tag:theconversation.com,2011:/fr/topics/edna-28757/articleseDNA – 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>
<figure class="align-center ">
<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>
<figcaption>
<span class="caption">In future, our marine parks may well have networks of buoys sampling eDNA at the surface and underwater drones sampling the depths.</span>
<span class="attribution"><span class="source">CSIRO</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>This is just the start. Imagine a future where eDNA data could be collected from the most remote oceans by autonomous vehicles, analysed by the drone or on board a research vessel, and integrated with other monitoring data so marine managers and the public can see near-real time data about the condition of the ocean. </p>
<p>Science fiction? Not any more. </p>
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<em>
<strong>
Read more:
<a href="https://theconversation.com/you-shed-dna-everywhere-you-go-trace-samples-in-the-water-sand-and-air-are-enough-to-identify-who-you-are-raising-ethical-questions-about-privacy-205557">You shed DNA everywhere you go – trace samples in the water, sand and air are enough to identify who you are, raising ethical questions about privacy</a>
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</p>
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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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<p>
<em>
<strong>
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>
<figcaption>
<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>
</figcaption>
</figure>
<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>
<hr>
<p>
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<strong>
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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<hr>
<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>
<figcaption>
<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>
</figcaption>
</figure>
<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>
<hr>
<p>
<em>
<strong>
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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</em>
</p>
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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/2077802023-06-21T14:50:05Z2023-06-21T14:50:05ZFive ways to know if a river is polluted – and whether it’s safe to go in the water<figure><img src="https://images.theconversation.com/files/532916/original/file-20230620-30-7dxcxb.jpg?ixlib=rb-1.1.0&rect=0%2C0%2C4281%2C2725&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/family-crossing-river-whilst-hiking-uk-1188687490">Monkey Business Images/Shutterstock</a></span></figcaption></figure><p>England’s rivers are <a href="https://publications.parliament.uk/pa/cm5802/cmselect/cmenvaud/74/summary.html">in a mess</a>. <a href="https://www.gov.uk/government/publications/state-of-the-water-environment-indicator-b3-supporting-evidence/state-of-the-water-environment-indicator-b3-supporting-evidence">Just 14%</a> are in good ecological condition – and that’s just the ones that are regularly assessed. </p>
<p>There are many reasons for this. They include growing pressure on ageing sewer systems from housing developments and extreme weather, <a href="http://www.connectright.org.uk/">misconnected drains</a>, intensive <a href="https://www.theguardian.com/environment/2023/jan/10/landmark-decision-mega-poultry-farm-life-or-death-of-river-wye-wales">livestock and poultry farms</a>, the <a href="https://www.nwl.co.uk/binthewipe">flushing of wet wipes</a>, and illegal waste dumping and littering. </p>
<p>In the older parts of English cities, combined sewers carry wastewater flushed from homes and public buildings with the water that runs off pavements and into drains. </p>
<p>To prevent flooding, overflows are permitted to release excess water into rivers when combined sewers cannot cope with a deluge. Via these overflows, urban runoff blended with sewage entered rivers and the sea on average <a href="https://www.bbc.co.uk/news/science-environment-65099906">825 times a day in 2022</a>.</p>
<p>Swimming in rivers or wading and splashing around in streams is one of the most pleasant things you can do on a hot summer day. Unfortunately, the bacterial water quality of England’s rivers is not routinely tested by authorities unless it contains an officially designated bathing site. </p>
<p>To assess the risk in my own city, Newcastle upon Tyne in north-east England, my research team and I undertook an extensive study to monitor the <a href="https://www.sciencedirect.com/science/article/pii/S0048969723029030">bacteria living in the river Ouseburn</a>.</p>
<p>We collected 40 water samples from the Ouseburn’s course in the summer and early autumn of 2021 at eight locations, including where the river flows through <a href="https://urbangreennewcastle.org/our-green-spaces/parks/jesmond-dene/">Newcastle’s most popular park</a>. </p>
<p>We found that water discharged from storm overflows contained a high concentration of faecal bacteria – about one hundred times higher than the acceptable standard for bathing water. </p>
<p>The river’s bacterial community shifted from predominantly freshwater species during dry weather to mostly sewage bacteria during heavy rain, when sewers were inundated and storm overflows were activated.</p>
<p>During one September storm, 72-77% of all bacteria in the Ouseburn downstream of storm overflows originated from the sewer system. Sewage bacteria in the river reached levels observed in storm overflow discharge, which implies that the natural flow of the river only slightly dilutes these discharges. </p>
<p>Levels of sewage bacteria fell substantially 24 hours after rainfall, but overall the Ouseburn would probably fail water quality standards if it were monitored as bathing water. People who accidentally ingest water when wading and splashing in the Ouseburn could contract diarrhoea or another gastrointestinal disease.</p>
<p>To avoid getting sick, here are five things you should do before entering a river.</p>
<h2>1. Check for storm overflows</h2>
<p>Water and sewerage companies in England and Wales update the Environment Agency on how long their storm overflows discharge over the course of a year. The Rivers Trust charity compiles this information in its <a href="https://experience.arcgis.com/experience/e834e261b53740eba2fe6736e37bbc7b/page/Map/">sewage map</a>.</p>
<figure class="align-center ">
<img alt="A pipe lodged in a concrete wall discharging brown water into a river." src="https://images.theconversation.com/files/532908/original/file-20230620-27-npid6e.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/532908/original/file-20230620-27-npid6e.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/532908/original/file-20230620-27-npid6e.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/532908/original/file-20230620-27-npid6e.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/532908/original/file-20230620-27-npid6e.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/532908/original/file-20230620-27-npid6e.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/532908/original/file-20230620-27-npid6e.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">Storm overflows are designed to take the pressure off sewers during heavy rain.</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/water-outflows-through-flood-drainage-system-1676682793">Ashadhodhomei/Shutterstock</a></span>
</figcaption>
</figure>
<p>Check this map for storm overflows that frequently discharge upstream of where you plan to swim. Keep in mind that the water in rivers moves fast over great distances. Our work suggested that the sewage didn’t dilute all that much downstream of the main discharge point over a stretch of river several kilometres long.</p>
<h2>2. Consider the size of the river – and what surrounds it</h2>
<p>Small rivers flowing in urban areas receive less water from their catchment than larger ones to dilute sewage. As our work showed, concentrations of sewer-related bacteria in a small urban river can be very high when it rains.</p>
<h2>3. Look out for sewage litter</h2>
<p>Plastic litter derived from sewage, such as wet wipes and sanitary products, is a sign that the sewer system is discharging into a river. This kind of litter is often tangled in tree roots or other vegetation along the high-flow line, or dumped on embankments that flood during storms.</p>
<figure class="align-center ">
<img alt="Tree roots overhanging a river covered with litter." src="https://images.theconversation.com/files/532242/original/file-20230615-27-rhruw9.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/532242/original/file-20230615-27-rhruw9.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/532242/original/file-20230615-27-rhruw9.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/532242/original/file-20230615-27-rhruw9.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/532242/original/file-20230615-27-rhruw9.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/532242/original/file-20230615-27-rhruw9.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/532242/original/file-20230615-27-rhruw9.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">Wet wipes can indicate that a sewage outflow is nearby.</span>
<span class="attribution"><span class="source">David Werner</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<h2>4. Avoid rivers during and after storms</h2>
<p>Heavy rain can cause storm overflows to release sewage, so avoid rivers during and after heavy rain (and flooded areas if a river has left its embankment). In a thunderstorm, heavy showers can fall upstream while the weather remains sunny even a short distance downstream. So avoid rivers when conditions are thundery.</p>
<h2>5. Avoid cloudy water</h2>
<p>We found that cloudier water tended to have more sewer bacteria. While rivers can be naturally cloudy following rainfall, it is often a sign of water pollution, not just from sewers but also farms.</p>
<p>These five tips should help you recognise the signs of pollution from sewers that could make you sick. You should also consider the risks of slips, trips and falls when venturing into a stream. Or the risk of drowning in deeper rivers. A river’s depth can change within a single step, currents can speed up, and cold temperatures can cause shock. Branches, boulders, and other hazards could be lurking out of sight. </p>
<p>Connecting with nature can <a href="https://www.mentalhealth.org.uk/our-work/research/nature-how-connecting-nature-benefits-our-mental-health">benefit your mental health</a>. To do this safely in England’s rivers, take these precautions.</p><img src="https://counter.theconversation.com/content/207780/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>David Werner receives research funding from a wide range of government, industry and charity sources including the Reece Foundation, UKRI, the Royal Society, Fera Science, Northumbrian Water, and UKWIR.</span></em></p>And other ways to enjoy open water safely this summer.David Werner, Professor in Environmental Systems Modelling, Newcastle 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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<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/1645292021-09-17T12:19:15Z2021-09-17T12:19:15ZScientists at work: We use environmental DNA to monitor how human activities affect life in rivers and streams<figure><img src="https://images.theconversation.com/files/420917/original/file-20210913-21-185he0a.jpg?ixlib=rb-1.1.0&rect=0%2C0%2C3259%2C1832&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Environmental DNA is a promising tool for tracking species in freshwater ecosystems like Oregon's Elkhorn Creek.</span> <span class="attribution"><a class="source" href="https://flic.kr/p/NZgE7n">Greg Shine, BLM/Flickr</a>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span></figcaption></figure><p>Rivers, lakes and wetlands cover just 1% of the Earth’s surface but are home to nearly 10% of all species, including fish, mammals, birds, insects and crustaceans. But these rich, <a href="https://wwfcee.org/pdf_collections/7/world_s_forgotten_fishes__final_april9_.pdf">diverse</a> ecosystems are <a href="https://wwf.panda.org/discover/our_focus/freshwater_practice/the_world_s_forgotten_fishes/">in free fall</a>. Worldwide, species are <a href="https://www.un.org/sustainabledevelopment/blog/2019/05/nature-decline-unprecedented-report/">declining faster now</a> than at any other time in human history, and fresh waters are losing more species than land or ocean ecosystems.</p>
<p>Today about <a href="https://www.iucn.org/theme/species/our-work/freshwater-biodiversity">1 in 4 freshwater creatures face extinction</a>. Wetlands are disappearing <a href="https://doi.org/10.1093/biosci/biaa002">three times faster than forests</a>. Across the globe, water quality is plummeting, polluted by <a href="https://uneplive.unep.org/media/docs/assessments/unep_wwqa_report_web.pdf">plastic, sewage, mining sludge, industrial and agricultural chemicals and much more</a>. </p>
<p>It’s challenging to study how these stresses are affecting aquatic life. There are many diverse threats, and river networks cover broad geographic regions. Often they run through remote, nearly inaccessible areas. Current techniques for monitoring freshwater species are <a href="https://doi.org/10.1111/j.1365-2664.2010.01864.x">labor-intensive and costly</a>.</p>
<p>In our <a href="https://esajournals.onlinelibrary.wiley.com/doi/10.1002/eap.2389">work</a> as <a href="https://scholar.google.fr/citations?user=rhmblP8AAAAJ&hl=fr">researchers</a> in <a href="https://scholar.google.com/citations?user=hxHYAA8AAAAJ&hl=en">ecology</a>, we are testing a new method that can vastly expand biomonitoring: using environmental DNA, or eDNA, in rivers to <a href="https://doi.org/10.1016/j.tree.2014.04.003">catalog and count species</a>. Federal and local agencies need this data to restore water quality and save dwindling species from extinction. </p>
<figure>
<iframe src="https://player.vimeo.com/video/66103145" width="500" height="281" frameborder="0" webkitallowfullscreen="" mozallowfullscreen="" allowfullscreen=""></iframe>
<figcaption><span class="caption">This preview of the film “Hidden Rivers” reveals the diverse and little-known life in Southern Appalachian waterways.</span></figcaption>
</figure>
<h2>Traditional methods are slow and expensive</h2>
<p>With traditional biomonitoring methods, scientists count individual species and their abundance at just <a href="https://doi.org/10.1111/j.1365-2664.2010.01864.x">a few sites</a>. For example, one recent study of <a href="https://doi.org/10.1086/676997">mountaintop mining impacts on fish in West Virginia</a> sampled just four sites with a team of four researchers. </p>
<p>Collecting and identifying aquatic organisms requires highly skilled ecologists and taxonomists with expertise in a wide variety of freshwater species. For each sample of fish or invertebrates collected in the field, it takes from hours to weeks to identify all of the species. Only wealthy nations can afford this costly process.</p>
<p>Conserving threatened and endangered species and keeping river ecosystems healthy requires monitoring broad areas over time. Sensitive aquatic insects and fish species are the freshwater equivalent of the proverbial canary in a coal mine: If these species are absent, that’s a strong indicator of water quality problems. The cause may be mining, agriculture, urbanization or other sources, as well as <a href="https://www.nwf.org/Magazines/National-Wildlife/2012/AugSept/Animals/Appalachian-Rivers">dams</a> that block animals’ downstream movements.</p>
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<iframe width="440" height="260" src="https://www.youtube.com/embed/W3lcHdFyzrQ?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">Scientists sample for fish in a Maryland stream by ‘electrofishing’ – stunning fish with a mild electrical pulse so they can be collected, identified and released after the shock wears off.</span></figcaption>
</figure>
<h2>Free-floating genetic evidence</h2>
<p>Innovations in genetic technology have created a powerful, affordable new tool that we are now testing. The process involves extracting eDNA from genetic material floating in the water – skin, scales, feces and single-celled organisms, such as bacteria. </p>
<p>By analyzing this genetic information, we can <a href="https://doi.org/10.1111/j.1365-294X.2012.05470.x">detect a wide range of species</a>. We started considering using eDNA for our research in 2018, after several studies demonstrated its power to monitor single species of interest or groups of organisms in <a href="https://doi.org/10.1016/j.tree.2014.04.003">rivers</a> and <a href="https://theconversation.com/fishing-for-dna-free-floating-edna-identifies-presence-and-abundance-of-ocean-life-75957">oceans</a>.</p>
<p>Collecting eDNA is easy: One 4-ounce water sample can capture remnant DNA from thousands of aquatic species. Another benefit is that it doesn’t require killing wildlife for identification.</p>
<p>In the lab, we analyze the DNA from different taxonomic groups one by one: bacteria, algae, fish and <a href="https://www.epa.gov/national-aquatic-resource-surveys/indicators-benthic-macroinvertebrates">macroinvertebrates</a> – organisms that lack backbones and are large enough to see, such as snails, worms and beetles. Many researchers study just one group, but we assess all of them at the same time. </p>
<p>We then match our DNA sequences with freshwater species that are already catalogued in existing databases. In this way, we can chart the distribution and abundance of these organisms within and across rivers.</p>
<p>This process requires just a cheap filter, a syringe and vials, and anyone can do it. Commercial eDNA companies charge less than $200 to extract and sequence a sample. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/421209/original/file-20210914-13-u7g2zq.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Graphic showing how scientists analyze eDNA to detect different species." src="https://images.theconversation.com/files/421209/original/file-20210914-13-u7g2zq.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/421209/original/file-20210914-13-u7g2zq.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=364&fit=crop&dpr=1 600w, https://images.theconversation.com/files/421209/original/file-20210914-13-u7g2zq.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=364&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/421209/original/file-20210914-13-u7g2zq.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=364&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/421209/original/file-20210914-13-u7g2zq.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=457&fit=crop&dpr=1 754w, https://images.theconversation.com/files/421209/original/file-20210914-13-u7g2zq.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=457&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/421209/original/file-20210914-13-u7g2zq.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=457&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Most eDNA the authors collect from streams is microbial (the gray DNA in the cartoon above). Without special techniques, they would not ‘see’ the less frequent DNA from other taxonomic groups, so their surveys would generate a species abundance curve like the one on the bottom left, in which most groups of conservation concern are too rare to detect or fall into the ‘long tail’ of rare occurrences. By using targeted primers – short stretches of DNA that are unique to specific groups of organisms – they can amplify the eDNA of less abundant groups, like algae, arthropods and fish, as shown on the right.</span>
<span class="attribution"><span class="source">Emily Bernhardt, produced using Biorender</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<h2>Altered rivers</h2>
<p>Using this method, we extensively surveyed 93 rivers in West Virginia – looking at the entire tree of life, from the tiniest bacteria to fish – in two days with a four-person team. </p>
<p>The Appalachian rivers that we study teem with life. These are some of the world’s most biologically diverse temperate freshwater ecosystems, home to <a href="https://www.conservationfisheries.org/appalachia">many fish species</a>, as well as salamanders, crayfish, mussels and aquatic insects. <a href="https://www.natureserve.org/publications/rivers-life-critical-watersheds-protecting-freshwater-biodiversity">Many are found nowhere else</a>. We tallied <a href="https://doi.org/10.1002/eap.2389">more than 10,000 different species</a> in those 93 waterways. </p>
<p>The area where we worked is an intensive coal mining region, which heavily affects waterways. Liquids draining from mines are <a href="https://www.epa.gov/nps/abandoned-mine-drainage">acidic</a>, but in this region they react with limestone rock, so the net effect is to make local streams alkaline. Mine drainage also increases streams’ salinity and concentrations of <a href="https://doi.org/10.1021/es301144q">sulfate and other contaminants</a>. Our research revealed that mined watersheds held 40% fewer species than areas without mining operations, and the organisms we detected were less abundant than in unaffected rivers. </p>
<h2>Assessing river health</h2>
<p>We believe this new approach represents a revolution for biomonitoring, expanding our ability to quantify and study freshwater life. It’s also an important new conservation tool, allowing scientists to track changes in populations of endangered or invasive species. Researchers also can use eDNA to monitor biodiversity or discover new species in oceans or soils. </p>
<p><div data-react-class="Tweet" data-react-props="{"tweetId":"1303976383178309633"}"></div></p>
<p>This <a href="https://doi.org/10.1002/fee.1490">open-science method</a> makes all DNA data widely available, with nearly all sequences placed in public repositories. Moving forward, we expect that it will aid many types of research, as well as state and local monitoring and conservation programs. Investments in collecting eDNA and identifying organisms and analyzing their genetic signatures will continue to make it a more effective tool.</p>
<p>[<em>Over 100,000 readers rely on The Conversation’s newsletter to understand the world.</em> <a href="https://theconversation.com/us/newsletters/the-daily-3?utm_source=TCUS&utm_medium=inline-link&utm_campaign=newsletter-text&utm_content=100Ksignup">Sign up today</a>.]</p>
<p>Efforts are underway to better target various individual species, focusing on those that are endangered, invasives that damage ecosystems and sensitive species that serve as indicators of river health. Scientists are freezing eDNA samples at -112 degrees F (-80 C) in expectation that technological advances may yield <a href="https://doi.org/10.1038/s41559-018-0614-3">more information in the future</a>.</p>
<p>Traditional monitoring approaches remain valuable, but eDNA adds an important new tool to the toolkit. Together, these approaches can begin to answer many questions about food webs, the conservation status of species, reproduction rates, species interactions, organisms’ health, disease and more.</p><img src="https://counter.theconversation.com/content/164529/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Marie Simonin is a research scientist at INRAE, the French National Research Institute for Agriculture, Food and Environment.</span></em></p><p class="fine-print"><em><span>Emily S. Bernhardt has received funding to research the impacts of mountaintop removal coal mining from the Foundation for the Carolinas and the National Science Foundation, which supported the work described in this article. She currently is engaged as an expert on these impacts by the US Department of Justice.</span></em></p>Rivers are among the most embattled ecosystems on Earth. Researchers are testing a new, inexpensive way to study river health by using eDNA to count the species that rivers harbor.Marie Simonin, Research Scientist, InraeEmily S. Bernhardt, Professor of Biology, Duke UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1620842021-06-28T04:31:28Z2021-06-28T04:31:28ZBreakthrough allows scientists to determine the age of endangered native fish using DNA<figure><img src="https://images.theconversation.com/files/408568/original/file-20210628-13-xaemas.jpg?ixlib=rb-1.1.0&rect=0%2C479%2C3982%2C2179&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>Identifying the age of animals is fundamental to wildlife management. It helps scientists know if a species is at risk of extinction and the rate at which it reproduces, as well as determining what level of fishing is sustainable. </p>
<p>Determining the age of fish has been difficult in the past — primarily involving extracting the inner ear bone, also known as the “otolith”. Layers of growth in the otolith are counted like rings on a tree to reveal an individual’s age. Unless a dead specimen is available, this method requires killing a fish, making it unsuitable for use on endangered populations. </p>
<p>However a non-lethal DNA test developed by the CSIRO enables researchers to determine fish age for three iconic and threatened Australian freshwater species: the Australian lungfish, the Murray cod and the Mary River cod. We outline the technological breakthrough in our <a href="https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13440">research</a> just published.</p>
<p>Our fast, accurate and cost-effective test can be adapted for other fish species. We now hope to share this method to improve the protection of wild fish populations and help promote sustainable fisheries around the world.</p>
<figure class="align-center ">
<img alt="gloved hands cut open fish with sciessors" src="https://images.theconversation.com/files/408566/original/file-20210628-25-1n3i312.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/408566/original/file-20210628-25-1n3i312.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=384&fit=crop&dpr=1 600w, https://images.theconversation.com/files/408566/original/file-20210628-25-1n3i312.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=384&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/408566/original/file-20210628-25-1n3i312.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=384&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/408566/original/file-20210628-25-1n3i312.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=483&fit=crop&dpr=1 754w, https://images.theconversation.com/files/408566/original/file-20210628-25-1n3i312.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=483&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/408566/original/file-20210628-25-1n3i312.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=483&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Traditionally, age could only be determined on a dead fish. The new method is non-lethal.</span>
<span class="attribution"><span class="source">Shutterstock</span></span>
</figcaption>
</figure>
<h2>Iconic species at risk</h2>
<p>Human activity has led to the population declines of the three Australian fish species at the centre of our research.</p>
<p>The threatened Australian lungfish is found in rivers and lakes in southeast Queensland. It’s often referred to as a “living fossil” because its extraordinary evolutionary history stretches back more than 100 million years, before all land animals including dinosaurs. </p>
<p>Man-made barriers in rivers reduce the movement of water, which lowers lungfish breeding rates. </p>
<p>Older lungfish do not have hard otolith structures, which makes determining their age difficult. Bomb radiocarbon, which analyses carbon levels in organic matter, has been used to age Australian lungfish, but this method is too expensive to be widely used. </p>
<figure class="align-center ">
<img alt="Australian lungfish" src="https://images.theconversation.com/files/405400/original/file-20210609-14804-dxzlxf.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/405400/original/file-20210609-14804-dxzlxf.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/405400/original/file-20210609-14804-dxzlxf.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/405400/original/file-20210609-14804-dxzlxf.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/405400/original/file-20210609-14804-dxzlxf.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/405400/original/file-20210609-14804-dxzlxf.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/405400/original/file-20210609-14804-dxzlxf.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">In the past, determining the age of Australian lungfish has been challenging.</span>
</figcaption>
</figure>
<p>The threatened <a href="https://www.mdba.gov.au/sites/default/files/archived/mdbc-NFS-reports/2202_factsheet_native_murray_cod.pdf">Murray cod</a> is Australia’s largest freshwater fish. The <a href="https://www.environment.gov.au/biodiversity/threatened/recovery-plans/mary-river-cod-research-and-recovery-plan-1996">Mary River cod</a> is one of Australia’s most endangered fish, found in less than 30% of its former range in Queensland’s Mary River. </p>
<p>Habitat destruction and overfishing are major threats to Murray cod and Mary River cod populations.</p>
<p>Otoliths can be used to determine age for both these cod species, however this has only been done on a population-wide scale for the more prevalent Murray cod. </p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/australias-smallest-fish-among-22-at-risk-of-extinction-within-two-decades-144115">Australia's smallest fish among 22 at risk of extinction within two decades</a>
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</p>
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<figure class="align-right ">
<img alt="Mary River cod" src="https://images.theconversation.com/files/405403/original/file-20210609-14622-b8aqvx.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/405403/original/file-20210609-14622-b8aqvx.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/405403/original/file-20210609-14622-b8aqvx.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/405403/original/file-20210609-14622-b8aqvx.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/405403/original/file-20210609-14622-b8aqvx.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/405403/original/file-20210609-14622-b8aqvx.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/405403/original/file-20210609-14622-b8aqvx.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">CSIRO estimated the age of Mary River cod.</span>
</figcaption>
</figure>
<h2>Our DNA breakthrough</h2>
<p>When cells divide to make new cells, DNA is replicated. This can lead to DNA methylation, which involves the addition or the loss of a “methyl group” molecule at places along the DNA strand. </p>
<p>Research has found the level of DNA methylation is a reliable predictor of age, particularly in mammals, <a href="https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-10-r115">including humans</a>. </p>
<p>To develop our test, we first worked with zebrafish. This species is useful when studying fish biology because it has a short lifespan and high reproductive rates. We took zebrafish whose ages were known, then removed a tiny clip of their fin. We then examined DNA methylation levels in the fin sample to identify the fish’s age. </p>
<p>Following this successful step, we transferred the method to Australian lungfish, Murray cod and Mary River cod. Again, we used fish of known ages, as well as bomb radiocarbon dating of scales and ages determined from otoliths.</p>
<p>We found despite the zebrafish and the study fish species being separated by millions of years of evolution, our method worked in all four species. This suggests the test can be used to predict age in many other fish species.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/good-news-from-the-river-murray-these-2-fish-species-have-bounced-back-from-the-millennium-drought-in-record-numbers-148433">Good news from the River Murray: these 2 fish species have bounced back from the Millennium Drought in record numbers</a>
</strong>
</em>
</p>
<hr>
<figure class="align-center ">
<img alt="DNA strand" src="https://images.theconversation.com/files/408567/original/file-20210628-17-h2rxxj.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/408567/original/file-20210628-17-h2rxxj.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=303&fit=crop&dpr=1 600w, https://images.theconversation.com/files/408567/original/file-20210628-17-h2rxxj.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=303&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/408567/original/file-20210628-17-h2rxxj.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=303&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/408567/original/file-20210628-17-h2rxxj.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=381&fit=crop&dpr=1 754w, https://images.theconversation.com/files/408567/original/file-20210628-17-h2rxxj.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=381&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/408567/original/file-20210628-17-h2rxxj.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=381&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">The test uses co-called DNA methylation to estimate age.</span>
<span class="attribution"><span class="source">Shutterstock</span></span>
</figcaption>
</figure>
<h2>A conservation management boom?</h2>
<p>In the same way human population demographers use census data to understand and model human populations, we now have the tools to do this with animals. </p>
<p>We are looking to expand this DNA-based method to determine the age of the endangered eastern freshwater cod and trout cod. We will also continue to test the method across other species including reptiles and crustaceans. </p>
<p>This work is part of CSIRO’s ongoing efforts to use DNA to measure and monitor the environment. This includes estimating the lifespan of vertebrate species such as long-lived fish and surveying biodiversity in seawater using DNA extracted from the environment.</p>
<p>We envisage that in the not too distant future, these methods may be used by other researchers to better understand and manage wild animal populations. </p>
<p><em><a href="https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13440">The paper</a> upon which this article was based was published in Molecular Ecology Resources with authors from CSIRO, Seqwater, Queensland Government, NSW Department of Primary Industries, University of Queensland and University of Western Australia.</em></p><img src="https://counter.theconversation.com/content/162084/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Benjamin Mayne 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>Determining the age of fish has been historically difficult, primarily involving lethal methods. A new DNA test solves this problem.Benjamin Mayne, Molecular biologist and bioinformatician, CSIROLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1582862021-04-21T12:29:03Z2021-04-21T12:29:03ZEnvironmental DNA – how a tool used to detect endangered wildlife ended up helping fight the COVID-19 pandemic<figure><img src="https://images.theconversation.com/files/396160/original/file-20210420-23-1rz2nzg.JPG?ixlib=rb-1.1.0&rect=0%2C0%2C6709%2C4466&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Looking for bits of DNA at the University of Florida.</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>Imagine discovering an animal species you thought had gone extinct was still living – without laying eyes on it. Such was the case with the Brazilian frog species <em>Megaelosia bocainensis</em>, whose complete disappearance in 1968 led scientists to believe it had become extinct. But through a novel genetic detection technique, <a href="https://doi.org/10.1111/mec.15594">it was rediscovered in 2020</a>. </p>
<p>Such discoveries are now possible thanks to a new approach that recovers and reads the trace amounts of DNA released into the environment by animals. It’s called environmental DNA, or eDNA – and it takes advantage of the fact that <a href="https://doi.org/10.1093/biosci/biab027">every animal sheds DNA into its environment</a> via skin, hair, scales, feces or bodily fluids as it moves through the world.</p>
<p><a href="https://scholar.google.com/citations?hl=en&user=3cQ6umoAAAAJ">As</a> <a href="https://scholar.google.com/citations?hl=en&user=LtNEh9gAAAAJ">wildlife</a> <a href="https://scholar.google.com/citations?hl=en&user=YJAXPpYAAAAJ">biologists</a> at the University of Florida’s <a href="https://www.whitney.ufl.edu/conservation--sea-turtle-hospital/">Whitney Laboratory for Marine Bioscience & Sea Turtle Hospital</a>, we <a href="https://doi.org/10.1038/s42003-021-01656-7">use eDNA to track a virus</a> responsible for a <a href="https://doi.org/10.1038/s42003-021-01656-7">sea turtle pandemic called fibropapillomatosis</a>, which <a href="https://theconversation.com/could-human-cancer-treatments-be-the-key-to-saving-sea-turtles-from-a-disfiguring-tumor-disease-98140">causes debilitating tumors</a>. We also use eDNA to detect sea turtles in the wild. </p>
<p>But in 2020, human health researchers began repurposing eDNA techniques to track the COVID-19 pandemic. This is a prime example of how research in one area – wildlife conservation – can be adapted to another area – human disease mitigation. Going forward, we believe eDNA will prove to be an essential tool for monitoring both human and animal health. </p>
<h2>From soil microbes to sea turtles</h2>
<p>Scientists in the 1980s began <a href="https://doi.org/10.1098/rstb.2013.0383">hunting for microbe DNA in soil samples</a>. Over the next 20 years, the technique was adapted for use with air and water samples, and scientists started using eDNA to <a href="https://doi.org/10.1371/journal.pone.0041781">detect larger animals</a> <a href="https://doi.org/10.1086/685882">and plants</a>. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/394859/original/file-20210413-21-g6e1rl.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="A flowchart of how snow/ice, freshwater, soil, sand or seawater samples can be collected and analyzed for their DNA." src="https://images.theconversation.com/files/394859/original/file-20210413-21-g6e1rl.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/394859/original/file-20210413-21-g6e1rl.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=420&fit=crop&dpr=1 600w, https://images.theconversation.com/files/394859/original/file-20210413-21-g6e1rl.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=420&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/394859/original/file-20210413-21-g6e1rl.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=420&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/394859/original/file-20210413-21-g6e1rl.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=528&fit=crop&dpr=1 754w, https://images.theconversation.com/files/394859/original/file-20210413-21-g6e1rl.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=528&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/394859/original/file-20210413-21-g6e1rl.png?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">Scientists now can detect DNA traces from many different environments.</span>
<span class="attribution"><span class="source">Liam Whitmore, University of Limerick</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>While the science behind eDNA techniques is complex, the actual process of collecting and testing a sample is relatively simple. Samples are filtered through very fine paper, which traps loose cells and strands of DNA. The techniques to read what DNA is present are the same as those used for tissue or blood samples, usually <a href="https://www.theguardian.com/science/2013/nov/28/meaning-technology-pcr-history-science">quantitative polymerase chain reaction</a> or <a href="https://www.theguardian.com/australia-news/2020/aug/18/what-is-genomic-sequencing-and-how-is-it-being-used-against-covid-19-in-australia">whole genome sequencing</a>. Scientists can either read all of the DNA present from every organism – or target just the DNA from species of interest. </p>
<p>Scientists now routinely use eDNA to <a href="https://doi.org/10.1371/journal.pone.0221120">detect endangered wildlife and invasive species</a>. The ability to tell whether an animal is present without ever needing to lay eyes or a lens on it is an incredible leap forward, decreasing the time, resources and human effort needed to monitor and protect vulnerable species. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/394860/original/file-20210413-21-1e4veem.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="A sea turtle on its back in an exam room. One of its flippers is severely deformed." src="https://images.theconversation.com/files/394860/original/file-20210413-21-1e4veem.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/394860/original/file-20210413-21-1e4veem.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/394860/original/file-20210413-21-1e4veem.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/394860/original/file-20210413-21-1e4veem.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/394860/original/file-20210413-21-1e4veem.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/394860/original/file-20210413-21-1e4veem.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/394860/original/file-20210413-21-1e4veem.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">Routine imaging of a juvenile green sea turtle patient afflicted with virus-triggered fibropapillomatosis at the Florida Whitney Sea Turtle Hospital.</span>
<span class="attribution"><span class="source">Devon Rollinson-Ramia</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>However, to truly protect endangered species, it’s not just the animals that need to be monitored, but the pathogens that threaten their survival. Environmental DNA is able to monitor the parasites, fungi and <a href="https://doi.org/10.3390/v11060526">viruses that can cause disease in wildlife</a>.</p>
<h2>Tracking COVID-19</h2>
<p>While scientists originally <a href="https://doi.org/10.1128/AEM.01561-10">applied eDNA to human pathogen detection</a> over a decade ago, it wasn’t until the beginning of the current COVID-19 human pandemic that the repurposing of eDNA took off on a large scale, allowing the technology to make staggering advancements in very short order.</p>
<p>Coronavirus genomes consist not of DNA, but rather its cousin molecule, RNA. So researchers have rapidly optimized a variation of eDNA – eRNA – to detect coronavirus RNA in air and human wastewater. </p>
<p>For example, at the University of Florida Health Shands Hospital, researchers collected air samples from the hospital room of two COVID-19 patients. Using eRNA, they <a href="https://doi.org/10.1016/j.ijid.2020.09.025">successfully isolated and sequenced the virus</a>. Confirming air as a key route of transmission directly influenced public health guidelines.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/395305/original/file-20210415-17-zjc5tl.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="A gloved hand holds a sealed plastic bottle of murky-looking water." src="https://images.theconversation.com/files/395305/original/file-20210415-17-zjc5tl.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/395305/original/file-20210415-17-zjc5tl.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/395305/original/file-20210415-17-zjc5tl.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/395305/original/file-20210415-17-zjc5tl.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/395305/original/file-20210415-17-zjc5tl.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/395305/original/file-20210415-17-zjc5tl.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/395305/original/file-20210415-17-zjc5tl.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">Collecting sewage samples to test for SARS-CoV-2 at Utah State University in September 2020.</span>
<span class="attribution"><span class="source">AP Photo/Rick Bowmer</span></span>
</figcaption>
</figure>
<p>When scientists apply eRNA to <a href="https://doi.org/10.1016/j.scitotenv.2020.138764">archived wastewater samples</a>, the <a href="https://doi.org/10.1101/2020.07.10.20150573">true dates of SARS-CoV-2 appearance can be detected</a>. <a href="https://doi.org/10.1016/j.watres.2020.115942">SARS-CoV-2 concentration in wastewater in Valencia, Spain</a>, peaked on March 9, 2020, but the number of clinical cases didn’t peak until the start of April 2020 because of the lag time between infection and severe clinical symptoms. </p>
<p>This sort of predictive monitoring has profound implications for health care systems, allowing time to prepare – not just for COVID-19, but for any future disease outbreaks that threaten human populations.</p>
<p>[<em>Understand new developments in science, health and technology, each week.</em> <a href="https://theconversation.com/us/newsletters/science-editors-picks-71/?utm_source=TCUS&utm_medium=inline-link&utm_campaign=newsletter-text&utm_content=science-understand">Subscribe to The Conversation’s science newsletter</a>.]</p>
<h2>Intersection of diseases</h2>
<p>It’s vital that human and animal diseases are studied together. <a href="https://www.rte.ie/brainstorm/2020/0702/1150996-pandemics-coronavirus-animals-birds-humans/">Sixty percent of emerging human pathogens come from animals</a> – with many of these (42%) originating in wildlife populations, including Ebola, Zika, West Nile and Marburg viruses. Alternatively, <a href="https://science.thewire.in/environment/reverse-zoonosis-when-humans-pass-diseases-on-to-animals/">people can also transmit pathogens to animals</a>.</p>
<p>SARS-CoV-2 has already infected <a href="https://apnews.com/article/animals-san-diego-health-coronavirus-pandemic-gorillas-ef6607498782226f58608d7ebfc60d1b">apes at a zoo in San Diego</a>, <a href="https://www.nationalgeographic.com/animals/article/tiger-coronavirus-covid19-positive-test-bronx-zoo">large cats at a zoo in New York</a> and <a href="https://www.theguardian.com/environment/2021/feb/18/mink-farms-a-continuing-covid-risk-to-humans-and-wildlife-warn-eu-experts">minks at farms in Europe</a> - the latter of which <a href="https://www.who.int/csr/don/03-december-2020-mink-associated-sars-cov2-denmark/en/">gave rise to new variants that could prove a new threat to people</a>.</p>
<p>Medics, veterinarians and scientists call this convergence of human, animal and environmental well-being <a href="https://www.cdc.gov/onehealth/index.html">OneHealth</a> or EcoHealth. Studying and treating human and wildlife disease together <a href="https://www.zoobiquity.com/">recognizes their commonalities</a> and often yields breakthroughs. </p>
<p>With eDNA, all pathogens can be monitored in an environment regardless of where they come from. An integrated eDNA monitoring program could cost-effectively provide advanced warning of human, livestock and wildlife diseases.</p><img src="https://counter.theconversation.com/content/158286/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Jessica Alice Farrell receives funding from the National Save The Sea Turtle Foundation, The Sea Turtle Conservancy, Florida Sea Turtle Grants Program, the Save Our Seas Foundation and the Gumbo Limbo Nature Center Inc d/b/a Friends of Gumbo Limbo (a 501c3 non-profit organization). She is affiliated with the University of Florida Whitney Laboratory for Marine Bioscience & Sea Turtle Hospital. </span></em></p><p class="fine-print"><em><span>David Duffy receives funding from the National Save The Sea Turtle Foundation, The Sea Turtle Conservancy, Florida Sea Turtle Grants Program, the Save Our Seas Foundation, the Welsh Government Sêr Cymru II and the European Union’s Horizon 2020 program. He is affiliated with the University of Florida and Wildlife Rehabilitation Ireland. </span></em></p><p class="fine-print"><em><span>Liam Whitmore is funded by a Irish Research Council Government of Ireland Postgraduate Scholarship, under project number GOIPG/2020/1056, and he is an editor at The Turtle Room (tTR) World Turtle News Blog (<a href="https://theturtleroom.org">https://theturtleroom.org</a>).</span></em></p>Technology that can identify stray bits of genetic material in the environment can help scientists monitor human and animal health.Jessica Alice Farrell, PhD Candidate in Biology, University of FloridaDavid Duffy, Assistant Professor of Wildlife Disease Genomics, University of FloridaLiam Whitmore, PhD Candidate, Department of Biological Sciences, University of LimerickLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1524772021-02-16T21:40:04Z2021-02-16T21:40:04ZHealthy rivers: Communities use DNA tool to keep tabs on freshwater quality<figure><img src="https://images.theconversation.com/files/376738/original/file-20201228-23-gp4wg1.jpg?ixlib=rb-1.1.0&rect=172%2C165%2C4428%2C3283&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Community members from Blueberry River First Nations collect STREAM samples in Fort St. John, B.C.</span> <span class="attribution"><span class="source">(Raegan Mallinson/Living Lakes Canada)</span>, <span class="license">Author provided</span></span></figcaption></figure><p>Photos of Canada often show the Great Lakes, expanses of wetlands and scenic rivers. The country is described as a <a href="https://www.canada.ca/en/environment-climate-change/services/water-overview/publications/water-in-canada.html">water-rich</a> nation, and it is, with seven per cent of the world’s renewable freshwater supply. However, freshwater sources are far from endless.</p>
<p>Many of Canada’s 25 watersheds are under threat from pollution, habitat degradation, water overuse and invasive species. For example, more than <a href="https://wwf.ca/wp-content/uploads/2020/10/WWF-Watershed-Report-2020-FINAL-WEB.pdf">half of Canada’s population</a> lives within the Great Lakes watershed, Ottawa basin and St. Lawrence basin, which face multiple threats that degrade water quality and undermine the ability of freshwater ecosystems to keep functioning. </p>
<figure class="align-right ">
<img alt="A creek courses through a forested area" src="https://images.theconversation.com/files/384030/original/file-20210212-21-15cfx3m.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/384030/original/file-20210212-21-15cfx3m.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/384030/original/file-20210212-21-15cfx3m.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/384030/original/file-20210212-21-15cfx3m.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/384030/original/file-20210212-21-15cfx3m.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/384030/original/file-20210212-21-15cfx3m.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/384030/original/file-20210212-21-15cfx3m.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">Curtis Creek, one of the tributaries within the Columbia Basin, B.C.</span>
<span class="attribution"><span class="source">(Salmo River Streamkeepers)</span></span>
</figcaption>
</figure>
<p>The story of the Great Lakes watershed is not unique in Canada. Ten additional watersheds, from the Winnipeg to the Fraser-Lower Mainland watershed, face high or very high levels of threats. The water quality in more than half of Canada’s 167 sub-watersheds (smaller freshwater systems that drain into a specific watershed) score poor or fair.</p>
<p>In Canada, these watersheds are vast and often inaccessible, making it difficult to monitor the health of these ecosystems. But with the help of a new tool, scientists and community members are collecting data to better understand the state of Canada’s rivers. </p>
<h2>Data deficiencies</h2>
<p>Rivers are full of all kinds of small creatures that are highly sensitive to environmental threats. The worms, fly larvae and snails — collectively called macroinvertebrates — that live in the sediment at the bottom of a river (the “benthos”) can serve as biological monitors for water quality. The presence of biological monitor species that are less tolerant of poor water quality is suggestive of a healthy river. </p>
<p>But it can be challenging to sample and identify these macroinvertebrates. Even when there is some data on them, <a href="https://doi.org/10.1016/j.ecolind.2019.02.008">the quality</a> of the data may not be good enough to <a href="https://doi.org/10.1038/s41598-017-13157-x">determine the health of the watershed</a>. To date, 64 per cent of sub-watersheds in Canada lack data on these species. </p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/376730/original/file-20201228-21-138f78c.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/376730/original/file-20201228-21-138f78c.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=179&fit=crop&dpr=1 600w, https://images.theconversation.com/files/376730/original/file-20201228-21-138f78c.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=179&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/376730/original/file-20201228-21-138f78c.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=179&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/376730/original/file-20201228-21-138f78c.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=225&fit=crop&dpr=1 754w, https://images.theconversation.com/files/376730/original/file-20201228-21-138f78c.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=225&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/376730/original/file-20201228-21-138f78c.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=225&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Left to right: Flatheaded mayfly larvae, green sedge caddisfly larvae and golden stonefly larvae. These species are macroinvertebrates known to be sensitive to changes in environmental conditions.</span>
<span class="attribution"><span class="source">(Chloe Robinson)</span></span>
</figcaption>
</figure>
<p>Gathering data on these species is challenging: Many watersheds are remote and difficult to access, and the cost of flying to them limits the amount of data that can be collected. We partnered with local community groups to collect river samples so that we could understand river health by identifying macroinvertebrates from their DNA. </p>
<h2>DNA profiling</h2>
<p><a href="https://pubmed.ncbi.nlm.nih.gov/22590728/">DNA technologies</a> have revolutionized the amount of data we can generate from a single river sample. </p>
<p>For example, one technique called “<a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0138432">environmental DNA metabarcoding</a>,” or eDNA for short, involves taking samples of soil or water and searching for fragments of DNA specific to certain species. This method eliminates the time-consuming process of sorting individual samples and enables us to identify the different species present in a river system. </p>
<figure class="align-center ">
<img alt="A flow chart showing two different processes for identifying species in environmental samples" src="https://images.theconversation.com/files/384335/original/file-20210215-17-18rorx2.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/384335/original/file-20210215-17-18rorx2.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=338&fit=crop&dpr=1 600w, https://images.theconversation.com/files/384335/original/file-20210215-17-18rorx2.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=338&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/384335/original/file-20210215-17-18rorx2.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=338&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/384335/original/file-20210215-17-18rorx2.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=424&fit=crop&dpr=1 754w, https://images.theconversation.com/files/384335/original/file-20210215-17-18rorx2.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=424&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/384335/original/file-20210215-17-18rorx2.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=424&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">The process of manually sorting and identifying macroinvertebrates (top) versus eDNA metabarcoding approach of species identification (bottom).</span>
<span class="attribution"><span class="source">(Chloe Robinson)</span></span>
</figcaption>
</figure>
<p>Once you’re at a river, collecting samples is fast and easy — all it takes is <a href="https://www.canada.ca/en/environment-climate-change/services/canadian-aquatic-biomonitoring-network.html">three minutes of kicking river sediment into a net to capture the macroinvertebrates that live in the benthos</a>. We taught this technique to people involved in a community-based monitoring network called CABIN to create a new biomonitoring project: <a href="https://stream-dna.com/">STREAM</a> (Sequencing the Rivers for Environmental Assessment and Monitoring). </p>
<p>Since 2019, STREAM scientists have trained more than 100 community members who have gone on to collect almost 1,000 samples across 10 watersheds. We’re close to our goal of 1,500 samples in 15 watersheds in Canada. Yet we’re already beginning to see how the STREAM project is filling in the blanks for freshwater health across Canada.</p>
<figure>
<iframe width="440" height="260" src="https://www.youtube.com/embed/ooOtSFwzyPg?wmode=transparent&start=4" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">STREAM video produced by Living Lakes Canada.</span></figcaption>
</figure>
<h2>STREAM case studies</h2>
<p>Not only has the STREAM project provided data on the health of the Great Lakes and Ottawa River watersheds — and the threats to them — it has <a href="https://news.uoguelph.ca/2020/06/u-of-g-researchers-partner-with-indigenous-communities-to-monitor-river-health/">enabled communities to ask questions about their aquatic ecosystems</a>.</p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/376722/original/file-20201228-17-q6yxc1.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="A woman kicking muddy water into a net" src="https://images.theconversation.com/files/376722/original/file-20201228-17-q6yxc1.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/376722/original/file-20201228-17-q6yxc1.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=338&fit=crop&dpr=1 600w, https://images.theconversation.com/files/376722/original/file-20201228-17-q6yxc1.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=338&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/376722/original/file-20201228-17-q6yxc1.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=338&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/376722/original/file-20201228-17-q6yxc1.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=424&fit=crop&dpr=1 754w, https://images.theconversation.com/files/376722/original/file-20201228-17-q6yxc1.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=424&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/376722/original/file-20201228-17-q6yxc1.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">Darcie Quamme from Integrated Ecological Research collecting a wetland benthic kick-net sample.</span>
<span class="attribution"><span class="source">(Darcie Quamme)</span></span>
</figcaption>
</figure>
<p>In collaboration with <a href="https://slocanriverstreamkeepers.wordpress.com/">Slocan River Streamkeepers</a>, an environmental stewardship group based in Winlaw, B.C., and <a href="https://integratedecologicalresearch.com/">Integrated Ecological Research</a>, an environmental consulting service based in Nelson, B.C., STREAM has been able to <a href="https://integratedecologicalresearch.files.wordpress.com/2020/07/six-mile-slough-pre-restoration-monitoring-final-report-july-10-2020.pdf">assess changes in macroinvertebrate communities after the completion of a wetland restoration project</a>. Although this project is ongoing, early results show the wetlands already have a high variety of macroinvertebrates, with 178 species identified. A quarter of these species are indicators of good wetland health, meaning water quality in the area is likely improving.</p>
<p>With Living Lakes Canada and the <a href="https://www.ghostwatershed.ca/GWAS/index.html">Ghost Watershed Alliance Society</a>, parts of the Bow River, in Alberta, are now being screened for <a href="https://stream-dna.com/2020/06/09/dna-metabarcoding-whirling-disease/">sludge worms</a>, which can carry the parasite that causes <a href="https://www.alberta.ca/whirling-disease.aspx">whirling disease</a>, an infection that can wipe out up to 90 per cent of young salmon, trout and whitefish. Loss of these fish has <a href="https://www.cabi.org/isc/datasheet/59563">ecological, economic</a> and social consequences in Alberta, where they are <a href="https://open.alberta.ca/dataset/9f9268b6-377d-4f91-a99e-ee944f143752/resource/b2394f1b-e347-40f0-bec7-3cae7a8ff8a5/download/whirlingdiseaseprogramreport-2017.pdf">important recreational and sustenance fisheries</a>. DNA results from 2019 indicated that the host sludge worms had not spread beyond the known whirling disease zone.</p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/378153/original/file-20210111-13-1c23phv.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/378153/original/file-20210111-13-1c23phv.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/378153/original/file-20210111-13-1c23phv.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/378153/original/file-20210111-13-1c23phv.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/378153/original/file-20210111-13-1c23phv.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/378153/original/file-20210111-13-1c23phv.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/378153/original/file-20210111-13-1c23phv.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">Members of Ghost Watershed Alliance Society at CABIN Training and Certification event with WWF-Canada Freshwater Specialist, Catherine Paquette (left) and Living Lakes Canada STREAM program manager, Raegan Mallinson (second from right).</span>
<span class="attribution"><span class="source">(Ghost Watershed Alliance Society)</span></span>
</figcaption>
</figure>
<p>STREAM provides a unique opportunity to bring benefits to both people and the environment. Through using DNA-based technology, it is possible to determine changes in water quality at local, sub-watershed and watershed levels. For continued monitoring of the Bow River for example, the rapid result turnaround provided by STREAM means any indications of sludge worm dispersion can be dealt with by <a href="https://albertawilderness.ca/wp-content/uploads/2017/03/20170300_ar_wla_update_whirling_disease.pdf">closing angling access to the area to prevent potential spread</a>. </p>
<p>STREAM empowers local communities to lead freshwater research and equips people to address their own environmental questions — and it can easily be applied to other countries as a means to monitor freshwater systems.</p><img src="https://counter.theconversation.com/content/152477/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Chloe Robinson receives funding from the Government of Canada through Genome Canada and Ontario Genomics. </span></em></p><p class="fine-print"><em><span>Mehrdad Hajibabaei receives funding from the Government of Canada through Genome Canada and Ontario Genomics. He is the founder and CSO of eDNAtec Inc. </span></em></p>In Canada, watersheds are vast and often inaccessible, making it difficult to monitor the health of these ecosystems. A new tool helps communities collect data to assess the state of Canada’s rivers.Chloe V. Robinson, Postdoctoral Fellow, Department of Integrative Biology, University of GuelphMehrdad Hajibabaei, Associate professor, Department of integrative biology, University of GuelphLicensed 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>
<hr>
<p>
<em>
<strong>
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>
</strong>
</em>
</p>
<hr>
<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>
<hr>
<p>
<em>
<strong>
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>
</strong>
</em>
</p>
<hr>
<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>
<figure class="align-center ">
<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">
<figcaption>
<span class="caption">Sampling soil for eDNA analysis.</span>
</figcaption>
</figure>
<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>
<hr>
<p>
<em>
<strong>
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>
</strong>
</em>
</p>
<hr>
<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/973072018-06-06T10:37:54Z2018-06-06T10:37:54ZWhy won’t scientific evidence change the minds of Loch Ness monster true believers?<figure><img src="https://images.theconversation.com/files/221867/original/file-20180605-119860-172rye3.jpg?ixlib=rb-1.1.0&rect=248%2C237%2C1907%2C1303&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">If you're convinced Nessie's real, would science unconvince you?</span> <span class="attribution"><a class="source" href="http://www.apimages.com/metadata/Index/AP-I-XSC-TRV-TRAVEL-TRIP-SCOTLAND/1c47fcab2710db11af9f0014c2589dfb/17/0">AP Photo/Norm Goldstein</a></span></figcaption></figure><p>You may have noticed a curious recent announcement: An international research team plans to use state-of-the-art DNA testing to establish once and for all <a href="https://www.smithsonianmag.com/smart-news/search-monster-dna-will-help-survey-life-loch-ness-180969151/">whether the Loch Ness monster exists</a>.</p>
<p>Regardless of the results, it’s unlikely the test will change the mind of anyone who firmly believes in Nessie’s existence. <a href="https://scholar.google.com/citations?user=WnCX7AcAAAAJ&hl=en&oi=ao">As a philosopher</a> working on the notion of evidence and knowledge, I still consider the scientists’ efforts to be valuable. Moreover, this episode can illustrate something important about how people think more generally about evidence and science.</p>
<h2>Discounting discomfiting evidence</h2>
<p>Genomicist <a href="https://scholar.google.com/citations?user=XGE4mdAAAAAJ&hl=en&oi=ao">Neil Gemmell</a>, who will lead the international research team in Scotland, says he looks forward to “<a href="https://www.otago.ac.nz/news/news/otago686785.html">(demonstrating) the scientific process</a>.” The team plans to collect and identify free-floating DNA from creatures living in the waters of Loch Ness. But whatever the eDNA sampling finds, Gemmell <a href="http://www.latimes.com/science/la-sci-loch-ness-monster-dna-20180523-story.html">is well aware</a> the testing results will most likely not convince everyone.</p>
<p>A long-standing theory in social psychology helps explain why. According to <a href="https://www.simplypsychology.org/cognitive-dissonance.html">cognitive dissonance theory</a>, <a href="https://www.sup.org/books/title/?id=3850">first developed by Leon Festinger</a> in the 1950s, people seek to avoid the internal discomfort that arises when their beliefs, attitudes or behavior come into conflict with each other or with new information. In other words, it doesn’t feel good to do something you don’t value or that contradicts your deeply held convictions. To deal with this kind of discomfort, people sometimes attempt to rationalize their beliefs and behavior.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/221870/original/file-20180605-119888-ah4zjv.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/221870/original/file-20180605-119888-ah4zjv.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/221870/original/file-20180605-119888-ah4zjv.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=240&fit=crop&dpr=1 600w, https://images.theconversation.com/files/221870/original/file-20180605-119888-ah4zjv.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=240&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/221870/original/file-20180605-119888-ah4zjv.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=240&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/221870/original/file-20180605-119888-ah4zjv.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=302&fit=crop&dpr=1 754w, https://images.theconversation.com/files/221870/original/file-20180605-119888-ah4zjv.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=302&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/221870/original/file-20180605-119888-ah4zjv.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=302&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">It’s hard to stop waiting for an expected UFO.</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/july-2017-hastings-mesa-ufolike-sunset-1090442363">Joseph Sohm/Shutterstock.com</a></span>
</figcaption>
</figure>
<p>In a classic study, Festinger and colleagues <a href="https://dx.doi.org/10.1037/10030-000">observed a small doomsday cult</a> in Chicago who were waiting for a UFO to save them from impending massive destruction of Earth. When the prophecy didn’t come true, instead of rejecting their original belief, members of the sect came to believe that the God of Earth changed plans and no longer wanted to destroy the planet.</p>
<p>Cult members so closely identified with the idea that a UFO was coming to rescue them that they couldn’t just let the idea go when it was proven wrong. Rather than give up on the original belief, they preferred to lessen the cognitive dissonance they were experiencing internally.</p>
<p><a href="http://www.lochnesssightings.com/index.asp">Loch Ness monster true believers</a> may be just like the doomsday believers. Giving up their favorite theory could be too challenging. And yet, they’ll be sensitive to any evidence they hear about that contradicts their conviction, which creates a feeling of cognitive discomfort. To overcome the dissonance, it’s human nature to try to explain away the scientific evidence. So rather than accepting that researchers’ inability to find Nessie DNA in Loch Ness means the monster doesn’t exist, believers may rationalize that the scientists didn’t sample from the right area, or didn’t know how to identify this unknown DNA, for instance.</p>
<p>Cognitive dissonance may also provide an explanation for other science-related conspiracy theories, such as flat Earth beliefs, climate change denial and so on. It may help account for reckless descriptions of reliable media sources as “fake news.” If one’s deeply held convictions don’t fit well with what media say, it’s easier to deal with any inner discomfort by discrediting the source of the new information rather than revising one’s own convictions.</p>
<h2>Philosophy of knowledge</h2>
<p>If psychology may explain why Loch Ness Monster fans believe what they do, philosophy can explain what’s wrong with such beliefs.</p>
<p>The error here comes from an implicit assumption that to prove a claim, one has to rule out all of the conceivable alternatives – instead of all the plausible alternatives. Of course scientists haven’t and cannot deductively rule out all of the conceivable possibilities here. If to prove something you have to show that there is no conceivable alternative to your theory, then you can’t really prove much. Maybe the Loch Ness monster is an alien whose biology doesn’t include DNA.</p>
<p>So the problem is not that believers in the existence of the Loch Ness monster or climate change deniers are sloppy thinkers. Rather, they are too demanding thinkers, at least with respect to some selected claims. They adopt too-high standards for what counts as evidence, and for what is needed to prove a claim. </p>
<p>Philosophers have long known that too-high standards for knowledge and rational belief lead to skepticism. Famously, 17th century French philosopher René Descartes suggested that only “clear and distinct perceptions” should function as the required markers for knowledge. So if only some special inner feeling can guarantee knowledge and we can be wrong about that feeling – say, due to some brain damage – then what can be known?</p>
<p>This line of thought has been taken to its extreme in contemporary philosophy <a href="https://global.oup.com/academic/product/ignorance-9780198244172?cc=us&lang=en&">by Peter Unger</a>. He asserted that knowledge requires certainty; since we are not really certain of much, if anything at all, we don’t know much, if anything at all.</p>
<p>One promising way to resist a skeptic is simply not to engage in trying to prove that the thing whose existence is doubted exists. A better approach might be to start with basic knowledge: assume we know some things and can draw further consequences from them.</p>
<p>A knowledge-first approach that attempts to do exactly this has recently gained popularity in epistemology, the philosophical theory of knowledge. British <a href="https://scholar.google.com/citations?user=IH-44VwAAAAJ&hl=en&oi=ao">philosopher Timothy Williamson</a> and others <a href="https://doi.org/10.1111/theo.12111">including me</a> have proposed that evidence, rationality, belief, assertion, cognitive aspects of action and so on can be explained <a href="https://global.oup.com/academic/product/knowledge-and-its-limits-9780199256563?q=Knowledge%20and%20its%20Limits&lang=en&cc=us">in terms of knowledge</a>.</p>
<p>This idea is in contrast to an approach popular in the 20th century, that knowledge is true justified belief. But counterexamples abound that show one can have true justified belief without knowledge.</p>
<p>Say, you check your Swiss watch and it reads 11:40. You believe on this basis that it is 11:40. However, what you haven’t noticed is that your typically super reliable watch has stopped exactly 12 hours ago. And by incredible chance it happens that, now, when you check your watch, it is in fact 11:40. In this case you have a true and justified or rational belief but still, it doesn’t seem that you know that it is 11:40 – it is just by pure luck that your belief that it’s 11:40 happens to be true.</p>
<p>Our newer knowledge-first approach avoids defining knowledge altogether and rather posits knowledge as fundamental. It’s its own fundamental entity – which allows it to undercut the skeptical argument. One may not need to feel certain or have a sensation of clarity and distinctness in order to know things. The skeptical argument doesn’t get off the ground in the first place.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/221868/original/file-20180605-119867-1og6e43.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/221868/original/file-20180605-119867-1og6e43.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/221868/original/file-20180605-119867-1og6e43.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=531&fit=crop&dpr=1 600w, https://images.theconversation.com/files/221868/original/file-20180605-119867-1og6e43.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=531&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/221868/original/file-20180605-119867-1og6e43.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=531&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/221868/original/file-20180605-119867-1og6e43.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=667&fit=crop&dpr=1 754w, https://images.theconversation.com/files/221868/original/file-20180605-119867-1og6e43.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=667&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/221868/original/file-20180605-119867-1og6e43.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=667&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">When it comes to science versus skeptic, evidence doesn’t always matter.</span>
<span class="attribution"><a class="source" href="http://www.apimages.com/metadata/Index/Loch-Ness-Monster/8380914232b04eba885c495dc2f946c4/2/0">AP Photo, File</a></span>
</figcaption>
</figure>
<h2>Knowledge and the skeptic</h2>
<p>The eDNA analysis of Loch Ness may not be enough to change the minds of those who are strongly committed to the existence of the lake’s monster. Psychology may help explain why. And lessons from philosophy suggest this kind of investigation may not even provide good arguments against conspiracy theorists and skeptics.</p>
<p>A different and, arguably, better argument against skepticism questions the skeptic’s own state of knowledge and rationality. Do you really know that we know nothing? If not, then there may be something we know. If yes, then we can know something and, again, you are wrong in claiming that knowledge is not attainable.</p>
<p>A strategy of this kind would challenge the evidential and psychological bases for true believers’ positive conviction in the existence of Nessie. That’s quite different from attempting to respond with scientific evidence to each possible skeptical challenge.</p>
<p>But the rejection of a few true believers doesn’t detract from the value of this kind of scientific research. First and foremost, this research is expected to produce much more precise and fine-grained knowledge of biodiversity in Loch Ness than what we have without it. Science is at its best when it avoids engaging with the skeptic directly and simply provides new knowledge and evidence. Science can be successful without ruling out all of the possibilities and without convincing everyone.</p><img src="https://counter.theconversation.com/content/97307/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Artūrs Logins receives funding from Swiss National Science Foundation (project "New Direction for Epistemic Normativity" n. 171464, <a href="http://p3.snf.ch/project-171464">http://p3.snf.ch/project-171464</a>). </span></em></p>If you’re committed to a belief, it’s hard to let go. Psychology and philosophy provide different ways to think about how skeptics respond to counterevidence.Artūrs Logins, Visiting Postdoctoral Researcher in Philosophy, USC Dornsife College of Letters, Arts and SciencesLicensed 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/857832017-10-16T22:01:25Z2017-10-16T22:01:25ZHow technology will help fight food fraud<figure><img src="https://images.theconversation.com/files/190492/original/file-20171016-30997-41t9t5.jpg?ixlib=rb-1.1.0&rect=165%2C0%2C2464%2C1466&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">A worker handles meat at the Doly-Com abattoir in Romania in 2013 when Europe was facing a scandal over incorrectly declared horsemeat. The problem of food fraud and its health and economic implications affect a broad range of foods around the world, but technology could soon end the problem.</span> <span class="attribution"><a class="source" href="http://www.cpimages.com/fotoweb/cpimages_details.pop.fwx?position=59&archiveType=ImageFolder&sorting=ModifiedTimeAsc&search=horsemeat&fileId=7ED4E565C8CEED2778801C7E3A1D5E69FE75CC55B658603987FEF24F300B62227BF497D18515FAB7978750CE214B0837D1853405FB9357B8BCCED882E87BBD23646AFBDDAAAB053B500C071FA9B0FB31E297922C28FCC5CFEB24C714341D0405F0E5BDA0B82DF2D81CEC86FBB1EFD40B60A801D21EF106A0884083FA795332F61C4105A3ABBEDCF0">(AP Photo/Vadim Ghirda)</a></span></figcaption></figure><p><a href="https://www.washingtonpost.com/news/wonk/wp/2017/09/18/lax-enforcement-at-ports-allows-bogus-organic-foods-to-reach-u-s-government-report-says/">Food fraud is everywhere</a>. In the aftermath of the <a href="https://www.theguardian.com/uk/horsemeat-scandal">horsemeat scandal</a> in Europe, and with cases reported <a href="http://www.producer.com/2017/03/brazilian-meat-fraud-rocks-markets/">around the world</a>, including <a href="http://www.ctvnews.ca/canada/1-in-5-sausages-contain-undeclared-meats-study-1.3532110">in Canada</a>, <a href="http://www.cbc.ca/news/canada/montreal/meat-fraud-quebec-ground-beef-1.4041156">awareness is high</a>. </p>
<p>Dalhousie University recently released a study on food fraud and the results were surprising: A whopping 63 per cent of Canadians are generally concerned about food fraud. Worse still, more than <a href="https://www.dal.ca/news/media/media-releases/2017/02/21/dalhousie_led_study_finds_that_majority_of_canadians_concerned_about_food_fraud.html">40 per cent of Canadians feel they have been victims of food fraud</a> already. These are alarming results that can’t be ignored.</p>
<p>Food fraud can take many forms. It can include adulteration — substituting one ingredient with a much cheaper one — or misrepresentation, which may include selling a product as organic when it is not. </p>
<h2>Canadian food fraud cases abound</h2>
<p>Food categories that are more vulnerable to food fraud are fish, seafood, liquids, spices, fruits, vegetables and meat products. Canada has seen its share of cases in recent months, one of the most notable ones is <a href="http://www.huffingtonpost.ca/2016/06/07/mislabelled-foods-canada-mucci-farms_n_10339214.html">Mucci Farms</a> in southwestern Ontario, near the tip of Lake Erie. The company was fined $1.5 million for selling Mexican tomatoes as a product of Canada. Mucci Farms denies that the labelling was intentional and faults their computer system. </p>
<p>Other cases have emerged through whistleblowers trying to draw attention to food fraud. <a href="https://beta.theglobeandmail.com/news/national/ontario-supplier-charged-with-mislabelling-organic-chicken/article32502431/">Cericola Farms, one of the largest poultry processors</a> in the country, was charged with fraud last year over allegations of organic mislabelling. </p>
<p><a href="https://beta.theglobeandmail.com/life/food-and-wine/food-trends/fighting-food-fraud-canada-is-playing-catch-up-in-a-war-against-theunknown/article31098377/">The number of cases is adding up</a>. The Canadian Food Inspection Agency has received over 40 complaints in 2016 and industry observers expect that number to increase in 2017.</p>
<h2>Serious health and economic risks</h2>
<p>Some may believe that food fraud is a victimless crime. This is not so. What is at stake is the entire food economy. </p>
<p>For any food business to grow and offer high-quality food products, it requires consumer trust. If trust is lost then everything the industry is trying to accomplish will become more challenging. Why would consumers pay more for a product they may deem fraudulent?</p>
<p>The majority of food companies are ethically sound, but you only need a few cases to damage the reputation of an entire industry. </p>
<p>Most importantly, the Dalhousie study suggests that consumers with allergies or intolerances to particular foods are likely to feel more vulnerable than other consumers when thinking of food fraud. Consequently, food fraud is as much a socioeconomic issue as it is one of public health.</p>
<h2>Technology a partial solution</h2>
<p><a href="https://techcrunch.com/2017/08/22/ibm-costco-walmart-and-others-team-up-to-improve-food-safety-with-blockchains/">Grocers</a> have made recent <a href="https://qz.com/1031861/blockchain-could-fix-a-key-problem-in-chinas-food-industry-the-fear-of-food-made-in-china/">investments in blockchain</a> technologies that provide a tool to detect products that may pose as counterfeit. </p>
<p>But these measures can only do so much. Companies can’t really report fraudulent rivals for fear of retaliation — food companies denouncing fraudulent cases are themselves accused of food fraud. They can’t win. </p>
<p>Regulators would have to sample-test everything, which would be operationally impractical and, frankly, impossible. Public regulators have been aware of the issue for quite some time but have struggled to find any solutions to address the issue. </p>
<p>A few provinces, including Ontario, have created provincewide <a href="https://www.canada.ca/en/health-canada/services/food-nutrition/public-involvement-partnerships/food-expert-advisory-committee/membership-list.html">committees on food integrity</a> to work with <a href="http://www.foodintegrity.ca/">industry</a> in finding fraudulent cases. However, their work will take a while before we see anything new.</p>
<h2>Exercise caution</h2>
<p>Meanwhile, consumers should shop for food and visit restaurants with extreme prejudice. Consumers should look for consistencies in pricing and quality. If a food product is much cheaper at one outlet, perhaps the deal is too good to be true. Consumers should also ask pointed questions about procurement strategies to retailers and restaurant operators to make the supply chain more transparent to them.</p>
<p>But humans are humans and food fraud has been going on for more than 2,000 years. The first known reported cases go back to the Roman Empire when suspicions around adulterated wines and oils were prevalent. Today, however, we have technologies allowing us to detect fraudulent behaviour. </p>
<p>Companies and research centres from around the world are currently developing <a href="https://theconversation.com/dna-barcodes-sci-fi-tech-to-safeguard-environment-79391">portable technologies that allow consumers themselves to validate the content of food labels</a>. Imagine testing your own products at home to see if that apple is really from Ontario or that olive oil is really from Italy. The technology exists, but costs are prohibitive. Some of these devices can cost more than $200,000.</p>
<p>One day though, consumers empowered by these technologies will become the most powerful regulators the food industry can ever imagine. Knowing that consumers can ultimately test the integrity of any product, the entire food supply chain will need to be more disciplined and the rotten apples will need to go, no pun intended.</p>
<p>Over time, humans themselves may not get rid of food fraud but technology will.</p><img src="https://counter.theconversation.com/content/85783/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Sylvain Charlebois 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>Food fraud is a common problem that technologies such as blockchain and DNA fingerprinting can help to solve.Sylvain Charlebois, Professor in Food Distribution and Policy, Dalhousie UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/793912017-06-25T23:58:39Z2017-06-25T23:58:39ZDNA barcodes — sci-fi tech to safeguard environment<figure><img src="https://images.theconversation.com/files/175524/original/file-20170626-31771-1g4vxlz.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Using passive eDNA detection, we won’t have to wait until we see massive algae blooms to know lakes are struggling. </span> </figcaption></figure><p><em>Editor’s note: Canada Day 2017 marks the sesquicentennial of Confederation. While the anniversary is a chance to reflect on the past, The Conversation Canada asked some of our academic authors to imagine what our world will be like in 2167 - or “Canada +150”. Scientist Robert Hanner looks at how an emerging technology of today will be part of our everyday life in the next century.</em></p>
<p>A Canadian technology that can identify a substance by scanning it — as a character in Star Trek might — could become a crucial tool to capture DNA data in the environment and protect it.</p>
<p>DNA barcoding, developed at the University of Guelph by <a href="https://www.uoguelph.ca/ib/hebert">Professor Paul Hebert</a>, uses genetic variations to identify different species. It’s similar to how a supermarket checkout scanner reads variations in a UPC barcode’s lines to identify a product you buy. </p>
<p>A team of researchers with the <a href="http://www.IBOL.org">International Barcode of Life network</a> (www.iBOL.org) has been busy building a library of DNA barcodes from expert-identified reference specimens for more than a decade. They have created DNA barcodes for more than 500,000 species so far.</p>
<p>DNA barcoding can already identify foreign biological material and contaminants in food, or insects, pests and carriers of disease. This may make the technology already seem futuristic, but it is just a taste of what is to come. </p>
<h2>Early warning system</h2>
<p>Today, we use this technology to identify individual specimens. By 2167, we will not only be able to identify single specimens of almost every animal, plant and microorganism on the planet, but will routinely identify individual species among millions of organisms in large and varied samples. We will do so virtually instantaneously, anywhere, rather than sending samples to a lab. </p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/175316/original/file-20170623-27915-1nyayrn.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/175316/original/file-20170623-27915-1nyayrn.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=733&fit=crop&dpr=1 600w, https://images.theconversation.com/files/175316/original/file-20170623-27915-1nyayrn.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=733&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/175316/original/file-20170623-27915-1nyayrn.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=733&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/175316/original/file-20170623-27915-1nyayrn.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=921&fit=crop&dpr=1 754w, https://images.theconversation.com/files/175316/original/file-20170623-27915-1nyayrn.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=921&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/175316/original/file-20170623-27915-1nyayrn.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=921&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">The technology uses genetic variations to identify different species.</span>
<span class="attribution"><span class="source">(Robert Hanner)</span></span>
</figcaption>
</figure>
<p>This will give us a better handle on how species are distributed in time and space, which will help us protect biodiversity (e.g. threatened species) or halt the spread of alien invasive species. It will also provide clues about how they interact. For example, we will be able to detect an aquatic organism simply by reading the DNA it sheds into the ecosystem. </p>
<p>This environmental DNA, or “eDNA,” will allow us to detect species without having to physically capture and identify them one-by-one, as we do now. Canadians will then more easily be able to protect natural resources, such as our lakes and rivers. </p>
<p>Passive eDNA detection will enable large-scale biomonitoring systems that identify entire biological communities in the water, down to different algae and bacteria. Changes to that diversity will help alert us to pollution or climate problems (or gains). We won’t have to wait until we see massive algae blooms to know our lakes are struggling. </p>
<p>Tracking key indicators such as invasive alien, at-risk, or toxin-producing species and disease vectors will help us respond sooner. The better understanding of a healthy ecosystem that we gain will also help us to assess remedies and promote biodiversity that functional, healthy ecosystems need.</p>
<h2>Weather-style ‘biodiversity forecasts’</h2>
<p>The benefits DNA barcoding affords natural habitats can equally aid Canadian agriculture and forestry in pest control. </p>
<p>Currently, land managers place sticky traps in greenhouses, farm fields and forests to catch insects in an effort to detect pests. They send captured critters to a lab to be visually identified, and then tailor pesticide applications accordingly. But this approach takes time and expertise, which doesn’t work well at a large scale, and can be difficult to use.</p>
<p>In another 150 years, advancements in barcoding will enable us to monitor the air, soil and water to determine what organisms are where, and how a community is changing. </p>
<p>Early and precise detection of changes will not only help with pest control, but also ensure that we sustain pollinators such as bees, natural predators of pests and other species required for healthy farms and forests. All this information will be available on-demand through internet-connected devices.</p>
<p>By the time Canada celebrates 300 years of Confederation, DNA barcoding will be an everyday part of our lives and we will receive biodiversity forecasts much in the way we do weather forecasts today. Armed with that information, we will not only be able to better respond to our country’s environment, but we will be better able to make it an ideal place to live.</p><img src="https://counter.theconversation.com/content/79391/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Robert Hanner works for the University of Guelph's Biodiversity Institute of Ontario. He owns shares in TRU-ID, Ltd. He receives research funding from the Canadian Food Inspection Agency, the Natural Sciences and Engineering Research Council, and others sources, including various industry partners. </span></em></p>By 2167, DNA barcoding scans will lead to weather-style “biodiversity forecasts,” enabling us to more easily protect and care for the environment.Robert Hanner, Associate professor, Biodiversity Institute of Ontario, Centre for Biodiversity Genomics, Department of Integrative Biology, University of GuelphLicensed 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.tag:theconversation.com,2011:article/616162016-08-09T09:24:42Z2016-08-09T09:24:42ZHow DNA evidence could be a game-changer in monitoring freshwater fish<figure><img src="https://images.theconversation.com/files/128083/original/image-20160624-28362-u129g1.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">Krzysztof Odziomek/shutterstock</span></span></figcaption></figure><p>Water may well be everywhere, but freshwater lake ecosystems are among some of the most vulnerable on Earth. In recent decades, freshwater species have suffered double the rate of decline of land species. And <a href="http://eur-lex.europa.eu/legal-content/EN/TXT/PDF/?uri=CELEX:52012DC0670&from=EN">nearly 50%</a> of fresh water lakes, rivers and streams across Europe failed to meet the <a href="http://ec.europa.eu/environment/water/water-framework/index_en.html">EU Water Framework Directive</a>, which aimed to achieve “good ecological status” of freshwater in Europe by 2015.</p>
<p>Part of the problem is that current tools used to monitor the so called “health” of a lake can be costly, time consuming, inefficient, and in some cases, lethal to the organisms they are sampling. Which is why our <a href="http://onlinelibrary.wiley.com/doi/10.1111/mec.13660/abstract">new research</a> is pioneering a new way of monitoring water species – using techniques more familiar to fans of crime TV shows.</p>
<p><a href="http://www.sciencedirect.com/science/article/pii/S0006320714004443">Environmental DNA</a>, also known as eDNA works in the same way as regular DNA testing, but rather than using saliva or hair, samples of water, soil or even air are taken and tested. The method works because every creature in freshwater leaves behind traces of its eDNA as it swims around, shedding minute flakes of skin, eggs, sperm or in the case of plants, pollen or seeds. </p>
<p>The majority of <a href="http://onlinelibrary.wiley.com/doi/10.1111/bij.12516/full">eDNA studies</a> so far have focused on detecting single species using highly specific DNA-based procedures which focus on detecting one species at a time. Our study instead used a form of DNA testing called “metabarcoding”. This is where a single region of DNA called a “barcode” is simultaneously sequenced from a whole community of organisms. This enabled us to analyse millions of DNA sequences from water samples, identifying the DNA of a broad range of species and looking at whole communities of organisms – rather than just detecting single species.</p>
<p>Metabarcoding of eDNA is a very new technology, and has only been tested in controlled conditions – such as in aquaria – or on a small scale in natural environments. But this technique has the potential to be a game changer for biodiversity monitoring, as it is completely non-invasive and extremely sensitive. It detects more species than established methods, and gives a surprisingly good indication of how abundant they are within the water environment. </p>
<h2>DNA in action</h2>
<p>We used this method of testing in Lake Windermere, England’s largest lake, to discover what fish species are living in the water and their relative abundance. And the information provided by these humble water samples exceeded all our expectations. </p>
<p>Windermere’s fish population has been monitored since the 1940s, by the <a href="https://www.fba.org.uk/">Freshwater Biological Association</a> and, more recently, the <a href="https://www.ceh.ac.uk/">Centre for Ecology and Hydrology</a>, using a combination of established fish survey methods such as netting, angler’s catches and hydroacoustics. </p>
<p>So to see how eDNA would compare to these established methods, earlier this year we braved all that the Lakeland weather could throw at us – from blizzards to glorious winter sunshine – to collect over 60, two-litre water samples – from the very northern tip to the southern tip of the lake.</p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/132040/original/image-20160726-7028-17rpxsd.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/132040/original/image-20160726-7028-17rpxsd.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/132040/original/image-20160726-7028-17rpxsd.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/132040/original/image-20160726-7028-17rpxsd.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/132040/original/image-20160726-7028-17rpxsd.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/132040/original/image-20160726-7028-17rpxsd.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/132040/original/image-20160726-7028-17rpxsd.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">Research in action.</span>
<span class="attribution"><span class="source">Ian Winfield</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>The eDNA metabarcoding detected 14 of the 16 species ever recorded in Windermere – perch, roach, brown trout, pike, Arctic charr, bream and eel were the most common. Only the two rarest species, river and sea lamprey, were missed, but it is possible they are not present in the lake at the time of sampling. Whereas only four species were detected in the corresponding net survey. </p>
<h2>Healthy lakes</h2>
<p><a href="http://onlinelibrary.wiley.com/doi/10.1111/bij.12516/full">Previous studies</a> suggested that estimating how many fish are in an area of water from eDNA data would be problematic. Encouragingly though, our data indicated that eDNA may be better as measuring the quantity than previously thought. And we also found a clear pattern in the spatial distribution of eDNA in the lake.</p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/132043/original/image-20160726-7064-dgzkgh.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/132043/original/image-20160726-7064-dgzkgh.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/132043/original/image-20160726-7064-dgzkgh.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/132043/original/image-20160726-7064-dgzkgh.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/132043/original/image-20160726-7064-dgzkgh.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/132043/original/image-20160726-7064-dgzkgh.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/132043/original/image-20160726-7064-dgzkgh.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">Views from the boat.</span>
<span class="attribution"><span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>Windermere is divided into two separate basins, the north and the south basin. With the South Basin more nutrient rich – also known as “eutrophic” – than the north. eDNA from species that don’t like nutrient rich conditions – such as Arctic charr – were found to be more common in the North Basin, while species that aren’t choosy were detected throughout the lake. This suggests that eDNA data could reliably indicate the ecological condition of lakes.</p>
<p>These results are a highly encouraging step towards eDNA becoming a game-changer in biodiversity monitoring. And we are now working closely with the Environment Agency and other groups to drive this research forward – to help ensure that the health our lakes is monitored in the most efficient and cost effective way possible.</p><img src="https://counter.theconversation.com/content/61616/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Lori Lawson Handley received funding from the Environment Agency and Scottish Environmental Protection Agency in relation to the work discussed in this article. </span></em></p>Scientists are pioneering a new way of monitoring water species, using techniques more familiar to fans of crime scene TV shows.Lori Lawson Handley, Senior Lecturer in Evolutionary Biology, University of HullLicensed as Creative Commons – attribution, no derivatives.