Category: Wildlife

Environmental DNA – how a tool used to detect endangered wildlife ended up helping fight the COVID-19 pandemic

Looking for bits of DNA at the University of Florida. David Duffy, CC BY-ND

by Jessica Alice Farrell & David Duffy (University of Florida) and Liam Whitmore, (University of Limerick)

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 Megaelosia bocainensis, whose complete disappearance in 1968 led scientists to believe it had become extinct. But through a novel genetic detection technique, it was rediscovered in 2020.

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 every animal sheds DNA into its environment via skin, hair, scales, feces or bodily fluids as it moves through the world.

As wildlife biologists at the University of Florida’s Whitney Laboratory for Marine Bioscience & Sea Turtle Hospital, we use eDNA to track a virus responsible for a sea turtle pandemic called fibropapillomatosis, which causes debilitating tumors. We also use eDNA to detect sea turtles in the wild.

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.

From soil microbes to sea turtles

Scientists in the 1980s began hunting for microbe DNA in soil samples. Over the next 20 years, the technique was adapted for use with air and water samples, and scientists started using eDNA to detect larger animals and plants.

A flowchart of how snow/ice, freshwater, soil, sand or seawater samples can be collected and analyzed for their DNA.
Scientists now can detect DNA traces from many different environments. Liam Whitmore, University of Limerick, CC BY-ND

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 quantitative polymerase chain reaction or whole genome sequencing. Scientists can either read all of the DNA present from every organism – or target just the DNA from species of interest.

Scientists now routinely use eDNA to detect endangered wildlife and invasive species. 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.

A sea turtle on its back in an exam room. One of its flippers is severely deformed.
Routine imaging of a juvenile green sea turtle patient afflicted with virus-triggered fibropapillomatosis at the Florida Whitney Sea Turtle Hospital. Devon Rollinson-Ramia, CC BY-ND

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 viruses that can cause disease in wildlife.

Tracking COVID-19

While scientists originally applied eDNA to human pathogen detection 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.

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.

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 successfully isolated and sequenced the virus. Confirming air as a key route of transmission directly influenced public health guidelines.

A gloved hand holds a sealed plastic bottle of murky-looking water.
Collecting sewage samples to test for SARS-CoV-2 at Utah State University in September 2020. AP Photo/Rick Bowmer

When scientists apply eRNA to archived wastewater samples, the true dates of SARS-CoV-2 appearance can be detected. SARS-CoV-2 concentration in wastewater in Valencia, Spain, 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.

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.

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Intersection of diseases

It’s vital that human and animal diseases are studied together. Sixty percent of emerging human pathogens come from animals – with many of these (42%) originating in wildlife populations, including Ebola, Zika, West Nile and Marburg viruses. Alternatively, people can also transmit pathogens to animals.

SARS-CoV-2 has already infected apes at a zoo in San Diego, large cats at a zoo in New York and minks at farms in Europe – the latter of which gave rise to new variants that could prove a new threat to people.

Medics, veterinarians and scientists call this convergence of human, animal and environmental well-being OneHealth or EcoHealth. Studying and treating human and wildlife disease together recognizes their commonalities and often yields breakthroughs.

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.

Jessica Alice Farrell, PhD Candidate in Biology, University of Florida; David Duffy, Assistant Professor of Wildlife Disease Genomics, University of Florida, and Liam Whitmore, PhD Candidate, Department of Biological Sciences, University of Limerick

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Novel computational framework seeks insight into eagle flight at wind plants

Read the full story from the National Renewable Energy Lab.

Golden eagles strike a cutting visage that, to put it mildly, grants the species an aura of regality. Occupying much of the Northern Hemisphere, many cultures view this species as a sacred messenger of the gods and kings and queens of the sky.

Not only are these birds highly revered, but highly protected—receiving protections under the Bald and Golden Eagle Protection Act and the Migratory Bird Treaty Act. As a result, their presence must be carefully considered by wind power plant operators and developers working in eagle territory, presenting challenges that can extend permitting timelines, add unanticipated project costs, and constrain energy output.

To address these challenges, National Renewable Energy Laboratory (NREL) scientists along with fellow researchers at the U.S. Geological Survey, Western EcoSystems Inc., and Conservation Science Global Inc. are developing a state-of-the-art computational framework for modeling golden eagle behavior near wind farms. In all hopes, this tool can help guide wind power plant siting decisions and dynamic curtailment strategies informed by real-time eagle flight path prediction.

Denver returns 14 bison to tribal land in reparations, conservation effort

Read the full story from NPR.

Fourteen American bison headed to their new homes on native land this month. Indigenous tribes received the bison from Denver Parks and Recreation as a form of reparations, the first gift in a 10-year ordinance to donate surplus bison that will also go toward tribal conservation efforts.

With smartphones, anyone can help track Brood X — and maybe unlock cicada mysteries

Read the full story in the Washington Post.

Quinn-Farber and tens of thousands of others have signed up to take part in an unprecedented crowdsourcing effort in the coming weeks to track the largest emergence of cicadas in the country. Using Cicada Safari, an app developed by researchers at Mount St. Joseph University in Cincinnati, their contributions will potentially offer the most comprehensive look at the cicada tsunami — and help scientists better understand how urban development may contribute to cicadas’ decline and why the insects emerge in 13- and 17-year intervals, a strange mating schedule that still puzzles entomologists.

Rat poison found in bodies of 80% of American eagles

Read the full story in The Guardian.

Rat poison has been found in the bodies of an estimated 80% of American eagles, according to a new study from the University of Georgia.

Minnesota Bird Songs

The Minnesota Department of Natural Resources has developed an easy guide to identifying bird songs. Simply go to the page and click on the image of the bird to hear its song.

All recordings are courtesy of The Cornell Lab of Ornithology, All About Birds.

Translocation is a viable option for problem bears

Read the full story from the Prairie Research Institute.

One way to manage bears who damage property and crops is to move them to a different area within their geographic range. Illinois Natural History Survey (INHS) scientists studying translocation have found that capture and release does not lower bears’ survival rates, so it’s a good option for handling nuisance bears.

Ever wondered what red foxes eat? There’s a database for that

Read the full story from the University of Sussex.

Researchers create a free, online database on global carnivore diets to help conservationists and educators.

Philadelphia is about to go completely dark at night. Here’s why

Read the full story at Fast Company.

After 15 years of effort, Audubon Mid-Atlantic and several other local organizations have succeeded in convincing building owners to do more. Beginning April 1, and running for the duration of both the spring and autumn bird migration periods, buildings across Philadelphia will be voluntarily turning off their lights at night.

The initiative, Lights Out Philly, runs from April 1 to May 31 and again from August 15 to November 15, and it calls on building owners and managers to turn off, dim, or block any lights within buildings that are typically left on at night. It also calls for nonessential lights, such as those illuminating building signs or sponsor logos, to be turned off or switched to green or blue colors that are less likely to attract birds than red or white. For these twice-annual migration periods, turning off lights can help reduce the potentially deadly lure and distraction of buildings, keeping the tens of millions of birds that travel through Philadelphia along the Atlantic Flyway on their flight path.

Bird Finder

This page (currently displaying data for Champaign, IL) shows the probability of a species appearing on a checklist during a given month. The change in probability from the previous month is also shown, to highlight which birds are coming and going. Rows with significant changes (< 0.5x or > 2x) are highlighted in red or green. This is based on historical data from eBird, and does not include the current month.

  • Enter a location to search a different region (works worldwide!).
  • Click on a species to see when and where best to find it.

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