tag:theconversation.com,2011:/uk/topics/dna-251/articlesDNA – The Conversation2024-02-27T12:41:39Ztag:theconversation.com,2011:article/2191402024-02-27T12:41:39Z2024-02-27T12:41:39ZCould a couple of Thai otters have helped the UK’s otter population recover? Our study provides a hint<p>Otter populations crashed in Britain around the 1960s from the lethal effects of chemical pollution in rivers and lakes – or so we thought. <a href="https://academic.oup.com/mbe/article/40/11/msad207/7275014">Our research</a> has looked more closely at what happened to otters in Britain over the last 800 years and has revealed a more complex picture. </p>
<p>Since Eurasian otters (<em>Lutra lutra</em>) are at the top of the aquatic food chain in Britain, any contamination consumed by their prey, and by the prey of their prey, <a href="https://pubs.acs.org/doi/10.1021/acs.est.1c05410">accumulates in otters</a>. So otters are particularly susceptible to any toxic chemicals in their environment. </p>
<p>Following the banning of many chemical pollutants, otter populations began to recover, and we now have otters in <a href="https://onlinelibrary.wiley.com/doi/10.1111/eva.13505">every county in Britain</a>. National otter surveys have been conducted in Wales, Scotland and England since 1977 and have helped to track population recovery. </p>
<p>However, we didn’t have a good grasp on what population sizes were like in the decades before this time. We only had anecdotal evidence that otter hunting was becoming less “successful” over time, and that both sightings and signs of otters were rarer. </p>
<h2>Otter population decline</h2>
<p>Our research shows that roughly between 1950 and 1970, an extreme population decline happened in the east of England, and a strong decline in south-west England. They were probably caused by chemical pollution. </p>
<p>In Scotland, otter populations showed a long-term, but smaller decline, which suggests less chemical pollution. There was a smaller population decline in Wales, which started around 1800, possibly linked to otter hunting and changes in how people shaped and used the landscape. </p>
<p>While both deal with DNA, genetics focuses on individual genes and their roles, while genomics examines the entire set of an organism’s DNA. Although there have been genetic studies of otters in Britain, our research was the first time genomics was used to study Eurasian otters anywhere in the world.</p>
<p>Working with scientists from the Smithsonian Conservation Biology Institute and the Wellcome Sanger’s Darwin Tree of Life project, we looked at the entire otter genome. The upgrade from genetics to genomics threw up a few surprises. </p>
<p>First, there was a mitochondrial DNA sequence found in the east of England, which was very different to the sequences in the rest of Britain. Mitochondrial DNA is a sequence of DNA found in a cell’s mitochondria, which is what generates the energy. Mitochondrial DNA is inherited only from the mother, while the rest of the DNA is a mix of both the mother’s and the father’s DNA.</p>
<p>Another <a href="https://www.tandfonline.com/doi/full/10.1080/19768354.2023.2283763">recent study</a> by our research group, in collaboration with colleagues in South Korea, suggested a divergence between these two lineages at least 80,000 years ago. Finding this mitochondrial lineage (that, based on our data, is otherwise restricted to Asia) in the UK was surprising. </p>
<p>Second, we found high levels of genetic diversity in the east of England. Normally, after an extreme population decline such as the one we identified in this area, genetic diversity decreases. Yet we saw much greater diversity here than in the population in Scotland, where there was no clear evidence for such a decline. </p>
<h2>Thai otters</h2>
<p>With a little detective work, we discovered that a pair of Eurasian otters (the same species that we have in the UK), were brought to Britain from Thailand in the 1960s. Populations of Eurasian otters range right across Europe and Asia. Although they are the same species, there are several genetically distinct subspecies, particularly in Asia. </p>
<p>It seems possible that these genetically different otters from Thailand bred with otters in the east of England. At the time of the population decline, when native UK populations were at their smallest, even a few individuals introduced into the population may have made a big difference. And they left unexpected marks on the genome. </p>
<p>We don’t know for sure if this is what happened, and we need to do more work to find out what effect this may have had on otters in the east of England. High genetic diversity is usually good for a population or species. But on the other hand, conservation often strives to maintain genetic differences between populations, rather than mixing distinct populations.</p>
<p>One way to find out more would be to compare the genome of a Eurasian otter from Thailand to the otters we see in the east of England. Unfortunately, it’s not that easy. Since the 1960s, otters in Thailand and across Asia have become increasingly rare. This is due to habitat loss, pollution and the illegal otter trade. So getting samples for genome sequencing is very difficult. It highlights the importance of conserving the species in Asia, despite population recoveries in Europe.</p>
<p>Our work shows the value of using modern genomic tools to look at the genetic diversity of a threatened species. The application of such tools can uncover surprising facts, even in supposedly well-studied species.</p>
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<img alt="Imagine weekly climate newsletter" src="https://images.theconversation.com/files/434988/original/file-20211201-21-13avx6y.png?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/434988/original/file-20211201-21-13avx6y.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=600&fit=crop&dpr=1 600w, https://images.theconversation.com/files/434988/original/file-20211201-21-13avx6y.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=600&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/434988/original/file-20211201-21-13avx6y.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=600&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/434988/original/file-20211201-21-13avx6y.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=754&fit=crop&dpr=1 754w, https://images.theconversation.com/files/434988/original/file-20211201-21-13avx6y.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=754&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/434988/original/file-20211201-21-13avx6y.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=754&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
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<p class="fine-print"><em><span>Frank Hailer receives funding from NERC and Dŵr Cymru Welsh Water. </span></em></p><p class="fine-print"><em><span>Elizabeth Chadwick receives funding from the UK Natural Environment Research Council and from the Environment Agency</span></em></p><p class="fine-print"><em><span>Sarah du Plessis receives funding from the UK Natural Environment Research Council and the Global Wales International Mobility Fund.</span></em></p>Research has revealed how British otters may have been able to recover from species loss in the 1950s with the help of otters from Asia.Frank Hailer, Senior Lecturer in Evolutionary Biology, Cardiff UniversityElizabeth Chadwick, Senior Lecturer at the School of Biosciences, Cardiff UniversitySarah du Plessis, PhD Candidate, Cardiff UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2190722024-02-22T18:16:18Z2024-02-22T18:16:18ZExtreme environments are coded into the genomes of the organisms that live there<p>An organism’s genome is a set of DNA instructions needed for its development, function and reproduction. The genome of a present-day organism contains information from its journey on an evolutionary path that starts with the
“<a href="https://doi.org/10.1007/978-3-030-30363-1_3">first universal common ancestor</a>” of all life on Earth and culminates with that organism. </p>
<p>Encoded within itself, an organism’s genome contains information that can reveal connections to its ancestors and its relatives.</p>
<h2>Other dimensions of the genome</h2>
<p>Our research explores the hypothesis that an organism’s genome could contain other types of information, <a href="https://doi.org/10.1038/s41598-023-42518-y">beyond genealogy or taxonomy</a>. We asked: Could the genome of an organism contain information that would allow us to determine the type of environment the organism lives in?</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/574213/original/file-20240207-16-upk4fk.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="a large black lake" src="https://images.theconversation.com/files/574213/original/file-20240207-16-upk4fk.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/574213/original/file-20240207-16-upk4fk.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=399&fit=crop&dpr=1 600w, https://images.theconversation.com/files/574213/original/file-20240207-16-upk4fk.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=399&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/574213/original/file-20240207-16-upk4fk.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=399&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/574213/original/file-20240207-16-upk4fk.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=502&fit=crop&dpr=1 754w, https://images.theconversation.com/files/574213/original/file-20240207-16-upk4fk.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=502&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/574213/original/file-20240207-16-upk4fk.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=502&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Extremophiles have been found in environments such as Pitch Lake in Trinidad and Tobago, the largest asphalt deposit in the world.</span>
<span class="attribution"><span class="source">(Shutterstock)</span></span>
</figcaption>
</figure>
<p>As unlikely as it seems, our team of computer science and biology researchers at the University of Waterloo and Western University found that to be the case for extremophiles — organisms that live and thrive in extremely harsh conditions. These environmental conditions range from extreme heat (over 100 C) to extreme cold (below -12 C), high radiation or extremes in acidity or pressure.</p>
<h2>DNA as a language</h2>
<p>We looked at genomic DNA as a text written in a “DNA language.” A DNA strand (or DNA sequence) consists of a succession of <a href="https://www.genome.gov/genetics-glossary/Nucleotide">basic units called nucleotides</a>, strung together by a sugar-phosphate backbone. There are four such different DNA units: <a href="https://www.genome.gov/genetics-glossary/acgt">adenine, cytosine, guanine and thymine (A,C,G,T)</a>. </p>
<p>Viewed abstractly, a DNA sequence can be thought of as a line of text, written with “letters” from the “DNA alphabet.” For example, “CAT” would be the three-letter “DNA word” corresponding to the three-unit DNA sequence cytosine-adenine-thymine.</p>
<p>In the 1990s, it was discovered that by <a href="https://doi.org/10.1093/nar/18.8.2163">counting occurrences</a> of such DNA words in a short DNA sequence extracted from the genome of an organism, one could identify <a href="https://doi.org/10.1093/oxfordjournals.molbev.a026048">the species of the organism</a> and the degree of its relatedness to other organisms in the evolutionary “<a href="https://doi.org/10.1038/nmicrobiol.2016.48">tree of life</a>.”</p>
<p>The mechanism of this identification or classification of an organism based on DNA word counts is similar to the process that allows us to differentiate an English book from a French book: By taking one page from each book one notices that the English text has many occurrences of the three-letter word “the,” while the French text has many occurrences of the three-letter word “les.”</p>
<p>Note that the word-frequency profile of each book is not dependent on the particular page we chose to read and on whether we considered multiple pages, a single page or an entire chapter. Similarly, the frequency profile of DNA words in a genome is not dependent on the location and on the length of the DNA sequence that was selected to represent that genome.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/574232/original/file-20240207-33-kdilvj.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="rows of lights with the letters C, A, G, T projected from them" src="https://images.theconversation.com/files/574232/original/file-20240207-33-kdilvj.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/574232/original/file-20240207-33-kdilvj.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=420&fit=crop&dpr=1 600w, https://images.theconversation.com/files/574232/original/file-20240207-33-kdilvj.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=420&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/574232/original/file-20240207-33-kdilvj.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=420&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/574232/original/file-20240207-33-kdilvj.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=528&fit=crop&dpr=1 754w, https://images.theconversation.com/files/574232/original/file-20240207-33-kdilvj.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=528&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/574232/original/file-20240207-33-kdilvj.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=528&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 DNA strand consists of a succession of basic units: adenine, cytosine, guanine and thymine (ACGT).</span>
<span class="attribution"><span class="source">(Shutterstock)</span></span>
</figcaption>
</figure>
<p>That DNA word-frequency profiles can act as a “genomic signature” of an organism was a significant discovery and, until now, it was believed that the DNA word-frequency profile of a genome only contained evolutionary information pertaining to the species, genus, family, order, class, phylum, kingdom or domain that the organism belonged to.</p>
<p>Our team set out to ask whether the DNA word-frequency profile of a genome could reveal other kinds of information — for example, information regarding the type of extreme environment that a microbial extremophile thrives in.</p>
<h2>Environment imprints in extremophile DNA</h2>
<p>We used a dataset of 700 microbial extremophiles living in extreme temperatures (either extreme heat or cold) or extreme pH conditions (strongly acidic or alkaline). We used both <a href="https://doi.org/10.1093/bioinformatics/btz918">supervised machine learning</a> and <a href="https://doi.org/10.1093/bioinformatics/btad508">unsupervised machine learning</a> computational approaches to test our hypothesis.</p>
<p>In both types of environmental conditions, we discovered that we could clearly detect an environmental signal indicating the type of extreme environment a particular organism inhabited. </p>
<p>In the case of unsupervised machine learning, a “blind” algorithm was given a dataset of extremophile DNA sequences (and no other information about either their taxonomy or their living environment). The algorithm was then asked to group these DNA sequences in clusters, based on whatever similarities it could find among their DNA word-frequency profiles. </p>
<p>The expectation was that all the clusters discovered this way would be along taxonomic lines: bacteria grouped with bacteria, and archaea grouped with archaea. To our great surprise, this was not always the case, and some archaea and bacteria were consistently grouped together, no matter what algorithms we used. </p>
<p>The only obvious commonality that could explain their being considered similar by the multiple machine learning algorithms was that they were heat-loving extremophiles.</p>
<h2>A shocking discovery</h2>
<p>The <a href="https://doi.org/10.1038/s41467-023-42924-w">tree of life</a>, a conceptual framework used in biology that <a href="https://doi.org/10.1073/pnas.87.12.4576">represents geneaological relationships</a> between species, has three major limbs, called domains: <a href="https://doi.org/10.1073/pnas.74.11.5088">bacteria, archaea and eukarya</a>.</p>
<p>Eukaryotes are organisms that have a membrane-bound nucleus, and this domain includes animals, plants, fungi and the unicellular microscopic protists. In contrast, bacteria and archaea are single-cell organisms that do not have a membrane-bound nucleus containing the genome. What distinguishes bacteria from archaea is the composition of their cell walls.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/576771/original/file-20240220-22-6gkrf4.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="a figure showing the three branches of the tree of life" src="https://images.theconversation.com/files/576771/original/file-20240220-22-6gkrf4.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/576771/original/file-20240220-22-6gkrf4.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=485&fit=crop&dpr=1 600w, https://images.theconversation.com/files/576771/original/file-20240220-22-6gkrf4.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=485&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/576771/original/file-20240220-22-6gkrf4.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=485&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/576771/original/file-20240220-22-6gkrf4.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=610&fit=crop&dpr=1 754w, https://images.theconversation.com/files/576771/original/file-20240220-22-6gkrf4.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=610&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/576771/original/file-20240220-22-6gkrf4.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=610&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">A schematic tree of life with the primary domains, archaea and bacteria, shown in purple and blue, respectively and the secondary domain, Eukaryotes, in green.</span>
<span class="attribution"><a class="source" href="https://www.eurekalert.org/multimedia/1006461">(Tara Mahendrarajah)</a>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<p>The three domains of life are dramatically different from each other and, genetically, a bacterium is as different from an archaeon as a polar bear (eukarya) is from an <em>E. coli</em> (bacteria). </p>
<p>The expectation was therefore that the genome of a bacterium and of an archaeon would be as far apart as possible in any clustering by any genomic similarity measure. Our finding of some bacteria and archaea clustered together, apparently just because they are both adapted to extreme heat, means that the extreme temperature environment they live in caused pervasive, genome-wide, systemic shifts in their genome language. </p>
<p>This discovery is akin to finding a completely new dimension of the genome, an environmental one, existent in addition to its well-known taxonomic dimension.</p>
<h2>Genomic impact of other environments</h2>
<p>Besides being unexpected, this finding could have implications for our understanding of the evolution of life on Earth, as well as guide our thinking into what it would take to live in outer space. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/576775/original/file-20240220-16-7aq8tz.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="an orange sphere with a tail" src="https://images.theconversation.com/files/576775/original/file-20240220-16-7aq8tz.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/576775/original/file-20240220-16-7aq8tz.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=449&fit=crop&dpr=1 600w, https://images.theconversation.com/files/576775/original/file-20240220-16-7aq8tz.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=449&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/576775/original/file-20240220-16-7aq8tz.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=449&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/576775/original/file-20240220-16-7aq8tz.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=565&fit=crop&dpr=1 754w, https://images.theconversation.com/files/576775/original/file-20240220-16-7aq8tz.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=565&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/576775/original/file-20240220-16-7aq8tz.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=565&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>Pyrococcus furiosus</em>, a thermophilic archaeon that was surprisingly grouped with thermophilic bacteria.</span>
<span class="attribution"><a class="source" href="https://commons.wikimedia.org/wiki/File:P_furiosus.jpg">(Michelle Kropf/Wikimedia Commons)</a>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<p>Indeed, our ongoing research is exploring the existence of an environmental signal in the genomic signature of radiation-resistant extremophiles, such as <a href="https://doi.org/10.1089/ast.2020.2424"><em>Deinococcus radiodurans</em></a>, which can survive radiation exposure, as well as <a href="https://doi.org/10.1101/cshperspect.a012765">cold</a>, <a href="https://doi.org/10.1128/jb.178.3.633-637.1996">dehydration</a>, <a href="https://doi.org/10.3389/fmicb.2019.00909">vacuum conditions</a> and acid, and was shown to be able to survive in <a href="https://doi.org/10.1089/ast.2020.2424">outer space for up to three years</a>.</p><img src="https://counter.theconversation.com/content/219072/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Kathleen A. Hill receives funding from the Natural Sciences and Engineering Research Council of Canada (NSERC).</span></em></p><p class="fine-print"><em><span>Lila Kari receives funding from the Natural Sciences and Engineering Research Council of Canada (NSERC). </span></em></p>Computer analysis of the genomes of extremophiles — organisms that live in extreme environments — reveals that their living conditions are recorded in their DNA.Kathleen A. Hill, Associate Professor Biology, Western UniversityLila Kari, Professor, Computer Science, University of WaterlooLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2232242024-02-21T13:04:38Z2024-02-21T13:04:38ZGut bacteria may explain why grey squirrels outcompete reds – new research<p>Across large parts of the UK, the native red squirrel has been replaced by the grey squirrel, a North American species. As well as endangering reds, grey squirrels pose a threat to our woodlands because of the damage they cause to trees. </p>
<p><a href="https://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.001793">New research</a> from my colleagues and I compared the gut bacteria of red and grey squirrels. We found that differences between the two may explain their competition and red squirrel decline, as well as why grey squirrels are so destructive to woodland.</p>
<p>Grey squirrels were introduced to the UK between 1876 and 1929 and have displaced reds in most areas of the UK. Greys carry a virus called “squirrelpox”, which doesn’t affect them but leads to sickness and often death in red squirrels.</p>
<p>Grey squirrels are bigger than red squirrels and compete with them <a href="https://www.frontiersin.org/articles/10.3389/fevo.2023.1083008/full">for food and habitat</a>.
Acorns, a widespread food source, contain tannins, which are hard for red squirrels to digest. But greys can digest acorns easily, giving them an extra edge in competing for resources. </p>
<p>Grey squirrels frequently strip the bark from deciduous trees. In commercial plantations, the damage can lead to fungal infection and result in the tree producing low quality timber. The annual cost is an <a href="https://rfs.org.uk/insights-publications/rfs-reports/report-overview-the-cost-of-grey-squirrel-damage-to-woodland-in-england-and-wales/">estimated £37 million.</a> with sycamore, oak, birch and beech frequently targeted. </p>
<p>The grey squirrels select the strongest growing trees as these have bark containing the largest volume of sap. Intriguingly, grey squirrels do not select trees with the <a href="https://www.researchgate.net/publication/230344319_Bark-stripping_by_Grey_squirrels_Sciurus_carolinensis">highest sugar content</a>. This observation has led scientists to posit that the squirrels consume bark to obtain <a href="https://www.sciencedirect.com/science/article/pii/S0378112716300421?via%3Dihub">certain micro-nutrients</a>. </p>
<h2>Gut bacteria</h2>
<p>All mammals have microorganisms living in their intestines. For example, the typical human colon is host to at least <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5847071/">160 bacterial species</a>, while in birds, research has found thousands of different bacterial species in <a href="https://pubmed.ncbi.nlm.nih.gov/33868800/">chicken intestines.</a></p>
<p>The bacteria break down foods and help synthesise vitamins, complementing the enzymes secreted by the body. The diversity of these microorganisms, known as the “microbiota”, can reflect the level of health and also the diet of an individual. But we don’t know enough about the microbiota living in squirrel intestines. </p>
<p>The types of microbes present vary between species, yet the extent to which they differ between grey and red squirrels is unclear. We explored this and investigated the potential for any differences to affect competition between the two squirrel species. We also examined whether gut bacteria might be playing a role in bark stripping behaviour.</p>
<p>We sampled bacterial DNA from red and grey squirrel intestinal contents and performed gene sequencing to identify the range of bacteria present in the samples. The results were analysed to compare any important differences between the two.</p>
<figure class="align-center ">
<img alt="A cute red squirrels with a large bushy tail stands on the branch of a tree." src="https://images.theconversation.com/files/576545/original/file-20240219-20-ivfdqj.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/576545/original/file-20240219-20-ivfdqj.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=430&fit=crop&dpr=1 600w, https://images.theconversation.com/files/576545/original/file-20240219-20-ivfdqj.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=430&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/576545/original/file-20240219-20-ivfdqj.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=430&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/576545/original/file-20240219-20-ivfdqj.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=541&fit=crop&dpr=1 754w, https://images.theconversation.com/files/576545/original/file-20240219-20-ivfdqj.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=541&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/576545/original/file-20240219-20-ivfdqj.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=541&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Ynys Môn off the north Wales coast is one of the few places in the UK where greys have been eradicated in favour of red squirrels.</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/red-squirrel-views-around-north-wales-2232607907">Gail Johnson/Shutterstock</a></span>
</figcaption>
</figure>
<h2>Calcium</h2>
<p>Calcium is an important nutrient in the body and is required for healthy bones, muscles and nerves. It is especially needed by lactating animals and ones that are young and growing.</p>
<p>We found that grey squirrels may have the capacity to obtain the calcium that exists in tree bark thanks to the presence of a bacteria called “oxalobacter” in their gut. The calcium in tree bark comes in an insoluble form and is hard for an animal to digest. But oxalobacter would be able to change this into a form that could be more digestible. </p>
<p>Calcium levels <a href="https://www.sciencedirect.com/science/article/pii/S0378112716300421?via%3Dihub">increase in trees</a> as active growth resumes after winter dormancy. This happens immediately before the main squirrel bark-stripping season of May to July. Our research may therefore help to explain the destructive behaviour of grey squirrels and why red squirrels appear to strip bark much less frequently.</p>
<p>Our research also identified a significantly higher diversity of bacteria in the intestines of grey squirrels compared to red squirrels. This could hold the key to further understanding why grey squirrels outcompete red squirrels in the UK. </p>
<p>A more diverse range of bacteria being sustained in the gut means that grey squirrels potentially may be able to access a broader range of resources than red squirrels in addition to acorns.</p>
<h2>Adenovirus</h2>
<p>The grey squirrel harbours not just the squirrelpox virus, but also another potential threat – adenovirus. While this virus causes severe intestinal lesions in some red squirrels, curiously, grey squirrels never exhibit the same symptoms.</p>
<p>This discrepancy underscores the fascinating and complex potential role of gut microbiota. Research increasingly reveals their influence on everything from digestion to immune response, and even susceptibility to disease.</p>
<p>In the context of red squirrels, understanding how variations in their gut bacteria might predispose them to adenovirus becomes crucial. This is especially pertinent for captive breeding programs, where adenovirus infections pose a hurdle to successful reintroductions of red squirrels into the wild.</p>
<p>Given we only sampled red and grey squirrels from north Wales, we hope that future studies will map the gut microbiota of other European populations too. Such future research will continue to improve our knowledge of the competition between red and grey squirrels.</p><img src="https://counter.theconversation.com/content/223224/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Craig Shuttleworth 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 the gut bacteria of red and grey squirrels differ significantly, potentially explaining the decline of the native red and the success of its grey counterpart.Craig Shuttleworth, Honorary Visiting Research Fellow, Bangor UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2225332024-02-14T16:55:57Z2024-02-14T16:55:57ZMen become less fertile with age, but the same isn’t true for all animals – new study<figure><img src="https://images.theconversation.com/files/573049/original/file-20240202-27-wscv4y.jpg?ixlib=rb-1.1.0&rect=0%2C34%2C5833%2C3938&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/colorful-balloons-spermatozoid-shape-on-blue-1100465771">olliulli/Shutterstock</a></span></figcaption></figure><p>We take it for granted that humans find it <a href="https://www.tandfonline.com/doi/full/10.3109/09513590.2010.501889">more difficult to conceive</a> as they grow older. But <a href="https://www.nature.com/articles/s41467-024-44768-4">our recent study</a>, which analysed data from 157 animal species, found that male reproductive ageing seems to be a lot less common in other male animals. </p>
<p>With fertility in men <a href="https://www.bmj.com/content/305/6854/609">declining worldwide</a>, understanding ageing of sperm in other animals could give new insights into our own fertility. </p>
<p>Human fertility declines with age because sperm and eggs of older people are <a href="https://academic.oup.com/humupd/article/11/3/261/759255">more deteriorated</a> or fewer in number than those of young people. Reproducing at an older age not only affects your fertility, but can also <a href="https://www.nature.com/articles/nrurol.2013.18">reduce the fertility</a>, survival rate and physical and cognitive performance of the children you conceive.</p>
<h2>Humans versus other animals</h2>
<p>Humans <a href="https://link.springer.com/article/10.1007/s00239-019-09896-2">live considerably longer</a> than we did just a century ago. This <a href="https://www.pnas.org/doi/full/10.1073/pnas.0909606106">recent, rapid extension</a> in our longevity might be one reason why humans reproductively age at faster rates than other animals. Our reproductive ageing rate hasn’t slowed down yet to match our longer lifespans. </p>
<p>Animals might also face greater evolutionary pressure to maximise their reproductive potential at all ages, because most animals reproduce throughout their lives. But this isn’t the case for humans. We rarely <a href="https://academic.oup.com/humrep/article/29/6/1304/625687">reproduce</a> in our late life. </p>
<p>Additionally, we have <a href="https://academic.oup.com/humrep/article/37/4/629/6515525">fewer offspring</a> compared to our ancestors. This makes it harder for natural selection to select genes that improve human reproduction due to less variation in the population’s fecundity. </p>
<h2>Females versus males</h2>
<p>Males and females in many species age reproductively at different rates. </p>
<p>For instance, in red wolves, male reproductive success declines with age but it <a href="https://link.springer.com/article/10.1007/s00265-016-2241-9">does not</a> for females. Yet female killifish show stronger decline in fertility with age <a href="https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/1365-2656.13382">than males</a>. Despite the fact human females live longer than males, they tend to become infertile <a href="https://www.science.org/doi/abs/10.1126/science.3755843">earlier than men</a>, and go through menopause. </p>
<p>In some species, including humans, where females help raise their grand-offspring (such as humans and whales), females live <a href="https://www.sciencedirect.com/science/article/pii/S0960982218316828?via%3Dihub">much beyond the age</a> of reproduction. An <a href="https://royalsocietypublishing.org/doi/full/10.1098/rsos.191972">evolutionary explanation</a> for this is that older females can better pass on their genes by helping their relatives survive and rear young than by reproducing themselves.</p>
<p>There are some hypotheses that try to explain these <a href="https://onlinelibrary.wiley.com/doi/full/10.1111/acel.13542">sex-specific differences</a> in reproductive ageing. </p>
<p>Sperm are continuously produced in males, but eggs in many species, <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8769179/">including humans</a>, are produced early in the life of females. This might lead eggs to <a href="https://academic.oup.com/humupd/article/6/6/532/616993">accumulate more damage</a> due to being stored for longer durations inside older females than sperm are stored in old males. </p>
<p>Another hypothesis suggests that males might age faster because sperm DNA <a href="https://elifesciences.org/articles/80008">accumulate more</a> mutations than egg DNA. Sperm have poorer DNA repair machinery than eggs, causing males to <a href="https://www.nature.com/articles/s41586-023-05752-y">pass on more mutations</a> to the next generation than females with advancing age, a pattern observed across vertebrate animals.</p>
<p>Sexes also face different environmental pressures. For instance, in many mammals, males, <a href="https://theconversation.com/of-mice-and-matriarchs-the-female-led-societies-of-the-animal-kingdom-186875">but not females</a>, disperse away from the family group when they mature. This sort of environmental pressure leads to differences in the strategies males and females use to pass on their genes, which can create differences in <a href="https://onlinelibrary.wiley.com/doi/full/10.1111/acel.13542">rates of reproductive ageing</a> between the sexes. </p>
<figure class="align-center ">
<img alt="Humpback whale mother with her calf" src="https://images.theconversation.com/files/573052/original/file-20240202-19-valjo5.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/573052/original/file-20240202-19-valjo5.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=397&fit=crop&dpr=1 600w, https://images.theconversation.com/files/573052/original/file-20240202-19-valjo5.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=397&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/573052/original/file-20240202-19-valjo5.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=397&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/573052/original/file-20240202-19-valjo5.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=499&fit=crop&dpr=1 754w, https://images.theconversation.com/files/573052/original/file-20240202-19-valjo5.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=499&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/573052/original/file-20240202-19-valjo5.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=499&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Female whales live long after their reproductive window.</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/humpback-whale-mother-calf-on-tonga-1907017690">Tomas Kotouc/Shutterstock</a></span>
</figcaption>
</figure>
<h2>Patterns of reproductive ageing in animals</h2>
<p>In our study, we showed that reproductive ageing rates in males <a href="https://www.nature.com/articles/s41467-024-44768-4">vary vastly</a> across the animal kingdom. We found invertebrates such as crustacea and insects have some of the slowest rates of reproductive ageing, compared to lab rodents who had some of the fastest rates.
Generally though, male animals showed few signs of age-related declines in their ejaculate traits (such as sperm quality and quantity). </p>
<p>We also found that different ejaculate traits, such as sperm viability, number, motility or velocity, aged at different rates.</p>
<p>In species that grow throughout their lives, such as some fish and crustacea, old animals have a lower mortality risk and larger gonads than young males. This can cause old males <a href="https://royalsocietypublishing.org/doi/full/10.1098/rspb.2021.2146">in such species</a> to age at slower rates, with older males producing larger ejaculates than younger males.</p>
<p>In animals such as lab rodents, who have some genetic lines selected for accelerated ageing, reproductive ageing was universal across ejaculate traits. Lab rodents are generally kept in highly controlled environments where ageing is easier to detect – due to fewer confounding effects that could mask ageing. This suggests that a lot of the variation in male reproductive ageing between different species could be due to their environment. </p>
<p>We also discovered that closely related species showed similar rates of decline in ejaculates with age, suggested that ageing is also shaped by an animal’s evolutionary history. </p>
<p>Some of the patterns we mention above also reflected methodological differences between studies. For example, when studies kept male animals as virgins, old males can <a href="https://www.pnas.org/doi/full/10.1073/pnas.2009053117">accumulate more sperm</a> than young males, leading to old males producing larger ejaculates. </p>
<p>Additionally, studies that only sampled young to middle-aged males showed an increase in sperm quality and quantity with age, compared to studies that sampled middle-aged to old males, suggesting that fertility peaks around middle age in male animals generally.</p>
<h2>Reproductive ageing</h2>
<p>Reproductive ageing occurs because as individuals grow older, their sperm and eggs <a href="https://www.nature.com/articles/nrurol.2013.18">accumulate damage</a>. Organisms have evolved to reproduce earlier in life rather than when old, which leads to a <a href="https://academic.oup.com/genetics/article/156/3/927/6051413">weaker ability of natural selection</a> to weed out bad genes that are expressed in old but not young organisms, in turn promoting ageing.</p>
<p>There are however, opposing forces that determine whether old individuals will leave more copies of their genes to successive lineages compared to young animals, and reproductive ageing is only one process determining this. </p>
<p><a href="https://onlinelibrary.wiley.com/doi/abs/10.1002/bies.201100157">An alternative hypothesis</a> is that parents who conceive at an older age would have more gene variants for longer lifespans which could benefit their offspring. This could lead to longer lived offspring from older conceiving parents. However evidence for this hypothesis is still limited. </p>
<p>While most scientists accept that at least some reproductive traits decline with age, biologists are still uncovering what the exact mechanisms and evolutionary reasons for these declines are. But by looking at other species to investigate the drivers of reproductive ageing, we can understand and perhaps even seek to alleviate our own reproductive decline with age.</p><img src="https://counter.theconversation.com/content/222533/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Krish Sanghvi receives funding from Society for the study of evolution (Rosemary grant award).</span></em></p><p class="fine-print"><em><span>Irem Sepil receives funding from the Royal Society, BBSRC and Wellcome Trust. </span></em></p><p class="fine-print"><em><span>Regina Vega-Trejo receives funding from Biotechnology and Biological Sciences Research Council.</span></em></p>Understanding how the ageing of sperm works in other animals is more important than ever as human male fertility is in decline.Krish Sanghvi, PhD student at the department of Biology, University of Oxford, University of OxfordIrem Sepil, Lecturer in Evolutionary Biology, University of OxfordRegina Vega-Trejo, Postdoctoral Research Assistant in Evolutionary Biology, University of OxfordLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2221002024-02-08T21:32:00Z2024-02-08T21:32:00ZSecrets of soil-enriching pulses could transform future of sustainable agriculture<figure><img src="https://images.theconversation.com/files/574321/original/file-20240208-20-86knbn.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Root nodules of legumes such as soybeans help fix nitrogen into the soil. </span> <span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/development-soybean-root-1248864754">Lidiane Miotto/Shutterstock</a></span></figcaption></figure><p>From lentils to chickpeas, and even the humble baked bean, pulses are perhaps best known as an alternative, plant-based source of protein. These plants are environmental heroes: they work together with soil microbes to “fix” nitrogen from the air, enriching the soil with nutrients to allow them to thrive.</p>
<p>As their nitrogen-fixing capacity is becoming better understood, scientists are hoping to find ways to increase productivity, and eventually apply some of these effective soil-enriching characteristics to other crops such as cereals. With the ability to fix nitrogen, crops would need less nitrogen fertiliser and soil health would simultaneously improve.</p>
<p>Pulses, the edible dry seeds of legume plants, are staple foods in the diets of both people and livestock around the world. Across Europe and the US, they are <a href="https://www.cbi.eu/market-information/grains-pulses-oilseeds/dried-beans/market-potential">commonly eaten</a> as tinned beans, chickpeas and lentils, while in sub-Saharan Africa, <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7794592/">cowpea</a> is among the most important legumes. </p>
<p>High in protein, carbohydrates, dietary fibres, vitamins and minerals, pulses play a fundamental role in <a href="https://www.frontiersin.org/articles/10.3389/fsufs.2022.878269/full">nutritious healthy diets</a>. Both the seeds and leaves are also used as <a href="https://www.un-ilibrary.org/content/books/9789210472579">feed for livestock</a>. For smallholder farmers in developing nations, nutritious pulses are a cost-effective substitute for animal protein and make up a large proportion of typical diets.</p>
<p>In Western Kenya, Rwanda and Burundi, people eat <a href="https://cgspace.cgiar.org/handle/10568/121077">more than 30kg beans a year</a> on average, while many African countries recommend pulses as a meat alternative in <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9370574/">dietary guidelines</a>. Pulses can also be stored for <a href="https://www.sciencedirect.com/science/article/abs/pii/S0022474X14000496">extended periods</a> without affecting their nutritional content.</p>
<h2>The magic inside root nodules</h2>
<p>Some <a href="https://doi.org/10.1016/j.jplph.2022.153765">100 million years ago</a>, legumes developed the natural ability to house beneficial bacteria inside dedicated structures called root nodules. Here, bacteria convert gaseous nitrogen from the air and soil into a form that’s accessible to the plant as nutrients.</p>
<p>So, legumes need less nitrogen fertiliser than cereal and other vegetable crops. A high-performing legume can fix up to <a href="https://www.frontiersin.org/articles/10.3389/fsufs.2021.767998/full">300kg of nitrogen per hectare</a>, which would otherwise cost farmers around $1 per kg in fertiliser to meet the nutrient needs of the plant. </p>
<p>At the <a href="https://www.ensa.ac.uk/">Enabling Nutrient Symbioses in Agriculture</a> project, we are trying to understand how exactly legumes do this. We are exploring how these nitrogen-fixing root nodules evolved in only legumes in the first place. With that knowledge, we hope to find ways to increase the efficiency of nitrogen fixation inside the root nodules and maximise the growth and yield of legume crops.</p>
<figure class="align-center ">
<img alt="microscopic image of pink cells - bacteria inside root nodules close up" src="https://images.theconversation.com/files/574454/original/file-20240208-18-zvrb8w.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/574454/original/file-20240208-18-zvrb8w.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/574454/original/file-20240208-18-zvrb8w.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/574454/original/file-20240208-18-zvrb8w.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/574454/original/file-20240208-18-zvrb8w.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/574454/original/file-20240208-18-zvrb8w.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/574454/original/file-20240208-18-zvrb8w.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Under the microscope, the nitrogen-fixing bacteria inside root nodules of a bean plant can be seen.</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/root-bacteria-nodules-bean-under-microscope-1114612907">ChWeiss/Shutterstock</a></span>
</figcaption>
</figure>
<h2>Beneficial bacteria</h2>
<p>My research group is investigating how legumes can engage with beneficial bacteria and avoid disease-causing microbes. While bacteria like the rhizobia in these root nodules help plants source nutrients, other soil microbes including bacteria and fungi could cause disease and prevent plants from converting as much nitrogen. So the plant must have a defence mechanism that keeps disease-causing microbes at bay. This may also prevent it from fully engaging with beneficial bacteria. </p>
<p>Our team of researchers has identified potential factors that limit nitrogen fixation in the nodules of <em>Medicago</em>, also known as barrel medic or barrel clover. This legume is frequently used for research and not grown for consumption. By studying these limiting factors, we hope to improve the efficiency of nitrogen fixation without affecting the crop’s in-built defence mechanisms to protect it from disease.</p>
<p>Having studied this mechanism in the research legume, researchers are now studying a few relevant crop legumes such as soybean and cowpea to understand how widespread and applicable the underlying biological mechanisms are, and whether they can be harnessed to improve other pulses in the future.</p>
<p>Despite being some of the oldest domesticated crops, many legumes are much less adapted to farming and so have significant potential for further improvement through breeding and genetic engineering, making them more suitable and sustainable for modern food systems.</p>
<p>The benefits of more efficient nitrogen fixing in legumes would include greater growth and biomass and, we hope, higher protein content in the seeds or pulses. This would increase the nutritional value per crop, meaning more high-quality nutrient-rich food could be produced per hectare.</p>
<p>Higher yields would create new opportunities for small-scale and subsistence farmers to grow and benefit from legumes – such as soybean – as cash crops to improve rural livelihoods. More productive legumes could be more effective as a <a href="https://link.springer.com/article/10.1007/s41130-018-0063-z">rotation crop</a> that improves soil health, which is especially important for farmers dealing with degraded soil, such as those found across sub-Saharan Africa. </p>
<p>The more we know about this unique ability of legumes, the greater our chance of successfully developing other crops with a similar ability. Such a development, though some years away, could transform sustainable agriculture, especially in areas where access to synthetic fertiliser is already limited by cost and availability.</p>
<p>Extending nitrogen fixing to other crops has long been an ambition of crop scientists around the world and as the study of plant biology advances, the pulse of progress is quickening.</p>
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<img alt="Imagine weekly climate newsletter" src="https://images.theconversation.com/files/434988/original/file-20211201-21-13avx6y.png?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/434988/original/file-20211201-21-13avx6y.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=600&fit=crop&dpr=1 600w, https://images.theconversation.com/files/434988/original/file-20211201-21-13avx6y.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=600&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/434988/original/file-20211201-21-13avx6y.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=600&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/434988/original/file-20211201-21-13avx6y.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=754&fit=crop&dpr=1 754w, https://images.theconversation.com/files/434988/original/file-20211201-21-13avx6y.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=754&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/434988/original/file-20211201-21-13avx6y.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=754&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
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<hr><img src="https://counter.theconversation.com/content/222100/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Sebastian Schornack receives funding from Bill and Melinda Gates Agricultural Innovations. He is also listed as an inventor on a patent filed by the University of Cambridge on a gene that seems to limit nitrogen fixation.</span></em></p>New technology could unlock the soil-enriching nitrogen-fixing ability of legumes…and one day apply this to other crops too.Sebastian Schornack, Senior research group leader in the Enabling Nutrient Symbioses in Agriculture (ENSA) project, University of CambridgeLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2196832024-02-05T23:06:31Z2024-02-05T23:06:31ZGenetic diseases: How scientists are working to make DNA repair (almost) a piece of cake<figure><img src="https://images.theconversation.com/files/564984/original/file-20231101-27-722eas.jpg?ixlib=rb-1.1.0&rect=5%2C0%2C992%2C561&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">An error in DNA is called a mutation.</span> <span class="attribution"><span class="source">(Shutterstock)</span></span></figcaption></figure><p>I have always been fascinated by genetics, a branch of biology that helps explain everything from the striking resemblance between different members of a family to the fact that strawberry plants are frost-resistant. It’s an impressive field!</p>
<p>I also have a personal connection to genetics. Growing up, I learned that members of my family had a form of <a href="https://doi.org/10.3390/jcm12186011">muscular dystrophy</a> called dysferlinopathy. I watched as my mother gradually lost the ability to climb stairs and had to use a cane, then a walker, and finally a wheelchair to get around. Her leg muscles were less and less able to repair themselves and became weaker with time.</p>
<p>My parents explained to me that all these changes were due to the error of a single letter among the billions of letters in a long DNA sequence. This error prevents the production of the protein <a href="https://doi.org/10.3390/jcm12144769">responsible for repairing arm and leg muscles</a>.</p>
<p>Today, I am a doctoral research student in molecular medicine. I study the treatment of hereditary diseases in order to be able to help families like my own. In this article, I will demystify hereditary diseases and show what research is being carried out to treat them.</p>
<h2>A piece of cake? Not quite</h2>
<p>Let’s start by imagining DNA as a recipe book. Each gene represents a different recipe. The page with the chocolate cake recipe has a nice picture, but there is some information missing. The recipe says to preheat the oven and measure the flour, but the rest of the page is torn. So it is impossible to make the cake. We go ahead and serve our meal made from all the other recipes, but there is no chocolate cake even though this is a particularly important part of the meal.</p>
<p>The same is true for hereditary diseases. In this case, the body can make all the proteins it needs except one. In dysferlinopathy, which affects my family, the missing recipe is the protein that repairs the muscles of the arms and legs. Each hereditary disease has its own damaged page in its recipe book.</p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/580032/original/file-20240305-21577-nvf7ba.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/580032/original/file-20240305-21577-nvf7ba.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=426&fit=crop&dpr=1 600w, https://images.theconversation.com/files/580032/original/file-20240305-21577-nvf7ba.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=426&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/580032/original/file-20240305-21577-nvf7ba.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=426&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/580032/original/file-20240305-21577-nvf7ba.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=535&fit=crop&dpr=1 754w, https://images.theconversation.com/files/580032/original/file-20240305-21577-nvf7ba.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=535&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/580032/original/file-20240305-21577-nvf7ba.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=535&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">A mutation can cause the absence of a protein that has its own function.</span>
<span class="attribution"><span class="source">(Camille Bouchard)</span>, <span class="license">Fourni par l'auteur</span></span>
</figcaption>
</figure>
<p>To be precise, an error in the DNA is called a mutation. There are different types of mutations. Some are caused by adding letters, like adding an ingredient to the recipe. This addition could lead to a delicious chocolate cake with strawberries, or to a cake that is no longer edible because we added motor oil to it.</p>
<p>Other mutations are caused by the removal (or elimination) of one or more letters (or ingredients), or by substitutions that replace one letter with another. All of these modifications can lead to favourable or non-impactful changes, such as the appearance of the first blue eyes in evolution, or the ability to breathe outside of water. But these modifications can also bring about unfavourable results, such as a hereditary disease or cancer.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/565888/original/file-20231214-19-3u3el2.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/565888/original/file-20231214-19-3u3el2.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/565888/original/file-20231214-19-3u3el2.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=616&fit=crop&dpr=1 600w, https://images.theconversation.com/files/565888/original/file-20231214-19-3u3el2.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=616&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/565888/original/file-20231214-19-3u3el2.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=616&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/565888/original/file-20231214-19-3u3el2.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=774&fit=crop&dpr=1 754w, https://images.theconversation.com/files/565888/original/file-20231214-19-3u3el2.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=774&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/565888/original/file-20231214-19-3u3el2.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=774&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">There are different types of mutations.</span>
<span class="attribution"><span class="source">(Camille Bouchard)</span>, <span class="license">Fourni par l'auteur</span></span>
</figcaption>
</figure>
<h2>Repairing DNA</h2>
<p>From a young age, I understood that my mother was sick due to the error of a gene, but that I would not develop the disease because my father did not have the same error. This is called a recessive disease, since there must be an error in the gene of each of the two parents in order for the disease to manifest. Other hereditary diseases are dominant, meaning that a mutation in the DNA passed down from just one parent is enough to impair the production of a protein.</p>
<p>As part of my research, I look at the DNA sequence of each dysferlinopathy patient to see where the error is.</p>
<p>To try to correct it, I use <a href="https://doi.org/10.3390/cells12040536">Prime editing</a>, a technique which makes it possible to cut the DNA near the mutation and rewrite the sequence correctly. Prime editing is a version of <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4975809/">CRISPR-Cas9</a>, a technique that allows DNA to be cut at a particular location.</p>
<p>Prime editing uses a protein called Cas9, which occurs naturally in bacteria. This protein allows bacteria to destroy the DNA sequences of viruses that could infect them. The mission of the Cas9 protein is to recognize a sequence and cut it.</p>
<p>When we use Cas9 in our human cells, we attach it to another protein, which rewrites the DNA sequence based on a template. In other words, we give the cell an error-free sequence so that it can go ahead and manufacture the protein on its own. It’s a bit like recovering the original page of the recipe book so you can finally serve the chocolate cake.</p>
<h2>A step in the right direction</h2>
<p>So why aren’t we hearing about Prime editing, when it could be used to treat a variety of diseases? Because the technology is not yet fully developed. At the moment we are able to repair DNA directly in cells in the laboratory, but we lack the means to deliver the two large proteins (Cas9 and the one that rewrites) to the cells to be treated (for example, to the centre of the affected muscles).</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/565889/original/file-20231214-21-z2b726.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/565889/original/file-20231214-21-z2b726.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/565889/original/file-20231214-21-z2b726.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=434&fit=crop&dpr=1 600w, https://images.theconversation.com/files/565889/original/file-20231214-21-z2b726.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=434&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/565889/original/file-20231214-21-z2b726.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=434&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/565889/original/file-20231214-21-z2b726.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=546&fit=crop&dpr=1 754w, https://images.theconversation.com/files/565889/original/file-20231214-21-z2b726.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=546&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/565889/original/file-20231214-21-z2b726.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=546&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Prime editing is a technique being studied to correct mutations in different genes.</span>
<span class="attribution"><span class="source">(Camille Bouchard)</span>, <span class="license">Fourni par l'auteur</span></span>
</figcaption>
</figure>
<p>In other words, we have found the chocolate cake recipe, but it’s written on a page that is too large to fit in an email or put in an envelope. Many laboratories, including mine, are looking for an efficient and safe vehicle that will be able to deliver these proteins.</p><img src="https://counter.theconversation.com/content/219683/count.gif" alt="La Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Camille Bouchard received funding from the Jain Foundation and the Fondation du CHU de Québec.</span></em></p>Many people know someone with a genetic disease, but few understand how gene mutations work.Camille Bouchard, Étudiante au doctorat en médecine moléculaire (correction génétique de maladies héréditaires), Université LavalLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2206292024-01-31T13:36:25Z2024-01-31T13:36:25Z‘Jaws’ portrayed sharks as monsters 50 years ago, but it also inspired a generation of shark scientists<figure><img src="https://images.theconversation.com/files/572002/original/file-20240129-17-8m3oe7.jpg?ixlib=rb-1.1.0&rect=37%2C0%2C4952%2C3261&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">A paleontologist wears a T-shirt showing _Strophodus rebecae_, a shark species with flat teeth that lived millions of years ago.</span> <span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/news-photo/palaeontologist-edwin-cadena-shows-a-t-shirt-with-an-image-news-photo/1241210531">Juan Pablo Pino/AFP via Getty Images</a></span></figcaption></figure><p>Human fear of sharks has deep roots. Written works and art from the ancient world contain references to <a href="https://www.artmajeur.com/en/magazine/5-art-history/sharks-in-art/331942">sharks preying on sailors</a> as early as the eighth century B.C.E. </p>
<p>Relayed back to land, stories about shark encounters have been <a href="https://etc.usf.edu/lit2go/42/moby-dick/747/chapter-66-the-shark-massacre/">embellished and amplified</a>. Together with the fact that from time to time – very rarely – sharks bite humans, people have been primed for centuries to imagine terrifying situations at sea.</p>
<p>In 1974, Peter Benchley’s <a href="https://www.penguinrandomhouse.ca/books/11203/jaws-by-peter-benchley/9780345544148/excerpt">bestselling novel “Jaws</a>” fanned this fear into a wildfire that spread around the world. The book sold more than 5 million copies in the U.S. within a year and was quickly followed by <a href="https://www.imdb.com/title/tt0073195/">Steven Spielberg’s 1975 movie</a>, which became the highest-grossing film in history at that time. Virtually all audiences embraced the idea, depicted vividly in the movie and its sequels, that sharks were malevolent, vindictive creatures that prowled coastal waters seeking to feed on unsuspecting bathers. </p>
<p>But “Jaws” also spawned widespread interest in better understanding sharks. </p>
<p>Previously, shark research had largely been the esoteric domain of a handful of academic specialists. Thanks to interest sparked by “Jaws,” we now know that there are many more kinds of sharks than scientists were aware of in 1974, and that sharks do more interesting things than researchers ever anticipated. Benchley himself became an avid <a href="https://www.latimes.com/archives/la-xpm-2006-feb-13-me-benchley13-story.html">spokesman for shark protection and marine conservation</a>.</p>
<p>In my own 30-year career studying <a href="https://scholar.google.com/citations?user=FKrC4FYAAAAJ&hl=en">sharks and their close relatives, skates and rays</a>, I’ve seen attitudes evolve and interest in understanding sharks expand enormously. Here’s how things have changed.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/572000/original/file-20240129-27-l4g7ei.jpg?ixlib=rb-1.1.0&rect=32%2C8%2C5434%2C3630&q=45&auto=format&w=1000&fit=clip"><img alt="A man stands on the prow of a boat, extending a pole into the water toward a large dark shape." src="https://images.theconversation.com/files/572000/original/file-20240129-27-l4g7ei.jpg?ixlib=rb-1.1.0&rect=32%2C8%2C5434%2C3630&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/572000/original/file-20240129-27-l4g7ei.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/572000/original/file-20240129-27-l4g7ei.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/572000/original/file-20240129-27-l4g7ei.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/572000/original/file-20240129-27-l4g7ei.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/572000/original/file-20240129-27-l4g7ei.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/572000/original/file-20240129-27-l4g7ei.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">Marine biologist Greg Skomal of the Massachusetts Division of Marine Fisheries captures video footage of a white shark off Cape Cod, Oct. 21, 2022.</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/news-photo/dr-greg-skomal-shark-researcher-for-massachusetts-marine-news-photo/1244267691">Joseph Prezioso/AFP via Getty Images</a></span>
</figcaption>
</figure>
<h2>Swimming into the spotlight</h2>
<p>Before the mid-1970s, much of what was known about sharks came via people who went to sea. In 1958, the U.S. Navy established the <a href="https://www.floridamuseum.ufl.edu/shark-attacks/">International Shark Attack File</a> – the world’s only scientifically documented, comprehensive database of all known shark attacks – to reduce wartime risks to sailors stranded at sea when their ships sank. </p>
<p>Today the file is managed by the <a href="https://www.floridamuseum.ufl.edu/">Florida Museum of Natural History</a> and the <a href="https://elasmo.org/">American Elasmobranch Society</a>, a professional organization for shark researchers. It works to inform the public about shark-human interactions and ways to reduce the risk of shark bites.</p>
<p>In 1962, <a href="https://www.fisheries.noaa.gov/feature-story/john-jack-casey-internationally-recognized-shark-researcher-mentor-and-narragansett">Jack Casey</a>, a pioneer of modern shark research, initiated the <a href="https://www.fisheries.noaa.gov/resource/document/cooperative-shark-tagging-program">Cooperative Shark Tagging Program</a>. This initiative, which is still running today, relied on Atlantic commercial fishermen to report and return tags they found on sharks, so that government scientists could calculate how far the sharks had moved after being tagged. </p>
<p>After “Jaws,” shark research quickly went mainstream. The American Elasmobranch Society was founded in 1982. Graduate students lined up to study shark behavior, and the number of published shark studies <a href="https://thefisheriesblog.com/2015/06/15/thank-you-jaws-the-upside-for-sharks-40-years-later/">sharply increased</a>.</p>
<p><div data-react-class="InstagramEmbed" data-react-props="{"url":"https://www.instagram.com/reel/Cz6muU6u3Mn/?utm_source=ig_web_copy_link\u0026igsh=MzRlODBiNWFlZA==","accessToken":"127105130696839|b4b75090c9688d81dfd245afe6052f20"}"></div></p>
<p>Field research on sharks expanded in parallel with growing interest in extreme outdoor sports like surfing, parasailing and scuba diving. Electronic tags enabled researchers to monitor sharks’ movements in real time. DNA sequencing technologies provided cost-effective ways to determine how different species were related to one another, what they were eating and how populations were structured.</p>
<p>This interest also had a sensational side, embodied in the Discovery Channel’s launch in 1988 of <a href="https://www.discovery.com/shark-week">Shark Week</a>. This annual block of programming, ostensibly designed to educate the public about shark biology and counter negative publicity about sharks, was a commercial venture that exploited the tension between people’s deep-seated fear of sharks and their yearning to understand what made these animals tick. </p>
<p>Shark Week featured made-for-TV stories that focused on <a href="https://www.washingtonpost.com/news/arts-and-entertainment/wp/2018/07/26/a-fake-shark-week-documentary-about-megalodons-caused-controversy-why-is-discovery-bringing-it-up-again/">fictional scientific research projects</a>. It was wildly successful and remains so today, in spite of critiques from some researchers who call it <a href="https://theconversation.com/beware-of-shark-week-scientists-watched-202-episodes-and-found-them-filled-with-junk-science-misinformation-and-white-male-experts-named-mike-195180">a major source of misinformation</a> about sharks and shark science.</p>
<h2>Physical, social and genetic insights</h2>
<p>Contrary to the long-held notion that sharks are mindless killers, they exhibit a wide range of traits and behavior. For example, the velvet belly lantern shark communicates through flashes of light from <a href="https://doi.org/10.4161/cib.4.3.14888">organs on the sides of its body</a>. Female hammerhead sharks can <a href="http://dx.doi.org/10.1098/rsbl.2007.0189">clone perfect replicas of themselves</a> without male sperm. </p>
<p>Sharks have the most sensitive electrical detectors thus far discovered in the natural world – networks of pores and nerves in their heads, known as <a href="https://www.scienceandthesea.org/program/201105/ampullae-lorenzini">ampullae of Lorenzini</a>, after Italian scientist Stefano Lorenzini, who first described these features in the 17th century. Sharks use these networks to navigate in the open ocean, <a href="https://doi.org/10.1016/j.cub.2021.03.103">using Earth’s magnetic field for orientation</a>. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/572016/original/file-20240129-17-i6lyza.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Three snorkelers swim above a large spotted shark." src="https://images.theconversation.com/files/572016/original/file-20240129-17-i6lyza.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/572016/original/file-20240129-17-i6lyza.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/572016/original/file-20240129-17-i6lyza.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/572016/original/file-20240129-17-i6lyza.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/572016/original/file-20240129-17-i6lyza.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/572016/original/file-20240129-17-i6lyza.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/572016/original/file-20240129-17-i6lyza.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">Snorkelers swim above a whale shark near the Maldives in the Indian Ocean. The largest fish in the sea, whale sharks are filter feeders that prey on plankton.</span>
<span class="attribution"><a class="source" href="https://flic.kr/p/gTntz7">Tchami/Flickr</a>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span>
</figcaption>
</figure>
<p>Another intriguing discovery is that some shark species, including makos and blue sharks, <a href="http://dx.doi.org/10.1098/rsbl.2008.0761">segregate by both sex and size</a>. Among these species, cohorts of males and females of different sizes are often found in distinct groups. This finding suggests that some sharks may have <a href="https://www.britannica.com/topic/hierarchy-social-science">social hierarchies</a>, like those seen in some primates and hoofed mammals. </p>
<p>Genetic studies have helped researchers explore questions such as why some sharks <a href="https://theconversation.com/why-do-hammerhead-sharks-have-hammer-shaped-heads-184372">have heads shaped like hammers or shovels</a>. They also show that sharks have the <a href="https://doi.org/10.1038/s41467-023-42238-x">lowest mutation rate of any vertebrate animal</a>. This is notable because mutations are the raw material for evolution: The higher the mutation rate, the better a species can adapt to environmental change. </p>
<p>However, sharks have been around for 400 million years and have been through some of the most extreme environmental changes on earth. It’s not known yet how they have persisted so successfully with such a low mutation rate.</p>
<figure>
<iframe width="440" height="260" src="https://www.youtube.com/embed/punSQuf-ZwQ?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">Gavin Naylor, director of the Florida Program for Shark Research, describes how DNA analysis provides insights into shark science.</span></figcaption>
</figure>
<h2>The marquee species</h2>
<p>White sharks, the focal species of “Jaws,” attract enormous public interest, although much about them is still unknown. They can live to age 70, and they routinely swim thousands of miles every year. Those in the Western North Atlantic tend to move north-south between Canada and the Gulf of Mexico; white sharks on the U.S. west coast move east-west between California and the Central Pacific. </p>
<p>We now know that juvenile white sharks feed almost exclusively on fishes and stingrays, and don’t start incorporating seals and other marine mammals into their diets until they are the equivalent of teenagers and have grown to about 12 feet long. Most confirmed white shark bites on humans seem to be by animals that are between 12 and 15 feet long. This supports the theory that almost all bites by white sharks on humans are <a href="https://doi.org/10.1098/rsif.2021.0533">cases of mistaken identity</a>, where humans resemble the seals that sharks prey on.</p>
<p><iframe id="9y7JJ" class="tc-infographic-datawrapper" src="https://datawrapper.dwcdn.net/9y7JJ/2/" height="400px" width="100%" style="border: none" frameborder="0"></iframe></p>
<h2>Still in the water</h2>
<p>Although “Jaws” had a <a href="https://www.today.com/popculture/jaws-took-chomp-out-pop-culture-40-years-ago-1d79919594">widespread cultural impact</a>, it didn’t keep surfers and bathers from enjoying the ocean. </p>
<p>Data from the International Shark Attack File on confirmed unprovoked bites by white sharks from the 1960s to the present day shows a continuous increase, although the number of incidents yearly is quite low. This pattern is consistent with growing numbers of people <a href="https://coast.noaa.gov/states/fast-facts/tourism-and-recreation.html">pursuing recreational activities at the coasts</a>. </p>
<p>Around the world, there have been 363 <a href="https://www.floridamuseum.ufl.edu/shark-attacks/maps/world-interactive/">confirmed, unprovoked bites by white sharks</a> since 1960. Of these, 73 were fatal. The World Health Organization estimates that there are <a href="https://www.who.int/news-room/fact-sheets/detail/drowning">236,000 deaths yearly due to drowning</a>, which translates to around 15 million drowning deaths over the same time period. </p>
<p>In other words, people are roughly 200,000 times more likely to drown than to die from a white shark bite. Indeed, surfers are more likely to die in a car crash on the way to the beach than they are to be bitten by a shark.</p><img src="https://counter.theconversation.com/content/220629/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Gavin Naylor receives funding from the National Science Foundation and the Lenfest Foundation.</span></em></p>‘Jaws,’ published in 1974, terrified the public of sharks, but it also brought shark research into the scientific mainstream.Gavin Naylor, Director of Florida Program for Shark Research, University of FloridaLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2196202024-01-18T16:38:26Z2024-01-18T16:38:26ZDNA from stone age chewing gum sheds light on diet and disease in Scandinavia’s ancient hunter-gatherers<figure><img src="https://images.theconversation.com/files/570142/original/file-20240118-27-aehxwa.jpg?ixlib=rb-1.1.0&rect=0%2C0%2C464%2C352&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">A mold cast of one of the chewed pitch pieces.</span> <span class="attribution"><span class="source">Verner Alexandersen</span>, <span class="license">Author provided</span></span></figcaption></figure><p>Some 9,700 years ago on an autumn day, a group of people were camping on the west coast of Scandinavia. They were hunter-gatherers that had been fishing, hunting and collecting resources in the area. </p>
<p>Some teenagers, both boys and girls, were chewing resin to produce glue, just after eating trout, deer and hazelnuts. Due to a severe gum infection (periodontitis), one of the teenagers had problems eating the chewy deer-meat, as well as preparing the resin by chewing it.</p>
<p>This snapshot of the Mesolithic period, just before Europeans started farming, comes from analysis of DNA left in the chewed resin that we have conducted, now <a href="https://www.nature.com/articles/s41598-023-48762-6">published in Scientific Reports</a>. </p>
<p>The location is now known as <a href="https://lup.lub.lu.se/search/publication/3c1fd58a-9495-4403-ab7d-d22104f2fafb">Huseby Klev</a>, situated north of Gothenburg (Göteborg), Sweden. <a href="https://www.cambridge.org/core/journals/antiquity/article/abs/wet-and-the-wild-followed-by-the-dry-and-the-tame-or-did-they-occur-at-the-same-time-diet-in-mesolithic-neolithic-southern-sweden/D91F7830FE704FD24DFAFB55E551039B">It was excavated</a> by archaeologists in the early 1990s, and yielded some 1,849 flint artefacts and 115 pieces of resin (mastic). The site has been radiocarbon dated to between 10,200 and 9,400 years ago, with one of the pieces of resin dated to 9,700 years ago.</p>
<p>Some of the resin has teeth imprints, indicating that children, actually teenagers, had been chewing them. Masticated lumps, often with imprints of teeth, fingerprints or both, are not uncommon to find in Mesolithic sites. </p>
<p>The pieces of resin we have analysed were made of <a href="https://www.nature.com/articles/s41467-019-13549-9">birch bark pitch</a>, which is known to have been used as an <a href="https://phys.org/news/2019-08-neanderthal-tool-making-simpler-previously-thought.html">adhesive substance in stone tool technology</a> from the Middle Palaeolithic onward. However, they were also chewed for recreational or medicinal purposes in traditional societies.</p>
<p>A variety of substances with similar properties, such as resins from coniferous trees, natural bitumen, and other plant gums, are known to have been used in analogous ways in many parts of the world.</p>
<h2>The power of DNA</h2>
<p>In some of the resin, half the <a href="https://www.nature.com/articles/s42003-019-0399-1">DNA extracted</a> was of human origin. This is a lot compared to what we often find in ancient bones and teeth. </p>
<p>It represents some of the oldest human genomes from Scandinavia. It has a particular ancestry profile common among Mesolithic hunter gatherers who once lived there. </p>
<p>Some of the resin contains male human DNA while others have female DNA. We think that teenagers of both sexes were preparing glue for use in tool making, such as attaching a stone axe to a wooden handle.</p>
<p>But what of the other half of the DNA that was of non-human origin? Most of this DNA is from organisms such as bacteria and fungi that have lived in the mastic since it was discarded 9,700 years ago. But some of it was from bacteria living in the human that chewed it, along with material the human had been chewing on before they put the birch bark pitch in their mouths.</p>
<p>Analysing all this DNA is a demanding task and treads new ground. We had to both adapt existing computing tools and also develop some new analytical strategies. As such, this work has become the starting point for developing a new workflow for this kind of analysis. </p>
<p>This includes mining the DNA using different strategies to characterise it, trying to piece together short DNA fragments into longer ones and using machine learning techniques to work out which DNA fragments belong to pathogens (harmful microorganisms). It also involves comparing the data to what we see in the mouths of modern people with <a href="https://www.ncbi.nlm.nih.gov/books/NBK551699/">tooth decay (caries)</a> and periodontitis.</p>
<h2>Higher organisms</h2>
<p>Naturally, we found the kind of bacteria that would be expected in an oral microbiome, the range of naturally occurring microorganisms found in the mouth. We also found traces of bacteria implicated in conditions such as tooth decay or caries (<em>Streptococcus mutans</em>), and systemic diseases such as Hib disease and endocarditis. There were also bacteria that can cause abscesses. </p>
<p>Although these pathogenic microorganisms were present at an elevated frequency, they were not clearly above the level expected for a healthy oral microbiome. There is thus no conclusive evidence that members of the group suffered from diseases these microorganisms are associated with. </p>
<p>What we did find, however, was an abundance of bacteria associated with serious gum disease – <a href="https://www.mayoclinic.org/diseases-conditions/periodontitis/symptoms-causes/syc-20354473">periodontitis</a>. When we applied a <a href="https://www.ibm.com/topics/machine-learning">machine learning</a> strategy (in this case, a technique called <a href="https://www.ibm.com/topics/random-forest">Random Forest modelling</a>) we reached the conclusion that the girl who chewed one of the pieces of resin had probably suffered from periodontitis – with more than a 75% probability.</p>
<p>We also found DNA from larger organisms than just bacteria. We found DNA for red deer, brown trout and hazelnuts. This DNA probably came from material the teenagers had been chewing before they put the birch pitch in their mouths. </p>
<p>However, we need to be a little bit cautious because exactly what we find is also dependent on the comparison data that we have. As genomes from eukaryotic organisms – the group that includes plants and animals – <a href="https://www.ncbi.nlm.nih.gov/books/NBK9846/">are larger and more complex</a> than those from microorganisms, it is more complicated to assemble a eukaryotic genome of high quality. </p>
<p>There are fewer eukaryotic genomes in the samples of resin, and they are of lower quality. This means that our brown trout, for example, may not actually be a brown trout, but we at least feel certain it is from the salmon family.</p>
<p>We also found a lot of fox DNA, but this is harder to interpret. Fox meat may have been a part of the diet, but these teenagers could also have chewed on tendons and fur from foxes for use in textiles. Alternatively, the fox DNA could even be from territorial marking and got into the resin after it was spat out.</p>
<p>However, what we have learned for sure represents a big step in understanding these fascinating records of human culture from the Stone Age. As we analyse more of these, even more surprises could emerge.</p><img src="https://counter.theconversation.com/content/219620/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Anders Götherström receives funding from: the Swedish Research Council (2019-00849_VR), Riksbankens Jubileumsfond (P16-0553:1)</span></em></p><p class="fine-print"><em><span>Emrah Kırdök does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>Genetic analysis reveals one of the teenagers probably had advanced gum disease.Anders Götherström, Professor in Molecular Archaeology, Department of Archaeology and Classical Studies, Stockholm UniversityEmrah Kırdök, Assistant Professor, Department of Biotechnology, Mersin UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2173792024-01-09T19:15:56Z2024-01-09T19:15:56ZViruses aren’t always harmful. 6 ways they’re used in health care and pest control<figure><img src="https://images.theconversation.com/files/564112/original/file-20231207-20-amgv6b.jpg?ixlib=rb-1.1.0&rect=33%2C67%2C5573%2C3665&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/male-nurse-pushing-stretcher-gurney-bed-156022646">Shutterstock</a></span></figcaption></figure><p>We tend to just think of viruses in terms of their damaging impacts on human health and lives. <a href="https://blogs.cdc.gov/publichealthmatters/2018/05/1918-flu/">The 1918 flu pandemic</a> killed around 50 million people. <a href="https://www.cdc.gov/smallpox/about/index.html">Smallpox</a> claimed 30% of those who caught it, and survivors were often scarred and blinded. More recently, we’re all too familiar with the health and economic impacts of COVID. </p>
<p>But viruses can also be used to benefit human health, agriculture and the environment. </p>
<p>Viruses are comparatively simple in <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7150055/">structure</a>, consisting of a piece of genetic material (RNA or DNA) enclosed in a protein coat (the capsid). Some also have an outer envelope. </p>
<p>Viruses get into your cells and use your cell machinery to copy themselves.
Here are six ways we’ve harnessed this for health care and pest control. </p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/how-do-viruses-get-into-cells-their-infection-tactics-determine-whether-they-can-jump-species-or-set-off-a-pandemic-216139">How do viruses get into cells? Their infection tactics determine whether they can jump species or set off a pandemic</a>
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</p>
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<h2>1. To correct genes</h2>
<p>Viruses are used in some gene therapies to correct <a href="https://www.mdpi.com/1999-4915/15/3/698#">malfunctioning genes</a>. <a href="https://www.genome.gov/genetics-glossary/Gene">Genes</a> are DNA sequences that code for a particular protein required for cell function. </p>
<p>If we remove viral genetic material from the capsid (protein coat) we can use the space to transport a “cargo” into cells. These modified viruses are called “<a href="https://www.nature.com/articles/s41392-021-00487-6">viral vectors</a>”. </p>
<figure class="align-right ">
<img alt="" src="https://images.theconversation.com/files/564099/original/file-20231207-15-g0knkm.png?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/564099/original/file-20231207-15-g0knkm.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=401&fit=crop&dpr=1 600w, https://images.theconversation.com/files/564099/original/file-20231207-15-g0knkm.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=401&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/564099/original/file-20231207-15-g0knkm.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=401&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/564099/original/file-20231207-15-g0knkm.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=504&fit=crop&dpr=1 754w, https://images.theconversation.com/files/564099/original/file-20231207-15-g0knkm.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=504&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/564099/original/file-20231207-15-g0knkm.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">
<figcaption>
<span class="caption">Viruses consist of a piece of RNA or DNA enclosed in a protein coat called the capsid.</span>
<span class="attribution"><a class="source" href="https://en.wikipedia.org/wiki/Introduction_to_viruses#/media/File:Basic_Scheme_of_Virus_en.svg">DEXi</a></span>
</figcaption>
</figure>
<p>Viral vectors can <a href="https://www.nature.com/articles/s41392-021-00487-6">deliver a functional gene</a> into someone with a genetic disorder whose own gene is not working properly. </p>
<p>Some <a href="https://www.mdpi.com/1999-4915/15/3/698#">genetic diseases</a> treated this way include haemophilia, sickle cell disease and beta thalassaemia. </p>
<h2>2. Treat cancer</h2>
<p>Viral vectors can be used to treat cancer. </p>
<p>Healthy people have p53, a tumour-suppressor gene. About <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8884858/">half</a> of cancers are associated with the loss of p53. </p>
<p>Replacing the damaged p53 gene using a viral vector stops the cancerous cell from replicating and tells it to suicide (<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3756401/">apoptosis</a>). </p>
<p>Viral vectors can also be used to deliver an <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8884858/">inactive drug</a> to a tumour, where it is then activated to kill the tumour cell. </p>
<p>This targeted therapy reduces the side effects otherwise seen with cytotoxic (cell-killing) drugs. </p>
<figure>
<iframe width="440" height="260" src="https://www.youtube.com/embed/Q6qk6Wh6cXU?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">Here’s how treatment, called gene therapy, works.</span></figcaption>
</figure>
<p>We can also use <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9888358/">oncolytic</a> (cancer cell-destroying) viruses to treat some types of cancer. </p>
<p>Tumour cells have often lost their antiviral defences. In the case of <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8884858/">melanoma</a>, a modified herpes simplex virus can kill rapidly dividing melanoma cells while largely leaving non-tumour cells alone. </p>
<h2>3. Create immune responses</h2>
<p>Viral vectors can create a protective immune response to a particular viral antigen. </p>
<p>One <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9317404/">COVID vaccine</a> uses a modified chimp adenovirus (adenoviruses cause the common cold in humans) to transport RNA coding for the SARS-CoV-2 spike protein into human cells. </p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/how-the-puzzle-of-viral-vector-vaccines-was-solved-leading-to-todays-covid-19-shots-167341">How the puzzle of viral vector vaccines was solved, leading to today’s COVID-19 shots</a>
</strong>
</em>
</p>
<hr>
<p>The RNA is then used to make spike protein copies, which stimulate our immune cells to replicate and “remember” the spike protein. </p>
<p>Then, when you are exposed to SARS-CoV-2 for real, your immune system can churn out lots of antibodies and virus-killing cells very quickly to prevent or reduce the severity of infection. </p>
<h2>4. Act as vaccines</h2>
<p>Viruses can be modified to act directly as vaccines themselves <a href="https://www.hhs.gov/immunization/basics/types/index.html">in several ways</a>. </p>
<p>We can weaken a virus (for an attenuated virus vaccine) so it doesn’t cause infection in a healthy host but can still replicate to stimulate the immune response. The chickenpox vaccine works like this. </p>
<p>The Salk vaccine for polio uses a whole virus that has been inactivated (so it can’t cause disease). </p>
<p>Others use a small part of the virus such as a capsid protein to stimulate an immune response (subunit vaccines). </p>
<p>An mRNA vaccine packages up viral RNA for a specific protein that will stimulate an immune response. </p>
<h2>5. Kill bacteria</h2>
<p>Viruses can – in limited situations <a href="https://phage.directory/capsid/phage-therapy-regulation-australia">in Australia</a> – be used to treat antibiotic-resistant bacterial infections.</p>
<p><a href="https://www.ncbi.nlm.nih.gov/books/NBK493185/">Bacteriophages</a> are viruses that kill bacteria. Each type of phage usually infects a particular species of bacteria. </p>
<p>Unlike antibiotics – which often kill “good” bacteria along with the disease-causing ones – phage therapy leaves your normal flora (useful microbes) intact. </p>
<figure class="align-center ">
<img alt="A phage" src="https://images.theconversation.com/files/564113/original/file-20231207-19-7ruzur.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/564113/original/file-20231207-19-7ruzur.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/564113/original/file-20231207-19-7ruzur.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/564113/original/file-20231207-19-7ruzur.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/564113/original/file-20231207-19-7ruzur.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/564113/original/file-20231207-19-7ruzur.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/564113/original/file-20231207-19-7ruzur.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">
<figcaption>
<span class="caption">Bacteriophages (red) are viruses that kill bacteria (green).</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/image-illustration/bacteriophages-viruses-that-attack-infect-bacteria-1391256956">Shutterstock</a></span>
</figcaption>
</figure>
<h2>6. Target plant, fungal or animal pests</h2>
<p>Viruses can be species-specific (infecting one species only) and even cell-specific (infecting one type of cell only). </p>
<p>This occurs because the proteins viruses use to attach to cells have a shape that binds to <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6083867/#">a specific type of cell receptor</a> or molecule, like a specific key fits a lock. </p>
<p>The virus can enter the cells of all species with this receptor/molecule. For example, <a href="https://www.cdc.gov/rabies/animals/index.html">rabies virus</a> can infect all mammals because we share the right receptor, and mammals have other characteristics that allow infection to occur whereas other non-mammal species don’t. </p>
<p>When the receptor is only found on one cell type, then the virus will infect that cell type, which may only be found in one or a limited number of species. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5869238/">Hepatitis B virus</a> successfully infects liver cells primarily in humans and chimps. </p>
<p>We can use that property of specificity to target <a href="https://pubmed.ncbi.nlm.nih.gov/37682594/">invasive plant species</a> (reducing the need for chemical herbicides) and pest insects (reducing the need for chemical insecticides). <a href="https://www.tandfonline.com/doi/full/10.1080/23311932.2023.2254139">Baculoviruses</a>, for example, are used to control caterpillars. </p>
<p>Similarly, <a href="https://www.ncbi.nlm.nih.gov/books/NBK493185/">bacteriophages</a> can be used to control bacterial <a href="https://www.annualreviews.org/doi/full/10.1146/annurev-phyto-021621-114208">tomato and grapevine diseases</a>. </p>
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Read more:
<a href="https://theconversation.com/phage-therapy-could-treat-some-drug-resistant-superbug-infections-but-comes-with-unique-challenges-207025">'Phage therapy' could treat some drug-resistant superbug infections, but comes with unique challenges</a>
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<p>Other viruses reduce plant damage from <a href="https://www.annualreviews.org/doi/full/10.1146/annurev-phyto-021621-114208">fungal pests</a>. </p>
<p><a href="https://csiropedia.csiro.au/myxomatosis-to-control-rabbits/">Myxoma virus and calicivirus</a> reduce rabbit populations and their environmental impacts and improve agricultural production. </p>
<p>Just like humans can be protected against by vaccination, plants can be “<a href="https://www.annualreviews.org/doi/full/10.1146/annurev-phyto-021621-114208">immunised</a>” against a disease-causing virus by being exposed to a milder version.</p><img src="https://counter.theconversation.com/content/217379/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Thea van de Mortel teaches into the Master of Infection Prevention and Control program at Griffith University. </span></em></p>We tend to just think of viruses in terms of their damaging impacts on human health and lives. But viruses can also be used to benefit human health, agriculture and the environment.Thea van de Mortel, Professor, Nursing, School of Nursing and Midwifery, Griffith UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2188102023-12-21T19:08:14Z2023-12-21T19:08:14ZWhat octopus DNA tells us about Antarctic ice sheet collapse<figure><img src="https://images.theconversation.com/files/563522/original/file-20231205-29-pymbyu.jpg?ixlib=rb-1.1.0&rect=17%2C26%2C5973%2C3961&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>If we want to understand the future, it’s often useful to look at the past. And even more useful if you use octopus DNA to peer into worlds long gone. </p>
<p>About 125,000 years ago, the Earth was in its last warm period between ice ages. Global average temperatures during this interglacial period were about 0.5–1.5°C warmer than pre-industrial levels. </p>
<p>This has strong parallels with our time. For a <a href="https://www.bbc.com/news/science-environment-66857354">third of 2023</a>, the Earth’s temperature has been 1.5°C warmer than the pre-industrial era, driven by climate change. </p>
<p>For <a href="https://www.nature.com/articles/271321a0">almost 50 years</a> physical scientists have sought the answer to whether or not the vast West Antarctic Ice Sheet collapsed the last time global temperatures were this high. Rather than relying only on geological sampling, we turned to the DNA of a small Antarctic octopus for clues to the deep past. </p>
<p>The DNA had an answer. Our <a href="https://science.org/doi/10.1126/science.ade0664">new research</a> shows yes, it most likely collapsed. </p>
<p>The West Antarctic Ice Sheet is <a href="https://www.science.org/doi/10.1126/science.aaz5487">very susceptible to warming</a>. If it melts, it has enough water to raise global sea levels by 3.3 to 5 metres.</p>
<h2>Of octopuses and giant ice sheets</h2>
<p>Sediment records and other ice cores show us that the ice sheet retreated at some point during the last ~1 million years in the late Pleistocene, but the exact timing and extent of any collapse remain ambiguous.</p>
<p>To get a more precise answer, we looked to cephalopod genetics. </p>
<p>Every organism’s DNA is a history book, and we now have the technology to read it. We can use DNA to look back in time and pinpoint when different populations of animals were interbreeding. </p>
<p>Turquet’s octopus (<em>Pareledone turqueti</em>) is fairly small, weighing up to 600 grams. They live on the seafloor all around Antarctica, but individuals don’t move far from home. Antarctica is so vast that populations in different regions cannot usually interbreed. </p>
<p>Deep under West Antarctica lies gaps in the rocks. At present, these are filled by the ice sheet, making the Weddell, Amundsen and Ross seas separate from each other. </p>
<p>If the ice melted, seaways would open up and connect these isolated basins. Octopuses could directly migrate into these regions and the evidence of their breeding would be laid down in DNA. </p>
<p>But if the ice sheet didn’t melt, we would only see evidence of breeding between octopus populations along the circumference of the continent.</p>
<p>We compared DNA patterns in Turquet octopus genomes all around Antarctica to see if there were direct and unique connections between octopus populations in the Weddell, Amundsen and Ross seas. We used statistical models to figure out if these connections could be explained by their present day connections around the Antarctic coastline.</p>
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<a href="https://theconversation.com/we-can-still-prevent-the-collapse-of-the-west-antarctic-ice-sheet-if-we-act-fast-to-keep-future-warming-in-check-215878">We can still prevent the collapse of the West Antarctic ice sheet – if we act fast to keep future warming in check</a>
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<p>The story was clear in the DNA: yes, there had been direct connections between these three octopus populations. Their connections could not be statistically explained by interbreeding around the present day Antarctic coastline. These populations could only come into contact through seaways now blocked by the West Antarctic Ice Sheet. </p>
<p>Even more interesting, we first found direct connections between the three populations during the mid-Pliocene, 3 million to 3.6 million years ago when temperatures were 2–3°C hotter and sea levels 25m higher than today. This supports <a href="https://www.nature.com/articles/nature07867">existing geological evidence</a> that the West Antarctic Ice Sheet collapsed during that era. </p>
<p>The most recent DNA signatures of direct connections between the octopuses of these three seas was during the last interglacial period around 125,000 years ago. That suggests the ice sheet collapsed when the global average temperature was around 1.5°C hotter than pre-industrial levels.</p>
<p>Our work provides the first empirical evidence the West Antarctic Ice Sheet could begin to collapse if we exceed the Paris Agreement goal of limiting warming to 1.5°C or even 2°C. </p>
<h2>This discovery took effort across disciplines and countries</h2>
<p>To use animal DNA as a proxy for changes in the ice sheet, we had to work across disciplines and countries. Bringing together physical scientists and biologists gave rise to new ways to answer long standing questions of vital importance to all of us. </p>
<p>We also turned to museum collections for samples. Some dated back three decades – well before the genetic sequencing and analytical techniques we used were available. This demonstrates the vital importance of careful sample preservation, linked with metadata, with specimens protected for future access.</p>
<p>Interdisciplinary science is hard. It requires time, effort, and an open mind to appreciate new terminologies, scales and approaches. Journal editors and scientists can be reluctant to review such papers, as some aspects of the research will necessarily be outside the area of their expertise. But we hope our results show the value of this approach. </p>
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<figcaption><span class="caption">The Antarctic seafloor is covered in marine life. Many of their ancestors also lived through climate changes in the past.</span></figcaption>
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<h2>What’s next?</h2>
<p>We hope to continue using DNA as a proxy to explore other parts of Antarctica with poorly understood climate histories. </p>
<p>There is a <a href="https://onlinelibrary.wiley.com/doi/10.1111/gcb.16356">wealth of information</a> on Antarctica’s recent and distant past also hidden in other types of biological data in moss beds and peat profiles, vertebrate animal colonies and living terrestrial and marine invertebrates. To date, very few of these biological archives have been brought into our understanding of Antarctica’s past climates. </p>
<p>As the world heats up at an unprecedented rate, we need to use these types of approaches to understand what else is likely to happen down on the ice. </p>
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Read more:
<a href="https://theconversation.com/increasing-melting-of-west-antarctic-ice-shelves-may-be-unavoidable-new-research-216030">Increasing melting of West Antarctic ice shelves may be unavoidable – new research</a>
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<p class="fine-print"><em><span>Sally Lau receives funding from the Australian Research Council (ARC). </span></em></p><p class="fine-print"><em><span>Jan Strugnell receives funding from the Australian Research Council (ARC), the Fisheries Research and Development Corporation (FRDC), the Department of Agriculture Water and the Environment through the National Environmental Science Program (NESP) and the Queensland Government through the Queensland Citizen Science Grants.</span></em></p><p class="fine-print"><em><span>Nerida Wilson receives funding from the Australian Research Council (ARC), Interact for Change and the Morris Animal Foundation (Wild Genomes).</span></em></p>Did the enormous West Antarctic Ice Sheet collapse the last time global temperatures were 1.5°C above preindustrial levels? The answer lay in the DNA of an octopus.Sally Lau, Postdoctoral Research Fellow, James Cook UniversityJan Strugnell, Professor Marine Biology and Aquaculture, James Cook UniversityNerida Wilson, Adjunct Senior Research Fellow, The University of Western AustraliaLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2196632023-12-14T13:19:15Z2023-12-14T13:19:15ZWe think we have found a cause of pregnancy sickness, and it may lead to a treatment<figure><img src="https://images.theconversation.com/files/565507/original/file-20231213-19-swroox.jpg?ixlib=rb-1.1.0&rect=48%2C0%2C5351%2C3540&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Pregnancy sickness is believed to affect 7 in 10 women. </span> <span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/woman-suffering-morning-sickness-bathroom-home-1041217495">Monkey Business Images/Shutterstock</a></span></figcaption></figure><p>Sickness in pregnancy, or hyperemesis gravidarum, is common and is thought to <a href="https://journals.lww.com/obgynsurvey/abstract/2013/09001/the_impact_of_nausea_and_vomiting_of_pregnancy_on.1.aspx">affect</a> seven out of ten women at some time in their pregnancy. But, until recently, very little has been known about why it happens. </p>
<p><a href="https://www.nature.com/articles/s41586-023-06921-9">New research</a> by our team has identified sensitivity to a hormone made in abundance by the developing pregnancy, GDF15, as a contributor to the risk of pregnancy sickness.</p>
<p>This condition can affect pregnant women’s quality of life, even in so-called mild cases. Between 1% and 3% of women <a href="https://pubmed.ncbi.nlm.nih.gov/31515515/">suffer</a> from a severe form of pregnancy sickness when nausea and vomiting are so severe that they lose weight or become dehydrated, or both. In one study, this condition was the most common reason that women were admitted to <a href="https://pubmed.ncbi.nlm.nih.gov/12100809/">hospital</a> in the first three months of pregnancy. </p>
<p>It has been <a href="https://onlinelibrary.wiley.com/doi/10.1111/ppe.12416">associated</a> with worse pregnancy outcomes and its effect lasts beyond the end of pregnancy with some women <a href="https://pubmed.ncbi.nlm.nih.gov/21635201/">reporting</a> psychological distress and being reluctant to <a href="https://pubmed.ncbi.nlm.nih.gov/28241811/">conceive again</a>. </p>
<p>The fact that it develops in early pregnancy and invariably resolves when pregnancy ends strongly suggests that the cause of the sickness comes from the developing pregnancy. But the detail on how and why it happens has remained elusive. This dearth of understanding makes the development of treatments difficult and arguably contributes to the considerable <a href="https://www.pregnancysicknesssupport.org.uk/documents/research%20papers/stigma-of-hg.pdf">stigma</a> associated with this condition. </p>
<h2>GDF15</h2>
<p>GDF15 is a hormone that suppresses food intake in mice by acting, probably exclusively, on a small group of cells at the base of the brain which are also known to induce nausea and vomiting. As such, GDF15 has been under investigation as an <a href="https://pubmed.ncbi.nlm.nih.gov/36754014/">obesity therapy</a>. </p>
<p>Early trials confirm it suppresses appetite in people, but it also causes <a href="https://pubmed.ncbi.nlm.nih.gov/36630958/">nausea and vomiting</a>. It has long been known that it is abundant in human placenta and is present at very high concentrations in the blood of healthy pregnant women. These factors make it a plausible cause, but a detailed understanding of if GDF15 affects the severity of sickness in pregnancy has been lacking. </p>
<p>We used a variety of methods to study how GDF15 increases the risk of pregnancy sickness. We measured GDF15 in the blood of pregnant women attending hospital due to sickness and those attending hospital for other reasons. </p>
<p>We found that women with pregnancy sickness did indeed have higher levels of GDF15. While this was in keeping with GDF15 contributing to the condition, levels of GDF15 in each group overlapped substantially. This suggests that factors other than the absolute amount of GDF15 coming from the developing pregnancy might determine the risk of sickness.</p>
<p>Natural variation in DNA of future mothers contributes to risk of pregnancy sickness. Previous <a href="https://pubmed.ncbi.nlm.nih.gov/29563502/">studies</a> have identified changes in DNA near GDF15 as the biggest determinants of risk of pregnancy sickness. In particular, one rare genetic mutation (present in around one in 1,500 people) that affects the make-up of the GDF15 protein in the blood, has a large <a href="https://pubmed.ncbi.nlm.nih.gov/35218128/">effect</a> on that risk. </p>
<p>To understand the potential impact of this genetic variant on GDF15 levels in the bloodstream, we studied its effects on the protein in lab-grown cells. We discovered that this mutated GDF15 molecule gets stuck inside cells. What’s more, it actually stuck to and trapped “normal” GDF15 – this creates a double hit that hinders the transport of GDF15 out of cells. Healthy people with this mutation have markedly lower levels of GDF15 in their blood, which is consistent with these findings.</p>
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<img alt="A pregnant woman sits on the edge of a bed clutching her bump." src="https://images.theconversation.com/files/565574/original/file-20231213-21-z851cx.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/565574/original/file-20231213-21-z851cx.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/565574/original/file-20231213-21-z851cx.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/565574/original/file-20231213-21-z851cx.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/565574/original/file-20231213-21-z851cx.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/565574/original/file-20231213-21-z851cx.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/565574/original/file-20231213-21-z851cx.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
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<span class="caption">Between 1% and 3% of women suffer from a severe form of pregnancy sickness.</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/pregnant-woman-sitting-on-bed-holding-310309151">Monkey Business Images/Shutterstock</a></span>
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<p>We discovered that DNA changes near GDF15, which are prevalent in about 15 to 30% of people, lower the levels of the hormone. These changes increase the risk of pregnancy sickness by small amounts. Conversely, women with the blood disorder <a href="https://www.nhs.uk/conditions/thalassaemia/">thalassaemia</a>, who have very high levels of GDF15 throughout life, actually reported much less nausea and vomiting in pregnancy.</p>
<h2>A roadmap to treatment</h2>
<p>The conclusion of these studies is clear –- predisposition to higher levels of GDF15 when not pregnant reduces the risk of pregnancy sickness. At first glance, this is rather perplexing because how can having higher levels of a hormone that makes you sick protect against pregnancy sickness? </p>
<p>In fact, several hormone systems exhibit a phenomenon resembling memory, where the sensitivity to a hormone is influenced by previous exposure to that hormone. This seemed like the most plausible explanation for our results. Supporting this theory, mice with persistently high levels of GDF15 in their bloodstream were relatively unresponsive to an acute surge in GDF15 levels. </p>
<p>Our findings suggest that lower levels of GDF15 before pregnancy result in women being hypersensitive to the large amounts of GDF15 being released from the developing pregnancy. This poses two obvious approaches to treatment of this condition –- desensitising women to GDF15 by increasing its levels before pregnancy or blocking its action during pregnancy. </p>
<p>The challenge now is to develop and test strategies to achieve these aims that are safe and acceptable to women at risk from this debilitating condition.</p><img src="https://counter.theconversation.com/content/219663/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Sam Lockhart is supported by a Wellcome Trust Clinical PhD Fellowship (225479/Z/22). SL is a named creator of a pending patent application relating to therapy for hyperemesis gravidarum filed by Cambridge Enterprise Limited (GB application No. 2304716.0; Inventor: Professor Stephen O’Rahilly.</span></em></p><p class="fine-print"><em><span>Stephen O'Rahilly has undertaken remunerated consultancy work for Pfizer, Third Rock Ventures, AstraZeneca, NorthSea Therapeutics and Courage Therapeutics. Part of the work in this paper is the subject of a pending patent application relating to therapy for hyperemesis gravidarum filed by Cambridge Enterprise Limited (GB application No. 2304716.0; Inventor: Professor Stephen O’Rahilly). SL and NR are named creators on this patent.</span></em></p>New research has uncovered the hormone that triggers morning sickness, offering hope for millions of women.Sam Lockhart, Wellcome Trust Clinical PhD Fellow, Institute of Metabolic Science and Medical Research Council Metabolic Diseases Unit, University of CambridgeStephen O'Rahilly, Professor and Co-Director of the Institute of Metabolic Science and Director of the Medical Research Council Metabolic Diseases Unit, University of CambridgeLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2129542023-12-04T21:36:02Z2023-12-04T21:36:02ZHumans, rats and dogs pushed the takahē into Fiordland – new genetic research maps its dramatic journey<p><a href="https://nzbirdsonline.org.nz/species/south-island-takahe">Takahē</a> are a striking bird and a national treasure in Aotearoa New Zealand. But the history and origin story of this flightless swamp hen have become a point of scientific debate.</p>
<p>Our <a href="https://onlinelibrary.wiley.com/doi/10.1111/mec.17227">latest research</a> uncovered the significant impact of humans and past climate change on takahē. Genetic analysis has also revealed that takahē are closely related to their extinct North Island cousin, the <a href="https://nzbirdsonline.org.nz/species/north-island-takahe">moho</a>, contrary to previous research and established ideas. </p>
<p>So what is the story behind this large, prehistoric bird, <a href="https://www.theguardian.com/environment/2023/aug/29/prehistoric-bird-once-thought-extinct-returns-to-new-zealand-wild">once believed to be extinct</a>? And how might this new knowledge improve efforts to protect the unique species?</p>
<h2>A debated origin story</h2>
<p>The evolutionary history of takahē and moho has long puzzled scientists. Previous <a href="https://www.jstor.org/stable/56680?seq=1">genetic analysis</a> of small fragments of DNA suggested they were not close relatives. Instead, it was believed they descended from two separate arrivals to New Zealand by an ancient species of swamp hen. </p>
<p>This evolutionary history has become <a href="https://www.rnz.co.nz/national/programmes/saturday/audio/2018891951/alison-ballance-the-rediscovery-and-recovery-of-the-takahe">conventional wisdom</a>. But it’s different to the origin story of the majority of New Zealand’s birds with related species in the North and South Islands (such as <a href="https://www.nzherald.co.nz/nz/dna-analysis-solves-mystery-of-wattle-bird-evolution-dividing-kokako-huia-and-tieke/GLY6UYZINJ7CMYTBNWMIE7WDKY/">tīeke and kōkako</a>). Most New Zealand birds descend from a single colonisation event, not two.</p>
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<a href="https://theconversation.com/how-did-ancient-moa-survive-the-ice-age-and-what-can-they-teach-us-about-modern-climate-change-183350">How did ancient moa survive the ice age – and what can they teach us about modern climate change?</a>
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<p>Our new research has upended the takahē origin story. Using <a href="https://www.cell.com/trends/ecology-evolution/fulltext/S0169-5347(20)30282-2">palaeogenetic techniques</a> we sequenced takahē and moho DNA from fossil, archaeological, historical and living individuals to reconstruct their evolutionary history. </p>
<p>Our findings suggest the Australian or Pacific swamp hen ancestor of takahē and moho arrived in New Zealand four million years ago, as the previously forested landscape began to open up with a cooling climate. </p>
<p>Around 1.5 million years ago, a <a href="https://teara.govt.nz/en/1966/geology-land-districts-of-new-zealand/page-4">land bridge between the North and South Islands</a> allowed the now possibly flightless swamp hen to evolve into takahē in the south, and the taller and slighter moho in the north. This land bridge eventually eroded with the development of Cook Strait around 500,000 years ago.</p>
<h2>Ice ages and human arrival</h2>
<p>Our genetic analyses and the fossil records show takahē were restricted to isolated areas in the northwestern and perhaps southern South Island at the height of the last ice age – 29,000 to 19,000 years ago. </p>
<p>As the climate warmed, takahē shifted their distribution to eastern and southern regions. The takahē in the northwest South Island (where the Heaphy Track is today) went locally extinct.</p>
<p>However, the biggest impact on takahē came with the arrival of East Polynesian colonists in the late 13th century. Over-hunting, <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0111328">habitat destruction</a> and predation from kiore (Polynesian rats) and <a href="https://www.frontiersin.org/articles/10.3389/fevo.2021.757988/full">kurī</a> (Polynesian dogs) resulted in the loss of takahē everywhere except Fiordland. </p>
<p>This dramatic contraction and population bottleneck resulted in a small and inbred population with little to no genetic variation. There is no evidence of the genetic lineage (a series of mutations or changes in the genetic code which connect an ancestor to its descendants) of living takahē in any archaeological or fossil specimens we examined.</p>
<p>This lineage may have only occurred in Fiordland, or was extremely rare in takahē and swept to dominance in this small population.</p>
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Read more:
<a href="https://theconversation.com/the-legend-of-pouwa-ancient-myths-of-new-zealands-black-swan-confirmed-by-fossil-dna-81611">The legend of Poūwa: ancient myths of New Zealand's black swan confirmed by fossil DNA</a>
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<p>Another possibility suggests this lineage occurred spontaneously – much like the <a href="https://en.wikipedia.org/wiki/Haemophilia_in_European_royalty">genetic mutation in Queen Victoria</a> that gave rise to haemophilia in members of Europe’s royal families. </p>
<p>We know from historical records that the arrival of Europeans and their furry companions no doubt resulted in further restriction of already rare takahē to the Murchison Mountains in Fiordland. However, we don’t see any further genetic bottleneck at this point, as the damage had already been done by earlier human activity. </p>
<p>The moho suffered the same fate as takahē, with the last probable sighting in the late 1800s. The demise of moho and the near extinction of takahē opened up a <a href="https://www.frontiersin.org/articles/10.3389/fevo.2019.00158/full">job vacancy in the ecosystem</a>, allowing the pūkeko to colonise New Zealand from Australia <a href="https://www.doc.govt.nz/nature/native-animals/birds/birds-a-z/pukeko/">around 500 years ago</a>.</p>
<h2>Improving conservation management</h2>
<p>The growing field of conservation palaeontology uses the fossil record to inform conservation management decisions. It is especially important for endangered animals where human impact has masked their true biological heritage.</p>
<p><a href="https://nzbirdsonline.org.nz/species/kea">Kea</a>, despite appearances, are <a href="https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.15978">not an alpine bird</a>. Likewise, the ideal habitat of takahē is not tussock. Rather, the fossil record suggests takahē preferred border habitats such as the edges of forests, grasslands and shrublands, where one habitat transitions to another. </p>
<p>Conservation palaeontology can and should be used to determine the range of suitable habitats across the country, based on the preferences of prehistoric takahē. This can be married with effective predator control to support takahē populations.</p>
<p>It has long been known that takahē underwent a population bottleneck upon human arrival, but what surprised us was its scale. Our research highlights the need for conservation efforts to maximise the amount of genetic variation passed down to each generation, and to minimise the amount and consequent impacts of inbreeding. </p>
<p>Although threats to our native wildlife exist in the here and now, the past can be a key to future efforts to conserve our precious biodiversity.</p><img src="https://counter.theconversation.com/content/212954/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Nic Rawlence receives funding from Te Apārangi Royal Society of New Zealand Marsden Fund. </span></em></p><p class="fine-print"><em><span>Alexander Verry 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>Examining the DNA of the takahē has upended long-held beliefs about how the flightless bird ended up on the southwestern tip of New Zealand. This new knowledge can help future conservation efforts.Nic Rawlence, Senior Lecturer in Ancient DNA, University of OtagoAlexander Verry, Researcher, Department of Zoology, University of OtagoLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2176072023-11-22T11:54:52Z2023-11-22T11:54:52ZFlorence Bell died unrecognised for her contributions to DNA science – decades on female researchers are still being sidelined<p>Almost 80 years ago, <a href="https://theconversation.com/florence-bell-the-housewife-who-played-a-key-part-in-our-understanding-of-dna-175220">Florence Bell</a> quietly laid the foundations for one of the biggest landmarks in 20th century science: the discovery of the structure of DNA. But when she died on November 23 2000, her occupation on her death certificate was recorded as “housewife”. </p>
<p>Decades later, female researchers are <a href="https://www.timeshighereducation.com/news/hostile-workplace-climate-pushing-women-out-academia">still being sidelined</a>. Research has shown that deep systemic problems <a href="https://lisampmunoz.com/">block women from advancing</a> or push them out of science. But this isn’t inevitable – there are changes universities could make to level the playing field. </p>
<p>While promotion criteria differ across universities, <a href="https://www.researchsquare.com/article/rs-3011208/v1">credibility in academia</a> is primarily established through the number of publications a researcher has authored. This means academics are under pressure to publish as much as they can even if quality suffers. </p>
<p>Women in academia are <a href="https://www.tandfonline.com/doi/abs/10.1080/03075079012331377521?casa_token=nszxYzuRl64AAAAA:Haz91A2VCZoitEBHZxT2Vq_IaPA0aNse0i1zxEqVZF3rlRyidHh5WRODBnVIcnbL0dO1o600sopzLg">more likely to work part time</a>, hold teaching jobs and do extra admin tasks. This means women researchers often get less time to focus on their research, to make discoveries and publish about them. Yet it is research publications, grants and citations that are used in promotions and salary negotiations. </p>
<p>The gender disparity is apparent through <a href="https://www.pnas.org/doi/abs/10.1073/pnas.1914221117">men’s higher publication rates</a>, and <a href="https://link.springer.com/article/10.1007/s10648-018-9452-8">men’s dominant representation</a> in academia research journal editorships. </p>
<h2>Why the problem isn’t going away</h2>
<p>The cycle of gender disparity in academia is complex. Larger grants often <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0155876">go to larger universities</a>, where researchers can prioritise writing and research. And where, historically, the recipients of prestigious positions and important grants have been men. </p>
<p>In some fields, for example the STEM field, women exit the workforce at <a href="https://awis.org/fighting-gender-bias/">double the rate of men</a>, often due to the biases, harassment and inequities they encounter. A woman I interviewed for <a href="https://www.routledge.com/Inspirational-Women-in-Academia-Supporting-Careers-and-Improving-Minority/Kucirkova-Fahad/p/book/9781032026459">research about the issue</a> revealed that her pregnancy was viewed negatively by her senior colleagues, which resulted in her role being replaced without maternity leave. She said she felt like she had to choose between her career and having a baby.</p>
<figure class="align-center ">
<img alt="Portrait of senior female professor explaining math formulas." src="https://images.theconversation.com/files/560711/original/file-20231121-20-gmmq92.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/560711/original/file-20231121-20-gmmq92.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/560711/original/file-20231121-20-gmmq92.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/560711/original/file-20231121-20-gmmq92.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/560711/original/file-20231121-20-gmmq92.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/560711/original/file-20231121-20-gmmq92.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/560711/original/file-20231121-20-gmmq92.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">The academic system still makes career progression harder for a lot of female scientists.</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/portrait-senior-professor-explaining-math-formulas-1665468775">Ground Picture/Shutterstock</a></span>
</figcaption>
</figure>
<p>The gender bias becomes even more pronounced for women from marginalised
backgrounds. This includes women with working class origins, those with disabilities, those from minority ethnic groups in their country of work and those for whom English is not their first language. </p>
<p>For example, in a survey of <a href="https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002184">908 environmental science researchers</a>, non-native English speakers, especially those early in their careers, said they spent more time on reading and writing papers, preparing English presentations and disseminating research in multiple languages. </p>
<p>In our book <a href="https://www.routledge.com/Inspirational-Women-in-Academia-Supporting-Careers-and-Improving-Minority/Kucirkova-Fahad/p/book/9781032026459">Inspirational Women in Academia</a>, Loleta Fahad (head of career development at University College London) and I explored how women from marginalised backgrounds bear the brunt of double disadvantages, often exacerbated by well-intentioned but poorly executed solutions implemented by the university system. </p>
<p>We found that high achieving women from underrepresented backgrounds are often
assigned mentorship and representative roles, for example. Universities typically don’t provide extra time for these mentorship roles. It is expected that these high achieving women “pay it forward” to the community they came from. A woman feels a duty to represent her group and mentor other women, but this responsibility diverts time from the very tasks that brought her recognition in the first place.</p>
<p>Consequently, burnout rates can be higher among women from marginalised
backgrounds – <a href="https://www.bmj.com/content/376/bmj-2021-065984">a trend documented</a> among female medical professionals with marginalised identities.</p>
<p>Yet research suggests that the most enriching mentorships happen when people are mentored by <a href="https://www.sup.org/books/title/?id=4315">someone from a different background</a> than them. For instance, a woman we <a href="https://www.routledge.com/Inspirational-Women-in-Academia-Supporting-Careers-and-Improving-Minority/Kucirkova-Fahad/p/book/9781032026459#:%7E:text=Description,age%2C%20ethnicity%2C%20and%20disability.">interviewed for our book</a>, said that her career benefited most from conversations with successful male academics, not women facing the same challenges as her. </p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/unravelling-dnas-structure-a-landmark-achievement-whose-authors-were-not-fairly-credited-200404">Unravelling DNA's structure: a landmark achievement whose authors were not fairly credited</a>
</strong>
</em>
</p>
<hr>
<p>While the tough research environment has cultivated a resilience that enables many women to prevail against considerable challenges, their success often entails personal and professional sacrifices.</p>
<p>I achieved success early in my career partly because of the additional hours I invested. I worked twice as hard, including at night and on weekends. My story, <a href="https://www.nature.com/articles/d41586-023-00241-8">featured in Nature</a>, garnered widespread attention because my account of overwork echoed the experiences of many others. </p>
<p>Indeed, the <a href="https://link.springer.com/article/10.1007/s10648-023-09727-3">most accomplished female academics</a> in psychology report working over 50 hours a week. Their routines typically involve starting the day early, working into the evening and dedicating weekends to writing. Women who want to succeed typically need to put in more effort, especially in some male-dominated fields where there is still an old boy’s club culture making it harder for women to get promoted.</p>
<p>For emerging academics in particular, there is a concerning notion that those who prioritise research above all else are the scholars who succeed, potentially at the expense of their health. Those from marginalised backgrounds run an even higher risk of burnout. </p>
<h2>There is a way forward</h2>
<p>Universities can make changes to promote equality. For example, giving equal credit and respect for teaching as they do for publications. The time spent on mentoring, contributions to public debate, or work with communities should also be considered as equal measures of success, promotion and respect for academics. Without such systemic reforms, the scientific community risks losing the diverse perspectives that female scientists bring. </p>
<p>Florence Bell wasn’t the only woman who laid the groundwork for our understanding of DNA. <a href="https://theconversation.com/unravelling-dnas-structure-a-landmark-achievement-whose-authors-were-not-fairly-credited-200404">In April 2023</a>, historic papers were discovered showing <a href="https://theconversation.com/rosalind-franklin-still-doesnt-get-the-recognition-she-deserves-for-her-dna-discovery-95536">Rosalind Franklin’s</a> contributions were more important than we realised. Imagine what other discoveries Franklin and Bell may have helped make had they been properly supported and recognised. Holding back female researchers limits our understanding of science.</p><img src="https://counter.theconversation.com/content/217607/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Natalia Kucirkova receives funding from The Norwegian Research Council, ESRC and The Jacobs Foundation. She is affiliated with The Open University and University of Stavanger. She leads the university spin-out WiKIT.</span></em></p>In the academic world, researchers are rewarded for publishing frequently. Not only is this affecting research quality but it is also hindering female scientists.Natalia I. Kucirkova, Professor Reading and Early Childhood Development, The Open UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2152782023-11-16T14:27:49Z2023-11-16T14:27:49ZJurassic Park: why we’re still struggling to realise it 30 years on<figure><img src="https://images.theconversation.com/files/556310/original/file-20231027-26-umzgc5.jpg?ixlib=rb-1.1.0&rect=29%2C5%2C3964%2C2658&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/human-hand-compare-real-dinosaur-footprint-1205774944">Rattana/Shutterstock</a></span></figcaption></figure><p>Jurassic Park is arguably the ultimate Hollywood blockbuster. Aside from the appeal of human-chomping dinosaurs, tense action sequences and ground-breaking cinematography, its release in 1993 was a movies-meet-science milestone.</p>
<p>As global audiences were soaking up the gory action, the premise of the movie - extracting DNA from fossil insects preserved in amber to resurrect dinosaurs - was given the credibility of publication by several <a href="https://www.nature.com/articles/363536a0">high-profile studies</a> on <a href="https://www.science.org/doi/10.1126/science.1411508">fossil amber</a>. The authors recovered ancient DNA from amber, and even <a href="https://www.science.org/doi/10.1126/science.7538699">revived</a> amber-hosted bacteria. The world seemed primed for a real-life Jurassic Park. </p>
<p>But since then, the science has taken many twists and turns. An increasing number of palaeontologists are reporting evidence of DNA and proteins, which also give genetic information, in fossils. These chemical traces could provide unprecedented insights into ancient life and evolution. But such reports are the source of ongoing debate and controversy among scientists. Our <a href="https://www.nature.com/articles/s41559-023-02177-8">recent study</a>, published in the journal Nature Ecology and Evolution, offers new insight.</p>
<h2>Ancient DNA</h2>
<p>DNA yields the most detailed information, compared to other molecules, on how closely species are related. However, DNA is extremely fragile and <a href="https://www.nature.com/articles/362709a0">decays rapidly</a> after an organism dies. </p>
<p>That said, DNA can sometimes survive in polar climates, because the freezing temperatures slow down decay. Geologically young DNA (thousands of years old) therefore has the potential to resurrect extinct animals from the last ice age through to the recent past. </p>
<p>Commercial companies such as <a href="https://reviverestore.org/pleistocene-patreon/">Pleistocene Park</a>, <a href="https://colossal.com/de-extinction/">Colossal</a> and <a href="https://reviverestore.org/projects/woolly-mammoth/">Revive & Restore</a> are working on projects to bring back the woolly mammoth and passenger pigeon. </p>
<p>There is a long time gap between these mammoths and dinosaurs, which went extinct 66 million years ago. There is some evidence, though, that genetic material may survive in fossils even on these timescales. </p>
<p>For example, fossil chromosomes – fragments of DNA smaller than a cell – have been <a href="https://www.science.org/doi/10.1126/science.1249884">found in plants</a> up to <a href="https://www.sciencedirect.com/science/article/abs/pii/S0034666720302694">180 million years old</a> and a 75 million-year-old <a href="https://doi.org/10.1093/nsr/nwz206">dinosaur</a>.</p>
<p>Scientists have yet to find evidence, however, that actual DNA can survive for tens of millions of years. </p>
<h2>Ancient proteins</h2>
<p>Proteins also code information (in the form of <a href="https://www.britannica.com/science/amino-acid/Standard-amino-acids">amino acid sequences</a>) that can shed light on the evolutionary links among species. </p>
<p>Scientists believe that proteins can survive for longer than DNA. Indeed, researchers have found many examples of fossilised proteins, most notably intact amino acid sequences of collagen (a protein found in connective tissues), but these are at most a few million years old.</p>
<p>Scientists don’t expect large protein fragments <a href="https://doi.org/10.1042/BIO02403012">to survive</a> for as long as these smaller ones. So the scientific community was electrified in 2007 by the report of <a href="https://www.science.org/doi/10.1126/science.1137614">68 million-year-old collagen fragments</a> in a <em>Tyrannosaurus rex</em> bone.</p>
<p>Controversy soon followed though as <a href="https://royalsocietypublishing.org/doi/10.1098/rspb.2017.0544">concerns mounted</a> about the <a href="https://www.science.org/doi/10.1126/science.1155006">team’s methodology</a>, such as the potential for contamination and the lack of rigorous controls and independent verification. </p>
<p>Similar debate surrounds more recent reports of degraded proteins and <a href="https://www.nature.com/articles/ncomms8352">collagen fibres</a> in fossils as old as <a href="https://www.nature.com/articles/ncomms14220">130 million years</a>. </p>
<h2>A way forward</h2>
<p>These studies highlight the difficulties of working with fossils, especially using analytical methods that may not be appropriate to use on ancient tissues. The evidence for survival of fossil protein remnants, however, has proved compelling. </p>
<p>These studies are also stimulating other researchers to explore new methods and analytical approaches that might be better suited for use with fossils. </p>
<p>Our <a href="https://doi.org/10.1038/s41559-023-02177-8">new study</a> explores one such approach, using a focused beam of light plus X-rays to irradiate samples of ancient feathers. These techniques reveal which chemical bonds are present, providing information on the structure of proteins. In turn, this helps us to detect traces of proteins in fossil feathers. </p>
<p>Our analyses of the 125 million-year-old feathered dinosaur <em>Sinornithosaurus</em> revealed abundant corrugated protein structures, consistent with a protein called beta-keratin, which is common in modern feathers. Spiral protein structures (indicative of another protein called alpha-keratin) were present only in small amounts. </p>
<p>When we simulated the process of fossilisation in laboratory experiments, we found that corrugated protein structures unravel and form spiral structures when heated. </p>
<p>These findings suggest that ancient feathers were remarkably similar in chemistry to modern-day feathers. It also suggests that spiral protein structures in fossils are probably artefacts of the fossilisation process. </p>
<p>But ultimately, our findings suggest traces of proteins do survive for hundreds of millions of years.</p>
<h2>Real-life Jurassic Park – science fact or fiction?</h2>
<p>Palaeontologists today can test fossils for evidence of ancient molecules using an arsenal of techniques that were not available 30 years ago. This has allowed us to identify fragments of molecules in fossil animals that are tens to hundreds of millions of years old.</p>
<p>Scientists have discovered haemoglobin, a protein in red blood cells, in 50-million-year-old insects, and melanin pigments in the ink sacs of 200-million-year-old squid. </p>
<p>Ultimately though, we need intact DNA to resurrect species. So although scientists have made a lot of progress, the prospect remains in the realm of science fiction. All data from fossils and experiments to date suggests that DNA is simply unlikely to survive for tens of millions of years. </p>
<p>Even if scientists did find DNA fragments in dinosaur fossils, these would probably be very short. Short fragments of DNA are unlikely to give us useful information about a species. And we don’t yet have the technology to validate such rare DNA fragments as original rather than random combinations of amino acids, generated during fossilisation. </p>
<p>Better lab protocols and fossilisation experiments are helping us to make more accurate interpretations of fossils. This is paving the way for more rigorous studies of ancient molecules. </p>
<p>In the future, these studies may challenge what we think we know about how long molecules can survive, and may even reshape our understanding of the evolution of life on Earth.</p><img src="https://counter.theconversation.com/content/215278/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Tiffany Shea Slater receives funding from the European Research Council and the Irish Research Council. </span></em></p><p class="fine-print"><em><span>Maria McNamara receives funding from the European Research Council and Science Foundation Ireland. </span></em></p>New laboratory experiments add analytical rigour to the search for ancient biomoleculesTiffany Shea Slater, Postdoctoral Researcher, Palaeobiology, University College CorkMaria McNamara, Professor, Palaeobiology, University College CorkLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2169892023-11-14T22:59:25Z2023-11-14T22:59:25ZIt sounds like science fiction. But we can now sample water to find the DNA of every species living there<figure><img src="https://images.theconversation.com/files/559205/original/file-20231114-19-zdguhr.jpg?ixlib=rb-1.1.0&rect=31%2C23%2C4175%2C3422&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>Figuring out what species live in an ecosystem, and which ones are rare or just good at hiding is an essential way to understand and care for them. Until now, it’s been very labour intensive.</p>
<p>But now we can do it differently. Take a sample from the ocean and match tiny traces of DNA in the water with the species living there. </p>
<p>It’s not science fiction – it’s environmental DNA sampling. This approach opens the door to rapid, broad detection of species. You can find if pest species have arrived, tell if a hard-to-find endangered species is still hanging on, and gauge ecosystem health.</p>
<p>Because eDNA testing is still new, there are questions about its strengths and weaknesses and how it can best be used. For instance, we can tell if <a href="https://www.int-res.com/abstracts/esr/v30/p109-116/">extremely rare freshwater sawfish</a> are present in a Northern Territory river – but not how many individual fish there are. </p>
<p>Today CSIRO <a href="http://www.csiro.au/eDNA-roadmap">released a roadmap</a> created through consultation with many experts to show how eDNA technologies can be best integrated into marine monitoring at a large scale – and what the future holds. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/558175/original/file-20231107-21-8sujdg.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="man collecting DNA samples in buckets of river water" src="https://images.theconversation.com/files/558175/original/file-20231107-21-8sujdg.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/558175/original/file-20231107-21-8sujdg.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=456&fit=crop&dpr=1 600w, https://images.theconversation.com/files/558175/original/file-20231107-21-8sujdg.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=456&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/558175/original/file-20231107-21-8sujdg.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=456&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/558175/original/file-20231107-21-8sujdg.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=574&fit=crop&dpr=1 754w, https://images.theconversation.com/files/558175/original/file-20231107-21-8sujdg.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=574&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/558175/original/file-20231107-21-8sujdg.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=574&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Here, lead author Maarten De Brauwer collects jerry cans of water from Tasmania’s Derwent River to document hundreds of species in the estuary.</span>
<span class="attribution"><span class="source">Bruce Deagle</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<h2>How does eDNA sampling work?</h2>
<p>Deoxyribonucleic acid (DNA) is a very special molecule. It acts as the code for all life on Earth, holding the cellular instructions to make everything from a beetle to a human. Because DNA is unique to each species, it’s like a product barcode in a supermarket. </p>
<p>As animals and plants live their lives, they shed fragments of their DNA into their environment through dead skin, hair, saliva, scat, leaves or pollen. These traces make up environmental DNA. There’s enough DNA in water and even air to tell species apart. </p>
<p>The real power of eDNA sampling is how broad a net it casts. With one sample, we can detect anything living, from bacteria to whales, and in potentially every environment with life, from the deep sea to underground caves. </p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/environmental-dna-how-a-tool-used-to-detect-endangered-wildlife-ended-up-helping-fight-the-covid-19-pandemic-158286">Environmental DNA – how a tool used to detect endangered wildlife ended up helping fight the COVID-19 pandemic</a>
</strong>
</em>
</p>
<hr>
<p>Importantly, this method lets scientists detect species even if we can’t see or capture them. This comes in handy when working with rare or very small species, or when working in environments such as murky water where it is impossible to see or catch them. It will, for example, make it easier to study <a href="https://onlinelibrary.wiley.com/doi/full/10.1002/edn3.365">critically endangered pipefish</a> in estuaries. </p>
<p>To date, much eDNA research has focused on detecting species in water, because it’s relatively easy to collect, concentrate and extract eDNA from liquids. But we now know we can produce species lists based on the eDNA in soil, scat, honey, or even the air. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/558781/original/file-20231110-15-hupxn2.PNG?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Figure of mountains, seas, rivers showing how environmental DNA sampling can track species" src="https://images.theconversation.com/files/558781/original/file-20231110-15-hupxn2.PNG?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/558781/original/file-20231110-15-hupxn2.PNG?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=424&fit=crop&dpr=1 600w, https://images.theconversation.com/files/558781/original/file-20231110-15-hupxn2.PNG?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=424&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/558781/original/file-20231110-15-hupxn2.PNG?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=424&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/558781/original/file-20231110-15-hupxn2.PNG?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=533&fit=crop&dpr=1 754w, https://images.theconversation.com/files/558781/original/file-20231110-15-hupxn2.PNG?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=533&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/558781/original/file-20231110-15-hupxn2.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">Environmental DNA sampling has a wide range of uses, from land to river to sea.</span>
<span class="attribution"><span class="source">Berry et al, doi.org/10.1002/edn3.173</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<h2>How do scientists actually measure eDNA?</h2>
<p>Typically, you collect samples, perform molecular analysis and interpret results. </p>
<p><strong>Collect samples:</strong> Scientists collect a sample from the environment. This can be water, soil, or virtually any environmental substrate which might contain eDNA. We then process the sample to concentrate and stabilise the DNA. You might collect two litres of water with a bucket, filter it and then freeze or chemically stabilise the eDNA coating the filter. </p>
<p><strong>Molecular analysis:</strong> The first step in the lab is to purify DNA from a sample. The next step depends on your goal. If you want to detect a single species, you would generally use a technique called quantitative polymerase chain reaction (<a href="https://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction">qPCR</a>), similar to how you test for COVID.</p>
<p>But to detect whole communities of species, you have to use <a href="https://en.wikipedia.org/wiki/Metabarcoding">high-throughput DNA sequencing</a>. Where detecting a single species with eDNA takes only a few days days, completing the labwork for species communities can take weeks to months. At the end, you arrive at a long list of thousands or even millions of DNA barcode sequences. </p>
<p><strong>Interpreting results</strong>: Single species interpretation is simple. Was DNA from your species of interest present or not? But when the goal is to identify multiple species, scientists use <a href="https://research.csiro.au/dnalibrary/">DNA reference libraries</a> to link the DNA barcodes detected in the sample back to individual species. </p>
<p>This works well – but only if we already have the species listed in these libraries. If not, you can’t detect it with eDNA methods. That means eDNA can’t be used to detect new species or those only known from photos and videos.</p>
<h2>Why does eDNA matter? Look at marine parks</h2>
<p>Australia boasts one of the world’s largest and most biodiverse networks of marine parks. But as ocean life reels from climate change, overfishing and plastic pollution, it’s certain the oceans of the future will look very different to that of today. </p>
<p>Gauging impact to support evidence-based decisions across such a vast, diverse and remote area poses challenges difficult to solve with standard hands-on survey methods like like diving, video or trawling.</p>
<p>That’s where eDNA methods can help, offering a powerful, non-destructive, cost-effective and quick form of monitoring that can complement other techniques.</p>
<p>eDNA means we can fine-tune monitoring for specific purposes, such as detecting pests, endangered, or dangerous species. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/558201/original/file-20231108-15-9w71wp.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="figure showing the many future uses for eDNA with underwater drones, samplers in buoys" src="https://images.theconversation.com/files/558201/original/file-20231108-15-9w71wp.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/558201/original/file-20231108-15-9w71wp.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=424&fit=crop&dpr=1 600w, https://images.theconversation.com/files/558201/original/file-20231108-15-9w71wp.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=424&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/558201/original/file-20231108-15-9w71wp.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=424&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/558201/original/file-20231108-15-9w71wp.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=533&fit=crop&dpr=1 754w, https://images.theconversation.com/files/558201/original/file-20231108-15-9w71wp.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=533&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/558201/original/file-20231108-15-9w71wp.jpg?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">In future, our marine parks may well have networks of buoys sampling eDNA at the surface and underwater drones sampling the depths.</span>
<span class="attribution"><span class="source">CSIRO</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>This is just the start. Imagine a future where eDNA data could be collected from the most remote oceans by autonomous vehicles, analysed by the drone or on board a research vessel, and integrated with other monitoring data so marine managers and the public can see near-real time data about the condition of the ocean. </p>
<p>Science fiction? Not any more. </p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/you-shed-dna-everywhere-you-go-trace-samples-in-the-water-sand-and-air-are-enough-to-identify-who-you-are-raising-ethical-questions-about-privacy-205557">You shed DNA everywhere you go – trace samples in the water, sand and air are enough to identify who you are, raising ethical questions about privacy</a>
</strong>
</em>
</p>
<hr>
<img src="https://counter.theconversation.com/content/216989/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Maarten De Brauwer receives funding from the CSIRO and the National Geographic Society. He is a board member at the Southern eDNA Society. </span></em></p><p class="fine-print"><em><span>Oliver Berry receives funding from the CSIRO, the Australian Government, and the Minderoo Foundation. He is a board member of the Southern eDNA Society (Australia and New Zealand's professional society for eDNA scientists and other stakeholders). </span></em></p>Every living thing leaves traces in its environment. By sampling water or even air for this environmental DNA, we can know which species live where.Maarten De Brauwer, Research fellow, CSIROOliver Berry, Leader, Environomics Future Science Platform, CSIROLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2170252023-11-13T21:44:00Z2023-11-13T21:44:00ZGulf of St. Lawrence: Analyzing fish blood can show us how healthy they are<figure><img src="https://images.theconversation.com/files/557461/original/file-20231003-21-bibw4p.jpeg?ixlib=rb-1.1.0&rect=30%2C12%2C3995%2C3005&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">The industrialization of the fishing industry and changes in the environment have raised many issues about the management of our fisheries.</span> <span class="attribution"><span class="source">(Fanny Fronton)</span>, <span class="license">Fourni par l'auteur</span></span></figcaption></figure><p>The Gulf of St. Lawrence is an invaluable resource for Canada. Fish and shellfish fisheries that date to the 16th century have remained an essential source of income for many communities, including those on the North Shore and Gaspésie or the Îles-de-la-Madeleine.</p>
<p>For example, in <a href="https://publications.gc.ca/collections/collection_2019/mpo-dfo/Fs124-10-2018-eng.pdf">Îles-de-la-Madeleine</a>, nearly 1,800 jobs (for a total of 12,500 inhabitants) were linked to fishing in 2015.</p>
<p>But the industrialization of fishing, and changes in the environment, have brought about many new problems in the management of our fisheries. The abundance of different fish species in the Gulf has fluctuated greatly over the last 20 years.</p>
<hr>
<figure class="align-right ">
<img alt="" src="https://images.theconversation.com/files/469058/original/file-20220615-9549-jj1phn.png?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/469058/original/file-20220615-9549-jj1phn.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=398&fit=crop&dpr=1 600w, https://images.theconversation.com/files/469058/original/file-20220615-9549-jj1phn.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=398&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/469058/original/file-20220615-9549-jj1phn.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=398&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/469058/original/file-20220615-9549-jj1phn.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=500&fit=crop&dpr=1 754w, https://images.theconversation.com/files/469058/original/file-20220615-9549-jj1phn.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=500&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/469058/original/file-20220615-9549-jj1phn.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=500&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
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<span class="caption"></span>
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<p><em>This article is part of our series, <a href="https://theconversation.com/ca-fr/topics/fleuve-saint-laurent-116908">The St. Lawrence River: In depth</a>.
Don’t miss new articles on this mythical river of remarkable beauty. Our experts look at its fauna, flora and history, and the issues it faces. This series is brought to you by <a href="https://theconversation.com/ca-fr">La Conversation</a>.</em></p>
<hr>
<p>A case in point: the number of Greenland halibut has declined drastically. This year, <a href="https://www.hi.no/hi/nettrapporter/imr-pinro-en-2023-6">landings</a> are six times lower for fishermen compared to last year.</p>
<p>But other species are benefiting from the situation. This is the case for the population of Atlantic halibut, which is at record levels today.</p>
<p>What is causing these changes? And can we predict further changes?</p>
<p>As a doctoral student in biology at the Institut national de la recherche scientifique (INRS), I am trying to find possible answers to these questions as part of my research work.</p>
<h2>A new health monitoring technique</h2>
<p>The means available for studying the health of fish at the individual level are limited. On the one hand, we can calculate indicators from the weight and height of individual fish. But these measurements are too vague and don’t tell us much.</p>
<p>The logistics of performing biopsies on the tissue of fish — which requires taking samples from their muscle or organs — are complex. To carry them out, researchers must have to travel to the ocean, physically collect samples and bring them back to a laboratory. And then there are ethical considerations, since obviously fish must be sacrificed to achieve this.</p>
<p>Even so, these methods are not very effective for detecting stress induced by environmental changes, and are not effective for detecting stress at early stages, before the physical effects can become manifest.</p>
<p>Yet in a context where the abundance of certain fish species is in rapid decline, an analysis of their overall health is necessary. Fortunately, a new tool is being developed: the <a href="https://www.nature.com/articles/s41598-023-32690-6">circulating microbiome</a>.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/551779/original/file-20231003-15-6ou9xh.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="viruses in the blood" src="https://images.theconversation.com/files/551779/original/file-20231003-15-6ou9xh.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/551779/original/file-20231003-15-6ou9xh.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=343&fit=crop&dpr=1 600w, https://images.theconversation.com/files/551779/original/file-20231003-15-6ou9xh.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=343&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/551779/original/file-20231003-15-6ou9xh.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=343&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/551779/original/file-20231003-15-6ou9xh.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=431&fit=crop&dpr=1 754w, https://images.theconversation.com/files/551779/original/file-20231003-15-6ou9xh.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=431&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/551779/original/file-20231003-15-6ou9xh.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=431&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">It is often wrongly believed that blood is sterile.</span>
<span class="attribution"><span class="source">(Shutterstock)</span></span>
</figcaption>
</figure>
<h2>A little-known practice</h2>
<p>The circulating microbiome is a biomarker, an alarm signal that can be detected in fish even before their health begins to deteriorate. A good biomarker is sensitive, easy to sample, and inexpensive.</p>
<p>The analysis of the circulating microbiome, made up of the DNA of bacteria found in the blood, is directly inspired by <a href="https://theconversation.com/ladn-%20circulating-a-new-simple-and-rapid-weapon-in-the-diagnosis-and-monitoring-of-cancers-206786">similar analyses performed on humans</a>, which provide a great deal of information.</p>
<p>In particular, these analyses make it possible to detect anomalies resulting from the effect of a stress factor on the body, or the development of a disease.</p>
<p>Changes in the environment can also be detected from studying the circulating microbiome. But a major problem emerges here: a fish is not a human. Humans are studied in such detail that knowledge about their health can then be used for an infinite amount of further research. However, sampling fish blood is not a common practice. So there is a great deal that needs to be done before we can properly evaluate the health of fish.</p>
<p>Since the analysis of the circulating microbiome in fish has never been studied before, a lot of work needs to be done to develop the technique.</p>
<h2>Traces of bacteria in the blood?</h2>
<p>As blood circulates throughout the body, it comes into contact specifically with bacteria that make up the other microbiomes (intestinal, oral, dermal). Both in fish and humans, these bacteria are essential for good health.</p>
<p>When we analyze bacterial DNA in the blood, it is therefore possible to find bacteria from the intestine, mouth, or skin. But the hypothesis that these are bacteria specific to the blood cannot be completely ruled out either.</p>
<p>While some continue to believe that blood is sterile, and therefore does not contain any bacteria, we have known since the 1970s that this hypothesis is false — it was confirmed <a href="https://doi.org/10.1128/jcm.39.5.1956-1959.2001">in the 2000s by genomic studies</a>. It’s possible that in 1674, the Dutch microbiologist Antonie Van Leeuwenhoek may even have observed bacteria in salmon blood <a href="https://doi.org/10.3389/fcimb.2019.00148">under a microscope</a>.</p>
<p>Today, we can analyze these bacteria in detail by targeting a very specific bacterial gene, the 16S ribosomal RNA gene. Present in all bacteria around the world, this gene varies slightly from one species to another. That makes it possible to identify and analyze the biodiversity of the microbiome.</p>
<h2>I eat, therefore I am</h2>
<p>Our recent work has made it possible to characterize, for the first time, the <a href="https://www.nature.com/articles/s41598-023-32690-6">circulating microbiomes of turbot and halibut</a>. We have demonstrated that the two fish species have circulating microbiomes dominated by the presence of the species <em>Pseudoalteromonas</em> and <em>Psychrobacter</em>. These bacteria are known to colonize cold environments, for example the bottom of the Gulf of St. Lawrence, which is around 5°C. They are also known to produce bioactive compounds (antibacterials and antifungals). They are more tenacious than other bacteria.</p>
<figure class="align-left zoomable">
<a href="https://images.theconversation.com/files/551768/original/file-20231003-29-qhulgz.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="person with blue gloves holds a fish" src="https://images.theconversation.com/files/551768/original/file-20231003-29-qhulgz.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/551768/original/file-20231003-29-qhulgz.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=800&fit=crop&dpr=1 600w, https://images.theconversation.com/files/551768/original/file-20231003-29-qhulgz.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=800&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/551768/original/file-20231003-29-qhulgz.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=800&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/551768/original/file-20231003-29-qhulgz.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=1005&fit=crop&dpr=1 754w, https://images.theconversation.com/files/551768/original/file-20231003-29-qhulgz.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=1005&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/551768/original/file-20231003-29-qhulgz.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=1005&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Greenland halibut.</span>
<span class="attribution"><span class="source">(Fanny Fronton)</span>, <span class="license">Fourni par l'auteur</span></span>
</figcaption>
</figure>
<p>However, differences can be observed between the two species. Turbot has more bacteria called <em>Vibrio</em>, some of which metabolize chitin, a molecule that makes up the shells of the invertebrates on which it feeds. Atlantic halibut, for its part, presents more <em>Acinetobacter</em> bacteria, typical of piscivorous (fish-eating) diets in the intestinal microbiomes. The circulating microbiome in these two fish species therefore seems to be influenced by intestinal bacteria, as is the case in humans. We could therefore potentially link a blood microbiome to the fish’s diet, which is often difficult to estimate.</p>
<h2>An embryonic, but promising technique</h2>
<p>So this first bacterial mapping of the blood of these two species probably reflects their respective intestinal microbiome. From this characterization, detection of a variation in the composition of bacteria could be linked to stress, a change in the environment or a physiological change in the animal.</p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/540859/original/file-20230802-23891-ctgz3u.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="comic strip" src="https://images.theconversation.com/files/540859/original/file-20230802-23891-ctgz3u.png?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/540859/original/file-20230802-23891-ctgz3u.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=907&fit=crop&dpr=1 600w, https://images.theconversation.com/files/540859/original/file-20230802-23891-ctgz3u.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=907&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/540859/original/file-20230802-23891-ctgz3u.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=907&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/540859/original/file-20230802-23891-ctgz3u.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=1140&fit=crop&dpr=1 754w, https://images.theconversation.com/files/540859/original/file-20230802-23891-ctgz3u.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=1140&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/540859/original/file-20230802-23891-ctgz3u.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=1140&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Comic strip illustrating the principle of analyzing the circulating microbiome.</span>
<span class="attribution"><span class="source">(Fanny Fronton)</span>, <span class="license">Fourni par l'auteur</span></span>
</figcaption>
</figure>
<p>For example, we know that in humans, the loss of <em>Actinobacteria</em> in the circulating microbiome is associated with severe acute <a href="https://doi.org/10.3389/fcimb.2018.00005">pancreatitis</a>. And there are dozens of examples like this in humans.</p>
<p>This study, the result of a collaboration between university researchers from INRS, the University of Québec at Rimouski and the Department of Fisheries and Oceans Canada, provides a small overview of the informative potential offered by the blood microbiomes of fish from the Gulf of St. Lawrence.</p>
<p>Further research will make it possible to estimate their health and better predict the evolution of their population. The dramatic collapse of the cod stock in the late 1980s had a major impact on fishermen. Several of them even fear that this situation will happen again with another species. As turbot remains a species at risk, it is essential to ensure better management of St. Lawrence species.</p>
<p>Only by refining our analysis techniques and deepening our scientific knowledge can we prevent this type of collapse from happening again in the future.</p><img src="https://counter.theconversation.com/content/217025/count.gif" alt="La Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Fanny Fronton received a grant from the Fondation Armand Frappier.</span></em></p>Blood isn’t sterile, and analyzing the bacteria in it could help assess the health of fish and prevent the collapse of their populations.Fanny Fronton, Doctorante en Écologie halieutique et biologie moléculaire, Institut national de la recherche scientifique (INRS)Licensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2157322023-10-26T13:38:18Z2023-10-26T13:38:18ZA mystery disease hit South Africa’s pine trees 40 years ago: new DNA technology has found the killer<figure><img src="https://images.theconversation.com/files/555224/original/file-20231023-29-u8m533.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">An unidentified fungal killer swept through a South African pine plantation in the 1980s. </span> <span class="attribution"><span class="source">Rodger Shagam</span></span></figcaption></figure><p>In the 1970s and 1980s, pine trees growing in various forestry plantations in South Africa’s Western Cape province began to die in patches. These trees succumbed to a mysterious root disease and the patches expanded gradually. Spontaneous regrowth of seedlings in the patches died dramatically. </p>
<p>As in many other true crime dramas, the finger was initially pointed at the most likely suspect: the root-infecting <em><a href="https://pubmed.ncbi.nlm.nih.gov/28519717/">Phytophthora cinnamomi</a></em>. Its name – plant (phyto) destroyer (phthora) – reveals its power to cause harm; the pathogen is known to cause disease in almost 5,000 different plants.</p>
<p>After further investigation and the collection of many samples, tree pathologists shifted the blame onto the fungus <em>Leptographium serpens</em> (now known as <em>Leptographium alacre</em>). This fungus is well known to be transported by insects and was previously only known in Europe. It was visually identified from the roots of the dying trees. Now it was the prime suspect. </p>
<p>Doubts lingered, though. Most <em>Leptographium</em> species are not known to act as primary disease agents and so <em>L. serpens</em> was most likely not able to cause the disease. Other fungi were also found within the roots of the diseased trees but could not be identified at the time due to a lack of more advanced techniques.</p>
<p>Knowing that the then-available technologies could not provide the complete answer to this mystery, the pathologists took more samples from the dead and dying pine trees, and stored them carefully. The hope was that one day they would have a better idea of the cause of this disease outbreak. </p>
<p>Fast forward to 2023 and a new character enters the mystery: DNA sequencing. This modern technology did what wasn’t possible a few decades ago, allowing our team of molecular mycologists <a href="https://link.springer.com/article/10.1007/s42161-023-01502-1">to identify the real culprit</a>.</p>
<p>This tale is a testament to the ever-evolving nature of scientific inquiry. It reinforces the idea that, in the pursuit of knowledge, no stone should be left unturned and no assumption should be taken for granted. Through a blend of perseverance, technology, and a touch of serendipity, it was possible to solve a decades-old mystery.</p>
<h2>Tracking a killer</h2>
<p>Back in the 1980s the samples were stored in the culture collection of the <a href="https://www.fabinet.up.ac.za">Forestry and Agricultural Biotechnology Institute</a> at the University of Pretoria. In 2020, the samples were revived by a team that included ourselves and several others who recently <a href="https://link.springer.com/article/10.1007/s42161-023-01502-1">published a paper</a> on the topic. </p>
<p>We sequenced the samples’ DNA to reveal their unique genetic code. By comparing this code against genetic databases, it was possible to figure out exactly what was causing the tree disease. And so, more than four decades after the disease was first described, the pathogen was finally identified as <em>Rhizina undulata</em>. <em>L. serpens</em>, the long time primary suspect, was finally exonerated. </p>
<p><em>Rhizina undulata</em> is <a href="https://doi.org/10.1080/00382167.1984.9629524">well known</a> to cause tree disease and death, mainly in Europe. This fungus is known colloquially as the “coffee fire fungus” because the intense heat caused by fires made by campers in a forest to brew coffee activates its dormant spores. This allows it to colonise the roots of conifers, including pines. <em>R. undulata</em> is also well known in South Africa, where it kills many pines in the aftermath of forest fire and when trees are felled to clear a plantation.</p>
<p>What remains a mystery, however, is the trigger that activated this fungus in the Western Cape plantations. No fires were known to have occurred during the relevant time period.</p>
<p>One potential clue to the trigger may lie in the soil in which these trees were planted. Known as Table Mountain sandstone, this soil is sandy and acidic. Acidic soil <a href="https://doi.org/10.1016/S0007-1536(67)80014-7">has been shown</a> in the laboratory to encourage <em>R. undulata</em> growth. This naturally occurring acidity may have been the nudge the pathogen needed to infect the pine trees. It is also possible that the fungus was activated by heat radiating from the quartz rocks that are common in the areas in which the dying trees were planted.</p>
<h2>It pays to be patient</h2>
<p>In the years since the mysterious Western Cape outbreak, <em>R. undulata</em> has become well known to foresters in pine plantations in other parts of South Africa and has done great damage to newly planted trees after fires. These fires can be accidental or due to what is known as slash-burning after trees are harvested. </p>
<p>Identifying <em>R. undulata</em> as the culprit in those (no longer active) Western Cape plantations means scientists have more data that might help to better understand the biology of the fungus – which may lead to better control strategies in the future.</p>
<p>Our work is also a testament to the timeliness of scientific progress and the importance of patience. This story could only be fully unravelled when more advanced techniques were developed. It shows the power of modern technologies to solve historical problems. This underlines the need for continued investment into research and the development of new tools, both in South Africa and worldwide.</p>
<p>Our study also strongly advocates for the preservation of diverse fungal cultures for extended periods of time, regardless of their perceived importance at the time they are collected. The lack of accessible culture collections for lesser-known fungi, in South Africa and internationally, highlights the need for innovative approaches to safeguard these invaluable resources. This shift could revolutionise the study of microbes, opening new avenues beyond traditional species descriptions.</p><img src="https://counter.theconversation.com/content/215732/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Andi Wilson receives funding from the National Research Foundation through a Scarce Skills Postdoctoral Fellowship. </span></em></p><p class="fine-print"><em><span>Brenda Wingfield receives funding from South African Department of Science and Innovation. DSI-NRF SARChI chair in Fungal Genomics</span></em></p><p class="fine-print"><em><span>Michael John Wingfield has previously received Grant funding from the South African National Research Foundation and the Department of Science and Innovation as the director of the DSI/NRF Center of Excellence in Tree Health Biotechnology</span></em></p>Through a blend of perseverance, technology, and a touch of serendipity, it was possible to solve a decades-old mystery.Andi Wilson, Postdoctoral fellow, University of PretoriaBrenda Wingfield, Previous Vice President of the Academy of Science of South Africa and DSI-NRF SARChI chair in Fungal Genomics, Professor in Genetics, University of Pretoria, University of PretoriaMichael John Wingfield, Professor, Advisor to the Executive, University of Pretoria, University of PretoriaLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2135562023-10-12T02:48:26Z2023-10-12T02:48:26ZFor generations, killer whales and First Nations hunted whales together. Now we suspect the orca group has gone extinct<figure><img src="https://images.theconversation.com/files/548727/original/file-20230918-21-qfq7hs.png?ixlib=rb-1.1.0&rect=0%2C4%2C3243%2C1784&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Whalers and Old Tom on the hunt </span> <span class="attribution"><a class="source" href="https://upload.wikimedia.org/wikipedia/commons/c/c5/Killer_whale_%28Old_Tom%29_and_whalers_-_original.jpeg">Charles Eden Wellings/WIkimedia Commons</a>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span></figcaption></figure><p>For generations, the Thaua people worked with killer whales to hunt large whales in the water of Twofold Bay, on the southern coast of New South Wales. Killer whales – commonly known as orcas – would herd their giant prey into shallower waters where hunters could spear them. Humans would get the meat, but the killer whales wanted a delicacy – the tongue.</p>
<p>After colonists dispossessed the Thaua, Europeans began capitalising on this longstanding partnership. From around 1844, commercial whalers worked with employed Thaua and killer whales to hunt these giants. The pods of killer whales would find a prized <a href="https://au.whales.org/whales-dolphins/what-is-baleen/">baleen whale</a>, herd it closer to shore and signal the whalers, who lived in the town of Eden.</p>
<p>The partnership has no parallel anywhere in the world: the top predator of the oceans working with the top predator on land.</p>
<p>One killer whale, Old Tom, <a href="https://blogs.scientificamerican.com/running-ponies/the-legend-of-old-tom-and-the-gruesome-law-of-the-tongue/">became legendary</a> due to his active role in the hunts for at least three decades. He was seven metres long and weighed six tonnes. </p>
<p>In 1930, he was found dead at a local beach – the last of his group in Eden. You can see his body preserved in Eden’s <a href="https://killerwhalemuseum.com.au/">Killer Whale Museum</a>. But questions have lingered. Do Old Tom’s descendants still roam the oceans, or did they die out? </p>
<p>Our <a href="https://academic.oup.com/jhered/advance-article/doi/10.1093/jhered/esad058/7308443">new research</a> suggests these famous killer whales are likely to be extinct.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/548733/original/file-20230918-27-y38zuy.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="killer whales of Eden, australia" src="https://images.theconversation.com/files/548733/original/file-20230918-27-y38zuy.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/548733/original/file-20230918-27-y38zuy.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=454&fit=crop&dpr=1 600w, https://images.theconversation.com/files/548733/original/file-20230918-27-y38zuy.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=454&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/548733/original/file-20230918-27-y38zuy.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=454&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/548733/original/file-20230918-27-y38zuy.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=570&fit=crop&dpr=1 754w, https://images.theconversation.com/files/548733/original/file-20230918-27-y38zuy.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=570&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/548733/original/file-20230918-27-y38zuy.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=570&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">The killer whales of Eden, including Old Tom at top right.</span>
<span class="attribution"><span class="source">Eden Killer Whale Museum</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<h2>Old Tom’s origins</h2>
<p>Adaptability, cultural traditions and female-led societies have made killer whales the ultimate ocean predator. These intelligent marine mammals are the world’s largest dolphin, and the only species known to successfully hunt adult <a href="https://esajournals.onlinelibrary.wiley.com/doi/10.1002/ecy.3875">great white sharks</a> and the world’s largest living animal – <a href="https://onlinelibrary.wiley.com/doi/abs/10.1111/mms.12906">blue whales</a>. </p>
<p>But different groups can live <a href="https://www.norwegianorcasurvey.no/about-orcas">very different lives</a>. Some are constantly on the move, while others stay living in a particular region. Some feed exclusively on one type of prey, while others feed on many. Across the globe, killer whale vocalisations differ greatly, with different dialects and languages unique to families and regions. </p>
<p>To find out where these killer whales of Eden came from, we drilled into one of Old Tom’s teeth and analysed the resulting powder to sequence his DNA. We used the same methods used to extract DNA from Neanderthal remains and million-year-old mammoths. </p>
<p>When we compared Old Tom’s DNA to a global data set of killer whales, his genome was most similar to those of modern New Zealand killer whales. He shared a most recent common ancestor with killer whales from the northern Pacific, northern Atlantic, and Australasia. </p>
<p>But there was no sign of any recent descendants in our modern killer whales data set. Old Tom’s DNA is mostly distinct from modern populations. That suggests the famous <a href="https://danielleclode.com.au/killers-in-eden">killers of Eden</a> may have died out. </p>
<h2>Whale brothers</h2>
<p>The ancestors of Steven Holmes, a Thaua Traditional Owner, had close ties to both the killer whales and to the colonist whalers. Steven has worked with us to give the Thaua perspective. His advocacy helped <a href="https://www.theguardian.com/australia-news/2022/sep/30/nsw-renames-national-park-over-pastoralist-ben-boyds-links-to-slavery-in-pacific">change the name</a> of Eden’s Ben Boyd National Park to Beowa, which is Thaua for killer whale. Ben Boyd was a whaler as well as a notorious slaver, forcing Pacific people onto boats and into indentured labour. </p>
<p>Steven told us: </p>
<blockquote>
<p>In Twofold Bay, the coastal Thaua people, part of the Yuin nation, had a connection with the killer whales through the Dreaming. Their long relationship was highly valued by the Thaua, who depended on the ocean for food and other resources. They considered the killer whales their brothers. When a Thaua died, they were believed to be reincarnated as killer whales. That way, the Thaua always remained one mob – whether whale or man.</p>
</blockquote>
<p>Thaua people used specialised hunting strategies that encouraged killer whales to herd baleen whales, such as humpbacks, closer to shore for them to kill. After a successful kill, the killer whales were rewarded with the tongue while the Thaua got the rest of the carcass. This became known as the “Law of the Tongue”. </p>
<p>After colonisation, white whalers capitalised on this relationship. They hired many skilled First Nations whalers. </p>
<p>When killer whales found a whale, some would slap their tails in front of the whaling station to alert the whalers. Some killer whales would herd the target into shallower water, while others would harry and tire it out. Eventually, the whalers would harpoon the exhausted whale, following it with the killing lance to pierce vital organs. </p>
<p>Old Tom was active in these hunts, reported to grab the lines of the boat to pull the whalers out faster, or tug on the line to drive the harpoon deeper and speed up the whale’s death. </p>
<p>The whalers left the carcass on a buoy for up to two days to allow the killer whales to eat the tongue and lips.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/548731/original/file-20230918-15-8qik2n.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="whalers and killer whales hunting whales together`" src="https://images.theconversation.com/files/548731/original/file-20230918-15-8qik2n.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/548731/original/file-20230918-15-8qik2n.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=380&fit=crop&dpr=1 600w, https://images.theconversation.com/files/548731/original/file-20230918-15-8qik2n.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=380&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/548731/original/file-20230918-15-8qik2n.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=380&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/548731/original/file-20230918-15-8qik2n.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=477&fit=crop&dpr=1 754w, https://images.theconversation.com/files/548731/original/file-20230918-15-8qik2n.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=477&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/548731/original/file-20230918-15-8qik2n.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=477&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">European whalers and killer whales on a hunt towards the end of whaling in Eden, some time between 1910 and 1920.</span>
<span class="attribution"><span class="source">Eden Killer Whale Museum</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<h2>Where did they go?</h2>
<p>Eden’s whaling station did not process any whales after 1928, as whale numbers had plummeted. The killer whales had already begun to vanish. </p>
<p>Why did they leave? We don’t know for sure, but hypotheses include a lack of other food or even a breach of the Law of the Tongue by whalers. </p>
<p>What we do know is the group has never returned, and our new DNA evidence suggests that Old Tom’s group does not have any descendants in our oceans today.</p>
<p>Since they left, there have been <a href="https://www.abc.net.au/news/2022-04-28/killer-whale-pod-spotted-off-nsw-far-south-coast/101012770">only a handful</a> of killer whale sightings off Eden. </p>
<p>While they are gone, they are not forgotten. The legacy of the killer whales of Eden lives on among Thaua people and local communities.</p><img src="https://counter.theconversation.com/content/213556/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>The authors do not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and have disclosed no relevant affiliations beyond their academic appointment.</span></em></p>On New South Wales’ southern coast, First Nations groups and European whalers hunted alongside orcas. But what happened to this unusual group?Isabella Reeves, PhD Candidate, Flinders UniversitySteven Holmes, Traditional knowledge holder, Indigenous KnowledgeLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2106262023-10-08T19:27:05Z2023-10-08T19:27:05ZThere are 750 unidentified human remains in Australia. Could your DNA help solve one of these cold cases?<figure><img src="https://images.theconversation.com/files/548232/original/file-20230914-15-etoudo.jpg?ixlib=rb-1.1.0&rect=0%2C112%2C4513%2C3016&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/skull-bones-ruined-wooden-coffin-1180841596">Shutterstock</a></span></figcaption></figure><p>Yesterday <a href="https://www.abc.net.au/news/2023-10-08/how-genetic-genealogy-is-solving-australias-coldest-cases/102870058">it was announced</a> the Australian Federal Police (AFP) <a href="https://www.missingpersons.gov.au/support/national-dna-program-unidentified-and-missing-persons">National DNA Program for Unidentified and Missing Persons</a> used advanced DNA technology to assist South Australia Police resolve a 40-year-old missing persons case. </p>
<p>In January 1983, skeletal remains were found in roadside scrub on Kangaroo Island. Forensic testing over the years revealed he was male, middle-aged, of European ancestry, blue-eyed, 162–173cm tall and wore full dentures. </p>
<p>But it wasn’t until June 2023 that advances in forensic genomics and genealogy gave William Hardie his name back.</p>
<p>The AFP DNA program used similar technology to direct-to-consumer DNA testing companies like <a href="https://www.ancestry.com.au/dna/">AncestryDNA</a> and <a href="https://www.23andme.com/en-int/">23andMe</a>. These companies market themselves as a DNA-based way <a href="https://theconversation.com/at-home-dna-tests-just-arent-that-reliable-and-the-risks-may-outweigh-the-benefits-194349">to explore your ancestral origins</a> by simply sending in a saliva sample. But how is this technology used to solve cold cases? </p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/if-youve-given-your-dna-to-a-dna-database-us-police-may-now-have-access-to-it-126680">If you've given your DNA to a DNA database, US police may now have access to it</a>
</strong>
</em>
</p>
<hr>
<h2>We share pieces of DNA with our relatives</h2>
<p>All humans are <a href="https://nigms.nih.gov/education/Inside-Life-Science/Pages/Genetics-by-the-Numbers.aspx">more than 99%</a> genetically identical. The genetic differences in the remaining 1% of the genome are what hints at our ancestors, as well as coding for other distinctive traits (for example, <a href="https://www.frontiersin.org/articles/10.3389/fgene.2018.00462/full">facial features</a> and <a href="https://www.science.org/content/article/landmark-study-resolves-major-mystery-how-genes-govern-human-height">height</a>).</p>
<p>Most consumer DNA testing companies use <a href="https://www.genome.gov/about-genomics/fact-sheets/DNA-Microarray-Technology">microarrays</a> to survey this non-identical DNA. Microarrays target a small fraction of the genome – up to a million genetic variants called single nucleotide polymorphisms or SNPs.</p>
<p>The reason we can match our DNA to relatives is because we inherit it from each of our biological parents. On average, half of our DNA (including the identical and non-identical parts) is shared with our parents and siblings – first degree relatives.</p>
<p>Going further, we share roughly a quarter of our DNA with second degree relatives, and an eighth with third degree relatives. As the genetic distance increases, we generally share <a href="https://dnapainter.com/tools/sharedcmv4">fewer and smaller pieces of DNA</a>.</p>
<p>Even so, it’s possible to detect the few small pieces of DNA we share with our ancestors (and their descendants) going back many generations.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/how-do-we-identify-human-remains-121315">How do we identify human remains?</a>
</strong>
</em>
</p>
<hr>
<h2>A challenge for forensic samples</h2>
<p>But there are unique challenges for forensic scientists trying to identify human remains using ancestral DNA. In long-term missing persons cases, often the only remains found are skeletal.</p>
<p>In this scenario, DNA has to be extracted from bones or teeth. However, the DNA contained in these hard tissues will degrade with time and exposure to adverse environmental conditions (for example, long periods in <a href="https://www.sciencedirect.com/science/article/pii/S0379073821001791">soil</a> and <a href="https://www.tandfonline.com/doi/full/10.1080/00450618.2023.2181395?src=">seawater</a>).</p>
<p>As a result, the quantity and quality of extracted DNA is often <a href="https://pubmed.ncbi.nlm.nih.gov/35272198/#full-view-affiliation-1">insufficient</a> for microarray analysis. Whole genome sequencing – which can recover all <a href="https://nigms.nih.gov/education/Inside-Life-Science/Pages/Genetics-by-the-Numbers.aspx">3.2 billion</a> letters that make up the genetic code – is proving <a href="https://pubmed.ncbi.nlm.nih.gov/31981902/">more successful</a> for such samples, but it’s not yet available in Australian forensic laboratories.</p>
<p>To overcome these challenges, the AFP DNA program recently <a href="https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4551904">validated</a> a forensic DNA kit for use in their accredited laboratory. The kit employs <a href="https://sapac.illumina.com/content/dam/illumina-marketing/documents/products/appspotlights/app_spotlight_forensics.pdf">targeted sequencing</a> to focus on about <a href="https://verogen.com/wp-content/uploads/2021/07/high-quality-outcomes-low-quality-samples-app-note-vd2021002-b.pdf">10,000 SNPs</a>.</p>
<p>While this new method doesn’t analyse as much DNA as microarrays or whole genome sequencing, it is enough to link genetic relatives <a href="https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4466078">up to the fifth degree</a> (for example, second cousins or great-great-great grandparents), or sometimes further.</p>
<figure class="align-center ">
<img alt="white gloved hands unpacking a cotton swab for a dna test" src="https://images.theconversation.com/files/541407/original/file-20230807-1249-63emwo.jpg?ixlib=rb-1.1.0&rect=221%2C113%2C3208%2C2340&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/541407/original/file-20230807-1249-63emwo.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/541407/original/file-20230807-1249-63emwo.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/541407/original/file-20230807-1249-63emwo.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/541407/original/file-20230807-1249-63emwo.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/541407/original/file-20230807-1249-63emwo.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/541407/original/file-20230807-1249-63emwo.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
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<span class="caption">A saliva sample contains enough DNA to sequence the whole genome of a living person, but for skeletonised human remains the DNA may be limited or damaged.</span>
<span class="attribution"><a class="source" href="https://unsplash.com/photos/aNEaWqVoT0g">Mufid Majnun/Unsplash</a></span>
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<h2>Combing through public databases and records</h2>
<p>Once a SNP profile is obtained – and after all other avenues of inquiry have been exhausted – the AFP DNA program will upload it to the <a href="https://pro.gedmatch.com/">GEDmatch PRO</a> and <a href="https://www.familytreedna.com/">FamilyTreeDNA</a> databases for comparison to the profiles of citizens who have volunteered their DNA to be used in this way.</p>
<p>If suitable genetic matches are found, a genetic genealogist will use public information to <a href="https://abcnews.go.com/2020/video/investigators-built-genetic-genealogy-leading-golden-state-killer-54949329">build out their family trees</a> until they discover (typically deceased) ancestors in common. From there, they will <a href="https://www.familysearch.org/en/wiki/Descendancy_Research">research</a> relevant family lines to find closer (ideally living) relatives of the unknown individual.</p>
<p>They may also work with police who can use investigative techniques, non-public information and <a href="https://www.yourdnaguide.com/ydgblog/targeted-dna-testing-family-history">targeted DNA testing</a> to fill in some branches of the tree and rule out others. The aim is to find a present-day family with a missing or unaccounted-for relative.</p>
<p>This process is known as <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9407302/">forensic investigative genetic genealogy</a>. It has revolutionised <a href="https://dnadoeproject.org/">John and Jane Doe investigations</a> and other <a href="https://www.intermountainforensics.com/understanding-genetic-geneaology">humanitarian efforts</a> in the United States. However, its use in Australia is still growing. It is also just one of <a href="https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wfs2.1484">many forensic identification tools</a> and often used as a last resort.</p>
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<strong>
Read more:
<a href="https://theconversation.com/australia-has-2-000-missing-persons-and-500-unidentified-human-remains-a-dedicated-lab-could-find-matches-90620">Australia has 2,000 missing persons and 500 unidentified human remains – a dedicated lab could find matches</a>
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<h2>750 unidentified and 2,500 missing persons</h2>
<p>Currently, there are around 2,500 long-term missing persons and <a href="https://www.sciencedirect.com/science/article/pii/S1875176822000208">750 unidentified human remains in Australia</a>.</p>
<p>AFP DNA program specialists are supporting state and territory police to identify these nameless individuals, link them to missing people and reunite them with families who’ve missed them for years.</p>
<p>So far, the AFP DNA program has been instrumental in resolving 46 cases. This includes identifying the remains of 15 missing Australians, including <a href="https://www.abc.net.au/news/2022-03-01/coroner-confirms-bones-belong-to-missing-whyalla-man/100870540">Mario Della Torre</a>, <a href="https://www.abc.net.au/news/2023-05-23/missing-person-owen-ryder-human-remains-identified-hermannsburg/102382936">Owen Ryder</a>, <a href="https://www.abc.net.au/news/2023-08-10/qld-police-identify-remains-found-buried-brisbane-unit-complex/102711418">Tanya Glover</a> and <a href="https://www.abc.net.au/news/2023-09-05/queensland-police-cold-case-murder-francis-foley-2008/102814926">Francis Foley</a>.</p>
<h2>How can you help if you have a missing relative?</h2>
<p>First, you should <a href="https://forms.afp.gov.au/online_forms/missing-person-details">report</a> them missing to the police if you haven’t already. Provide all known information relevant to the forensic investigation (including physical appearance, medical history and dentist’s details).</p>
<p>Second, you can <a href="https://www.missingpersons.gov.au/support/national-dna-program-unidentified-and-missing-persons#faq-DNA-testing-information">provide a reference DNA sample</a>. This simple procedure involves you swabbing the inside of your cheek and can be done at your local police station when making a missing persons report.</p>
<p>Your DNA profile will be uploaded to Australia’s <a href="https://www.acic.gov.au/services/biometric-and-forensic-services">national DNA database</a> so it can be compared to DNA profiles from unknown deceased persons across Australia with your consent.</p>
<p>This is critical for decades-old missing persons cases where few close genetic relatives remain.</p>
<h2>You can help if you’ve taken a consumer DNA test</h2>
<p>You may be distantly related to one of the unknown Australians without even knowing it.</p>
<p>Anyone who has done a consumer DNA test <a href="https://www.missingpersons.gov.au/support/national-dna-program-unidentified-and-missing-persons#faq-Forensic-Investigative-Genetic-Genealogy-information">can potentially help</a> identify missing people. To do so, you need to <a href="https://www.gedmatch.com/how-it-works/">download</a> your DNA data file, upload it to <a href="https://www.gedmatch.com/">GEDmatch</a> and choose to opt in or out of “law enforcement matching”. </p>
<p>If you opt in, you consent to your DNA being included in searches by police worldwide for the purpose of identifying human remains and solving violent crimes like homicides.</p>
<p>If you opt out, your DNA can still be used by the AFP DNA program to resolve unidentified and missing persons cases, but it won’t be used for criminal cases.</p>
<p>Without the leads from distant genetic relatives who had previously opted in to this type of DNA matching, it wouldn’t have been possible to connect human remains found on Kangaroo Island in 1983 to the family of William Hardie, who’ve missed him for over 40 years.</p>
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<strong>
Read more:
<a href="https://theconversation.com/is-your-genome-really-your-own-the-public-and-forensic-value-of-dna-95786">Is your genome really your own? The public and forensic value of DNA</a>
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<img src="https://counter.theconversation.com/content/210626/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Jodie Ward is also employed by the Australian Federal Police as the Program Lead of the National DNA Program for Unidentified and Missing Persons. She was involved in applying forensic investigative genetic genealogy to the unidentified human remains case found on Kangaroo Island, which assisted the South Australia Police to identify the remains as belonging to William Hardie. The National DNA Program for Unidentified and Missing Persons commenced in July 2020 and is currently funded under the Proceeds of Crime Act 2002 (Cth) until December 2023.</span></em></p><p class="fine-print"><em><span>Dennis McNevin has been seconded to the Australian Federal Police National DNA Program for Unidentified and Missing Persons. He has also provided commercial scientific services to the NSW Police Force. He has previously received fuding for research on forensic genetics from the Australian Research Council, the AMP Tomorrow Fund, the ANU Connect Ventures Discovery Translation Fund and the US Army International Technology Center - Pacific.</span></em></p>DNA volunteered by citizens worldwide is helping to restore the identity of human remains found across Australia.Jodie Ward, Associate Professor, Centre for Forensic Science, University of Technology SydneyDennis McNevin, Professor of Forensic Genetics, University of Technology SydneyLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2129352023-09-18T14:25:22Z2023-09-18T14:25:22ZWild animals leave DNA on plants, making them easier to track – here’s what scientists found in a Ugandan rainforest<p>The world is losing animals at an alarming <a href="https://doi.org/10.1126/science.1244693">rate</a> due to habitat degradation, climate change and illegal human activities in the wildlife protected areas. In fact, it is estimated that, by 2100, <a href="https://www.ipbes.net/sites/default/files/spm_africa_2018_digital.pdf#page=25">more than half</a> of Africa’s bird and mammal species could be lost. </p>
<p>Efforts to conserve biodiversity depend on information about which animals are where. Tracking wildlife is instrumental. Existing tracking methods include camera trapping and line transects, which are specific areas and designed trails respectively, that can be revisited from time to time to monitor habitat conditions and species changes. These methods can be expensive, labour intensive, time consuming and difficult to use, and might not detect all the species that are present in an area. Dense rainforests present a particular problem for tracking, since the vegetation is often very thick and doesn’t let much light in.</p>
<p>Recent research has shown that vertebrates leave their DNA in the environment, both as <a href="https://www.sciencedirect.com/science/article/pii/S0960982221016900?via%3Dihub">airborne particles</a> and on <a href="https://www.nature.com/articles/s41598-023-27512-8">vegetation</a>. This offers a useful new way to monitor species. </p>
<p>Our international research team, working in the rainforest of Uganda’s Kibale National Park, wondered whether the environmental DNA methods would be useful to us. We reasoned that if animal DNA was in the air, perhaps it settled and got stuck to leaves. Waxy, sticky or indented leaf surfaces might even be ideal DNA traps. Would simply swabbing leaves collect enough DNA to monitor species and map biodiversity?</p>
<p>Our <a href="https://doi.org/10.1016/j.cub.2023.06.031">study</a> demonstrated that many birds and mammals can be detected using this simple, low tech method. It’s a promising tool for large-scale biomonitoring efforts.</p>
<h2>Kibale National Park</h2>
<p><a href="https://ugandawildlife.org/national-parks/kibale-national-park/">Kibale National Park</a> in Uganda is famous for its rich biodiversity and has earned its place as the “primate capital” of the world. It is home to 13 species of non-human primates including the endangered Red colobus monkey and chimpanzees. </p>
<p>To test our idea, the research team went into the park’s dense tropical forest armed with 24 cotton buds. Our task was to swab as many leaves as possible with each bud in three minutes.</p>
<p>To tell which animals gave rise to the DNA in the swabs, the team sequenced a short piece of DNA, called a barcode. Barcodes are distinct for each animal, so the barcode found in the swabs could be compared to a barcode library containing all animals sampled to date.</p>
<p>The team didn’t expect great results, because in rainforest conditions – hot by day, cold at night, humid and wet – DNA degrades quickly.</p>
<p>So we were surprised when the results came back from the DNA sequencer. We’d picked up over 50 species of mammals and birds and a frog, with swabs collected in just over an hour, on only 24 cotton buds.</p>
<p>We detected nearly eight animal species on each of the cotton buds. These species spanned a huge diversity, from the very large and endangered African elephant to a very small species of sunbird. </p>
<p>Detected animals included the hammer-headed fruit bat, which has a wing-span of up to one metre, monkeys like the elusive L’Hoest’s monkey and the endangered ashy red colobus, as well as rodents such as the forest giant squirrel. A great variety of birds was detected too, including the great blue turaco and the endangered gray parrot.</p>
<p>The high diversity of animals, coupled with the impressive animal detection rate per swab, suggests we can now collect a lot of animal DNA simply from leaves. The ease of sampling, a task we can ask anyone on our team to do quickly when they are in the forest, suggests we could use this method to track animal diversity in the park, particularly in areas that are rapidly changing.</p>
<p>One of the team members, Emmanuel Opito, is studying exactly these areas in the park for his doctoral project. He is trying to understand how the invasive <em>Lantana camara</em> and the woody herb <em>Acanthus pubescens</em> inhibit forest regeneration. With this leaf swabbing method, it will be easier to explore how removing invasive species and allowing the forest to regenerate will help animal biodiversity recover. </p>
<h2>Easy way to gather information</h2>
<p>Monitoring animal populations is crucial to comprehend the scale of ecosystem changes and to guide the development of effective management strategies. New technologies like these environmental DNA approaches offer promising support for these efforts. </p>
<p>Because leaf swabbing does not require fancy and expensive equipment or much training to carry out, it can easily be carried out by the staff at Uganda Wildlife Authority, field assistants or biologists working in the forest. </p>
<p>The method can also be scaled up because DNA sequencing technology is becoming more accessible and affordable post-COVID-19. There is a lot of potential for environmental DNA to contribute to biodiversity monitoring at a much larger scale and to inform biodiversity management initiatives.</p><img src="https://counter.theconversation.com/content/212935/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Patrick Omeja was supported by the International Development Research Centre.</span></em></p>Many animal species can be detected using a simple, low tech method of collecting DNA from the environment.Patrick Omeja, Senior Research Fellow and Field Director, Makerere University Biological Field Station, Makerere UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2117992023-08-24T14:51:27Z2023-08-24T14:51:27ZNew research reveals that Ötzi the iceman was bald and probably from a farming family – what else can DNA uncover?<p>In 1991, hikers came across a body that <a href="https://www.iceman.it/en/the-discovery/">was partially contained in ice</a> high up in the Alpine province of South Tyrol, Italy. Initially thought to be from a recent death, the body was later discovered to be 5,300 years old – from a time known as <a href="https://en.wikipedia.org/wiki/Chalcolithic">the Copper Age</a>.</p>
<p>This amazing find would subsequently become known as Ötzi the iceman. His body and belongings were extensively studied, prompting numerous questions: what was he doing here? Where was he from? How did he live – and die?</p>
<p>Researchers from the Max Planck Institute for Evolutionary Anthropology in Germany have just added another piece to this jigsaw, <a href="https://www.cell.com/cell-genomics/pdfExtended/S2666-979X(23)00174-X">describing the physical appearance of Ötzi</a> based on new DNA information. They say he probably had relatively dark skin and was balding. But how reliable are these predictions and could they be used in forensics?</p>
<p>Much of this depends on the quality of the samples. Ötzi died in the Otzal Alps and was frozen almost immediately, remaining in the permafrost until discovery.</p>
<p><a href="https://www.iceman.it/en/the-iceman/">The body is currently stored in low temperature conditions</a> at the South Tyrol Museum of Archaeology. His unique preservation enabled the sequencing of Ötzi’s whole genome – the complete “instruction booklet” for building a human. The chemical building blocks of DNA are called bases. These are nitrogen-containing chemical compounds called adenine, thymine, cytosine and guanine, known by the letters A, T, C and G. The human genome consists of billions of these bases arranged in different sequences - making up the genetic code.</p>
<p>Much of the genome’s DNA sequence is common to all humans, but there are places where a change from one base to another results in changes to our physical appearance. </p>
<p>The Ötzi paper isn’t the first study that has tried to predict a person’s appearance from ancient remains. King Richard III was killed in the Battle of Bosworth in 1485. When his body was discovered in 2012, under a car park in Leicester, only his bones remained. But it was enough for a team led by Turi King at the University of Leicester to extract <a href="https://www.nature.com/articles/ncomms6631">fragments of DNA from them</a>.</p>
<figure class="align-center ">
<img alt="Representation of the DNA molecule." src="https://images.theconversation.com/files/544058/original/file-20230822-21-xnyapv.jpg?ixlib=rb-1.1.0&rect=14%2C0%2C4947%2C2799&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/544058/original/file-20230822-21-xnyapv.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=337&fit=crop&dpr=1 600w, https://images.theconversation.com/files/544058/original/file-20230822-21-xnyapv.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=337&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/544058/original/file-20230822-21-xnyapv.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=337&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/544058/original/file-20230822-21-xnyapv.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=424&fit=crop&dpr=1 754w, https://images.theconversation.com/files/544058/original/file-20230822-21-xnyapv.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=424&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/544058/original/file-20230822-21-xnyapv.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=424&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
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<span class="caption">Representation of the DNA molecule.</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/blue-helix-human-dna-structure-1669326868">Billion Photos / Shutterstock</a></span>
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<h2>Crime scene samples</h2>
<p>These fragments, comprising hundreds of DNA bases, were sequenced. They were able to predict his hair and eye colour and he was reliably matched to a living relative – assigning a clear identity to the remains. This means that if I ate an apple and threw the core away, I could also be identified by the DNA I left on the core. </p>
<p>Sequencing a genome, which comprises billions of DNA bases, enables scientists to evaluate regions of the human genome that contribute to appearance. These are known as highly variable regions.</p>
<p>For more than 30 years, forensic scientists have looked at specific highly variable regions in DNA to match these to crime scene samples, or to relatives of a suspect or victim. So how likely is it that DNA from such a sample could accurately paint a picture of me? </p>
<p>Let’s take facial shape. Can forensic scientists build a kind of identikit photo from a crime scene DNA sample? Some efforts have <a href="https://snapshot.parabon-nanolabs.com/">already been taken in this regard</a>. But our understanding of the gene variants involved in face shape are incomplete. </p>
<p>Many of the identikit pictures built from DNA analysis alone <a href="https://snapshot.parabon-nanolabs.com/posters">bear a resemblance</a> to actual images of the individuals. But when DNA is the only evidence available to build a portrait, the prediction of facial appearance can be skewed by body composition which is significantly affected by diet and lifestyle.</p>
<p>However, other aspects of appearance can be predicted with high accuracy: red hair, for example. Base variations in the <a href="https://onlinelibrary.wiley.com/doi/epdf/10.1002/humu.20476">melanocortin receptor 1 (MC1R) gene</a> are linked to red hair, fair skin and freckling. In rarer cases, variations in two other genes <a href="https://www.snpedia.com/index.php/Rs12913832">HERC2</a> and <a href="https://www.snpedia.com/index.php/Rs2378249">PIGU/ASIP</a> are also linked to red hair.</p>
<p>The human genome is packaged into 23 pairs of chromosomes. On chromosome 15 there are many regions which influence eye colour and skin pigmentation. Eye colour can be reliably predicted, with blue eye colour the most accurate. Hair colour can be predicted from DNA, but <a href="https://www.sciencedirect.com/science/article/pii/S1872497312001810">darker shades of hair are more accurately predicted</a> than blonde hair. </p>
<p>Aside from the complications posed by hair dye, predicting blonde hair is complicated because some individuals have very blonde hair in childhood that darkens to light brown with the onset of adulthood. </p>
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Read more:
<a href="https://theconversation.com/how-does-genetics-explain-non-identical-identical-twins-55479">How does genetics explain non-identical identical twins?</a>
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<h2>Environmental factors</h2>
<p>Several genes contribute to produce hair pigments and a spectrum of hair colour is seen in humans, ranging from light blonde to black. <a href="https://www.sciencedirect.com/science/article/pii/S1872497312001810">Commercially sold laboratory kits such as Hirisplex</a> can simultaneously evaluate several DNA regions to predict the hair and eye colour from a biological sample. However, unlike eye colour, hair colour prediction from DNA is only of value until midlife, when the natural processes of ageing lead to greying or white hair. </p>
<p>These processes also lead to hair loss in some people and more than 300 gene variants have been linked to baldness. Future research should determine more clearly how these gene variants affect hair density. However, stress, diet, medication, and disease, in addition to genetics, all influence hair loss. </p>
<p>Individual DNA bases can become chemically modified as we age. This is known as an epigenetic change. Identical twins start life with the same DNA, but as they age, some physical differences become apparent.</p>
<p>Some of those differences are <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4276927/">due to DNA bases changing</a> as cells divide but most are due to base changes caused by lifestyle and the environment. This is an exciting area of research for understanding ageing and disease. It can also be used as a forensic tool to distinguish between twins.</p>
<p>There is currently a lot of DNA information from people of European origin, but fewer whole genomes exist from populations elsewhere. This can influence the accuracy when scientists try to predict both appearance and ancestry.</p>
<p>More representative data from the rest of the world will therefore enhance studies in forensic archaeology, such as the Ötzi research. It will also have implications for forensics and assist in the identification of missing individuals.</p><img src="https://counter.theconversation.com/content/211799/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Caroline Smith 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>We can predict hair and eye colour with reasonable accuracy from DNA, but other characteristics are being investigated.Caroline Smith, Assistant Head, School of Life Sciences, University of WestminsterLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2121122023-08-24T04:51:52Z2023-08-24T04:51:52ZThe ‘weird’ male Y chromosome has finally been fully sequenced. Can we now understand how it works, and how it evolved?<p>The Y chromosome is a never-ending source of fascination (particularly to men) because it bears genes that determine maleness and make sperm. It’s also small and seriously weird; it carries few genes and is full of junk DNA that makes it horrendous to sequence. </p>
<p>However, new “<a href="https://www.nature.com/articles/s41592-022-01730-w">long-read</a>” sequencing techniques have finally provided a reliable sequence from one end of the Y to the other. The paper describing this Herculean effort has been <a href="https://www.nature.com/articles/s41586-023-06457-y">published</a> in Nature.</p>
<p>The findings provide a solid base to explore how genes for sex and sperm work, how the Y chromosome evolved, and whether – as predicted – it will disappear in a few million years.</p>
<h2>Making baby boys</h2>
<p>We have known for <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5443938/#">about 60 years</a> that specialised chromosomes <a href="https://theconversation.com/what-makes-you-a-man-or-a-woman-geneticist-jenny-graves-explains-102983">determine birth sex</a> in humans and other mammals. Females have a pair of X chromosomes, whereas males have a single X and a much smaller Y chromosome.</p>
<p>The Y chromosome is male-determining because it bears a gene <a href="https://pubmed.ncbi.nlm.nih.gov/1695712/">called SRY</a>, which directs the development of a ridge of cells into a testis in the embryo. The embryonic testes make male hormones, and these hormones direct the development of male features in a baby boy.</p>
<p>Without a Y chromosome and a SRY gene, the same ridge of cells develops into an ovary in XX embryos. Female hormones then direct the development of female features in the baby girl.</p>
<h2>A DNA junkyard</h2>
<p>The Y chromosome is very different from X and the 22 other chromosomes of the human genome. It is smaller and bears few genes (only 27 compared to about 1,000 on the X).</p>
<p>These include SRY, a few genes required to make sperm, and several genes that seem to be critical for life – many of which have partners on the X.
Many Y genes (including the sperm genes RBMY and DAZ) are present in multiple copies. Some occur in weird loops in which the sequence is inverted and genetic accidents that duplicate or delete genes are common.</p>
<p>The Y also has a lot of DNA sequences that don’t seem to contribute to traits. This “junk DNA” is comprised of highly repetitive sequences that derive from bits and pieces of old viruses, dead genes and very simple runs of a few bases repeated over and over. </p>
<p>This last DNA class occupies big chunks of the Y that literally glow in the dark; you can see it down the microscope because it preferentially binds fluorescent dyes.</p>
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Read more:
<a href="https://theconversation.com/we-discovered-a-missing-gene-fragment-thats-shedding-new-light-on-how-males-develop-147348">We discovered a missing gene fragment that's shedding new light on how males develop</a>
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<h2>Why the Y is weird</h2>
<p>Why is the Y like this? Blame evolution.</p>
<p>We have a lot of evidence that 150 million years ago the X and Y were just a pair of ordinary chromosomes (they still are in birds and platypuses). There were two copies – one from each parent – as there are for all chromosomes.</p>
<p>Then SRY evolved (from an ancient gene with another function) on one of these two chromosomes, defining a new proto-Y. This proto-Y was forever confined to a testis, by definition, and subject to a barrage of mutations as a result of a lot of cell division and little repair. </p>
<p>The proto-Y degenerated fast, losing about 10 active genes per million years, reducing the number from its original 1,000 to just 27. A small “pseudoautosomal” region at one end retains its original form and is identical to its erstwhile partner, the X.</p>
<p>There has been great debate about whether this <a href="http://theconversation.com/sex-genes-the-y-chromosome-and-the-future-of-men-32893">degradation continues</a>, because at this rate the whole human Y would disappear in a few million years (as it already has in some rodents).</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/men-are-slowly-losing-their-y-chromosome-but-a-new-sex-gene-discovery-in-spiny-rats-brings-hope-for-humanity-195903">Men are slowly losing their Y chromosome, but a new sex gene discovery in spiny rats brings hope for humanity</a>
</strong>
</em>
</p>
<hr>
<h2>Sequencing Y was a nightmare</h2>
<p>The first draft of the human genome was completed in 1999. Since then, scientists have managed to sequence all the ordinary chromosomes, including the X, with just a few gaps. </p>
<p>They’ve done this using short-read sequencing, which involves chopping the DNA into little bits of a hundred or so bases and reassembling them like a jigsaw.</p>
<p>But it’s only recently that new technology has allowed sequencing of bases along individual long DNA molecules, producing long-reads of thousands of bases. These longer reads are easier to distinguish and can therefore be assembled more easily, handling the confusing repetitions and loops of the Y chromosome.</p>
<p>The Y is the last human chromosome to have been sequenced end-to-end, or T2T (telomere-to-telomere). Even with long-read technology, assembling the DNA bits was often ambiguous, and researchers had to make several attempts at difficult regions – particularly the highly repetitive region.</p>
<h2>So what’s new on the Y?</h2>
<p>Spoiler alert – the Y turns out to be just as weird as we expected from decades of gene mapping and the previous sequencing.</p>
<p>A few new genes have been discovered, but these are extra copies of genes that were already known to exist in multiple copies. The border of the pseudoautosomal region (which is shared with the X) has been pushed a bit further toward the tip of the Y chromosome.</p>
<p>We now know the structure of the centromere (a region of the chromosome that pulls copies apart when the cell divides), and have a complete readout of the complex mixture of repetitive sequences in the fluorescent end of the Y.</p>
<p>But perhaps the most important outcome is how useful the findings will be for scientists all over the world.</p>
<p>Some groups will now examine the details of Y genes. They will look for sequences that might control how SRY and the sperm genes are expressed, and to see whether genes that have X partners have retained the same functions or evolved new ones.</p>
<p>Others will closely examine the repeated sequences to determine where and how they originated, and why they were amplified. Many groups will also analyse the Y chromosomes of men from different <a href="https://www.biorxiv.org/content/10.1101/2022.12.01.518658v2.abstract">corners of the world</a> to detect signs of degeneration, or recent evolution of function.</p>
<p>It’s a new era for the poor old Y.</p><img src="https://counter.theconversation.com/content/212112/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Jenny Graves receives funding from the Australian Research Council.</span></em></p>DNA of the male-determining Y chromosome has been completely sequenced end-to-end, and it’s just as weird as we expected. Will we finally be able to understand how it works?Jenny Graves, Distinguished Professor of Genetics and Vice Chancellor's Fellow, La Trobe UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2121412023-08-23T15:50:07Z2023-08-23T15:50:07ZScientists find the last remnants of the human genome that were missing in the Y chromosome<figure><img src="https://images.theconversation.com/files/544284/original/file-20230823-23-eua6vx.jpg?ixlib=rb-1.1.0&rect=0%2C0%2C3000%2C1994&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><a class="source" href="https://www.shutterstock.com/es/image-illustration/xychromosomes-on-background-medical-symbol-gene-559732429">Rost9/Shutterstock</a></span></figcaption></figure><p>More than 20 years ago, the <a href="https://www.nature.com/articles/35057062">human genome was first sequenced</a>. While the first version was full of “holes” representing missing DNA sequences, the genome has been gradually improved in <a href="https://www.science.org/doi/10.1126/science.abj6987">successive rounds</a>. Each has increased the quality of the genome and, in so doing, resolved most of the blank spaces that prevented us from having a complete reading of our genetic material.</p>
<p>The fundamental difficulty researchers faced in reading the genome from end to end is the enormous number of repeated sequences that populate it. The 20,000 or so genes we humans have occupy barely 2% of the entire genome. The remaining 98% is essentially made up of these families of repeated sequences, mobile elements known as <a href="https://www.nature.com/scitable/topicpage/transposons-the-jumping-genes-518/">transposons</a> and retrotransposons, and – to a lesser but functionally important extent – gene expression regulatory sequences. These function as switches that determine when and where genes are turned on and off.</p>
<p>In March 2022, a <a href="https://doi.org/10.1126/science.abj6987">major revision</a> of the genome was published in the journal <em>Science</em>. An <a href="https://www.genome.gov/about-genomics/telomere-to-telomere">international consortium of researchers known as “T2T”</a> (telomere to telomere, which are the ends of chromosomes) used a novel strategy based a type of cell (CHM13) that retains only one copy of each chromosome.</p>
<p>Combined with the latest techniques for sequencing DNA, the researchers managed to add some 200 million letters to the human genome, resolving most of the holes in chromosomes 1 to 22.</p>
<p>The only one left out was the smallest of all the chromosomes we humans have: Y. It’s an exclusively male chromosome that is also the most complex, with repeated sequences of all kinds.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/544280/original/file-20230823-19-lwlf2d.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/544280/original/file-20230823-19-lwlf2d.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/544280/original/file-20230823-19-lwlf2d.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=257&fit=crop&dpr=1 600w, https://images.theconversation.com/files/544280/original/file-20230823-19-lwlf2d.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=257&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/544280/original/file-20230823-19-lwlf2d.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=257&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/544280/original/file-20230823-19-lwlf2d.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=323&fit=crop&dpr=1 754w, https://images.theconversation.com/files/544280/original/file-20230823-19-lwlf2d.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=323&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/544280/original/file-20230823-19-lwlf2d.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=323&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Cell, chromosome, DNA molecule (double helix) and base pairs.</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/es/image-vector/diagram-cell-structure-chromosome-dnadeoxyribonucleic-acid-2175697245">Dee-sign/Shutterstock</a></span>
</figcaption>
</figure>
<h2>The Y chromosome, finally complete</h2>
<p>Each of us has <a href="https://www.genome.gov/genetics-glossary/Chromosome">46 chromosomes</a> in our cells, arranged in pairs. There are actually 23 pairs of chromosomes, 22 pairs of autosomal chromosomes (1 to 22) and one pair of sex chromosomes (which can be X or Y).</p>
<p>From each pair of chromosomes we inherit one from our father and one from our mother. Most females have the 46XX chromosome configuration – the last pair of chromosomes, 23, is made up of two copies of the X chromosome. Most males have the 46XY chromosome configuration, meaning that the sex chromosome pair consists of an X and a Y chromosome.</p>
<p>The Y chromosome, present only in males, contains the genes responsible for the development of the male sex organs, in particular the <a href="https://es.wikipedia.org/wiki/SRY">master gene <em>SRY</em></a>, which triggers a cascade of events that eventually converts an initial undifferentiated gonad into the testes, where sperm are produced. In the absence of the <em>SRY</em> gene (as in 46XX females), this primordial gonad eventually develops into the ovaries, where eggs are produced.</p>
<p>The T2T consortium solved the technical problems that prevented the completion of the Y chromosome sequence, and in so doing, discovered 40 previously unknown protein-coding genes. As detailed in an <a href="https://www.nature.com/articles/s41586-023-06457-y">article in the journal <em>Nature</em></a>, this adds 30 million more letters to the length of the total human genome, which would now have 3.23 billion letters. The new reference genome, called T2T-CHM13+Y, has been made available to the entire research community by the authors of the study.</p>
<p>Alongside the complete sequence of the Y chromosome, <em>Nature</em> has published <a href="https://www.nature.com/articles/s41586-023-06425-6">a second study</a> on the sequences of 43 Y chromosomes derived from humans who lived over the last 183,000 years. Their analysis reveals great diversity in both the size and structure of this Y chromosome over the course of evolution. The researchers have detected, among other things, large sequence inversions – DNA fragments that are flipped and inserted upside down.</p>
<p>That we know more about the Y chromosome is great news. Just about a year ago we saw another scientific breakthrough correlating the common loss of the Y chromosome in many cells with <a href="https://theconversation.com/por-que-hay-mas-viudas-que-viudos-187187">a shorter life expectancy for men compared to women</a>. And it is clear that much more valuable information is hidden in the genes.</p>
<h2>The pangenome initiative</h2>
<p>These two new studies significantly increase our knowledge of human DNA, resolving what we have yet to discover about the smallest but most complex chromosome in our genome. They come on the heels of the <a href="https://montoliu.naukas.com/2023/05/21/por-que-necesitabamos-un-pangenoma-humano/">pangenome initiative</a>, which aims to capture the genetic variability that exists among human beings. While we all share a large part of our genome, we differ by approximately 0.1%. This corresponds to a difference of more than 3 million pairs of letters between any two individuals.</p>
<p>With the pangenome initiative, we will no longer have a single reference genome, but hundreds that will more reliably illustrate our genetic similarities and differences. Among other things, this should help us more easily detect gene mutations associated with the thousands of congenital diseases.</p><img src="https://counter.theconversation.com/content/212141/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>The contents of this publication and the views expressed are solely those of the author and this document should not be considered as representing an official position of CSIC nor does it commit CSIC to any liability of any kind.</span></em></p>The smallest chromosome in humans, the men-specific Y chromosome, has just been sequenced after considerable hurdles.Lluís Montoliu, Investigador científico del CSIC, Centro Nacional de Biotecnología (CNB - CSIC)Licensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1847232023-08-22T21:54:17Z2023-08-22T21:54:17ZNew research into genetic mutations may pave the way for more effective gene therapies<figure><img src="https://images.theconversation.com/files/543314/original/file-20230817-8328-bdaz8a.jpg?ixlib=rb-1.1.0&rect=44%2C0%2C5000%2C3315&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">A lab dish containing embryos that have been injected with Cas9 protein and PCSK9 sgRNA is seen in a laboratory in Shenzhen in southern China's Guangdong province.</span> <span class="attribution"><span class="source">(AP Photo/Mark Schiefelbein)</span></span></figcaption></figure><iframe style="width: 100%; height: 100px; border: none; position: relative; z-index: 1;" allowtransparency="" allow="clipboard-read; clipboard-write" src="https://narrations.ad-auris.com/widget/the-conversation-canada/new-research-into-genetic-mutations-may-pave-the-way-for-more-effective-gene-therapies" width="100%" height="400"></iframe>
<p>Consider a living cell, which can have thousands of genes. Now think of these genes as dials that can be tweaked to change how the cell grows in a given environment. Tweaking a gene can either increase or decrease growth, and this is made more complex considering these dials are interconnected with each other, like cogs in a machine. </p>
<p>While scientists are now able to edit genes in laboratory conditions and attempt to produce findings that may lead to cures, evolution has been doing this for billions of years. Evolution is the natural process that turns these dials, allowing populations to adapt. However, unlike scientists, evolution turns these dials randomly as mutations affect the function of genes.</p>
<p>One underlying hypothesis in evolutionary theory — the evolutionary contingency hypothesis — has been that this tuning can have chaotic behaviours. Or, in other words, dials tweaked early in the process can dramatically alter later evolutionary potential.</p>
<p>Stephen Jay Gould was a famous proponent of this theory, arguing in his 1989 book <a href="https://wwnorton.com/books/9780393307009"><em>Wonderful Life</em></a> that since beneficial mutations occur randomly, chance must play an important role in evolutionary diversification.</p>
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<strong>
Read more:
<a href="https://theconversation.com/does-our-dna-really-determine-our-intelligence-and-health-199266">Does our DNA really determine our intelligence and health?</a>
</strong>
</em>
</p>
<hr>
<p>If this hypothesis is true, it affects how scientists should edit genes in the laboratory as they will face the chaotic interconnections of our cells. Our work set out to test this hypothesis.</p>
<h2>Resolving an evolutionary paradox</h2>
<p>We can observe the process of evolution in the laboratory under extremely well-controlled conditions. We have done so by growing populations of micro-organisms for hundreds — <a href="https://doi.org/10.7554/eLife.63910">even thousands — of days</a>. </p>
<p>Since these organisms divide and reproduce so quickly, this process represents thousands of generations of growth. These experiments have allowed us to pinpoint <a href="https://doi.org/10.1038/s41586-019-1749-3">precisely when</a>, and how, beneficial mutations co-occur and compete to take over the population.</p>
<figure class="align-center ">
<img alt="Image of a human genome." src="https://images.theconversation.com/files/543310/original/file-20230817-41912-psfxhj.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/543310/original/file-20230817-41912-psfxhj.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=418&fit=crop&dpr=1 600w, https://images.theconversation.com/files/543310/original/file-20230817-41912-psfxhj.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=418&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/543310/original/file-20230817-41912-psfxhj.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=418&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/543310/original/file-20230817-41912-psfxhj.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=525&fit=crop&dpr=1 754w, https://images.theconversation.com/files/543310/original/file-20230817-41912-psfxhj.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=525&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/543310/original/file-20230817-41912-psfxhj.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=525&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Image readout of a human genome.</span>
<span class="attribution"><span class="source">(NHGRI via AP)</span></span>
</figcaption>
</figure>
<p>One striking observation from every single one of these experiments is that increases in fitness slow down over time at a rate that is surprisingly reproducible. Despite accumulating different mutations, different populations show remarkably predictable diminishing returns in how fast they adapt.</p>
<p>In contrast with the seemingly chaotic behaviour of mutations, fitness or growth changes are highly predictable. This has led many to hypothesize that this order of mutation is an <a href="https://doi.org/10.3389/fgene.2015.00099">inherent consequence</a> of the way biological systems have evolved. </p>
<p>This striking hypothesis is at odds with the idea that the <a href="https://doi.org/10.1038/s41559-020-01286-y">specifics of an organism’s biology matter for evolution</a>. In other words, it has been difficult to prove that the order in which evolution turns dials has any impact on the future.</p>
<h2>The answer to the paradox</h2>
<p>My team was able to show that the answer to resolving this paradox lies within the interconnected gene network of the cell itself. </p>
<p>For evolution to work, the dial-tuning must be precise: even if the net outcome is beneficial, adjusting one set of linked dials can trickle down and affect other previously correctly placed dials. As evolution continues, the probability of breaking harmoniously-tuned dials grows. This seemingly simple principle explains why the rate of evolutionary improvements typically slows down over time. </p>
<figure class="align-center ">
<img alt="A tray containing human DNA samples ready for genetic sequencing." src="https://images.theconversation.com/files/543312/original/file-20230817-23-a743da.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/543312/original/file-20230817-23-a743da.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=521&fit=crop&dpr=1 600w, https://images.theconversation.com/files/543312/original/file-20230817-23-a743da.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=521&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/543312/original/file-20230817-23-a743da.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=521&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/543312/original/file-20230817-23-a743da.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=654&fit=crop&dpr=1 754w, https://images.theconversation.com/files/543312/original/file-20230817-23-a743da.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=654&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/543312/original/file-20230817-23-a743da.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=654&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">A tray containing human DNA samples ready for genetic sequencing.</span>
<span class="attribution"><span class="source">(AP Photo/Patricia McDonnell)</span></span>
</figcaption>
</figure>
<p>Resolving this paradox experimentally was not an easy task. After all, how can one show the entanglement of dials within the cell? <a href="https://doi.org/10.1126/science.abm4774">In our recent study</a>, we tackled this challenge by systematically trying out every possible combination of 10 key beneficial mutations and looking at how they affect the growth of cells.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/human-genome-editing-offers-tantalizing-possibilities-but-without-clear-guidelines-many-ethical-questions-still-remain-200983">Human genome editing offers tantalizing possibilities – but without clear guidelines, many ethical questions still remain</a>
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</p>
<hr>
<p>By testing out combinations of mutations, we were able to reliably understand which mutations were entangled together (this entanglement is known as epistasis) and for just 10 mutations, over 1,000 combinations had to be generated.</p>
<h2>How this affects genetic precision medicine</h2>
<p>Current futuristic technologies tout the ability to generate precise single mutations within our own genomes with the hope that this can be used to repair non-functional genetic variants. For example, <a href="https://doi.org/10.1038/s41586-019-1711-4">prime editing</a> is an effective “search-and-replace” genome editing technology.</p>
<p>One important concern with these approaches is they can introduce undesired mutations at the same time. However, even as scientists solve these concerns, the field of human genetics has often <a href="https://doi.org/10.1038/s41576-019-0127-1">overlooked the importance of the interconnectedness of genes</a>.</p>
<p>Our study demonstrates that bioengineers should think not only about the effect a mutation has on the gene it is in, but also about the effect of the mutation in the context of all other variations in our genomes. Altering the function of any of our genes can affect our interconnected cellular networks. </p>
<p>This is compounded by the fact that all of us carry hundreds of extremely rare variants, which means each of us carries a unique interconnected network of genes. These personalized networks make us who we are. </p>
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<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/somatic-genome-editing-therapies-are-becoming-a-reality-but-debate-over-ethics-equitable-access-and-governance-continue-201234">Somatic genome editing therapies are becoming a reality – but debate over ethics, equitable access and governance continue</a>
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<p>Genome interpretation is at the heart of genetic testing for disease. And while scientists have made some progress in identifying key pathogenic genetic variants (those that can cause disease), our findings demonstrate that classifying a variant as pathogenic or benign requires us to also understand how the other genetic dials in our cells are tuned.</p><img src="https://counter.theconversation.com/content/184723/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Alex Nguyen Ba receives funding from the Natural Sciences and Engineering Research Council of Canada. </span></em></p>New research sheds light on the interconnected nature of the human genome and what this means for future gene therapies.Alex Nguyen Ba, Assistant Professor, Biology, University of TorontoLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2115892023-08-18T12:39:32Z2023-08-18T12:39:32ZIdentifying fire victims through DNA analysis can be challenging − a geneticist explains what forensics is learning from archaeology<figure><img src="https://images.theconversation.com/files/543315/original/file-20230817-17-h1y2zw.jpg?ixlib=rb-1.1.0&rect=0%2C0%2C1024%2C683&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Identifying victims after a disaster can offer closure to loved ones.</span> <span class="attribution"><a class="source" href="https://newsroom.ap.org/detail/APTOPIXHawaiiFires/2b2bf672bfc14794b8fbc20138f36c62">AP Photo/Jae C. Hong</a></span></figcaption></figure><p>Fire devastates communities and families, and it makes <a href="https://doi.org/10.1111/j.1556-4029.2012.02083.x">identification of victims challenging</a>. In the aftermath of the wildfire that swept through Lahaina, Hawaii, <a href="https://www.staradvertiser.com/2023/08/14/hawaii-news/maui-families-provide-dna-to-help-id-remains-of-fire-victims/">officials are collecting DNA samples</a> from relatives of missing persons in the hope that this can aid in identifying those who died in the fire. </p>
<p>But how well does DNA hold up under such extreme conditions, and what is the best way to recover DNA from fire victims? </p>
<p>I am an <a href="https://scholar.google.com/citations?user=xqKVKIwAAAAJ&hl=en">anthropological geneticist</a> who studies degraded DNA in archaeological and forensic contexts. <a href="https://stone.lab.asu.edu">My research group</a> applies ancient DNA and forensic analysis methods to optimize DNA recovery from burned bones. Retrieving DNA from severely burned remains in order to identify victims is a particular challenge.</p>
<h2>Forensic DNA analysis</h2>
<p>In a typical forensic investigation, <a href="https://www.forensicsciencesimplified.org/dna/how.html">DNA is extracted</a> from a sample – whether some blood, pieces of tissue or bone – collected from the scene of the disaster or crime. This process chemically separates the DNA from other components of cells within the sample, such as proteins, and purifies it. </p>
<p>This DNA is used as a template for <a href="https://www.genome.gov/about-genomics/fact-sheets/Polymerase-Chain-Reaction-Fact-Sheet">polymerase chain reaction, or PCR, analysis</a>, a method that is essentially the Xerox copier of molecular biology. Even if there are only a few cells present in the sample, PCR can amplify those DNA molecules into thousands or millions of copies. This creates a sufficient amount of DNA for subsequent tests.</p>
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<iframe width="440" height="260" src="https://www.youtube.com/embed/7onjVBsQwQ8?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">DNA analysis can help identify victims by comparing genetic similarities between people.</span></figcaption>
</figure>
<p>In forensics, the specific DNA targeted in PCR is usually a set of highly repetitive markers called <a href="https://strbase-archive.nist.gov/intro.htm">microsatellites, or short tandem repeats</a>. Law enforcement agencies around the world use specific sets of these markers for identification purposes. In the U.S., forensic analysts target 20 of these DNA repeats. Each person has two unique alleles, or genetic variants, at each of these markers, and these alleles are uploaded to the FBI’s <a href="https://www.fbi.gov/how-we-can-help-you/dna-fingerprint-act-of-2005-expungement-policy/codis-and-ndis-fact-sheet">Combined DNA Index System database</a> to identify matches. </p>
<p>DNA taken from the <a href="https://namus.nij.ojp.gov/services/dna#faq-what-is-a-family-reference-sample">relatives of missing people</a> will likely be analyzed for short tandem repeat markers and their allele profiles uploaded to the Relatives of Missing Persons index within the database. The expectation is that victims and their biological relatives share a percentage of alleles for these markers. For example, parents and children share 50% of their alleles, since a child inherits half of their DNA from each parent.</p>
<h2>Challenge of degraded DNA</h2>
<p>In forensic contexts, the time between death and DNA sampling is usually short enough that the DNA is often still in fairly good shape, both in terms of quantity and quality. However, DNA is often not found in ideal conditions after a disaster. </p>
<p>Time and the elements <a href="https://doi.org/10.1080/20961790.2018.1515594">take their toll</a>. After death, the process of decomposition releases enzymes that can cleave or damage DNA, and additional damage occurs over time depending on the environment in which the body is found. DNA also degrades faster in warm, wet, acidic environments and slower in colder, drier environments that are more pH neutral or slightly basic. </p>
<p>In addition, DNA preservation may vary considerably among the tissues, bones and teeth recovered. For example, researchers found that DNA identification of victims of the <a href="https://doi.org/10.1111/j.1556-4029.2009.01045.x">World Trade Center attacks</a> in 2001 was most successful when using bones of the feet and legs, compared with bones from the head and torso.</p>
<p>DNA damage can take different forms. Nicks and breaks in the DNA make it difficult to analyze. Chemical modification of the DNA can result in changes to the original sequence or make it unreadable. This includes changes to the building blocks of DNA <a href="https://www.genome.gov/genetics-glossary/Nucleotide">called nucleotides</a> that make up an identifiable sequence. For example, exposure to water can cause a chemical reaction <a href="https://doi.org/10.1101/cshperspect.a012567">called deamination</a> that changes the nucleotide cytosine such that it appears to be the nucleotide thymine upon analysis. Exposures to other chemicals or UV light can <a href="https://chem.libretexts.org/Ancillary_Materials/Exemplars_and_Case_Studies/Exemplars/Biology/Cross-Linking_in_DNA">cause cross-linking</a>, which essentially ties the DNA into knots. As a result, the PCR enzymes used to copy or read the DNA sequence can’t move linearly along the DNA strand. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/543323/original/file-20230817-33902-1dr1ti.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Rows of burnt houses and cars in the aftermath of the Lahaina fires." src="https://images.theconversation.com/files/543323/original/file-20230817-33902-1dr1ti.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/543323/original/file-20230817-33902-1dr1ti.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/543323/original/file-20230817-33902-1dr1ti.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/543323/original/file-20230817-33902-1dr1ti.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/543323/original/file-20230817-33902-1dr1ti.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/543323/original/file-20230817-33902-1dr1ti.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/543323/original/file-20230817-33902-1dr1ti.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">Exposure to intense and extended fires can make victim identification through DNA analysis difficult.</span>
<span class="attribution"><a class="source" href="https://newsroom.ap.org/detail/HawaiiFires/185896ea7dfd43b99850521649cf5be6">AP Photo/Jae C. Hong</a></span>
</figcaption>
</figure>
<h2>Applying methods from archaeology</h2>
<p>Researchers encounter similar issues in handling degraded genetic material when analyzing the DNA of ancient remains that are thousands of years old. To address these challenges, forensic geneticists and ancient DNA researchers like me employ a number of tricks to <a href="https://doi.org/10.1038/s43586-020-00011-0">optimize DNA retrieval</a>.</p>
<p>First, we tend to target dense bone or teeth for sampling, since they are more impervious to the environment. We also use DNA extraction methods that enhance the recovery of short fragments of DNA. </p>
<p>Second, we use PCR to amplify even shorter genetic markers, including mini-short tandem repeats, or sections of the <a href="https://www.genome.gov/genetics-glossary/Mitochondrial-DNA">mitochondrial genome</a>. Mitochondria are structures within each cell that produce energy, and each one has its own DNA. Mitochondrial DNA is passed down from mother to child and can be found in hundreds of copies within each mitochondrion, which make it easier to recover and analyze. However, mitochondrial DNA <a href="https://doi.org/10.1146/annurev.genom.4.070802.110352">may not provide sufficient information</a> for identification, since people who are maternally related, even very distantly, will share the same sequence.</p>
<p>Researchers are also testing newer methods of DNA analysis common in the ancient DNA field for forensic purposes. For example, <a href="https://doi.org/10.1038/s43586-020-00011-0">special enzymes</a> can remove chemically modified nucleotides, such as deaminated cytosines, to prevent misreading of the DNA sequence. Researchers can also use DNA baits to “fish” for specific sequences. This method of <a href="https://doi.org/10.1038/nmeth.1419">targeted enrichment</a> can recover very small fragments that can be used to piece together the full genetic sequence.</p>
<h2>DNA analysis of burned remains</h2>
<p>For <a href="https://doi.org/10.1002/9781119682691.ch12">fire victims</a>, particularly those caught in intense, extended fires, the DNA may be highly fragmented, making analysis difficult. High temperatures cause bonds between molecules, including nucleotides, to break. This results in fragmentation and ultimately destruction of the DNA.</p>
<p>Because hard tissue – bones and teeth – are often all that remains after a fire, forensic researchers have studied how bone characteristics such as color and composition <a href="https://doi.org/10.1016/j.fsigen.2010.08.008">change with temperature</a>. My research team used this information to classify the level of burning that human bone samples have been subjected to.</p>
<p>In investigating DNA preservation in those samples, we found that there is a <a href="https://doi.org/10.1016/j.fsigen.2020.102272">significant point of DNA degradation</a> when bones reached temperatures between 662 degrees Fahrenheit (350 degrees Celsius) and 1,022 F (550 C). For comparison, <a href="https://www.cremationassociation.org/page/CremationProcess">commercial cremation</a> is 1,400 to 1,600 F (760 to 871 C) for 30 to 120 minutes, and <a href="https://doi.org/10.1016/j.csite.2017.08.001">vehicle fires</a> typically reach 1,652 degrees F (900 C) but can last a shorter period of time.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/543318/original/file-20230817-25-qy54jc.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="People walking down street past the rubble of wildfire damage in Lahaina" src="https://images.theconversation.com/files/543318/original/file-20230817-25-qy54jc.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/543318/original/file-20230817-25-qy54jc.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=338&fit=crop&dpr=1 600w, https://images.theconversation.com/files/543318/original/file-20230817-25-qy54jc.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=338&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/543318/original/file-20230817-25-qy54jc.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=338&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/543318/original/file-20230817-25-qy54jc.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=424&fit=crop&dpr=1 754w, https://images.theconversation.com/files/543318/original/file-20230817-25-qy54jc.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=424&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/543318/original/file-20230817-25-qy54jc.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=424&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Survivors of the Lahaina wildfires, which began on Aug. 8, 2023, walk through the aftermath.</span>
<span class="attribution"><a class="source" href="https://newsroom.ap.org/detail/HawaiiFiresPowerLines/6643e5e332e44e8e8fedbb01c15ece9c">AP Photo/Rick Bowmer</a></span>
</figcaption>
</figure>
<p>Our team also found that the likelihood of generating high-quality short tandem repeat data or mitochondrial DNA sequence data, whether using forensic or ancient DNA methods, decreases significantly at temperatures <a href="https://doi.org/10.1016/j.fsigen.2021.102610">greater than 1,022 F</a> (550 C). </p>
<p>In sum, as temperature and exposure time increase, the amount of remaining DNA decreases. This leads to only partial DNA profiles, which can limit analysts’ ability to match a victim to a relative with high statistical certainty or prevent results altogether.</p>
<p>DNA evidence is not the only method used for identification. Investigators <a href="https://doi.org/10.1016/j.forsciint.2008.09.019">combine DNA with other evidence</a> – such as dental, skeletal and contextual information – to identify a victim conclusively. Together, this information hopefully will help bring closure for families and friends.</p><img src="https://counter.theconversation.com/content/211589/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Anne Stone receives funding from the National Institute of Justice. </span></em></p>Maui officials have asked relatives to provide DNA samples to help identify victims of the Lahaina wildfires. Time and exposure to the elements, however, can make DNA retrieval from remains difficult.Anne Stone, Professor of Human Evolution and Social Change, Arizona State UniversityLicensed as Creative Commons – attribution, no derivatives.