p>We also looked at where the color words themselves came from. Some were old in the family, and seemed to go back as color terms. Others relate to the environment (like <em>tyimpa</em> for “black” in Yandruwandha, which is related to a word which means “ashes” in other languages) or to other color words (compare Yolŋu <em>miku</em> for “red,” which also sometimes means simply “colored”). So Australian languages show similar sources of color terms to languages elsewhere in the world: color words change when people draw analogies with items in their environment.</p>
<p>Our research shows the potential for using language change to study areas of science that have previously been more closely examined by fields such as psychology. Psychologists and psycholinguists have described how constraints from our vision systems lead to particular areas of the color spectrum being named. We show that these constraints apply to color loss as well as gain. Just as it’s a lot easier to see a chameleon when it moves, language change makes it possible to see how words are working.</p><img src="https://counter.theconversation.com/content/68641/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Claire Bowern receives funding from the National Science Foundation and the Australian Research Council. She is Vice-President of the Endangered Language Fund. </span></em></p>New research investigates how people sequentially add new color terms to languages over time – and the results hold surprises about assumptions linguists have made for 40 years.Claire Bowern, Associate Professor of Linguistics, Yale UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/629242016-07-25T15:56:38Z2016-07-25T15:56:38ZStudy tracing ancestor microorganisms suggests life started in a hydrothermal environment<figure><img src="https://images.theconversation.com/files/131753/original/image-20160725-31202-dtl57k.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Grand Prismatic Spring and Midway Geyser Basin from above.</span> <span class="attribution"><span class="source">Brocken Inaglory/wikimedia</span>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span></figcaption></figure><p>It’s one of the greatest mysteries of modern science: how did life begin exactly? While most scientists believe that all lifeforms evolved from a common, primitive ancestor microorganism, the details are blurry. What kinds of genes did this lifeform carry and where did it live? A new study, <a href="http://nature.com/articles/doi:10.1038/nmicrobiol.2016.116">published in Nature Microbiology</a>, now sheds some light on this early organism and the environment it evolved in.</p>
<p>Experimental scientists interested in the origins of life generally tackle the problem in two distinct ways. One is a <a href="http://pubs.acs.org/doi/abs/10.1021/la503933x">bottom-up approach</a> in which they try to imagine how early life might have emerged and then try to recreate the key steps in the laboratory. The alternative, a <a href="http://www.sciencedirect.com/science/article/pii/S0092867413001359">top-down approach</a>, is to analyse or strip down modern cells to simplify them and deduce how the key stages in the evolution of complexity might have taken place. </p>
<p>Informaticians interested in this problem exploit the huge amounts of data emerging from the revolution in DNA sequencing. This has resulted in a sea of information about the genomes of organisms – from bacteria to humans. Hidden in this should be the echoes of DNA sequences from primitive cells – the first cells on the planet to use the modern genetic code – passed on through billions of generations. </p>
<p>The “last universal common ancestor” is a hypothetical very early single cell from which all life on Earth descended. The relationship between this ancestor and modern organisms is often visualised in the form of evolutionary trees, of which the most famous early examples were those by Charles Darwin. </p>
<p>The advent of DNA sequencing provided a wonderful, highly quantitative measure of genetic relatedness that transcended the whole of biology. The same four-base code of A, C, G and T is used by virtually all organisms on the planet. So in principle, it can be used to construct evolutionary trees for the whole of life. We know that certain genes, such as the one encoding a small <a href="http://microbe.net/simple-guides/fact-sheet-ribosomal-rna-rrna-the-details/">RNA subunit of the ribosome</a> (the protein synthesisers of a cell), existed at the dawn of cellular life on Earth and seem to have been inherited by all subsequent forms of life. Over four billion years, copies of this particular gene – <a href="http://www.ncbi.nlm.nih.gov/pubmed/18828852">16S rRNA</a> – have gradually changed by random mutation in the separate lineages that have led to different forms of life. This means each has a characteristic sequence that is similar in recently diverged organisms but increasingly different in lineages that diverged earlier in evolution.</p>
<p>The <a href="http://www.pnas.org/content/87/12/4576.long">first analyses of these “universal” DNA sequences</a> about 30 years ago led to dramatic changes in our appreciation of the diversity of life on Earth, and especially the staggering degree of diversity in single celled organisms with no nucleus (the prokaryotes). It also highlighted the existence of a huge new “domain” of prokarytic life – now called the archaea. </p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/131738/original/image-20160725-31195-1k1mej9.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/131738/original/image-20160725-31195-1k1mej9.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=405&fit=crop&dpr=1 600w, https://images.theconversation.com/files/131738/original/image-20160725-31195-1k1mej9.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=405&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/131738/original/image-20160725-31195-1k1mej9.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=405&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/131738/original/image-20160725-31195-1k1mej9.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=509&fit=crop&dpr=1 754w, https://images.theconversation.com/files/131738/original/image-20160725-31195-1k1mej9.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=509&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/131738/original/image-20160725-31195-1k1mej9.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=509&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">A speculatively rooted tree for rRNA genes, showing the three life domains Bacteria, Archaea, and Eucaryota, and linking the three branches of living organisms to the last universal common ancestor (the black trunk at the bottom of the tree). Note that the most modern models now place the origin of the eukaryotes within the archaeal lineage.</span>
<span class="attribution"><span class="source">wikimedia</span>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span>
</figcaption>
</figure>
<p>Attempts to develop truly universal trees that would define how all modern cells descended from this last universal ancestor have been thwarted by a number of technical issues. One problem lies in the sheer number of groups that have separated from each other since life first began. What’s more, bacteria can also exchange genes with each other, which makes it harder to identify how they’ve been passed down.</p>
<h2>Hydrogen-powered organism?</h2>
<p>The researchers behind the new study applied a sophisticated state-of-the-art method to organise some 6m sequenced prokaryotic genes into families. They then looked for patterns of similarity across all bacterial groups and found a small set of genes that were present in both archaea and bacteria. They could show that these genes were really likely to have been inherited directly from a common ancestor rather than by lateral exchange along the way.</p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/131744/original/image-20160725-31162-1dbu4s0.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/131744/original/image-20160725-31162-1dbu4s0.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=408&fit=crop&dpr=1 600w, https://images.theconversation.com/files/131744/original/image-20160725-31162-1dbu4s0.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=408&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/131744/original/image-20160725-31162-1dbu4s0.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=408&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/131744/original/image-20160725-31162-1dbu4s0.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=513&fit=crop&dpr=1 754w, https://images.theconversation.com/files/131744/original/image-20160725-31162-1dbu4s0.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=513&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/131744/original/image-20160725-31162-1dbu4s0.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=513&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Scanning electron micrograph of Clostridium difficile bacteria from a stool sample.</span>
<span class="attribution"><span class="source">CDC/ Lois S. Wiggs/wikimedia</span></span>
</figcaption>
</figure>
<p>The result is important because it identifies specific groups of bacteria (<a href="http://www.ncbi.nlm.nih.gov/books/NBK8219/">clostridia</a>) and archaea (<a href="http://www.nature.com/nrmicro/journal/v6/n8/full/nrmicro1931.html">methanogens</a>) that carry early versions of these genes, meaning they are very ancient and may be similar to the very earliest organisms that gave rise to the separate bacterial and archaeal lineages. </p>
<p>More importantly, the nature of the genes that are conserved tells an amazing story about the kind of environment in which this last common ancestor lived – including how it extracted energy to survive and thrive. The study suggests that the world inhabited by these organisms nearly four billion years ago was very different to the one we live in now. There was no available oxygen, but according to the genes, this common ancestor probably obtained energy from hydrogen gas, presumably made by geochemical activity in the Earth’s crust. “Inert” gases including carbon dioxide and nitrogen would have provided the key building blocks for making all cellular structures. Iron was freely available, with no oxygen to turn it into insoluble rust, and so this element was used by many enzymes in the early cell. Some of the genes are believed to be involved in adaptation to high temperatures, which suggests these organisms evolved in a hydrothermal environment – perhaps equivalent to modern hydrothermal vents or hot springs, where some bacteria still thrive. </p>
<p>Sadly, without a time machine, there is no way to directly verify these results. Nevertheless, this information will now be of great interest, not least to those scientists wishing to use the information to inform their bottom-up experiments in recreating modern forms of primitive life. But it will not be easy, given the requirement for high temperature, nitrogen, carbon dioxide and explosive hydrogen gas.</p><img src="https://counter.theconversation.com/content/62924/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Jeff Errington receives funding from the European Research Council and the Wellcome Trust.. </span></em></p>Scientists have uncovered genes they believe have been passed down from an ancestor organism that all life evolved from.Jeff Errington, Director of the Centre for Bacterial Cell Biology, Newcastle UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/202712013-11-13T23:42:39Z2013-11-13T23:42:39ZAs they spread, folktales evolve like biological species<figure><img src="https://images.theconversation.com/files/35189/original/7gqdqshq-1384368585.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Granny, why are your eyes so big?</span> <span class="attribution"><span class="source">Gustave Dore</span></span></figcaption></figure><p>We all know the story: Once upon a time there was a young girl who took a walk through the woods to visit her grandmother, carrying a basket of goodies. When she arrived she found her granny ill in bed. </p>
<p>But something else was wrong.</p>
<p>Why did Granny’s eyes look so big?! And her ears?! And her teeth?! By the time the girl finally realised that “Granny” was, in fact, a wolf in disguise, it was too late – she was gobbled up in an instant. And that was the end of Little Red Riding Hood.</p>
<p>Or was it? Maybe the story you know has the little girl rescued by a passing huntsman, who cuts her out of the wolf’s belly and kills the beast. Or perhaps her father stormed in with a shotgun, and blew the wolf’s head off just as he was about to devour her. In French and Italian oral tradition, the girl doesn’t need any man to rescue her – she uses her own wits to escape from the wolf. (Interestingly, this more empowered heroine has been reincarnated in some modern versions of the tale, such as Angela Carter’s Company of Wolves, David Slade’s superb Hitchcockian fairy-tale movie Hard Candy and the recent Hollywood flop Red Riding Hood).</p>
<h2>Chinese whispers</h2>
<p>Like all folktales, there is no single “correct” version of Little Red Riding Hood. Although the basic structure of the story remains recognisable, many of the details of the plot and characters have been modified as they get passed on from person to person. We can think of it as being like a game of “Chinese Whispers” (or, as Americans call it, “Broken Telephone”), whereby as people learn and re-tell the tale they omit some elements, while adding and distorting others. </p>
<p>In folklore, this game is not only played vertically across generations, but horizontally across space as tales spread from society to society, with some – like Little Red Riding Hood – spreading globally. Over time, these so-called “international tale types” evolve into locally distinctive forms (known as <a href="http://books.google.co.uk/books?id=I6QrAQAAMAAJ">oikotypes</a>) as they adapt to different cultural and ecological contexts. This process is directly analogous to the emergence of new species in biological evolution and, I argue, can be studied using the same kinds of tools.</p>
<p>The idea is to use a biologist’s tool, like <a href="http://bip.weizmann.ac.il/education/course/introbioinfo/03/lect12/phylogenetics.pdf">phylogenetic analysis</a> which looks at genetic relationships among species, to investigate the evolution of folktales. This is because folktales not only evolve through similar processes as biological species (variation, selection and inheritance), but the problems of reconstructing them are also comparable. Just as the fossil record bears witness to a tiny proportion of extinct ancestral species, the literary record provides scarce textual evidence about early forms of folktales because they have been mainly transmitted through oral means. Phylogenetics can fill these gaps by using information about the past that has been preserved through the mechanism of inheritance.</p>
<h2>Just like genes</h2>
<figure class="align-right ">
<img alt="" src="https://images.theconversation.com/files/35191/original/wbn8dtb3-1384371832.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/35191/original/wbn8dtb3-1384371832.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=772&fit=crop&dpr=1 600w, https://images.theconversation.com/files/35191/original/wbn8dtb3-1384371832.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=772&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/35191/original/wbn8dtb3-1384371832.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=772&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/35191/original/wbn8dtb3-1384371832.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=970&fit=crop&dpr=1 754w, https://images.theconversation.com/files/35191/original/wbn8dtb3-1384371832.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=970&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/35191/original/wbn8dtb3-1384371832.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=970&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption"></span>
<span class="attribution"><span class="source">Gustave Dore</span></span>
</figcaption>
</figure>
<p>Take the example of the long-running debate about the relationship between Little Red Riding Hood and similar tales from other regions of the world. These include East Asian tales in which a group of sisters are home alone when they hear a knock at the door. It is a tiger (or leopard, or some other predator) disguised as their grandmother. Despite her suspicious appearance (“Granny, why are your eyes so big?!”) they let her in. That night they share a bed, and the tiger eats the youngest girl to the horror of her sisters, who manage to escape. </p>
<p>Another tale, from central and southern Africa, involves a young girl who is tricked by an ogre pretending to be her brother. When her brother finds out he tracks down the ogre, kills him and cuts her out of the villain’s belly. Both these tales bear a clear resemblance to Little Red Riding Hood. But they are also similar to another well-known international type tale: “<a href="http://www.pitt.edu/%7Edash/grimm005.html">The Wolf and the Kids</a>”, in which a group of goat kids are devoured by a wolf who gets into their house by impersonating their mother.</p>
<p>By analysing variables in the plots and characters of 58 folktales using three methods of phylogenetic analysis, I was able to establish, in a paper just published in <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0078871">PLOS ONE</a>, that the African tales are clearly more closely related to The Wolf and the Kids than they are to Little Red Riding Hood. The East Asian tales evolved by blending together elements from both these tales and from local folktales. </p>
<p>Previous writers have suggested, based on resemblances, that the East Asian tales were the source of the western tales. My findings turn that theory on its head, suggesting that the Asian tales are in fact derived from a western source, not vice versa. The kind of approach I have used promises new insights into the origins and relationships among story-telling traditions from different countries around the world. But ultimately I believe it can deliver more than that. </p>
<p>Folktales, more than any other type of story, embody our shared fantasies, fears and experiences. Understanding which elements of them remain stable and which ones change as they get transmitted across generations and societies can therefore provide a unique window into universal and variable aspects of the human condition. As such, they represent a potentially rich point of contact between anthropologists, folklorists, literary scholars, biologists and cognitive scientists.</p><img src="https://counter.theconversation.com/content/20271/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Jamie Tehrani receives funding from Research Councils UK.</span></em></p>We all know the story: Once upon a time there was a young girl who took a walk through the woods to visit her grandmother, carrying a basket of goodies. When she arrived she found her granny ill in bed…Jamie Tehrani, Lecturer, Durham UniversityLicensed as Creative Commons – attribution, no derivatives.