Freshwater connectivity can transport environmental DNA through the landscape

A new paper published in the journal Proceedings of the Royal Society B used environmental DNA (eDNA) metabarcoding to analyze fish and zooplankton communities. The study found that the movement of water between freshwater bodies, or freshwater connectivity, can transport eDNA. This highlights the potential of eDNA to provide a comprehensive view of freshwater biodiversity.

Aquatic ecosystems are connected by waterways, which allow fish, plants, and other organisms to move from one place to another. This connectivity is important for the resilience of aquatic populations, but it can also make it difficult to track the DNA of these organisms.

The study, led by Dr Joanne Littlefair, a lecturer in biological sciences at Queen Mary University of London, looked at three lake networks containing 21 lakes in Canada's Boreal Forest at IISD Experimental Lakes Area. The researchers found that within-lake eDNA generally reflected the habitat preferences of the species, but that some eDNA was also transported into downstream lakes. Lakes with a higher degree of connectivity had more eDNA detections that could not be explained by conventional monitoring techniques.

The findings have implications for the use of eDNA to monitor biodiversity in freshwater ecosystems. eDNA is a promising tool for biodiversity monitoring, but data must be interpreted in light of connectivity in the landscape.

"eDNA can be used to detect the presence of species that are not easily monitored using conventional methods, including invasive species, or for monitoring the presence of rare or endangered species," said Dr Littlefair." "Our study showed that eDNA surveys can be carefully designed to consider the connectivity of the freshwater system being studied. In systems with high levels of connectivity, it is important to collect samples from multiple locations, which will allow us to build a complete picture of the biodiversity present."

The study also highlights the need for more research on the factors, such as effects of water movement, influencing the spatial resolution of eDNA detection. For example, if the water in an ecosystem is moving quickly, then it may be necessary to collect more samples to increase the chances of detecting eDNA. This research will help to improve scientists' understanding of how eDNA can be used to monitor and conserve aquatic biodiversity.

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Human DNA is everywhere. That's a boon for science -- and an ethical quagmire

On the beach. In the ocean. Traveling along riverways. In muggy Florida and chilly Ireland. Even floating through the air.

We cough, spit, shed and flush our DNA into all of these places and countless more. Signs of human life can be found nearly everywhere, short of isolated islands and remote mountaintops, according to a new University of Florida study.

That ubiquity is both a scientific boon and an ethical dilemma, say the UF researchers who sequenced this widespread DNA. The DNA was of such high quality that the scientists could identify mutations associated with disease and determine the genetic ancestry of nearby populations. They could even match genetic information to individual participants who had volunteered to have their errant DNA recovered.

David Duffy, the UF professor of wildlife disease genomics who led the project, says that ethically handled environmental DNA samples could benefit fields from medicine and environmental science to archaeology and criminal forensics. For example, researchers could track cancer mutations from wastewater or spot undiscovered archaeological sites by checking for hidden human DNA. Or detectives could identify suspects from the DNA floating in the air of a crime scene.

But this level of personal information must be handled extremely carefully. Now, scientists and regulators must grapple with the ethical dilemmas inherent in accidentally -- or intentionally -- sweeping up human genetic information, not from blood samples but from a scoop of sand, a vial of water or a person's breath.

Published May 15 in Nature Ecology and Evolution, the paper by Duffy's group outlines the relative ease of collecting human DNA nearly everywhere they looked.

"We've been consistently surprised throughout this project at how much human DNA we find and the quality of that DNA," Duffy said. "In most cases the quality is almost equivalent to if you took a sample from a person."

Because of the ability to potentially identify individuals, the researchers say that ethical guardrails are necessary for this kind of research. The study was conducted with approval from the institutional review board of UF, which ensures that ethical guidelines are adhered to during research studies.

"It's standard in science to make these sequences publicly available. But that also means if you don't screen out human information, anyone can come along and harvest this information," Duffy said. "That raises issues around consent. Do you need to get consent to take those samples? Or institute some controls to remove human information?"

Duffy's team at UF's Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital has successfully used environmental DNA, or eDNA, to study endangered sea turtles and the viral cancers they are susceptible to. They've plucked useful DNA out of turtle tracks in the sand, greatly accelerating their research program.

The scientists knew that human eDNA would end up in their turtle samples and probably many other places they looked. With modern genetic sequencing technology, it's now straightforward to sequence the DNA of every organism in an environmental sample. The questions were how much human DNA there would be and whether it was intact enough to harbor useful information.

The team found quality human DNA in the ocean and rivers surrounding the Whitney Lab, both near town and far from human settlement, as well as in sand from isolated beaches. In a test facilitated by the National Park Service, the researchers traveled to part of a remote island never visited by people. It was free of human DNA, as expected. But they were able to retrieve DNA from voluntary participants' footprints in the sand and could sequence parts of their genomes, with permission from the anonymous participants.

Duffy also tested the technique in his native Ireland. Tracing along a river that winds through town on its way to the ocean, Duffy found human DNA everywhere but the remote mountain stream where the river starts, far from civilization.

The scientists also collected room air samples from a veterinary hospital. They recovered DNA matching the staff, the animal patient and common animal viruses.

Now that it's clear human eDNA can be readily sampled, Duffy says it's time for policymakers and scientific communities to take issues around consent and privacy seriously and balance them against the possible benefits of studying this errant DNA.

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Solving Everest's wildlife mysteries with eDNA

A team of scientists led by the Wildlife Conservation Society (WCS) and Appalachian State University used environmental DNA (eDNA) to document the breadth of high-alpine biodiversity present on Earth's highest mountain, 29,032-foot Mt. Everest (8,849 m).

Describing their findings in the journal iScience, the team collected eDNA from water samples over a four-week period in ten ponds and streams between 14,763 feet (4,500 meters) and 18,044 feet (5,500 meters). The sites included areas of the alpine zone that exist above the tree line and contain an array of flowering plants and shrub species, along with the aeolian zone that reaches beyond the range of flowering plants and shrubs at the uppermost reaches of the biosphere. From just 20 liters of water, they identified organisms belonging to 187 taxonomic orders, which corresponds to 16.3 percent, or one sixth, of the total known orders across the tree of life -- a family tree of Earth's biodiversity.

eDNA searches for trace amounts of genetic material left behind by organisms and wildlife and offers a more accessible, rapid, and comprehensive approach to increasing survey capacity for assessing biodiversity in aquatic environments. Samples are collected using a sealed cartridge containing a filter that captures genetic material that is later analyzed at a lab using DNA metabarcoding and other sequencing methodologies. WCS has been using eDNA for detection of rare and threatened species from humpback whales to Swinhoe's softshell turtle, one of the rarest species on the planet.

Although the Everest study focused on identification at the order level, the team was able to identify many organisms to the genus or species level.

For example, the team identified both rotifers and tardigrades, two tiny animal organisms that are known to occur in the harshest and most extreme environments and are considered to be among the most resilient animals known on Earth. In addition, they identified Tibetan snow cock, which are found in Sagarmatha National Park, and were surprised to find species such as domestic dog and chicken, representing how human activities are influencing the landscape.

They also identified pine trees, which only are found far downhill from where they sampled, demonstrating how wind-blown pollen can make its way high up into these watersheds. Another organism they identified from several sites were mayflies, which are known indicator species for environmental change.

The eDNA inventory will aid future high-Himalayan biomonitoring and retrospective molecular studies to assess changes over time as climate-driven warming, glacial melt, and human-caused influences reshape this rapidly transforming world-renowned ecosystem.

Said Dr. Tracie Seimon of WCS's Zoological Health Program, co-lead of the Everest biology field team and lead of the study: "High-alpine and aeolian environments, which have often been thought of as barren and mostly devoid of life, in fact have abundant biodiversity. High mountain environments including Mount Everest should be recognized as a target for sustained long-term biodiversity monitoring of high-alpine taxa to complement bioclimatic monitoring and climate change impact assessments."

Said Dr. Marisa Lim of the Wildlife Conservation Society: "We went in search for life on the roof of the world. This is what we found. However, the story does not end here. There is more to be discovered and we hope our findings help to inform future exploration."

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