tag:theconversation.com,2011:/us/topics/environmental-dna-37791/articlesEnvironmental DNA – The Conversation2024-03-20T19:03:24Ztag:theconversation.com,2011:article/2255642024-03-20T19:03:24Z2024-03-20T19:03:24ZWe need faster, better ways to monitor NZ’s declining river health – using environmental DNA can help<figure><img src="https://images.theconversation.com/files/583001/original/file-20240320-18-n3pzxx.jpg?ixlib=rb-1.1.0&rect=72%2C252%2C5925%2C3053&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><span class="source">Getty Images/Julia Crim</span></span></figcaption></figure><p>New Zealand’s rivers are not in a good shape. The Ministry for the Environment’s <a href="https://environment.govt.nz/publications/our-freshwater-2023/">latest freshwater report</a> shows an estimated 45% of total river length is no longer suitable for swimming and 48% is partially inaccessible to endangered migratory fish. </p>
<p>The science is clear. Inputs of nitrogen and phosphorous, coupled with invasive species, stress some rivers to the point where they can’t sustain healthy ecosystems. The state of rivers and groundwater also impacts on the quality of drinking water.</p>
<p>The government’s <a href="https://www.beehive.govt.nz/release/government-takes-first-steps-towards-pragmatic-and-sensible-freshwater-rules">intention to replace</a> the <a href="https://environment.govt.nz/acts-and-regulations/national-policy-statements/national-policy-statement-freshwater-management/">national policy statement on freshwater management</a> brings the topic of freshwater quality back into the national spotlight. </p>
<p>But irrespective of political debates, given the perilous state of New Zealand’s freshwater, effective monitoring based on sound evidence is needed in order to weigh trade-offs and understand if we are managing rivers sustainably. </p>
<p>This is where environmental DNA (eDNA) comes in. </p>
<p>Aotearoa New Zealand will always need multiple methods to monitor the thousands of rivers and streams across the country, but we hope our <a href="https://peerj.com/articles/16963/">new eDNA method</a> will help by making freshwater monitoring faster, cheaper, more comprehensive and better suited to countrywide surveys.</p>
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Read more:
<a href="https://theconversation.com/it-sounds-like-science-fiction-but-we-can-now-sample-water-to-find-the-dna-of-every-species-living-there-216989">It sounds like science fiction. But we can now sample water to find the DNA of every species living there</a>
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<h2>Rivers are full of life</h2>
<p>The life found in New Zealand’s rivers is a vital component of their health. Microbial diversity is continually degrading and recycling nutrients that sustain new life and maintain river health.</p>
<p>Whether fish, frog or falcon, all organisms shed bits of genetic material into the environment. These DNA “breadcrumbs” provide vital clues about what is living in the area. We can test all these DNA signals without actually ever seeing an animal.</p>
<p>The same ultra-sensitive technology is already being used to <a href="http://www.poops.nz">detect COVID in wastewater</a> by tracking SARS-CoV-2 variants and concentrations of the virus.</p>
<p>Until eDNA was developed, the primary method we had to monitor river health involved catching (often killing) and sorting thousands of invertebrates or electric fishing. Such methods are time consuming, costly, require specialist expertise and typically need five-year windows to detect a change in river health.</p>
<p>The game changer with eDNA is its ability to detect many species at once, employing an easy-to-use (filtration) sampling method. This opens up a raft of possible applications.</p>
<figure class="align-center ">
<img alt="A close-up of someone taking a sample of river water." src="https://images.theconversation.com/files/582728/original/file-20240319-30-v9h68o.png?ixlib=rb-1.1.0&rect=33%2C7%2C1187%2C810&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/582728/original/file-20240319-30-v9h68o.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=625&fit=crop&dpr=1 600w, https://images.theconversation.com/files/582728/original/file-20240319-30-v9h68o.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=625&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/582728/original/file-20240319-30-v9h68o.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=625&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/582728/original/file-20240319-30-v9h68o.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=786&fit=crop&dpr=1 754w, https://images.theconversation.com/files/582728/original/file-20240319-30-v9h68o.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=786&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/582728/original/file-20240319-30-v9h68o.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=786&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">A small sample of river water can help detect the presence of many species.</span>
<span class="attribution"><span class="source">Author provided</span>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span>
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<p>The Department of Conservation is using eDNA to detect <a href="https://www.rnz.co.nz/news/national/488225/dna-technology-helps-discover-critically-threatened-clutha-flatheads">new populations of endangered galaxid fish</a> and the Ministry for Primary Industries is using it to track the spread of the <a href="https://www.rnz.co.nz/news/national/490630/newly-discovered-invasive-gold-clam-can-produce-400-offspring-a-day">freshwater golden clam</a> that invaded the Waikato river. </p>
<p>But there is much more to eDNA than detecting a favourite (or least favourite) animal. The real shift is the ability to read eDNA barcodes across the “tree of life”. </p>
<h2>‘Seeing’ entire ecosystems</h2>
<p>Rather than focusing on just a few select indicator species, eDNA helps us to <a href="https://s3.ap-southeast-2.amazonaws.com/wilderlab.openwaters/reports/f207132b0f954602.html">consider the ecosystem more holistically</a>, such as the example below from the Waikato River, from a single litre of filtered water.</p>
<figure class="align-center ">
<img alt="A graphic showing the tree of life." src="https://images.theconversation.com/files/581156/original/file-20240312-20-e5hzh3.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/581156/original/file-20240312-20-e5hzh3.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=600&fit=crop&dpr=1 600w, https://images.theconversation.com/files/581156/original/file-20240312-20-e5hzh3.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=600&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/581156/original/file-20240312-20-e5hzh3.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=600&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/581156/original/file-20240312-20-e5hzh3.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=754&fit=crop&dpr=1 754w, https://images.theconversation.com/files/581156/original/file-20240312-20-e5hzh3.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=754&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/581156/original/file-20240312-20-e5hzh3.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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<span class="caption">An eDNA analysis of one litre of water from the Waikato River shows all the species detected.</span>
<span class="attribution"><span class="source">Wilderlab and Wai Tuwhera o Te Taiao</span>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span>
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<p>In a partnership between the eDNA company <a href="https://www.wilderlab.co.nz/">Wilderlab</a>, the Department of Conservation, the Ministry for the Environment and regional councils, we harnessed this holistic ecosystem data to develop a new index to measure river health called the <a href="https://www.wilderlab.co.nz/tici">Taxon-Independent Community Index</a>, or TICI. </p>
<p>Using regularly monitored river sites across Aotearoa New Zealand, we focused on 3,000 eDNA barcodes from bacteria, fungi, plants and animals that are indicators of river nutrification.</p>
<p>The TICI index is a score from 60 to 140, based on which of the 3,000 barcode signatures are present. Some barcodes push the dial in a positive direction, others nudge it negative.</p>
<p>Raw DNA data can be complex. The TICI index distils the genetic code into a metric that people can more easily engage with. From zero river samples profiled using eDNA in 2019, we now have more than 50,000 eDNA records, including 16,000 TICI scores. Collectively, this has generated one of the most powerful global eDNA datasets, and opens a number of new applications. </p>
<p>Teichelmann Creek in the predator-free Perth Valley (in South Westland) currently tops the leader board with a TICI score of 135.03 (pristine). At the other end of the table, Papanui Stream in the Hawke’s Bay generated a TICI of 68.05 (very poor).</p>
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<img alt="An infographic that shows TICI scores across New Zealand." src="https://images.theconversation.com/files/581550/original/file-20240313-30-57zbs9.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/581550/original/file-20240313-30-57zbs9.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=657&fit=crop&dpr=1 600w, https://images.theconversation.com/files/581550/original/file-20240313-30-57zbs9.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=657&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/581550/original/file-20240313-30-57zbs9.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=657&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/581550/original/file-20240313-30-57zbs9.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=825&fit=crop&dpr=1 754w, https://images.theconversation.com/files/581550/original/file-20240313-30-57zbs9.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=825&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/581550/original/file-20240313-30-57zbs9.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=825&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">This infographic shows TICI scores across New Zealand and how they change along a river’s length.</span>
<span class="attribution"><span class="source">Wilderlab</span>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span>
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<h2>Where to next for eDNA?</h2>
<p>We envisage that eDNA-based indicators, like the TICI index, will provide a practical way for people to track health in their local rivers. </p>
<p>Communities are already engaging with this tool through the <a href="https://www.epa.govt.nz/community-involvement/open-waters-aotearoa/">Wai Tuwhera o te Taiao programme</a>. Farmers are <a href="https://ourlandandwater.nz/outputs/using-edna-to-identify-taonga-species-te-miro-farm-case-study/">getting on board</a> and eDNA techniques feature in the <a href="https://www.doc.govt.nz/globalassets/documents/about-doc/long-term-insights-briefings/2023/ltib2023-doc-linz.pdf">futures thinking</a> of central government.</p>
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Read more:
<a href="https://theconversation.com/consumers-want-nz-farmers-to-comply-with-regulations-better-monitoring-and-transparency-would-help-to-build-trust-204682">Consumers want NZ farmers to comply with regulations -- better monitoring and transparency would help to build trust</a>
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<p>In a 2019 <a href="https://pce.parliament.nz/publications/focusing-aotearoa-new-zealand-s-environmental-reporting-system/">report on New Zealand’s environmental reporting system</a>, the Parliamentary Commissioner for the Environment identified deficiencies and fragmentation in New Zealand’s environmental data gathering and reporting, including for freshwater. We argue that eDNA gets us a step closer to fixing some of these issues. </p>
<p>Using the eDNA toolkit it is within our technical (and budgetary) reach for regular monitor of all rivers in Aotearoa to help prioritise where, when and how much management (or restoration) is needed. </p>
<p>And there is more to come on the eDNA monitoring front, including methods of sampling eDNA from the air, household taps, shipping containers and around aquaculture facilities.</p><img src="https://counter.theconversation.com/content/225564/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Michael Bunce has received funding from Australia & New Zealand on the use of eDNA technologies, including to work with community groups as part of the Wai Tuwhera o Te Taiao programme at the Environmental Protection Authority. He is currently Chief Science advisor at the Department of Conservation.</span></em></p><p class="fine-print"><em><span>Simon Jarman currently works with eDNA Frontiers and Wilderlab, companies which offer fee-for-service eDNA services. </span></em></p>Monitoring methods based on environmental DNA are faster, more comprehensive and cheaper than traditional ecological surveys. They help fill gaps in New Zealand’s data on river health.Michael Bunce, Honarary Professor in Environmental Genomics, University of OtagoSimon Jarman, Professor of Environmental Genomics, Curtin UniversityLicensed 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>
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<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>
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<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>
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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>
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<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>
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<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>
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<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>
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<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>
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<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>
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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>
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<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/2126512023-10-03T12:10:37Z2023-10-03T12:10:37ZEven platypuses aren’t safe from bushfires – a new DNA study tracks their disappearance<p>When the Black Summer bushfires swept across eastern Australia in 2019–20, <a href="https://onlinelibrary.wiley.com/doi/full/10.1111/geb.13473">thousands of animal species lived</a> in the path of these megafires. </p>
<p>You’d be forgiven for thinking water-dwelling animals like platypuses were spared. Surely animals living in rivers and streams would be safe?</p>
<p>But our new research, published today in <a href="https://doi.org/10.1016/j.biocon.2023.110219">Biological Conservation</a>, reveals platypuses are disappearing from waterways after fire.</p>
<p>We took water samples from streams and rivers across south-eastern Australia to test for platypus DNA. We found platypuses were less likely to be found in burnt catchment areas, six months after fire. But the species returned after 18 months. We hope our findings will support conservation actions in the event of future bushfires.</p>
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Read more:
<a href="https://theconversation.com/a-platypus-can-glow-green-and-hunt-prey-with-electricity-but-it-cant-climb-dams-to-find-a-mate-193707">A platypus can glow green and hunt prey with electricity – but it can't climb dams to find a mate</a>
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<h2>An evolutionary masterpiece</h2>
<p>Platypuses are much loved and unique to Australia. As monotremes, they lay eggs. They’re one of only five species of mammals that does – the other four are echidnas. </p>
<p>They have webbed feet for swimming. And they have <a href="https://www.britannica.com/science/electroreception">electroreceptors</a> in their bills to help them find food in rivers and streams.</p>
<p>But they can be hard to find. It’s difficult to determine whether there’s a platypus living in a particular waterway. </p>
<p>Monitoring allows us to detect changes in populations or communities. There may be gradual changes over time, or rapid responses to a big disturbance, such as a fire. Quick, efficient methods are vital for surveying species that occupy large areas.</p>
<h2>DNA detective work</h2>
<p>Platypuses are found in waterways throughout the east coast of Australia, from Cooktown in northern Queensland to Tasmania. </p>
<p>Little is known about how platypuses and other aquatic or semi-aquatic animals respond to fire. Ideally we would have good data on species before and after a fire, to draw comparisons. But that is rare. </p>
<p>Other research shows aquatic invertebrates (animals with no backbones) and fish can be harmed by bushfire, especially when rain follows fire. </p>
<p>Bushfires burn and kill the vegetation that stabilises the soil around rivers or streams. When rain follows fire, a lot of ash, soil and other debris can be washed into waterways. The water chemistry might change or there might be big increases in sediment, which makes the river or stream inhospitable for invertebrates and fish. </p>
<p>As platypuses feed on aquatic invertebrates such as yabbies, these flow on effects of fire could also impact them. </p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/551317/original/file-20231002-15-55pavu.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="A grey mud-covered platypus on the bank of a creek with foliage and sticks next to it" src="https://images.theconversation.com/files/551317/original/file-20231002-15-55pavu.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/551317/original/file-20231002-15-55pavu.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=792&fit=crop&dpr=1 600w, https://images.theconversation.com/files/551317/original/file-20231002-15-55pavu.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=792&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/551317/original/file-20231002-15-55pavu.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=792&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/551317/original/file-20231002-15-55pavu.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=995&fit=crop&dpr=1 754w, https://images.theconversation.com/files/551317/original/file-20231002-15-55pavu.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=995&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/551317/original/file-20231002-15-55pavu.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=995&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
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<span class="caption">Platypus feed on invertebrates, which find debris- and sediment-filled waterways inhospitable.</span>
<span class="attribution"><span class="source">Shutterstock</span></span>
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<p>Just as people leave traces behind as they move through the environment (such as fingerprints, hair and skin cells), so do animals. These traces contain genetic material that can be analysed to identify the likely source. </p>
<p>We used this “environmental DNA” to detect where platypuses were present across the study area. </p>
<p>We sampled 118 rivers and creeks across Victoria, New South Wales and the Australian Capital Territory a year before the Black Summer fires, for a project on platypus distribution. This was fortuitous, because it provided a baseline for us to determine the effects of the unprecedented fires. </p>
<p>We took more environmental DNA samples from the same 118 sites at six months after the megafires, and also 12–18 months post-fire, giving us three data points for the same rivers and creeks. </p>
<p>The sampling sites were spread across burnt and unburnt areas, giving us unaffected (control) sites to use as a comparison. </p>
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Read more:
<a href="https://theconversation.com/scientists-at-work-we-use-environmental-dna-to-monitor-how-human-activities-affect-life-in-rivers-and-streams-164529">Scientists at work: We use environmental DNA to monitor how human activities affect life in rivers and streams</a>
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<h2>What we found</h2>
<p>Six months after the megafires, platypuses were less likely to be living at sites that experienced fire. But the difference between burnt and unburnt sites was negligible after 18 months. </p>
<p>The combination of severe fire and rainfall minimised the chance of finding platypuses living at a site. </p>
<p>Watersheds are areas of land that drain rainwater into local streams and creeks. We used the watershed of each site to calculate the area over which rain would drain to a site. </p>
<p>We also looked at what proportion of the watershed was burnt at high severity, as we thought this would increase the chance of destabilised soils and ash being washed into the waterways. We classified high severity fire as fire which removed all of the leaves from trees and burnt grasslands or pasture. </p>
<p>From our work, we predicted that sites where the watershed had at least 25% of its area burnt at high severity, and also experienced high rainfall, had a less than 10% chance of platypuses occupying those sites.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/551318/original/file-20231002-23-nafgj6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="A black ground with thin dead black trees, the aftermath of a fire" src="https://images.theconversation.com/files/551318/original/file-20231002-23-nafgj6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/551318/original/file-20231002-23-nafgj6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/551318/original/file-20231002-23-nafgj6.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/551318/original/file-20231002-23-nafgj6.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/551318/original/file-20231002-23-nafgj6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/551318/original/file-20231002-23-nafgj6.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/551318/original/file-20231002-23-nafgj6.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>
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<span class="caption">The ash and debris from bushfires can get washed into nearby waterways, affecting the water chemistry and wildlife habitat.</span>
<span class="attribution"><span class="source">Shutterstock</span></span>
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<h2>Understanding change</h2>
<p>Climate change is predicted to lead to more <a href="https://www.nature.com/articles/s41467-021-27225-4">frequent</a>, <a href="https://onlinelibrary.wiley.com/doi/10.1111/geb.13514">severe and extensive bushfires</a> in south-eastern Australia, as well as to more <a href="https://nespclimate.com.au/wp-content/uploads/2018/12/ESCC-NESP-Southern-Australia-6pp-WEB.pdf">extreme rainfall events</a>. </p>
<p>Our work adds to our understanding of how just one species could be harmed by the climate crisis. </p>
<p>We need these types of systematic surveys to provide baselines and monitor how populations and communities are changing. Monitoring will also help us respond more efficiently to major disturbances like the Black Summer bushfires, where, for many species, there wasn’t enough data to inform the initial emergency conservation response. </p>
<p><em>We would like to acknowledge Josh Griffiths, Reid Tingley and Luke Collins for their invaluable contribution to this work and Jaana Dielenberg for early discussions about this article.</em></p>
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Read more:
<a href="https://theconversation.com/worried-about-heat-and-fire-this-summer-heres-how-to-prepare-212443">Worried about heat and fire this summer? Here's how to prepare</a>
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<img src="https://counter.theconversation.com/content/212651/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Emily McColl-Gausden receives funding from San Diego Zoo Wildlife Alliance, The University of Melbourne and the Ecological Society of Australia. </span></em></p><p class="fine-print"><em><span>Andrew Weeks is a Director at EnviroDNA, a company that offers eDNA based services to industry. He receives funding from San Diego Zoo Wildlife Alliance and the Australian Research Council.</span></em></p>We sampled 118 rivers and creeks before and after the Black Summer bushfires, searching for platypus DNA. Here’s what we found.Emily McColl-Gausden, Research fellow, The University of MelbourneAndrew Weeks, Associate Senior Research Scientist, The University of MelbourneLicensed 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/1992292023-06-01T12:30:00Z2023-06-01T12:30:00ZInvasive lionfish have spread south from the Caribbean to Brazil, threatening ecosystems and livelihoods<figure><img src="https://images.theconversation.com/files/528927/original/file-20230529-34716-wug34x.jpg?ixlib=rb-1.1.0&rect=16%2C0%2C3591%2C2396&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">An invasive lionfish at Flower Garden Banks National Marine Sanctuary in the Gulf of Mexico.</span> <span class="attribution"><a class="source" href="https://flic.kr/p/23YKdEZ">G. P. Schmahl/NOAA</a>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span></figcaption></figure><p>Brazil’s coastal waters teem with a rich array of species that paint a living tapestry beneath the waves. This underwater world is particularly special because many of its species are <a href="https://www.britannica.com/science/endemic-species">endemic</a> – they are found nowhere else on Earth. The southwestern Atlantic is home to <a href="https://doi.org/10.1111/ddi.12729">111 endemic reef fish species</a>, each of which plays a crucial role in the intricate web of marine life. </p>
<p>An uninvited guest has arrived in these tropical waters: the <a href="https://invasions.si.edu/nemesis/species_summary/166883">Pacific red lionfish</a> (<em>Pterois volitans</em>). Renowned for its stunning appearance and voracious appetite, the lionfish was first detected off of Florida in 1985 and has spread throughout the Caribbean, <a href="https://www.fisheries.noaa.gov/southeast/ecosystems/impacts-invasive-lionfish">killing reef fish in large numbers</a>. </p>
<p>Now it has breached a formidable obstacle: the Amazon-Orinoco river plume, which flows into the Atlantic from northeastern Brazil. This massive discharge of fresh water has long <a href="http://dx.doi.org/10.1111/jbi.14398">functioned as a barrier</a> separating Caribbean fish species from those farther south along Brazil’s coastline.</p>
<p>Scientists and environmental managers widely agree that the lionfish invasion in Brazil is a potential ecological disaster. As a <a href="https://scholar.google.com.au/citations?user=_ArEYYMAAAAJ&hl=en">marine ecologist</a>, I believe mitigating the damage will require a comprehensive approach that addresses the ecological, social and economic harms wrought by this predatory fish.</p>
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<figcaption><span class="caption">Lionfish have no known predators and feed on the juveniles of important commercial fish species, such as grouper and snapper.</span></figcaption>
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<h2>Tracing the lionfish’s spread</h2>
<p>It’s easy to see why lionfish <a href="https://www.petco.com/content/petco/PetcoStore/en_US/pet-services/resource-center/caresheets/lionfish.html">appeal to aquarium enthusiasts</a>. Native to the warm waters of the Indo-Pacific ocean, they are 12 to 15 inches long, with red and white stripes and long, showy fins. They protect themselves with dorsal spines that deliver painful venomous stings.</p>
<p>Lionfish were first detected in the Atlantic Ocean <a href="https://myfwc.com/wildlifehabitats/profiles/saltwater/lionfish/">in 1985 off Dania Beach, Florida</a>, probably discarded by a tropical fish collector. Since then they have spread throughout the Caribbean Sea, the Gulf of Mexico and northward as far as <a href="https://www.pbsnc.org/blogs/science/rethinking-the-lionfish-invasion-hint-its-still-a-problem/">Bermuda and North Carolina</a> – one of the <a href="https://doi.org/10.1016/j.biocon.2013.04.014">most successful marine invasions on record</a>. A close relative, the common lionfish or devil firefish (<em>Pterois miles</em>), has <a href="https://doi.org/10.1111/jfb.14340">invaded the Mediterranean Sea</a> and is spreading rapidly there.</p>
<p>Lionfish can be eaten safely if they are properly prepared to remove their venomous spines. In Florida and the Caribbean, <a href="https://myfwc.com/fishing/saltwater/recreational/lionfish/events/">lionfish hunting tournaments</a> have become popular as a control method. However, lionfish <a href="https://doi.org/10.1007/s10530-016-1358-0">move to deeper waters as they grow</a>, so hunting alone can’t prevent them from spreading. </p>
<p>Marine scientists have anticipated for years that lionfish would someday arrive along the eastern coast of South America. <a href="https://doi.org/10.1038/nature.2015.17414">A single sighting in 2014</a>, far removed from the Amazon-Orinoco plume, was likely a result of an aquarium release rather than a natural migration. </p>
<p>Then in December 2020, local fishermen caught a pair of lionfish on coral reefs in the <a href="https://flowergarden.noaa.gov/about/mesophotic.html#">mesophotic, or “twilight,” zone</a> several hundred feet <a href="https://doi.org/10.1007/s10530-021-02575-8">below the mighty Amazon River plume</a>. A scuba diver also encountered a lionfish in the oceanic archipelago of <a href="https://whc.unesco.org/en/list/1000/">Fernando de Noronha</a>, 220 miles (350 kilometers) off Brazil’s tropical coast. </p>
<p>New invasion fronts have quickly opened along Brazil’s north and northeast coasts, covering eight states and diverse marine habitats. <a href="https://doi.org/10.3389/fmars.2022.956848">More than 350 lionfish have been tallied</a> along a 1,720-mile (2,765-kilometer) swath of coastline. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/528934/original/file-20230529-15-37nsp4.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/528934/original/file-20230529-15-37nsp4.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/528934/original/file-20230529-15-37nsp4.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=415&fit=crop&dpr=1 600w, https://images.theconversation.com/files/528934/original/file-20230529-15-37nsp4.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=415&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/528934/original/file-20230529-15-37nsp4.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=415&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/528934/original/file-20230529-15-37nsp4.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=521&fit=crop&dpr=1 754w, https://images.theconversation.com/files/528934/original/file-20230529-15-37nsp4.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=521&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/528934/original/file-20230529-15-37nsp4.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=521&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Map visualizing the spread of lionfish in the Atlantic, with orange dots representing recorded sightings as of 2023 from the ‘Lionfish Monitoring Dashboard,’ a collaborative project spearheaded by researchers at the Federal University of Ceará, Brazil.</span>
<span class="attribution"><a class="source" href="https://monitoramentos.shinyapps.io/LionfishWatch/">Lionfish Watch</a>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<h2>Aggressive predators without natural enemies</h2>
<p>Like many introduced species, lionfish in the Atlantic don’t face natural population control mechanisms such as predation, disease and parasitism that limit their numbers in the Indo-Pacific. A 2011 study found that lionfish on reefs in the Bahamas were <a href="https://doi.org/10.1007/s10530-011-0020-0">larger and more abundant</a> than their Pacific counterparts.</p>
<p>Lionfish thrive in many marine habitats, from mangroves and seagrass beds to deepwater reefs and shipwrecks. They are aggressive, persistent hunters that <a href="https://www.fisheries.noaa.gov/southeast/ecosystems/impacts-invasive-lionfish">feed on smaller fish</a>, including species that keep coral reefs clean and others that are food for important commercial species like snappers and groupers. In a 2008 study, when lionfish appeared on reefs in the Bahamas, populations of small juvenile reef fish <a href="https://doi.org/10.3354/meps07620">declined by 80% within five weeks</a>.</p>
<p>Brazil’s northeast coast, with its rich artisanal fishing activity, stands on the front line of this invasive threat. Lionfish are present in coastal <a href="https://oceanservice.noaa.gov/facts/mangroves.html">mangrove forests</a> and <a href="https://oceanservice.noaa.gov/facts/estuary.html">estuaries</a> – brackish water bodies where rivers meet the sea. These areas serve as nurseries for important commercial fish species. Losing them would increase the risk of hunger in a region that is already grappling with substantial social inequality. </p>
<p>Fishers also face the threat of lionfish stings, which are not lethal to humans but <a href="https://dan.org/alert-diver/article/lionfish-stings/">can cause painful wounds</a> that may require medical treatment.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/529112/original/file-20230530-23-r3sjuy.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Five people on a small boat near shore" src="https://images.theconversation.com/files/529112/original/file-20230530-23-r3sjuy.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/529112/original/file-20230530-23-r3sjuy.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/529112/original/file-20230530-23-r3sjuy.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/529112/original/file-20230530-23-r3sjuy.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/529112/original/file-20230530-23-r3sjuy.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/529112/original/file-20230530-23-r3sjuy.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/529112/original/file-20230530-23-r3sjuy.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">Fishing is a major income source for Brazilians along the coast, like these in Cabo Frio, and could suffer if lionfish predation reduces catches.</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/news-photo/fishing-activity-is-a-major-source-of-income-for-the-news-photo/609864872">Luiz Souza/NurPhoto via Getty Images</a></span>
</figcaption>
</figure>
<h2>Facing the invasion: Brazil’s challenges</h2>
<p>Biological invasions are easiest to control in early stages, when the invader population is still growing slowly. However, Brazil has been slow to react to the lionfish incursion. </p>
<p>The equatorial southwestern Atlantic, where the invasion is taking place, has been less thoroughly surveyed than the Caribbean. There has been little high-resolution seabed mapping, which would help scientists identifying potential lionfish habitats and anticipate where lionfish might spread next or concentrate their populations. Understanding of the scale of the invasion is largely based on estimates, which likely underrepresent its true extent. </p>
<p>Moreover, turbid waters along much of Brazil’s coast make it hard for scientists to monitor and document the invasion. Despite their distinctive appearance, lionfish are difficult to spot and record in murky water, which makes it challenging for scientists, divers and fishers to keep an accurate record of their spread. </p>
<p>Still another factor is that from 2018 through 2022, under former President Jair Bolsonaro, Brazil’s government <a href="https://doi.org/10.1590/0001-3765202020200700">sharply cut the national science budget</a>, reducing funding for field surveys. The COVID-19 pandemic further reduced field research because of lockdowns and social distancing measures.</p>
<p><div data-react-class="Tweet" data-react-props="{"tweetId":"1655705639665168385"}"></div></p>
<h2>Making up for lost time</h2>
<p>Brazil has a history of inadequately monitoring for <a href="http://dx.doi.org/10.1126/science.abb7255">early detection of marine invasions</a>. The lionfish is no exception. Actions thus far have been reactive and often initiated too late to be fully effective. </p>
<p>As one of many Brazilian scientists who <a href="http://dx.doi.org/10.3354/meps10383">warned repeatedly</a> about a potential lionfish invasion over the past decade, I’m disheartened that my country missed the window to take early action. Now, however, marine researchers and local communities are stepping up.</p>
<p>Given the length of Brazil’s coast, traditional monitoring methods are often insufficient. So we’ve turned to citizen science and information technology to fill the gaps in our knowledge. </p>
<p>In April 2022, a group of academic researchers spearheaded the launch of an <a href="https://monitoramentos.shinyapps.io/LionfishWatch/">online dashboard</a>, which is updated continuously with data from scientific surveys and local community self-reports. This interactive platform is maintained by a research group led by marine scientists <a href="https://scholar.google.com/citations?user=HE-s5mUAAAAJ&hl=it">Marcelo Soares</a> and <a href="https://scholar.google.com.br/citations?user=FoB0KPgAAAAJ&hl=pt-BR">Tommaso Giarrizzo</a> from the Federal University of Ceará. </p>
<p>The dashboard allows anyone, from fishers to recreational divers and tourists, to upload data on lionfish observations. This information supports rapid response efforts, strategic planning for preventive measures in areas still free from lionfish, and the development of localized lionfish removal programs.</p>
<figure>
<iframe width="440" height="260" src="https://www.youtube.com/embed/IWfcuaSA-9w?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">Artisanal fishers on Costa Rica’s southern Caribbean coast are working with regulators to curb the spread of invasive lionfish.</span></figcaption>
</figure>
<p>I believe lionfish are here to stay and will integrate over time into Brazil’s marine ecosystems, much as they have in the Caribbean. Given this reality, our most pragmatic and effective strategy is to reduce lionfish populations below levels that cause unacceptable ecological harm.</p>
<p>Regions along the coast that are still lionfish-free might benefit from early and preventive actions. Comprehensive surveillance plans should include environmental education programs about exotic species; early detection approaches, using techniques such as analyzing environmental DNA; citizen science initiatives to monitor and report lionfish sightings, participate in organized culls and help collect research data; and genetic surveys to identify patterns of connectivity among lionfish populations along Brazil’s coast and between Brazilian and Caribbean populations. </p>
<p>Brazil missed its initial opportunity to prevent the lionfish invasion, but I believe that with strategic, swift action and international collaboration, it can mitigate the impacts of this invasive species and safeguard its marine ecosystems. </p>
<p><em>This article has been updated to reflect that the correct number of endemic reef fish species in the southwestern Atlantic is 111.</em></p><img src="https://counter.theconversation.com/content/199229/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Osmar J. Luiz does not work for, consult, own shares in or receive funding from any company or organization that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>One of the most damaging invasive species in the oceans has breached a major barrier – the Amazon-Orinoco river plume – and is spreading along Brazil’s coast. Scientists are trying to catch up.Osmar J. Luiz, Senior Research Fellow in Aquatic Ecology, Charles Darwin UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2055572023-05-15T15:01:09Z2023-05-15T15:01:09ZYou 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<figure><img src="https://images.theconversation.com/files/525993/original/file-20230512-24221-4caajm.png?ixlib=rb-1.1.0&rect=0%2C0%2C2121%2C1412&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">A casual stroll on the beach can leave enough intact DNA behind to extract identifiable information.</span> <span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/photo/human-footprint-on-the-sand-royalty-free-image/1030780262">Comezora/Moment via Getty Images</a></span></figcaption></figure><p>Human DNA can be sequenced from small amounts of water, sand and air in the environment to <a href="https://www.nature.com/articles/s41559-023-02056-2">potentially extract identifiable information</a> like genetic lineage, gender, and health risks, according to our new research.</p>
<p>Every cell of the body <a href="https://calteches.library.caltech.edu/2687/1/bonner.pdf">contains DNA</a>. Because each person has a unique genetic code, DNA can be <a href="https://theconversation.com/genetic-paparazzi-are-right-around-the-corner-and-courts-arent-ready-to-confront-the-legal-quagmire-of-dna-theft-178866">used to identify individual people</a>. Typically, medical practitioners and researchers obtain human DNA through direct sampling, such as blood tests, swabs or biopsies. However, all living things, including animals, plants and microbes, <a href="https://doi.org/10.1016/j.biocon.2014.11.019">constantly shed DNA</a>. The water, soil and even the air contain microscopic particles of biological material from living organisms.</p>
<p>DNA that an organism has shed into the environment is known as <a href="https://doi.org/10.1093/biosci/biab027">environmental DNA, or eDNA</a>. For the last couple of decades, scientists have been able to collect and sequence eDNA from soil or water samples to <a href="https://theconversation.com/fishing-for-dna-free-floating-edna-identifies-presence-and-abundance-of-ocean-life-75957">monitor biodiversity, wildlife populations</a> and <a href="https://theconversation.com/environmental-dna-how-a-tool-used-to-detect-endangered-wildlife-ended-up-helping-fight-the-covid-19-pandemic-158286">disease-causing pathogens</a>. Tracking rare or elusive endangered species <a href="https://doi.org/10.1007/s00114-019-1605-1">through their eDNA</a> has been a boon to researchers, since traditional monitoring methods such as observation or trapping can be difficult, often unsuccessful and intrusive to the species of interest.</p>
<figure>
<iframe width="440" height="260" src="https://www.youtube.com/embed/q7mp1wxLoyA?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">The authors and their colleagues use environmental DNA to study sea turtles.</span></figcaption>
</figure>
<p>Researchers using eDNA tools usually focus only on the species they’re studying and disregard DNA from other species. However, humans <a href="https://theconversation.com/genetic-paparazzi-are-right-around-the-corner-and-courts-arent-ready-to-confront-the-legal-quagmire-of-dna-theft-178866">also shed</a>, cough and <a href="https://theconversation.com/who-sees-what-you-flush-wastewater-surveillance-for-public-health-is-on-the-rise-but-a-new-survey-reveals-many-us-adults-are-still-unaware-193007">flush DNA</a> into their surrounding environment. And as our team of geneticists, <a href="https://scholar.google.com/citations?user=czRqHV4AAAAJ&hl=en&oi=ao">ecologists</a> and <a href="https://scholar.google.com/citations?user=3cQ6umoAAAAJ&hl=en">marine biologists</a> in the <a href="https://scholar.google.com/citations?hl=en&user=LtNEh9gAAAAJ">Duffy Lab</a> at the University of Florida found, <a href="https://www.nature.com/articles/s41559-023-02056-2">signs of human life can be found everywhere</a> but in the most isolated locations. </p>
<h2>Animals, humans and viruses in eDNA</h2>
<p>Our team uses environmental DNA to study <a href="https://doi.org/10.1111/1755-0998.13617">endangered sea turtles and the viral tumors</a> to which they are susceptible. Tiny hatchling sea turtles shed DNA as they crawl along the beach on their way to the ocean shortly after they are born. <a href="https://doi.org/10.1111/1755-0998.13617">Sand scooped from their tracks</a> contains enough DNA to provide valuable insights into the turtles and the chelonid herpesviruses and <a href="https://theconversation.com/could-human-cancer-treatments-be-the-key-to-saving-sea-turtles-from-a-disfiguring-tumor-disease-98140">fibropapillomatosis tumors that afflict them</a>. Scooping a liter of <a href="https://doi.org/10.1038/s42003-021-02085-2">water from the tank</a> of a recovering sea turtle under veterinary care equally provides a wealth of genetic information for research. Unlike blood or skin sampling, collecting eDNA causes no stress to the animal.</p>
<p><a href="https://theconversation.com/genomic-sequencing-heres-how-researchers-identify-omicron-and-other-covid-19-variants-172935">Genetic sequencing technology</a> used to decode DNA has improved rapidly in recent years, and it is now possible to easily sequence the DNA of every organism in a sample from the environment. Our team suspected that the sand and water samples we were using to study sea turtles would also contain DNA from a number of other species – including, of course, humans. What we didn’t know was <a href="https://www.nature.com/articles/s41559-023-02056-2">just how informative</a> the human DNA we could extract would be. </p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/525991/original/file-20230512-33762-xb83ft.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Two people on a boat collecting water samples from a river" src="https://images.theconversation.com/files/525991/original/file-20230512-33762-xb83ft.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/525991/original/file-20230512-33762-xb83ft.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=800&fit=crop&dpr=1 600w, https://images.theconversation.com/files/525991/original/file-20230512-33762-xb83ft.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=800&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/525991/original/file-20230512-33762-xb83ft.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=800&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/525991/original/file-20230512-33762-xb83ft.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=1005&fit=crop&dpr=1 754w, https://images.theconversation.com/files/525991/original/file-20230512-33762-xb83ft.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=1005&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/525991/original/file-20230512-33762-xb83ft.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=1005&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">The researchers were able to collect intact human DNA in water samples from a river in Florida.</span>
<span class="attribution"><span class="source">Todd Osborne</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>To figure this out, we took samples from a variety of locations in Florida, including the ocean and rivers in urban and rural areas, sand from isolated beaches and a remote island never usually visited by people. We found human DNA in all of those locations except the remote island, and these samples were high quality enough for analysis and sequencing. </p>
<p>We also tested the technique in Ireland, tracing along a river that winds from a remote mountaintop, through small rural villages and into the sea at a larger town of 13,000 inhabitants. We found human DNA everywhere but in the remote mountain tributary where the river starts, far from human habitation.</p>
<p>We also collected air samples from a room in our wildlife veterinary hospital in Florida. People who were present in the room gave us permission to take samples from the air. We recovered DNA matching the people, the animal patient and common animal viruses present at the time of collection.</p>
<p>Surprisingly, the human eDNA found in the local environment was intact enough for us to identify mutations associated with disease and to determine the genetic ancestry of people who live in the area. Sequencing DNA that volunteers left in their footprints in the sand even yielded part of their sex chromosomes.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/526004/original/file-20230513-16755-kheuum.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Diagram depicting eDNA collection sources and analysis workflow" src="https://images.theconversation.com/files/526004/original/file-20230513-16755-kheuum.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/526004/original/file-20230513-16755-kheuum.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=420&fit=crop&dpr=1 600w, https://images.theconversation.com/files/526004/original/file-20230513-16755-kheuum.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=420&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/526004/original/file-20230513-16755-kheuum.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=420&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/526004/original/file-20230513-16755-kheuum.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=528&fit=crop&dpr=1 754w, https://images.theconversation.com/files/526004/original/file-20230513-16755-kheuum.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=528&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/526004/original/file-20230513-16755-kheuum.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">Human eDNA can be collected and analyzed from a variety of sources.</span>
<span class="attribution"><span class="source">Liam Whitmore/Created with BioRender.com</span>, <a class="license" href="http://creativecommons.org/licenses/by-nc-nd/4.0/">CC BY-NC-ND</a></span>
</figcaption>
</figure>
<h2>Ethical implications of collecting human eDNA</h2>
<p>Our team dubs inadvertent retrieval of human DNA from environmental samples <a href="https://www.nature.com/articles/s41559-023-02056-2">“human genetic bycatch.”</a> We’re calling for deeper discussion about how to ethically handle human environmental DNA. </p>
<p>Human eDNA could present significant advances to research in fields as diverse as conservation, epidemiology, forensics and farming. If handled correctly, human eDNA could help archaeologists <a href="https://theconversation.com/who-owned-this-stone-age-jewellery-new-forensic-tools-offer-an-unprecedented-answer-204797">track down undiscovered ancient human settlements</a>, allow biologists to <a href="https://doi.org/10.1038/s42003-021-01656-7">monitor cancer mutations in a given population</a> or provide law enforcement agencies <a href="https://doi.org/10.1016/j.forsciint.2023.111599">useful forensic information</a>.</p>
<figure class="align-left zoomable">
<a href="https://images.theconversation.com/files/525989/original/file-20230512-7632-rct90g.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Footprints in the sand at a beach" src="https://images.theconversation.com/files/525989/original/file-20230512-7632-rct90g.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/525989/original/file-20230512-7632-rct90g.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=899&fit=crop&dpr=1 600w, https://images.theconversation.com/files/525989/original/file-20230512-7632-rct90g.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=899&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/525989/original/file-20230512-7632-rct90g.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=899&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/525989/original/file-20230512-7632-rct90g.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=1130&fit=crop&dpr=1 754w, https://images.theconversation.com/files/525989/original/file-20230512-7632-rct90g.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=1130&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/525989/original/file-20230512-7632-rct90g.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=1130&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 researchers extracted identifiable genetic information from footprints in the sand.</span>
<span class="attribution"><span class="source">David Duffy</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>However, there are also myriad ethical implications relating to the inadvertent or deliberate collection and analysis of human genetic bycatch. Identifiable information can be extracted from eDNA, and accessing this level of detail about individuals or populations comes with <a href="https://theconversation.com/how-a-south-african-communitys-request-for-its-genetic-data-raises-questions-about-ethical-and-equitable-research-166940">responsibilities relating to consent and confidentiality</a>.</p>
<p>While we conducted our study with the approval of our <a href="https://doi.org/10.2146/ajhp070066">institutional review board</a>, which ensures that studies on people adhere to ethical research guidelines, there is no guarantee that everyone will treat this type of information ethically. </p>
<p>Many questions arise regarding human environmental DNA. For instance, who should have access to human eDNA sequences? Should this information be made publicly available? Should consent be required before taking human eDNA samples, and from whom? Should researchers remove human genetic information from samples originally collected to identify other species?</p>
<p>We believe it is vital to implement regulations that ensure collection, analysis and data storage are carried out ethically and appropriately. Policymakers, scientific communities and other stakeholders need to take human eDNA collection seriously and balance consent and privacy against the possible benefits of studying eDNA. Raising these questions now can help ensure everyone is aware of the capabilities of eDNA and provide more time to develop protocols and regulations to ensure appropriate use of eDNA techniques and the ethical handling of human genetic bycatch.</p><img src="https://counter.theconversation.com/content/205557/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Jessica Alice Farrell received funding from the Gumbo Limbo Nature Center d/b/a Friends of Gumbo Limbo (a 501c3 non-profit organization) through a generous donation through their Graduate Research Grant programme</span></em></p><p class="fine-print"><em><span>Jenny Whilde does not work for, consult, own shares in or receive funding from any company or organization that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>Environmental DNA provides a wealth of information for conservationists, archaeologists and forensic scientists. But the unintentional pickup of human genetic information raises ethical questions.Jenny Whilde, Adjunct Research Scientist in Marine Bioscience, University of FloridaJessica Alice Farrell, Postdoctoral associate, University of FloridaLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1932292023-01-03T10:01:31Z2023-01-03T10:01:31ZDNA in the water shows South African scientists where to find a rare pipefish<figure><img src="https://images.theconversation.com/files/491866/original/file-20221026-25-sv6gb2.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">The estuarine pipefish is not easy to find - it camouflages itself amid seagrass.</span> <span class="attribution"><span class="source">Louw Claassens</span></span></figcaption></figure><p>Keeping track of the world’s wildlife populations is fundamental to conservation efforts in the face of the <a href="https://www.science.org/content/article/are-we-middle-sixth-mass-extinction">continued deterioration of global biodiversity</a>. </p>
<p>But some species are harder to study than others. Some aquatic species, for instance, elude detection because they are extremely rare and sparsely distributed. </p>
<p>One especially elusive example is the estuarine pipefish (<em>Syngnathus watermeyeri</em>). It is the only critically endangered <a href="https://www.inaturalist.org/projects/syngnathids-of-africa">syngnathid</a> (the family of fishes that includes seahorses, pipefishes and seadragons) in the world. It is only found on the African continent and is endemic to just a few estuaries on the Eastern Cape of South Africa.</p>
<p>It has long been apparent that the estuarine pipefish is threatened. The species was classified as <a href="https://journals.co.za/doi/pdf/10.10520/AJA00382353_7781">extinct in 1994</a> before being <a href="http://vital.seals.ac.za:8080/vital/access/manager/Repository/vital:15021?site_name=GlobalView&exact=sm_title%3A%22Ichthyofaunal+characteristics+of+a+typical+temporarily+open%2Fclosed+estuary+on+the+southeast+coast+of+South+Africa%22&collection=vital%3A91">rediscovered in 1996</a>. There are an estimated <a href="https://www.iucnredlist.org/fr/species/41030/67621860">100-250 remaining globally</a>, but not much more is known.</p>
<p>The biggest challenge is keeping count. Population survey methods that work for other species – such as netting, counting and tagging – are simply not as effective for the elusive <em>S. watermeyeri</em>. They are just too small: adults reach between 10cm and 15cm and they are experts at camouflaging amid seagrass to avoid detection.</p>
<p>New technologies may solve the problem. One is environmental DNA (or eDNA). This refers to genetic material derived from organisms – skin cells, blood, faeces and so on – that can be extracted from environmental samples such as water, soil, ice or air. Since it <a href="https://www.sciencedirect.com/science/article/pii/S0006320714004443">degrades within days or weeks in aquatic environments</a>, eDNA can provide an up-to-date snapshot of the biodiversity within a region. Analysing this material can reveal the presence of rare species that may have otherwise remained hidden.</p>
<p>Our <a href="https://onlinelibrary.wiley.com/doi/full/10.1002/edn3.365">recent study</a> set out to determine whether eDNA is a good tool for monitoring estuarine pipefish. The answer is a resounding “yes”. It is far more successful at detection than the conventional method of seine netting. </p>
<p>We argue that eDNA holds great value as a complementary approach or a method for investigating species’ presence in a particular environment.</p>
<p>Our research was about testing eDNA as a monitoring method, not about updating the estimates on pipefish. But it will help identify priority areas for their conservation, and which habitat characteristics are important for supporting this species. </p>
<p>This knowledge represents a crucial first step to establishing a long-term monitoring and recovery plan for the estuarine pipefish. Now that we know where it is and what habitat it needs, we can identify possible locations to reintroduce the species and then use eDNA to monitor the success of these programmes.</p>
<h2>The search</h2>
<p>In the spring of 2019, we set out to look for the pipefish and test the use of eDNA as a monitoring tool for this rare species. We conducted seine netting surveys simultaneously to compare the sensitivity of both methods for estuarine pipefish detection. </p>
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<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/how-an-underwater-photo-led-to-the-discovery-of-a-tiny-new-seahorse-species-136962">How an underwater photo led to the discovery of a tiny new seahorse species</a>
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</em>
</p>
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<p>We sampled all estuaries in South Africa’s Eastern Cape province where the species had been recorded historically: the Kariega, Bushmans, Kasouga, and East and West Kleinemonde estuaries. A total of 39 sites were visited across these five estuaries. At each site, water samples were collected for eDNA, and seine net sweeps were carried out. </p>
<p>It proved to be a laborious task to sweep the seine net through thick beds of seagrass and seaweed while sinking into the muddy estuary banks, but the method was successful. With this method alone, the estuarine pipefish was found at five sites – four within the Bushmans Estuary and one site in the Kariega Estuary.</p>
<figure class="align-right ">
<img alt="Two people are standing in a large body of water, a big seine net between them." src="https://images.theconversation.com/files/491846/original/file-20221026-23-adtnmp.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/491846/original/file-20221026-23-adtnmp.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/491846/original/file-20221026-23-adtnmp.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/491846/original/file-20221026-23-adtnmp.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/491846/original/file-20221026-23-adtnmp.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/491846/original/file-20221026-23-adtnmp.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/491846/original/file-20221026-23-adtnmp.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">Researchers at work in an estuary, trying to net pipefish.</span>
<span class="attribution"><span class="source">Nina de Villiers</span></span>
</figcaption>
</figure>
<p>We didn’t immediately know what the water samples would reveal – they had to be processed. The samples were filtered shortly after collection and taken to the <a href="https://research.curtin.edu.au/scieng/trend-lab/">TrEnD laboratory</a> at Curtin University in Perth, Western Australia, which has been specially set up for trace and environmental DNA work like this. </p>
<p>A species-specific assay developed for this study was used to detect the estuarine pipefish in our samples. Following extensive laboratory work and data analysis, this approach proved to be a success: we successfully detected <em>S. watermeyeri</em> using eDNA at 20 out of 30 sites within the Kariega and Bushmans estuaries.</p>
<h2>Some populations already lost</h2>
<p>Our eDNA findings held some bad news about the estuarine pipefish. The study <a href="https://onlinelibrary.wiley.com/doi/epdf/10.1002/aqc.3742">reinforced</a> several others that have <a href="https://onlinelibrary.wiley.com/doi/epdf/10.1002/aqc.3742">suggested</a> <em>S. watermeyeri</em> is extinct at the Kasouga and East and West Kleinemonde estuaries. This highlights the importance of conserving the Kariega and Bushmans estuaries as a sanctuary for the Critically Endangered syngnathid. </p>
<p>We also confirmed a detail noted in previous surveys: the pipefish is far more likely to be found where there are dense beds of <em>Zostera capensis</em> (a <a href="https://www.sciencedirect.com/science/article/pii/S0254629916336511?via%3Dihub">seagrass endemic to southern African estuaries</a>). And we identified <em>Codium</em> seaweed, which formed large free-floating beds among the <em>Zostera</em> seagrass, as an important pipefish habitat. </p>
<p>These findings point to the delicate ecosystems in estuaries – coastal waterbodies found where rivers meet the sea. It underscores how estuaries provide crucial habitats for plants and creatures. Unfortunately, <a href="https://theconversation.com/south-africas-estuaries-face-a-growing-threat-from-pollution-we-took-a-close-look-at-four-184489">estuaries are under great pressure</a>, particularly from pollution. </p>
<p>This research now means that scientists have a much better picture of the estuarine pipefish’s status. This provides a foundation for developing a long-term monitoring programme for the species. It also exemplifies how new technologies, like eDNA, will be the key to guiding the conservation of the world’s biodiversity.</p><img src="https://counter.theconversation.com/content/193229/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Georgia May Nester received funding from National Geographic Society (NGS-59431C-19) for this project. Other projects are funded by West Australian Museum, PADI SCUBA, and the Australian Antarctic Division.</span></em></p><p class="fine-print"><em><span>Louw Claassens received funding from National Geographic Society (NGS-59431C-19). </span></em></p>Environmental DNA like skin cells, blood and faeces can be extracted from water, soil, ice or air to provide a good snapshot of an ecosystem.Georgia May Nester, PhD candidate, Curtin UniversityLouw Claassens, Research Associate of Zoology and Entomology, Rhodes UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1960442022-12-07T19:05:36Z2022-12-07T19:05:36ZThe oldest DNA ever found reveals a snapshot of a vanished world<figure><img src="https://images.theconversation.com/files/499392/original/file-20221207-16-7qtkic.jpeg?ixlib=rb-1.1.0&rect=57%2C9%2C6366%2C3945&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><span class="source">Beth Zaiken</span></span></figcaption></figure><p>At the icy northern tip of Greenland, far into the Artic Circle, a deep bed of sediment beneath the mouth of a fjord has lain frozen and undisturbed for 2 million years.</p>
<p>Known as the Kap København Formation, this relic of a vanished world dates to a period when Earth was much warmer than it is today. The sediment built up in a shallow bay over a period of 20,000 years, before being buried beneath ice and permafrost.</p>
<p>Our team, led by Kurt Kjær, Mikkel Winter Pedersen and Eske Willerslev at Copenhagen University, has extracted and analysed the oldest DNA ever recovered from samples of this Greenlandic sediment. It reveals the plants, animals and microorganisms that thrived in an ecosystem unlike anything in the modern world.</p>
<p>As we <a href="https://www.nature.com/articles/s41586-022-05453-y">report today in Nature</a>, this DNA is more than a million years older than the previous record. We can now recover and directly study molecules that were made inside plants and animals 2 million years ago, opening a new window into the history of life on Earth.</p>
<h2>A snapshot of an extinct ecosystem</h2>
<p>Two million years ago, northern Greenland was a very different place. Average winter temperatures were more than 10°C warmer, and there was less carbon dioxide in Earth’s atmosphere. </p>
<p>Our study, carried out by more than 40 scientists from Denmark, the UK, France, Sweden, Norway, the USA and Germany, pieced together minuscule fragments of DNA and matched them to sequences of known species. We found genetic traces of ancestors of modern reindeer, hares and lemmings, as well as mastodon – extinct elephant-like creatures which were not previously known to have lived in Greenland. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/499415/original/file-20221207-14-gnsmah.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="A photograph showing layers of sediment." src="https://images.theconversation.com/files/499415/original/file-20221207-14-gnsmah.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/499415/original/file-20221207-14-gnsmah.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/499415/original/file-20221207-14-gnsmah.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/499415/original/file-20221207-14-gnsmah.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/499415/original/file-20221207-14-gnsmah.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/499415/original/file-20221207-14-gnsmah.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/499415/original/file-20221207-14-gnsmah.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=566&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Layers of sediment retain traces of the rich flora and fauna that lived 2 million years ago in Kap København in North Greenland.</span>
<span class="attribution"><span class="source">Kurt H. Kjær</span></span>
</figcaption>
</figure>
<p>We also found DNA traces of plants including birch and poplar trees, as well as algae and other microorganisms – and a large proportion of DNA fragments we could not match to any known species.</p>
<p>But it is not just the specific species that are of interest but also how they co-existed in the same prehistoric ecosystem that was much warmer than today. This can tell us a lot about the possible impact on the biodiversity during warming periods and how it may drive their evolutionary response.</p>
<p>In essence, our study is similar to the “environmental DNA” (eDNA) research ecologists do today to understand biodiversity in modern ecosystems. The difference is that we are looking at an ecosystem that disappeared millions of years ago, which is why the recovery and bioinformatic analysis of these short, degraded molecules becomes a lot more challenging.</p>
<h2>Watching evolution</h2>
<p>We know that the DNA inside cells of all living organisms mutates slowly, as environmental changes drive adaptation and evolution over many generations. However, we very rarely have a “time machine” to go back and look directly at the old DNA molecules.</p>
<p>To understand how DNA has changed over time, we usually compare the genomes of modern species and work backwards to create an evolutionary family tree. However, the possibility of studying DNA that is millions of years old means we will be able to directly observe the deep-time process of molecular evolution, instead of being restricted to the current genetic “snapshot” in present-day species.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/how-to-grow-an-evolutionary-tree-65722">How to grow an evolutionary tree</a>
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</em>
</p>
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<p>What’s more, the DNA of the ancestors of modern species may show how they adapted to conditions that are very different from the ones they face today. We don’t gain those insights in this study, but if we can study those prehistoric genetic adaptations in detail in the future, it may allow us to predict if species are able to adapt to changes such as the ongoing global warming.</p>
<h2>How long can DNA survive?</h2>
<p>Despite what the Jurassic Park movies may tell you, DNA doesn’t last forever. It decays steadily over time – though the rate of decay depends on circumstances like temperature.</p>
<p>About a decade ago, my colleagues and I published <a href="https://royalsocietypublishing.org/doi/10.1098/rspb.2012.1745">a study of moa fossils</a> that calculated a “half-life” for long-term DNA decay in bones. We predicted that recognisable fragments of DNA should be able to last more than one million years under ideal conditions, such as the deep freeze of permafrost.</p>
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<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/moa-bones-reveal-dna-half-life-but-jurassic-park-remains-fiction-10067">Moa bones reveal DNA half-life but Jurassic Park remains fiction</a>
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</em>
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<p>And, indeed, in 2021 researchers <a href="https://www.nature.com/articles/s41586-021-03224-9">recovered DNA</a> from the tooth of a mammoth that lived in Siberia approximately 1.2 million years ago. </p>
<p>However, the new research shows something quite surprising. It seems that DNA can actually survive much longer as free molecules in sediment than in the bones of the animal it originally belonged to. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/499418/original/file-20221207-4529-7qtkic.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="A photo showing old fragments of wood on dusty ground next to a shovel." src="https://images.theconversation.com/files/499418/original/file-20221207-4529-7qtkic.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/499418/original/file-20221207-4529-7qtkic.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/499418/original/file-20221207-4529-7qtkic.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/499418/original/file-20221207-4529-7qtkic.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/499418/original/file-20221207-4529-7qtkic.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/499418/original/file-20221207-4529-7qtkic.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/499418/original/file-20221207-4529-7qtkic.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=566&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Remains of wooden branches from the forest that grew at Kap København 2 million years ago.</span>
<span class="attribution"><span class="source">Svend Funder</span></span>
</figcaption>
</figure>
<p>DNA molecules can bind to the surface of particles of clay which somehow protect them from the ravages of time. We do not know exactly how long DNA can survive in sediment, but if the preservation conditions are ideal, there is no reason to believe that we have found the limit here at two million years.</p>
<p>Once we know more about what kinds of sediment preserve DNA best, we will be able to hunt for it all over the world – though we are unlikely ever to realise the dream of examing 65 million year–old sequences of dinosaur DNA. I would be very happy to be proven wrong though!</p>
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<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/whats-next-for-ancient-dna-studies-after-nobel-prize-honors-groundbreaking-field-of-paleogenomics-191899">What’s next for ancient DNA studies after Nobel Prize honors groundbreaking field of paleogenomics</a>
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</p>
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<img src="https://counter.theconversation.com/content/196044/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Morten Allentoft does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>DNA frozen for 2 million years paints a picture of an extinct ecosystem.Morten Allentoft, Professor, Molecular and Life Sciences, Curtin UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1358442020-05-04T14:25:37Z2020-05-04T14:25:37ZWhy Nigeria needs to manage electronic waste better<figure><img src="https://images.theconversation.com/files/331114/original/file-20200428-110785-1x8pqpm.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Electronic waste heap from used discarded computer parts and cases </span> <span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/photo/electronic-waste-heap-from-used-discarded-computer-royalty-free-image/1175564260?adppopup=true">Ladislav Kubes/Getty Images </a></span></figcaption></figure><p>In most of Nigeria’s cities, there are visible piles of refuse that have built up on roads, river banks and swampy land. These waste dumps smell bad and are breeding grounds for germs that cause diseases. </p>
<p>Perhaps less well-known is the electronic waste that’s becoming a serious problem in parts of the country. This is obsolete electrical and electronic equipment that has been discarded. Because Nigeria does not have a formal recycling sector for safe management of e-waste, every month <a href="https://www.tandfonline.com/doi/abs/10.1080/02772248.2011.561949">about 500,000 tons</a> of electronic and electrical equipment is dumped in workshops, open spaces, water sources and landfills. More than half of this is near end of life or <a href="https://www.trtworld.com/magazine/nigeria-has-become-an-e-waste-dumpsite-for-europe-us-and-asia-24197">completely damaged</a> .</p>
<p>When rain falls on informal waste dumps, polluted liquids leach out. These liquids contain toxic chemicals and metals, bacteria and viruses. They find their way into the ground and surface water, and can be taken up by plants and end up in animals and people. </p>
<p>Electronic waste is one of the <a href="https://www.tandfonline.com/doi/abs/10.1080/02772248.2011.561949">fastest-growing types of waste</a> in some parts of the world. Globally, the eco-friendly recycling of e-waste is optimally low. So more than half of almost <a href="http://www.saicm.org/Portals/12/Documents/EPI/ewastesafework.pdf">50 million metric tonnes of e-waste</a> generated worldwide ends up in landfills or is illegally transported.</p>
<p>Some of Nigeria’s e-waste is equipment that was imported when new and is discarded after its useful life. Some is imported second-hand. Out of an <a href="https://www.unenvironment.org/news-and-stories/press-release/nigeria-turns-tide-electronic-waste">average of 500,000 tonnes</a> of used electrical and electronics equipment imported into Nigeria, more than 25% is dead on arrival.</p>
<p>I have carried out several <a href="https://www.sciencedirect.com/science/article/pii/S0048969712001374?via%3Dihub">studies</a> over the years into the environmental and health impacts of this electronic waste. My <a href="https://www.tandfonline.com/doi/abs/10.1080/15376516.2017.1349228?journalCode=itxm20">findings</a> show that metals from waste have contaminated land and water and that these substances are <a href="https://europepmc.org/article/med/31104299">harmful</a> to living organisms. </p>
<p>My studies <a href="https://www.sciencedirect.com/science/article/abs/pii/S0147651313001759?via%3Dihub">standard and advanced techniques</a> to explore the <a href="https://www.tandfonline.com/doi/abs/10.1080/02772248.2011.561949">genotoxic and mutagenic effects</a> and <a href="https://www.ajol.info/index.php/tzool/article/view/142147">potential environmental and health impacts</a> of this electronic waste. Specifically, I have shown how e-waste from Alaba international market and Computer Village in Lagos State induced genetic damage in the cells of microorganisms, plants, animals and people.</p>
<h2>What we found</h2>
<p>Even though these e-waste dump sites are a health hazard, many people make their living on them. According to the International Labour Organisation, up to <a href="https://www.unenvironment.org/news-and-stories/press-release/nigeria-turns-tide-electronic-waste">100,000 people </a> work in the informal e-waste recycling sector in Nigeria. They <a href="https://www.ajol.info/index.php/tzool/article/view/142147">collect and dismantle electronics by hand</a> to reclaim components that can then be sold. </p>
<p>These people are at risk of infection and physical injury from handling waste. They are in danger of direct chemical poisoning leading to organ dysfunction, or disorders that are an indirect result of exposure to hazardous chemicals. E-waste can also induce <a href="https://europepmc.org/article/med/31104299">genetic damage</a> that could affect future generations. </p>
<p>In one <a href="https://link.springer.com/article/10.1007/s12011-019-01745-z">study</a>, we collected blood samples and cheek cell samples from teenagers who were sorting through waste at the Alaba international electronic market. We found their blood contained much higher levels of heavy metals than a control group. </p>
<p>Within this group, higher levels also corresponded with longer periods spent in contact with e-waste, genetic predisposition (that is an individual’s genetic susceptibility), previous or concurrent exposures to other substances (such as cigarette smoke and alcohol), and the concentrations and types of toxic substances the person had been exposed to. </p>
<p>Genetic damage is usually due to exposure to chronic concentration or doses of xenobiotics. The most worrisome aspect is when the effect is not expressed in an individual but transferred onto another generation before it is expressed. </p>
<p>Genetic damage has been implicated as a cause of <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5979367/">cancer</a> and certain other disorders such as <a href="https://www.researchgate.net/publication/305954666_Mercury_toxicity_and_DNA_damage_in_patients_with_Down_syndrome">Down syndrome</a> and <a href="https://www.cell.com/ajhg/fulltext/S0002-9297(16)30282-8">nerve disorders</a> although our studies did not provide evidence of such linkages in Nigeria. We hope to provide evidence of such linkage in future studies.</p>
<h2>What needs to be done</h2>
<p>There is an urgent need for greater awareness of the dangerous substances found in the environment. The attitude of Nigerians towards waste disposal should change: waste should be managed sustainably by reducing, reusing, recovering and recycling materials safely. </p>
<p>The government should build properly engineered landfills to contain waste. Residential areas should be separated from electronic markets. Contaminated soil and water should be treated to protect workers and residents.</p>
<p>Nigeria also needs legislation that deals specifically with electronic waste. The country could be guided by examples provided by the <a href="https://www.europarl.europa.eu/sides/getDoc.do?type=REPORT&reference=A7-2011-0334&language=EN&mode=XML">European Union</a>and <a href="https://collections.unu.edu/eserv/UNU:1624/ewaste-in-china.pdf">China’s National Development and Reform Commission</a>.</p><img src="https://counter.theconversation.com/content/135844/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Adekunle Bakare receives funding from McArthur Foundation/University of Ibadan Grant and Academy of Science for the Third World- TWAS. </span></em></p>There is an urgent need for greater awareness of the dangerous substances found in the environment.Adekunle Bakare, Professor of Genetics, Cellular and Molecular Toxicology , University of IbadanLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1165172019-05-05T20:10:29Z2019-05-05T20:10:29ZSit! Seek! Fly! Scientists train dogs to sniff out endangered insects<p>Three very good dogs – named Bayar, Judd and Sasha – have sniffed out the endangered Alpine Stonefly, one of the smallest animals a dog has been trained to successfully detect in its natural habitat.</p>
<p>The conservation of threatened species is frequently hampered by the lack of relevant data on their distributions. This is particularly true for insects, where the difficulty of garnering simple information means the threatened status of many species remains unrecognised and unmanaged. </p>
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<a href="https://theconversation.com/how-many-species-on-earth-why-thats-a-simple-question-but-hard-to-answer-114909">How many species on Earth? Why that's a simple question but hard to answer</a>
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<p>In alpine areas there is a pressing need for innovative methods to better reveal the distribution and abundance of threatened insects. </p>
<p>Alpine regions rely on cool temperatures, and since climate change will bring warmer weather and lower rainfalls, insects like the Alpine Stonefly, which lives in the alpine freshwater system, will struggle to survive.</p>
<p>And while insects might not be appealing to everyone, they are extremely important for ecosystem function.</p>
<p>Traditional survey detection methods are often labour intensive, and hard-to-find species provide limited information. This is where the labrador, border collie and samoyed came to the rescue.</p>
<p>La Trobe’s Anthrozoology Research Group <a href="https://www.latrobe.edu.au/school-psychology-and-public-health/anthrozoology-research-group-dog-lab">Dog Lab</a> in Bendigo, Victoria have been training a pool of local community volunteers and their dogs in conservation detection to use with environmental DNA sampling. Using both environmental DNA and detection dogs has the potential to generate a lot of meaningful data on these threatened stoneflies.</p>
<p>For seven weeks in a special program, dogs were trained to memorise the odour of the Alpine Stonefly (<em>Thaumatoperla alpina</em>), a threatened but iconic insect in the high plains. </p>
<p>The dogs have previously been trained to sniff out animal nests or faeces but not an animal itself, so this was a new approach and an Australian first.</p>
<h2>Stoneflies are hard to catch</h2>
<p>The Alpine Stonefly are brightly coloured aquatic insects and are difficult to find, especially as larvae in water where they live as predators for up to two years in the streams on the Bogong High Plains, Mount Buller-Mount Stirling, Mt Baw Baw and the Yarra Ranges. </p>
<p>They often burrow underneath cobbles, boulders and into the stream bed while the adults only emerge from the water for a few months between January and April to reproduce. </p>
<p>With all this in mind, it’s easy to understand why traditional detection methods can be time consuming and often ineffective. </p>
<p>We predominately focused on the endangered Alpine Stonefly, found across the Bogong High Plains. Their restricted distribution and habitat made them an ideal candidate to trial detection dogs and environmental DNA techniques.</p>
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Read more:
<a href="https://theconversation.com/we-need-a-bank-of-dna-from-dirt-and-water-to-protect-australias-environment-98633">We need a bank of DNA from dirt and water to protect Australia's environment</a>
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<h2>How dogs and environmental DNA help</h2>
<p>We collected water samples from across the Bogong High Plains, Mount Buller and Mount Stirling with trace DNA, such as cells shed from the insect. The ability to quickly take these samples from a broad area to indicate the presence of a species is important to understand distribution. But this approach limits the amount of ecological information that is gathered. </p>
<p>Initial training introduced the dogs to the odour of the Alpine Stonefly in a controlled laboratory setting. Then they graduated from the laboratory to small areas of bushland to search for the insect. </p>
<p>Once the dogs successfully completed their training, it was time to trial the dogs in the alpine environment and survey Alpine Stoneflies in their natural environment.</p>
<p>The trial was conducted at Falls Creek with the dogs’ three volunteer handlers. And the surveys were successful, with all three dogs finding Alpine Stoneflies in their natural habitats. </p>
<p>So could this success be transferred to a similar species? </p>
<p>Absolutely. In preliminary trials, Bayar, Judd and Sasha detected the Stirling Stonefly, a related species of <em>Thaumatoperla</em> that lives in Mount Buller and Mount Stirling, suggesting detection dogs can transfer their conservation training from one species to another. </p>
<p>This is a great find as it means this technique can be used to survey yet another species of <em>Thaumatoperla</em> that lives in Mt Baw Baw and the Yarra Ranges.</p>
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Read more:
<a href="https://theconversation.com/its-not-worth-wiping-out-a-species-for-the-yeelirrie-uranium-mine-116059">It's not worth wiping out a species for the Yeelirrie uranium mine</a>
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<p>Our research is showing that these new sampling techniques supporting conservation are an important part of keeping biodiversity protected in alpine regions. </p>
<p>Now that we’ve successfully trained three dogs, we’re hoping to secure funding to conduct future and more thorough surveys on the Alpine and Stirling Stonefly, and eventually on the third species of stonefly. </p>
<p>By developing creative techniques to detect these species, we boost our ability to document them and, importantly, to protect them.</p><img src="https://counter.theconversation.com/content/116517/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Julia Mynott has previously received funding from the Victorian Government and the Australian Government.</span></em></p>Just in case you needed another reason to love dogs.Julia Mynott, Research Officer, Centre for Freshwater Ecosystems, La Trobe UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/986332018-07-08T19:58:33Z2018-07-08T19:58:33ZWe need a bank of DNA from dirt and water to protect Australia’s environment<figure><img src="https://images.theconversation.com/files/225826/original/file-20180702-116117-18b1pkb.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Water sampling for eDNA analysis. </span> <span class="attribution"><span class="source">Photograph credit: Katrina West.</span>, <span class="license">Author provided</span></span></figcaption></figure><p>Measuring biodiversity used to mean laboriously collecting samples and manually identifying the plants, animals and fungi. This might involve careful inspection under a microscope to spot identifying features. This takes a lot of time and generally requires an expert who has specific knowledge of each group of organisms. </p>
<p>In the last decade, however, DNA sequencing technology has revolutionised this process. We can now identify the species present in an area faster, cheaper and more accurately by measuring “environmental DNA” (eDNA), collected from soil, water or even air. </p>
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Read more:
<a href="https://theconversation.com/monster-hunt-using-environmental-dna-to-survey-life-in-loch-ness-98721">Monster hunt: using environmental DNA to survey life in Loch Ness</a>
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<p>But the explosion of eDNA brings with it some problems. The technology is developing so fast – and the research is so fragmented – that it’s difficult for scientists to compare past work with their own. In our recent correspondence in <a href="https://rdcu.be/2j8h">Nature Ecology & Evolution</a>, we argue that some simple forward-thinking solve these issues.</p>
<h2>How “eDNA” works</h2>
<p>The development of <a href="http://science.sciencemag.org/content/360/6394/1180/tab-pdf">“environmental DNA” metabarcoding</a> has transformed scientists’ ability to measure the diversity of multicellular life. </p>
<p>Substrates such as soil, water and even air contain DNA fragments left behind by organisms. Reading the sequences of a carefully-chosen subset of these DNA fragments enables taxonomic identification of the organisms. Reference databases for identifying the species belonging to the “DNA barcodes” of each species are <a href="http://www.ibol.org/">now well established</a>. </p>
<p>This analysis has led to many innovative ways of analysing biodiversity. For example, mammal diversity can be determined from <a href="http://www.nrcresearchpress.com/doi/10.1139/gen-2015-0193#.Wyswi6mYMmo">DNA taken from blowflies</a> that have touched the mammals. Diversity of indoor arthropods can be determined from <a href="https://onlinelibrary.wiley.com/doi/full/10.1111/mec.13944">eDNA collected by robotic vacuum cleaners</a>. </p>
<p>Sampling a bucket of <a href="https://www.nature.com/articles/s41598-017-12501-5">seawater from near a coral reef</a> allows the fish species present in the area to be identified from eDNA without even seeing them. More than 200 papers based on eDNA metabarcoding have been published since 2012. The field is now so well established that its first <a href="http://www.oxfordscholarship.com/view/10.1093/oso/9780198767220.001.0001/oso-9780198767220">comprehensive textbook</a> was published a couple of months ago. </p>
<p>A major enabler of eDNA research has been rapid advancements in high throughput DNA sequencing. However <a href="https://www.nature.com/articles/nature24286">rapidly-changing high-technology</a> means that research methods quickly become redundant. When new DNA sequencing systems are adopted, past experiments cannot be replicated because the equipment is no longer manufactured. </p>
<p>Another problem is that eDNA metabarcoding does not have universal standards that would allow datasets generated by different technologies to be compared. This lack of comparability limits eDNA metabarcoding research to end-point analysis using one specific methodology. </p>
<h2>We need biobanking</h2>
<p>Our solution is “eDNA biobanking”. “<a href="https://www.sciencedirect.com/science/article/pii/S0011224017304078">Biobanking</a>” in medicine is the standardised sampling, curation and long-term storage of healthy and diseased human tissues. Centralising sample storage allows comparisons that are impossible with single studies. Biobanking eDNA means that old and new samples can be combined and analysed with the contemporary technologies of the future. </p>
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Read more:
<a href="https://theconversation.com/we-reconstructed-the-genome-of-the-first-animal-95900">We reconstructed the genome of the 'first animal'</a>
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<p>Ecosystem monitoring based on metabarcoding of biobanked eDNA will provide records of contemporary biodiversity for future research. This will be particularly useful where industries such as mining, forestry and fisheries move into new areas: biobanking can provide a biodiversity baseline, and allow the impact of new development to be assesed. </p>
<p>We anticipate that in the near future, regulatory bodies such as Environment Protection Agencies will require samples to be biobanked. This will allow the true effects of environmentally-damaging incidents such as oil spills to be measured against the undisturbed baseline. </p>
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<img alt="" src="https://images.theconversation.com/files/225829/original/file-20180702-116129-1nnragn.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/225829/original/file-20180702-116129-1nnragn.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/225829/original/file-20180702-116129-1nnragn.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/225829/original/file-20180702-116129-1nnragn.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/225829/original/file-20180702-116129-1nnragn.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/225829/original/file-20180702-116129-1nnragn.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/225829/original/file-20180702-116129-1nnragn.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=566&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
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<span class="caption">Sampling soil for eDNA analysis.</span>
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<p>This demonstrates the value of eDNA biobanking to long-term ecosystem monitoring. Many environmental regulatory bodies depend on annual updates of ecosystem health. Yearly updates are only possible to a limited extent with eDNA metabarcoding because at some point the underlying technology becomes obsolete. </p>
<p>For example, the diet of Adelie penguins is used to measure biodiersity in the Southern Ocean. A 2013 DNA-based study of the diet of Adelie penguins produced data showing geographic and <a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0082227">inter-annual changes in dietary biodiversity</a>. However, these results cannot be compared to any future studies because this DNA sequencing technology has been discontinued. </p>
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Read more:
<a href="https://theconversation.com/ancient-dna-changes-everything-we-know-about-the-evolution-of-elephants-94426">Ancient DNA changes everything we know about the evolution of elephants</a>
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<p>The lack of comparability among environmental DNA studies is a significant problem. It will not be solved until we adopt a systems of reference standards that allow comparisons among studies. For the foreseeable future, the best solution is environmental DNA biobanking. This will ensure that eDNA technologies will be “future-proofed”, allowing best-practice stewardship of our environment.</p><img src="https://counter.theconversation.com/content/98633/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Simon Jarman receives funding from the CSIRO and Curtin University. He receives funding from the Australian Research Council and has received funding from the Australian Antarctic Science grants scheme.</span></em></p><p class="fine-print"><em><span>Michael Bunce receives funding from the Australian Research Council and has worked on projects together with state conservation agencies and the oil/gas sector on biodiversity studies using DNA.</span></em></p><p class="fine-print"><em><span>Oliver Berry does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>DNA sequencing means a scientist can take a bucket of seawater and ID every fish in the area. Now we need a universal ‘biobank’ of samples to make a truly powerful environment monitoring tool.Simon Jarman, Associate professor, Curtin UniversityMichael Bunce, Professor, Head of Trace and Environmentl DNA (TrEnD) Laboratory, Curtin University, Curtin UniversityOliver Berry, Leader Environomics Future Science Platform, CSIROLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/987212018-06-26T19:49:41Z2018-06-26T19:49:41ZMonster hunt: using environmental DNA to survey life in Loch Ness<figure><img src="https://images.theconversation.com/files/224548/original/file-20180624-26576-1k61oxw.png?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">With the help of environmental DNA, scientists are compiling a census of life in Loch Ness, which should establish if there is any scientific basis to the centuries-old legend of the Loch Ness monster.</span> <span class="attribution"><span class="source">Supplied</span>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span></figcaption></figure><p>Reported sightings of the Loch Ness monster go back to the Dark Ages, but now our <a href="https://www.lochnesshunters.com/">Super Natural History team</a> is using the 21st-century technology of <a href="https://www.theguardian.com/uk-news/2018/may/23/scientists-dna-hunt-loch-ness-monster-scotland">environmental DNA to survey all life</a> in the famous Scottish lake. </p>
<p>The premise of environmental DNA (eDNA) is simple. Life is messy, and living things leave behind skin, hair, feathers, poo, bark, pollen and spores as part of their day-to-day activities. </p>
<p>These traces result in a potpourri of organic material in our soil and water from which DNA can be extracted and sequenced. Our aim is to produce a census of life in Loch Ness and to establish if there is any scientific basis for the centuries-old monster legend.</p>
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Read more:
<a href="https://theconversation.com/why-wont-scientific-evidence-change-the-minds-of-loch-ness-monster-true-believers-97307">Why won't scientific evidence change the minds of Loch Ness monster true believers?</a>
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<h2>Sampling a legend</h2>
<p>There have been more than 1,000 <a href="http://www.lochnesssightings.com/">registered sightings</a> of the Loch Ness “monster”, including two in the last month. They have sparked various theories. Some say the loch is home to a prehistoric relic, while others believe it’s a giant sturgeon, catfish, or just a log or a boat wake.</p>
<p>Obviously, the hook here is that if Nessie is present in the deep, dark and mysterious waters of Loch Ness (for the record I am not a believer, but open to being wrong) then we might find DNA sequences that will help us figure out its biological basis.</p>
<p>We have now finished two weeks of field work for this project, having collected 259 water samples from various parts of the loch, including its chilly depths, more than 200 metres down. </p>
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<img alt="" src="https://images.theconversation.com/files/224573/original/file-20180625-152137-3o1ltj.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/224573/original/file-20180625-152137-3o1ltj.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/224573/original/file-20180625-152137-3o1ltj.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/224573/original/file-20180625-152137-3o1ltj.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/224573/original/file-20180625-152137-3o1ltj.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/224573/original/file-20180625-152137-3o1ltj.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/224573/original/file-20180625-152137-3o1ltj.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
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<span class="caption">The team took water samples from several sites on the lake, as well as from deep waters.</span>
<span class="attribution"><span class="source">Kieran Hennigan</span>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span>
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<p>Miraculously, for the Highlands, the wind stayed light and the rain stayed away which meant we were able to send teams out to sample right around Loch Ness by car and small boat, as well as several nearby lochs as controls. We have also used the <a href="http://www.lochness.com/exhibition.aspx">Loch Ness Centre</a> boat to sample up and down Loch Ness, particularly targeting the loch’s depths. </p>
<h2>Decoding life</h2>
<p>Our days were long, frequently starting as early as 6am and finishing as late as midnight. Our project was also hard on equipment – we broke two of our three sampling devices deploying to depth. Now, with sample collection behind us, we are onto the next phase of work. </p>
<p>The DNA is currently being extracted from our filtered water samples at the <a href="https://www.hull.ac.uk/faculties/fse.aspx">University of Hull</a>. From there it will go to French and Swiss laboratories to be metabarcoded and sequenced.</p>
<p>What will we find? Well undoubtedly there will be DNA sequences derived from bacteria, protists, algae, invertebrates, and the traces of fish, birds and other vertebrate life known from the loch. </p>
<p>What we’ll get is a comprehensive survey of the biodiversity of Loch Ness, but whether we’ll find anything unusual, such as a giant catfish, sturgeon or eel, or a species unknown to science, who knows. Nessie believers will have to wait a few more months for the final results.</p>
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Read more:
<a href="https://theconversation.com/bigfoot-the-kraken-and-night-parrots-searching-for-the-mythical-or-mysterious-75695">Bigfoot, the Kraken and night parrots: searching for the mythical or mysterious</a>
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<h2>It all started with a tweet</h2>
<p>About two years ago <a href="https://www.scientificamerican.com/author/darren-naish/">Darren Naish</a> had just published a book, <a href="https://blogs.scientificamerican.com/tetrapod-zoology/my-new-book-hunting-monsters-cryptozoology-and-the-reality-behind-the-myths/">Hunting Monsters</a>, which included a section on Loch Ness. Over a few tweets I asked him if, in his research for the book, he had stumbled on anyone who was using eDNA to search for evidence of Nessie. The answer was no, but we both thought it a splendid idea.</p>
<p>I was becoming increasingly enamoured with the power of eDNA as a means to monitor the natural environment. Our team at the <a href="http://www.otago.ac.nz">University of Otago</a> was undertaking <a href="http://sustainableseaschallenge.co.nz/programmes/dynamic-seas/quantifying-marine-biodiversity">eDNA work</a> that demonstrated amazing accuracy at identifying the species that resided in the marine ecosystems we studied.</p>
<p>Based on this, I was already thinking about how we might use eDNA to search for and identify the creatures that live in areas of our planet that are hard to investigate using traditional approaches – deep oceans, subterranean water systems and the like. Loch Ness seemed a perfect fit for that sort of project.</p>
<h2>Career killer or opportunity?</h2>
<p>As with many science ideas, that tweet ended up going into the “this is quite interesting” basket and there it sat until I got an email from Scottish journalist <a href="https://www.sundaypost.com/author/johnpaulbreslin/">John Paul Breslin</a>. When his <a href="https://www.sundaypost.com/fp/so-what-really-does-lie-beneath/">article</a> appeared in early April, many took it for an April Fool’s joke, but the story rapidly spread from Scotland to the rest of the world.</p>
<p>The media interest was overwhelming but I wasn’t sure if this was something I really wanted to do. At the time I was the head of a large department at a respected university, with an international reputation for doing quality work in the areas of molecular ecology and evolution. Some colleagues suggested the idea might be a career killer. </p>
<p>The turning point arrived one morning when I was dropping my son off at school. A large posse of eight- and nine-year-olds told me they thought the idea of hunting for the Loch Ness monster was the coolest thing ever. It resonated with me and led to this opportunity to engage the public, particularly kids, in the scientific process. </p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/224549/original/file-20180624-26564-txw910.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/224549/original/file-20180624-26564-txw910.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/224549/original/file-20180624-26564-txw910.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/224549/original/file-20180624-26564-txw910.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/224549/original/file-20180624-26564-txw910.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/224549/original/file-20180624-26564-txw910.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/224549/original/file-20180624-26564-txw910.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">Loch Ness expert, Adrian Shine (right), had dredged the deep lake many times and is now helping to sample DNA traces of life.</span>
<span class="attribution"><span class="source">Kieran Hennigan</span>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span>
</figcaption>
</figure>
<p>One of the first stops was Loch Ness expert, <a href="http://www.lochnessproject.org/">Adrian Shine</a>, who had dredged Loch Ness many times with nets and other devices and agreed to provide a boat and skipper. Several other <a href="https://www.lochnesshunters.com/team/">colleagues</a> all agreed to join the project and the team grew as we realised the Loch Ness monster hunt would describe the biodiversity of the lake in unprecedented fashion, add information about the movements of migratory fish species such as salmon, eels and lamprey, and be a hell of a science communication platform. </p>
<p>So, our <a href="https://www.lochnesshunters.com">project</a> is not a simple monster hunt (although wouldn’t it be amazing if we did find something extraordinary during our investigation). Rather it is an amalgam of basic science, linked to major current initiatives, with a strong science communication aspect. Ultimately, we may find no DNA evidence that explains the monster myth, but I doubt that will ever dent belief. As Adrian Shine quips, absence of evidence is not evidence of absence, and those that wish to will continue to believe in monsters.</p><img src="https://counter.theconversation.com/content/98721/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Neil Gemmell works for the University of Otago</span></em></p>Scientists are using environmental DNA to compile a census of life in Loch Ness and to establish if there is any scientific basis for the centuries-old monster legend.Neil Gemmell, Professor of Reproduction and Genomics, University of OtagoLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/959662018-05-02T18:07:03Z2018-05-02T18:07:03Z‘Hidden sharks’: how we found a new way to detect them<figure><img src="https://images.theconversation.com/files/217264/original/file-20180502-153878-1p7zmdc.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><span class="source">Normana Karia / shutterstock</span></span></figcaption></figure><p>Imagine studying animals without seeing them. Does that sound ludicrous? To people like us, who first got interested in biology because we love animals and enjoy studying them, yes, it sounds like a poor deal. Yet, if you think about what forensic investigators do when they seek DNA evidence at a crime scene, or what doctors do when they detect a pathogen in a patient’s blood, it is exactly that: they detect life forms without seeing them.</p>
<p>DNA is life’s blue print. It is present in virtually every organism on Earth, and we usually study it by extracting it from a piece of tissue or a blood sample. But DNA, really, is everywhere: animals shed it constantly, when they scratch themselves, when they release urine, eggs, saliva, excrement and, of course, when they die. Every environment, from your bed to the deepest recesses of the oceans, is full of “biological dust”, mostly cellular material, which contains the DNA of the organisms that left it behind. This, we call “environmental DNA”, or eDNA.</p>
<p>Assisted by increasingly fast, accurate and affordable technology, scientists have begun, in recent years, to sequence this trace DNA from many <a href="https://onlinelibrary.wiley.com/doi/full/10.1111/mec.13900">environments</a>. And this “micro” approach has even proved to be useful to scientists investigating environments as vast as the oceans.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/217282/original/file-20180502-153914-jaog7b.PNG?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/217282/original/file-20180502-153914-jaog7b.PNG?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/217282/original/file-20180502-153914-jaog7b.PNG?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=336&fit=crop&dpr=1 600w, https://images.theconversation.com/files/217282/original/file-20180502-153914-jaog7b.PNG?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=336&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/217282/original/file-20180502-153914-jaog7b.PNG?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=336&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/217282/original/file-20180502-153914-jaog7b.PNG?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=422&fit=crop&dpr=1 754w, https://images.theconversation.com/files/217282/original/file-20180502-153914-jaog7b.PNG?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=422&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/217282/original/file-20180502-153914-jaog7b.PNG?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=422&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Judith swimming with a hammerhead in the Bahamas: sharks are hard to survey and track as the ocean is so vast.</span>
<span class="attribution"><span class="source">Nicolo Roccatagliata</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>Many marine animals are large, rare, elusive and highly mobile. Sharks are an obvious example: in the oceans they make up a small proportion of the biomass, most of them are pretty <a href="https://www.youtube.com/watch?v=ucj8Ftgvwdg">difficult to catch</a>, and they have been in conflict with humans since we started venturing at sea. With a few exceptions, they avoid us, and <a href="https://www.sciencedirect.com/science/article/pii/S0308597X13000055">because of us</a> many have become threatened with extinction. </p>
<p>This is why we thought it would be interesting to see if, just by sampling a few bottles of ocean water (and the DNA fragments therein), we could rapidly map shark presence and distribution, without engaging in wild chases or employing time and resource-intensive shark fishing methods. We were happy to find out that, indeed, <a href="https://www.nature.com/articles/s41598-017-17150-2">this was possible</a>, and that different species could be detected in different geographical regions, although the areas that had been more affected by humans would show scant presence of sharks.</p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/217276/original/file-20180502-153914-1y8btgv.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/217276/original/file-20180502-153914-1y8btgv.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/217276/original/file-20180502-153914-1y8btgv.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=800&fit=crop&dpr=1 600w, https://images.theconversation.com/files/217276/original/file-20180502-153914-1y8btgv.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=800&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/217276/original/file-20180502-153914-1y8btgv.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=800&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/217276/original/file-20180502-153914-1y8btgv.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=1005&fit=crop&dpr=1 754w, https://images.theconversation.com/files/217276/original/file-20180502-153914-1y8btgv.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=1005&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/217276/original/file-20180502-153914-1y8btgv.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">Stefano sampling in Belize.</span>
<span class="attribution"><span class="source">Judith Bakker</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>But the true measure of the efficiency of this eDNA approach to shark monitoring would only be revealed when contrasted against established, <a href="https://www.dropbox.com/s/xf679djp8eshqbs/eDNA_ScienceADvances_Sound_EN.mp4?dl=0">tried-and-tested methodologies</a>, such as scuba-diving visual censuses or baited underwater camera recordings. </p>
<p>This was the focus of our most recent study, conducted with colleagues based in the South Pacific archipelago of New Caledonia, France, Australia and the US, and now published in the journal <a href="http://advances.sciencemag.org/content/4/5/eaap9661">Science Advances</a>. The results were very exciting: 22 water samples collected over a few weeks detected more sharks than hundreds of baited underwater camera observations over two years, and thousands of scuba dives over a period of decades. Nearly half of the species detected through environmental DNA could not be found at all using traditional methods. And while eDNA could detect the presence of some sharks in about 90% of the samples, underwater cameras could only manage just over 50%, and scuba diving around 15%. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/217286/original/file-20180502-153873-7fqkt6.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/217286/original/file-20180502-153873-7fqkt6.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/217286/original/file-20180502-153873-7fqkt6.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=401&fit=crop&dpr=1 600w, https://images.theconversation.com/files/217286/original/file-20180502-153873-7fqkt6.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=401&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/217286/original/file-20180502-153873-7fqkt6.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=401&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/217286/original/file-20180502-153873-7fqkt6.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/217286/original/file-20180502-153873-7fqkt6.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/217286/original/file-20180502-153873-7fqkt6.png?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">New Caledonia: just 22 eDNA water samples (red stars) detected more sharks than numerous camera recordings (blue) or scuba dives (green).</span>
<span class="attribution"><a class="source" href="http://advances.sciencemag.org/content/4/5/eaat7955">Boussarie & Bakker et al (2018)</a></span>
</figcaption>
</figure>
<p>Interestingly, eDNA outperformed the other methods in both pristine and impacted areas. A range of shark species were detected even in busy, noisy and depleted areas, where they were thought to be extirpated. This suggests some “dark diversity” may still be present, in the form of remnant individuals and groups requiring protection. Similarly, eDNA can help by revealing the appearance of newly established, alien species that are expanding their range. All of this is good news for everyone, and this is why.</p>
<p>Given the speed and efficiency of eDNA sampling, a much larger portion of the sea can be screened, in a shorter time, to gather an overview of the patterns of diversity across large areas and habitats, along various environmental gradients, and at different times. Potentially, we could rapidly build maps of species diversity and use them to create predictive models and identify the factors that influence diversity, while methods are <a href="https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.12888">being developed</a> to improve the quantitative aspect of eDNA detection, also in other <a href="https://www.frontiersin.org/articles/10.3389/fmars.2018.00133/full">charismatic species</a>. All of it will be of great help to those who must devise plans to protect crucial habitats and ecosystems. </p>
<p>Environmental DNA science is still rapidly developing. The databases that we use to match the unknown sequences retrieved from the sea must be enriched with new DNA references of many existing species – every multi-species eDNA study to date has detected large amounts of sequences that could not be matched against any reference. A significant proportion of these belong to organisms that are <a href="http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001127">yet to be described</a> by scientists. </p>
<p>The “DNA probes” currently available will have to become longer, as short sequences may sometimes fail to distinguish closely related species. For instance, the blacktip shark shared some identical sequences with the grey reef shark along the DNA stretch used in our study. Nevertheless, all the initial indications suggest that this approach can get us a step closer to understanding and better managing the largest ecosystem on Earth.</p><img src="https://counter.theconversation.com/content/95966/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Stefano Mariani receives funding from the Natural Environment Research Council, the Pew Charitable Trusts, the European Union H2020 and Interreg schemes. </span></em></p><p class="fine-print"><em><span>Judith Bakker receives funding from the Pew Charitable Trusts and the University of Salford R&E strategy funding. </span></em></p>We cannot spot every shark in the ocean. But we can detect their ‘environmental DNA’.Stefano Mariani, Chair in Conservation Genetics, University of SalfordJudith Bakker, Research Fellow, Environment & Life Sciences, University of SalfordLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/759572017-04-12T18:01:33Z2017-04-12T18:01:33ZFishing for DNA: Free-floating eDNA identifies presence and abundance of ocean life<figure><img src="https://images.theconversation.com/files/164726/original/image-20170410-31882-15i73ly.jpg?ixlib=rb-1.1.0&rect=12%2C84%2C813%2C449&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Fish leave bits of DNA behind that researchers can collect.</span> <span class="attribution"><span class="source">Mark Stoeckle/Diane Rome Peebles images</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span></figcaption></figure><p>Ocean life is largely hidden from view. Monitoring what lives where is costly – typically requiring big boats, big nets, skilled personnel and plenty of time. An emerging technology using what’s called environmental DNA gets around some of those limitations, providing a quick, affordable way to figure out what’s present beneath the water’s surface. </p>
<p>Fish and other animals shed DNA into the water, in the form of cells, secretions or excreta. About 10 years ago, researchers in Europe first demonstrated that small volumes of pond water contained enough <a href="https://dx.doi.org/10.1098/rsbl.2008.0118">free-floating DNA to detect resident animals</a>.</p>
<p>Researchers have <a href="https://dx.doi.org/10.1371/journal.pone.0023398">subsequently</a> <a href="https://dx.doi.org/10.1371/journal.pone.0035868">looked for</a> <a href="https://doi.org/10.1016/j.biocon.2014.11.025">aquatic eDNA</a> <a href="https://doi.org/10.1111/1755-0998.12433">in multiple</a> <a href="https://doi.org/10.1016/j.biocon.2014.11.020">freshwater systems</a>, and <a href="https://dx.doi.org/10.1371/journal.pone.0041732">more recently</a> in <a href="https://dx.doi.org/10.1371/journal.pone.0041781">vastly larger</a> and <a href="https://dx.doi.org/10.1371/journal.pone.0086175">more complex</a> <a href="https://doi.org/10.1111/mec.13481">marine</a> <a href="https://dx.doi.org/10.1371/journal.pone.0165252">environments</a>. While the principle of aquatic eDNA is well-established, we’re just beginning to explore its potential for detecting fish and their abundance in particular marine settings. The technology promises many practical and scientific applications, from helping set sustainable fish quotas and evaluating protections for endangered species to assessing the impacts of offshore wind farms.</p>
<h2>Who’s in the Hudson, when?</h2>
<p><a href="https://doi.org/10.1371/journal.pone.0175186">In our new study</a>, <a href="https://phe.rockefeller.edu/barcode/blog/nycnj-aquatic-vertebrate-edna-project/">my colleagues and I</a> tested how well aquatic eDNA could detect fish in the Hudson River estuary surrounding New York City. Despite being the most heavily urbanized estuary in North America, water quality has <a href="http://www.nyc.gov/html/dep/pdf/hwqs2011.pdf">improved dramatically</a> over the past decades, and the estuary has partly recovered its role as essential habitat for many fish species. The improved health of local waters is highlighted by the now <a href="https://www.nytimes.com/2016/07/10/nyregion/the-great-new-york-whale-census.html">regular fall appearance of humpback whales</a> feeding on large schools of <a href="http://discovermagazine.com/2001/sep/featfish">Atlantic menhaden</a> at the borders of New York harbor, within site of the Empire State Building. </p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/164947/original/image-20170411-26730-1vpceyd.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/164947/original/image-20170411-26730-1vpceyd.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/164947/original/image-20170411-26730-1vpceyd.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=751&fit=crop&dpr=1 600w, https://images.theconversation.com/files/164947/original/image-20170411-26730-1vpceyd.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=751&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/164947/original/image-20170411-26730-1vpceyd.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=751&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/164947/original/image-20170411-26730-1vpceyd.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=943&fit=crop&dpr=1 754w, https://images.theconversation.com/files/164947/original/image-20170411-26730-1vpceyd.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=943&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/164947/original/image-20170411-26730-1vpceyd.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=943&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Preparing to hurl the collecting bucket into the river.</span>
<span class="attribution"><span class="source">Mark Stoeckle</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>Our study is the first recording of spring migration of ocean fish by conducting DNA tests on water samples. We collected one liter (about a quart) water samples weekly at two city sites from January to July 2016. Because the Manhattan shoreline is armored and elevated, we tossed a bucket on a rope into the water. Wintertime samples had little or no fish eDNA. Beginning in April there was a steady increase in fish detected, with about 10 to 15 species per sample by early summer. The eDNA findings largely matched our existing knowledge of fish movements, hard won from decades of traditional seining surveys.</p>
<iframe src="https://datawrapper.dwcdn.net/4bGEP/4/" frameborder="0" allowtransparency="true" allowfullscreen="allowfullscreen" webkitallowfullscreen="webkitallowfullscreen" mozallowfullscreen="mozallowfullscreen" oallowfullscreen="oallowfullscreen" msallowfullscreen="msallowfullscreen" width="100%" height="500"></iframe>
<p>Our results demonstrate the “Goldilocks” quality of aquatic eDNA – it seems to last just the right amount of time to be useful. If it disappeared too quickly, we wouldn’t be able to detect it. If it lasted for too long, we wouldn’t detect seasonal differences and would likely find DNAs of many freshwater and open ocean species as well as those of local estuary fish. Research suggests <a href="https://doi.org/10.1021/acs.est.6b03114">DNA decays over hours to days</a>, depending on temperature, currents and so on.</p>
<figure class="align-left zoomable">
<a href="https://images.theconversation.com/files/164948/original/image-20170411-26733-15fdz4w.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/164948/original/image-20170411-26733-15fdz4w.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/164948/original/image-20170411-26733-15fdz4w.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=734&fit=crop&dpr=1 600w, https://images.theconversation.com/files/164948/original/image-20170411-26733-15fdz4w.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=734&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/164948/original/image-20170411-26733-15fdz4w.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=734&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/164948/original/image-20170411-26733-15fdz4w.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=922&fit=crop&dpr=1 754w, https://images.theconversation.com/files/164948/original/image-20170411-26733-15fdz4w.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=922&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/164948/original/image-20170411-26733-15fdz4w.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=922&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Fish identified via eDNA in one day’s sample from New York City’s East River.</span>
<span class="attribution"><span class="source">New York State Department of Environmental Conservation: alewife (herring species), striped bass, American eel, mummichog; Massachusetts Department of Fish and Game: black sea bass, bluefish, Atlantic silverside; New Jersey Scuba Diving Association: oyster toadfish; Diane Rome Peeples: Atlantic menhaden, Tautog, Bay anchovy; H. Gervais: conger eel.</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>Altogether, we obtained eDNAs matching 42 local marine fish species, including most (80 percent) of the locally abundant or common species. In addition, of species that we detected, abundant or common species were more frequently observed than were locally uncommon ones. That the species eDNA detected matched traditional observations of locally common fish in terms of abundance is good news for the method – it supports eDNA as an index of fish numbers. We expect we’ll eventually be able to detect all local species – by collecting larger volumes, at additional sites in the estuary and at different depths. </p>
<p>In addition to local marine species, we also found locally rare or absent species in a few samples. Most were fish we eat – Nile tilapia, Atlantic salmon, European sea bass (“branzino”). We speculate these came from wastewater – even though the Hudson is cleaner, <a href="https://www.riverkeeper.org/wp-content/uploads/2015/06/Riverkeeper_WQReport_2015_Final.pdf">sewage contamination persists</a>. If that is how the DNA got into the estuary in this case, then it might be possible to determine if a community is consuming protected species by testing its wastewater. The remaining exotics we found were freshwater species, surprisingly few given the large, daily freshwater inflows into the saltwater estuary from the Hudson watershed. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/164945/original/image-20170411-26730-11e9w3d.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/164945/original/image-20170411-26730-11e9w3d.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/164945/original/image-20170411-26730-11e9w3d.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=337&fit=crop&dpr=1 600w, https://images.theconversation.com/files/164945/original/image-20170411-26730-11e9w3d.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=337&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/164945/original/image-20170411-26730-11e9w3d.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=337&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/164945/original/image-20170411-26730-11e9w3d.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=424&fit=crop&dpr=1 754w, https://images.theconversation.com/files/164945/original/image-20170411-26730-11e9w3d.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=424&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/164945/original/image-20170411-26730-11e9w3d.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">Filtering the estuary water back in the lab.</span>
<span class="attribution"><span class="source">Mark Stoeckle</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<h2>Analyzing the naked DNA</h2>
<p>Our protocol uses methods and equipment standard in a molecular biology laboratory, and follows the same procedures used to analyze human microbiomes, for example.</p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/164946/original/image-20170411-26741-1ns4wwu.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/164946/original/image-20170411-26741-1ns4wwu.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/164946/original/image-20170411-26741-1ns4wwu.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=800&fit=crop&dpr=1 600w, https://images.theconversation.com/files/164946/original/image-20170411-26741-1ns4wwu.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=800&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/164946/original/image-20170411-26741-1ns4wwu.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=800&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/164946/original/image-20170411-26741-1ns4wwu.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=1005&fit=crop&dpr=1 754w, https://images.theconversation.com/files/164946/original/image-20170411-26741-1ns4wwu.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=1005&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/164946/original/image-20170411-26741-1ns4wwu.jpeg?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">eDNA and other debris left on the filter after the estuary water passed through.</span>
<span class="attribution"><span class="source">Mark Stoeckle</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>After collection, we run water samples through a small pore size (0.45 micron) filter that traps suspended material, including cells and cell fragments. We extract DNA from the filter, and amplify it using polymerase chain reaction (PCR). PCR is like “xeroxing” a particular DNA sequence, producing enough copies so that it can easily be analyzed.</p>
<p>We targeted mitochondrial DNA – the genetic material within the mitochondria, the organelle that generates the cell’s energy. Mitochondrial DNA is present in much higher concentrations than nuclear DNA, and so easier to detect. It also has regions that are the same in all vertebrates, which makes it easier for us to amplify multiple species.</p>
<p>We tagged each amplified sample, pooled the samples and sent them for next-generation sequencing. Rockefeller University scientist and co-author Zachary Charlop-Powers created the bioinformatic pipeline that assesses sequence quality and generates a list of the unique sequences and “read numbers” in each sample. That’s how many times we detected each unique sequence.</p>
<p>To identify species, each unique sequence is compared to those in the public database GenBank. Our results are consistent with read number being proportional to fish numbers, but more work is needed on the precise relationship of eDNA and fish abundance. For example, some fish may shed more DNA than others. The effects of fish mortality, water temperature, eggs and larval fish versus adult forms could also be at play.</p>
<p>Just like in television crime shows, eDNA identification relies on a comprehensive and accurate database. <a href="https://doi.org/10.1371/journal.pone.0175186">In a pilot study</a>, we identified local species that were missing from the GenBank database, or had incomplete or mismatched sequences. To improve identifications, we sequenced 31 specimens representing 18 species from scientific collections at Monmouth University, and from bait stores and fish markets. This work was largely done by student researcher and co-author Lyubov Soboleva, a senior at John Bowne High School in New York City. We deposited these new sequences in GenBank, boosting the database’s coverage to about 80 percent of our local species. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/164982/original/image-20170412-26730-m2nkq4.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/164982/original/image-20170412-26730-m2nkq4.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/164982/original/image-20170412-26730-m2nkq4.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=473&fit=crop&dpr=1 600w, https://images.theconversation.com/files/164982/original/image-20170412-26730-m2nkq4.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=473&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/164982/original/image-20170412-26730-m2nkq4.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=473&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/164982/original/image-20170412-26730-m2nkq4.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=594&fit=crop&dpr=1 754w, https://images.theconversation.com/files/164982/original/image-20170412-26730-m2nkq4.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=594&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/164982/original/image-20170412-26730-m2nkq4.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=594&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Study’s collection sites in Manhattan.</span>
<span class="attribution"><span class="source">Mark Stoeckle</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>We focused on fish and other vertebrates. Other research groups have applied an aquatic eDNA approach to invertebrates. In principle, the technique could assess the diversity of all animal, plant and microbial life in a particular habitat. In addition to detecting aquatic animals, eDNA reflects terrestrial animals in nearby watersheds. In our study, the commonest wild animal detected in New York City waters was the brown rat, a common urban denizen.</p>
<p>Future studies might employ autonomous vehicles to routinely sample remote and deep sites, helping us to better understand and manage the diversity of ocean life.</p><img src="https://counter.theconversation.com/content/75957/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Mark Stoeckle receives funding from Monmouth University-Rockefeller University Marine Science Policy Initiative (MURU). </span></em></p>Animals shed bits of DNA as they go about their lives. A new study of the Hudson River estuary tracked spring migration of ocean fish by collecting water samples and seeing whose DNA was present when.Mark Stoeckle, Senior Research Associate in the Program for the Human Environment, The Rockefeller UniversityLicensed as Creative Commons – attribution, no derivatives.