What Is: Environmental DNA (eDNA)

Scientific Frontline: Extended "At a Glance" Summary

The Core Concept: A non-invasive monitoring technique that detects the presence of species by extracting and analyzing genetic material shed into the environment (water, soil, air) rather than isolating the organism itself.

Key Distinction/Mechanism: Unlike traditional ecology which relies on physical capture or visual observation ("macro-organismal" interaction), eDNA focuses on the "molecular" traces—such as mucus, skin cells, and gametes—organisms leave behind, effectively reading the environment as a biological archive.

Origin/History: Initially developed in the 1980s as a niche method for identifying soil microbes, it has since evolved into a global surveillance network for monitoring macro-organisms across diverse ecosystems.

Major Frameworks/Components:

• Physical States: Exists as intracellular (within cells), extracellular (free-floating), or particle-bound DNA, with varying persistence rates.
• Genetic Targets: Primarily targets mitochondrial DNA (mtDNA) markers (e.g., COI, 12S rRNA) due to their exponential abundance compared to nuclear DNA.
• Analytical Workflows: Utilizes qPCR/dPCR for targeted "needle in a haystack" detection (single species) and Metabarcoding for community-wide ecosystem inventories.
• Fate and Transport: Modeling how genetic material moves through systems (e.g., downstream flow) and degrades due to environmental factors like UV radiation, temperature, and microbial activity.

Branch of Science: Molecular Ecology, Conservation Biology, Genetics, Bioinformatics.

Future Application: Enhanced "early warning systems" for invasive species (e.g., Burmese Python in Florida), non-invasive tracking of endangered wildlife in inaccessible habitats, and "ghost" censuses of ancient human history via cave sediments.

Why It Matters: It dismantles the limitations of physical accessibility in science, enabling proactive, scalable, and highly sensitive biodiversity stewardship that can detect invisible pathogens or elusive predators without disrupting the ecosystem.

Humboldt marten (Martes caurina humboldtensis): The Metazoa Explorer

Humboldt marten (Martes caurina humboldtensis)
Image Credit: Scientific Frontline / stock image

Taxonomic Definition

The Humboldt marten is a critically imperiled subspecies of the Pacific marten (Martes caurina), belonging to the family Mustelidae and order Carnivora. It is biologically distinct from the American marten (Martes americana) and is historically endemic to the humid, coastal coniferous forests of Northern California and Oregon. Currently, the taxon is restricted to four fragmented, isolated population areas (extant population areas or EPAs) along the Pacific coast, relying heavily on dense shrub understories in old-growth redwood and Douglas-fir ecosystems.

Muntjac (Muntiacus): The Metazoa Explorer

Red Muntjac female, Muntiacus vaginalis in Khao Yai national park, Thailand
Photo Credit: Tontantravel
(CC BY-SA 4.0)

Taxonomic Definition

The Muntjac (Muntiacus) constitutes a genus of small-to-medium-sized ungulates within the family Cervidae, specifically placed in the tribe Muntiacini. Often recognized as the oldest lineage of extant deer, they are endemic to South and Southeast Asia, ranging from Pakistan and India through China, Vietnam, and the Indonesian archipelago, with introduced populations establishing in the United Kingdom and Japan.

Timber rattlesnake (Crotalus horridus): The Metazoa Explorer

Timber rattlesnake (Crotalus horridus)
Photo Credit: Peter Paplanus
(CC BY 4.0)

Taxonomic Definition

The Timber rattlesnake (Crotalus horridus) is a venomous pit viper belonging to the family Viperidae and the subfamily Crotalinae. It is the sole member of its genus found in the populous northeastern United States, though its range extends south to northern Florida and west to eastern Texas and Minnesota. As a sexually dimorphic species, it is characterized by dorsal chevron patterns and a distinct rattle structure, occupying diverse habitats from deciduous forests to cane thickets.

Tigers (Panthera tigris): The Metazoa Explorer

Taxonomic Definition

Panthera tigris constitutes the largest extant species within the family Felidae and the genus Panthera. Taxonomically situated within the Order Carnivora, this obligate carnivore is historically distributed across much of Asia, ranging from the temperate forests of the Russian Far East to the tropical mangroves of the Sundarbans and the rainforests of Sumatra. It is defined by its distinct dark vertical stripes on orange-brown fur with a lighter underside, a phenotype resulting from specific expression of the Agouti and Tabby signaling pathways.

What Is: Invasive Species

Image Credit: Scientific Frontline / stock image

Scientific Frontline: Extended "At a Glance" Summary

The Core Concept: Invasive species are non-native organisms that, upon introduction to a new environment, escape the evolutionary checks of their native ranges to cause significant ecological, economic, or human health harm. This phenomenon represents a systemic disruption of biophysical systems rather than merely the presence of an unwanted plant or animal.

Key Distinction/Mechanism: The defining characteristic separating "invasive" from "non-native" is impact; while many non-native species (like agricultural crops) are beneficial, invasive species actively dismantle native ecosystems. They often succeed via the Enemy Release Hypothesis, flourishing because they have left behind natural predators and diseases, or through Priority Effects, such as leafing out earlier than native flora to monopolize resources.

Origin/History: While natural translocation has occurred for eons, the current crisis is driven by the "relentless engine of human globalization" in the Anthropocene. The concept is underscored by the "Ten Percent Rule," a statistical filter noting that roughly 10% of transported species survive, 10% of those establish, and 10% of those become destructive invaders.

Identical micro-animals live in two isolated deep-sea environments. How is that possible?

The researchers traveled on the research vessel Polarstern to South Sandwich Trench where they collected sediment samples.
Photo Credit: ©Anni Glud/SDU

Halalaimus is a microscopic nematode genus commonly found in sediment on the seafloor. It lives 1–5 cm below the sediment surface and grazes on bacteria or organic materials in the sediment. 

It does so in the Aleutian Trench as well, which lies in the northern Pacific Ocean, near the Bering Sea. We now know this because PhD Yick Hang Kwan from Danish Center for Hadal Research at the Department of Biology has isolated its eDNA in sediment samples collected from the depths of the Aleutian Trench. 

“But we also found its eDNA in sediment samples from the South Sandwich Trench, which lies 17,000 km away in the South Atlantic. And that inevitably makes you ask: How is it possible that the same nematode genus exists in such extremely isolated deep-sea environments so far apart, when it has a very limited ability to move – and when the trenches are up to eight kilometers deep?” Kwan asks rhetorically. 

Counting salmon is a breeze with airborne eDNA

A male Coho salmon, featuring the characteristic hooked nose, returns to spawn from the Oregon Coast.
Photo Credit: NOAA Fisheries

During the annual salmon run last fall, University of Washington researchers pulled salmon DNA out of thin air and used it to estimate the number of fish that passed through the adjacent river. Aden Yincheong Ip, a UW research scientist of marine and environmental affairs, began formulating the driving hypothesis for the study while hiking on the Olympic Peninsula.

“I saw the fish jumping and the water splashing and I started thinking — could we recover their genetic material from the air?,” he said.

The researchers placed air filters at several sites on Issaquah Creek, near the Issaquah Salmon Hatchery in Washington. To their amazement, the filters captured Coho salmon DNA, even 10 to 12 feet from the river. Scientists collect environmental DNA, or eDNA, to identify species living in or passing through an area, but few have attempted to track aquatic species by sampling air.

Plucking key evidence from air

PhD candidate Emily Bibbo and Dr Mariya Goray at the DNA forensics research room at Flinders University.
Photo Credit: Courtesy of Flinders University

Culprits may one day be found using a new technique to potentially pick up and record key airborne forensic DNA evidence from crime scenes wiped clean of fingerprints and other trace evidence.

A new study led by Flinders University forensic science researchers puts the new method to the test with conventional air-conditioning units as well as a portable, commercially available air collection device regularly used to test for COVID19 and other airborne viruses in hospitals, schools and nursing homes.

“Human DNA can be found in the air after people have spoken or breathed (via saliva droplets), shed skin cells or dislodged and aerosolized from surfaces and collected for DNA analysis,” says Emily Bibbo, a PhD candidate at Flinders University’s College of Science and Engineering.

“We may be able to use this as evidence to prove if someone has been in the room, even if they wore gloves or wiped surfaces clean to remove the evidence.”

Collection of trace DNA, comprising just a few human cells, is commonly used in criminal investigations. For example, 62% of all samples processed by Forensic Science SA in 2020 were trace or touch evidence, yet success rates with this type of evidence remain poor.

Lightning, camera, gamma ray!

Lightning captured with the highspeed camera at 40,000 frames per second.
Photo Credit: Rasha Abbasi

In September 2021, an unprecedented thunderstorm blew across Utah’s West Desert. Lightning from this storm produced at least six gamma ray flashes that beamed downward to Earth’s surface and activated detectors at the University of Utah-led Telescope Array. The storm was noteworthy on its own—the array usually clocks one or two of the lightning-triggered gamma rays per year—but recent upgrades led to a new observation by the Telescope Array scientists and their lightning collaborators.

For the first time ever, they captured video footage of lightning-triggered downward terrestrial gamma-ray flashes (TGFs). A special camera running at 40,000 frames per second gave an unprecedented look at how gamma rays burst downwards to the Earth’s surface from cloud-to-ground lightning strikes. They found that not only were multiple gamma rays produced at later lightning stages than previously thought, but the rays were also associated with a pulse of optical light that had never been recorded.

“This is an important step in lightning research that could lead us to the physics producing these downward gamma rays,” said lead author Dr. Rasha Abbasi, now an assistant professor of physics at Loyola University Chicago. Abbasi began the research on TGFs as a postdoctoral scholar at the University of Utah.

Tracing the flow of water with DNA

Oliver Schilling analyzing spring water at Mount Fuji.
Photo Credit: T. Schilling

Environmental DNA analysis of microbial communities can help us understand how a particular region’s water cycle works. Basel hydrogeologist Oliver Schilling recently used this method to examine the water cycle on Mount Fuji. His results have implications for Switzerland as well.

Where does the water come from that provides drinking water to people in a particular region? What feeds these sources and how long does it take for groundwater to make its way back up to the surface? This hydrological cycle is a complex interplay of various factors. A better grasp of the system allows us to understand, for example, why pollution is worse in some spots than others, and it can help us implement sustainable water management policies and practices.

Environmental DNA (eDNA) provides some important data to improve our understanding. In combination with the evaluation of other natural tracers – noble gases, for example – this microbial data provides important glimpses into the flow, circulation and functioning of complex groundwater systems. “It’s a vast toolbox that’s new to our field of research,” says Oliver Schilling, Professor of Hydrogeology at the University of Basel and at Eawag, the Swiss Federal Institute of Aquatic Science and Technology. Quantitative hydrogeology maps out where and how quickly new groundwater will accumulate.

Environmental DNA uncovers a 2-million-year-old ecosystem in Greenland

Reconstruction of the Kap København formation two-million years ago, in a time where the temperature was significantly warmer than northernmost Greenland today.
Illustration Credit: Beth Zaiken.

Around 2 million years ago, climate in Greenland resembled the forecast of a future under global warming: with trees such as poplars and birch and animals like hare, lemmings, mastodons and reindeer.

Paleoclimatic records show strong polar amplification with annual temperatures of 11–19 degrees Celsius above current values. The biological communities inhabiting the Arctic during this time remain poorly known because animal fossils are rare.

An international team, including a researcher from Lawrence Livermore National Laboratory (LLNL), report the oldest ancient environmental DNA (eDNA) record to date, describing the rich plant and animal assemblages of the Kap København Formation in north Greenland that existed 2 million years ago. The research appears on the cover of the Dec. 7 issue of the journal Nature.

Ancient DNA has been used to map a two-million-year-old ecosystem, which weathered extreme climate change. Researchers hope the results could help to predict the long-term environmental toll of today’s global warming.

Sea turtle conservation gets boost from new DNA detection method

DNA “fingerprints” left behind by sea turtles offer scientists a simple, powerful way of tracking the health and whereabouts of these endangered animals, a key step forward in their conservation.

A study led by University of Florida researchers is the first to sequence environmental DNA, or eDNA, from sea turtles — genetic material shed as they travel over beaches and in water. The research project is also the first to successfully collect animal eDNA from beach sand. The techniques could be used to trace and study other kinds of wildlife, advancing research and informing conservation strategies.

“We wanted to test the boundaries of this technology, which hadn't really been applied to sea turtles before and certainly not on sand,” said David Duffy, UF assistant professor of wildlife disease genomics and Rising Star Condron Family Endowed Assistant Professor. “This is a way to survey areas for elusive animals or species that can be hard to study otherwise. It’s essentially wildlife forensics.”

Nearly all of the planet’s sea turtle species are endangered and face a multitude of threats, including warming temperatures, habitat destruction and degradation, disease, hunting and pollutants such as plastics. Conserving sea turtles is further complicated by the fact that current survey methods rely on spotting them in one of their multiple habitats — in the open sea, coastal ecosystems or on beaches where they nest. This makes it difficult to monitor their numbers, genetic diversity and overall health and tailor conservation efforts accordingly, Duffy said.

Arthritis-related gene also regenerates cartilage in joints and growth plates

Spine from a healthy mouse (left) and a mouse with
genetically disrupted cartilage progenitor cells 
Image by Dawei Geng and Tea Jashashvili

The IL-6 family of proteins has a bad reputation: it can promote inflammation, arthritis, autoimmune disease and even cancer. However, a new USC-led study published in Communications Biology reveals the importance of IL-6 and associated genes for maintaining and regenerating cartilage in both the joints and in the growth plates that enable skeletal growth in children.

“We show, for the first time, that the IL-6 family, previously almost exclusively associated in the musculoskeletal field with arthritis, bone and muscle loss, and other chronic inflammatory diseases, is required for the maintenance of skeletal stem and progenitor cells, and for the healthy growth and function of the joints and spine,” said the study’s corresponding author Denis Evseenko, who is the J. Harold and Edna LaBriola Chair in Genetic Orthopedic Research, and an associate professor of orthopaedic surgery, and stem cell biology and regenerative medicine at USC. “Our study establishes a link between inflammation and regeneration, and may explain why stem and progenitors are exhausted in chronic inflammation.”

In the study, first author Nancy Q. Liu from USC and her colleagues took a close look at a key gene activated by IL-6: STAT3. In both lab-grown human cells and in mice, the scientists demonstrated that STAT3 is critical for the proliferation, survival, maturation and regeneration of cartilage-forming cells in the joints and growth plates. When the gene ceased to function, cartilage-forming cells became increasingly dysfunctional over time, resulting in smaller body size, prematurely fused growth plates, underdeveloped skeletons and mildly degenerated joint cartilage.

Mice experienced the same issues when they lacked a protein called glycoprotein 130 (gp130), which all IL-6 proteins use to activate Stat3. Deactivating another gene Lifr, which encodes a protein that works with gp130 to recognize one of the IL-6 proteins called Lif, produced similar but milder skeletal and cartilage changes.