Environmental DNA – a tool that transforms ecology and conservation

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Environmental DNA can be collected from any environmental sample such as soil, pollen, or mossАлексей Мойса, Unsplash

When you mention an ecologist at work, you might picture someone counting species of pine trees, marveling at obscure fossils, or sampling myriad snails. However, this is a certain picture of the past. If you see them today collecting soil and lake water, or standing in a lab indistinguishable from the molecular geneticists, don’t worry – they’re probably just collecting and decoding environmental DNA.

Environmental DNA (eDNA) is genetic material obtained from environmental samples such as water and sediment. It is an animal’s natural ecological footprint over its lifetime, including cell shedding, excretory waste, carcasses, and even bacterial DNA that can digest foreign DNA and incorporate it into itself. It has traditionally been assumed that DNA deposited in this way could not possibly last long on its own, or that even if it did, it would be too similar across samples to reveal anything about the surrounding ecology. Instead, studies of biodiversity have relied on measuring and sampling organism samples in the field and then classifying them based on morphology, a laborious but necessary endeavor—or so it was thought.

“More than just a ‘quick-and-dirty’ source, eDNA can identify species more accurately and comprehensively than previous methods”

Therefore, it came as a surprise to everyone when scientists discovered that eDNA varied greatly not only between environmental sample types (e.g. soil, pollen) but also between different ecological environments using the same sample type. eDNA can bind to soil particles to slow their degradation and persist in cold, dry permafrost for up to hundreds of thousands of years, granting us unprecedented genetic reach into the past. Importantly, it is a fast, simple and inexpensive source of data, as eDNA is ubiquitous and there is little harm to the organisms and their habitats, which is necessary for sample collection. But eDNA is more than just a “quick-and-dirty” source: it can identify species more accurately and comprehensively, bypassing subjective interpretations of morphology and identifying hard-shelled or low-abundance species allows. Many have therefore spoken for the potential of eDNA to revolutionize conservation science.

To understand eDNA, its analysis must be coupled with our latest DNA sequencing technology. eDNA contains an immense wealth of genetic information consisting of thousands of organisms that need to be identified and quantified. The two main decoding approaches used are metabarcoding and metagenomics sequencing. Metabarcoding tests eDNA with short DNA sequences called “marker sequences” that are conserved within a single species but vary between species. eDNA matching the marker can be sequenced and compared to a database of genomes from known species to identify those present. Alternatively, metagenomics sequences all of the DNA in the sample, rather than just those selected by markers. This more comprehensive approach allows measuring the regional abundance of immobile species such as plants and trace populations over time, albeit less cost-effectively. A combination of the two is often used in a process known as enrichment. Environmental samples used in these genetic analyzes are drilled from multiple layers of sediment corresponding to different stratigraphic time periods to provide an evolutionary snapshot of all flora and fauna in the region. This has been used to unravel complex evolutionary problems.

Successes of eDNA: from the spruce in Scandinavia to the extinction of the megafauna

The origin of trees in Scandinavia has long been a mystery. It was widely believed that no tree survived the Last Glacial Maximum, an event that occurred 25-15 kya (thousand years ago) that covered most of North America and northern Eurasia with ice sheets, and present-day species migrated from the south or east Scandinavia 9 kya after the ice cap melts. However, the first eDNA analysis showed otherwise. After sequencing various spruce samples, the researchers found a rare and conserved gene cluster in the cell’s mitochondria, the so-called “powerhouse of the cell” that produces ATP for energy and respiration. This rare gene cluster is unique to Scandinavian spruce and could therefore represent species that survived glaciation. The researchers then analyzed eDNA from nearby lake sediments in Norway, dating as far back as 22–17.7 kya, and found this distinctive gene cluster. They concluded that some conifers survived in the ice-free refuge of Scandinavia during the last ice age and the history of trees up to before the last ice age. This has prompted scientists to extend the timeframe for studying plant development and to reconsider vegetation responses to climate change.

Simultaneously, the 50-11 kya megafauna extinction unfolded as large land-migratory mammals gradually disappeared from Earth — and conjectures about why this happened have been split between climate change and human activity. The “Blitzkrieg” hypothesis posits that the rapid decline of the megafauna spiraled after human contact, leading to excess hunting and infectious diseases. However, by analyzing ancient DNA against climate data, the researchers showed that by and large, megafaunal population patterns map to environmental changes rather than the human timeline. This picture was supplemented by eDNA analyzes of the arctic vegetation. Glaciation severely reduced vegetative diversity, transforming arctic flora from arid tundra to wet land dominated by woody plants and grasses. This removed herbs as an important protein-rich food source, continuing the explanatory narrative of megafauna extinction.

These two cases are just a glimpse of the extensive use of eDNA in answering diverse, complex questions about plant and animal evolutionary history, population dynamics, and species migration. The inclusion of eDNA in the analytical toolkit represents a transition between theories of evolutionary ecology and methods of molecular genetics, a collaborative interdisciplinary synthesis that is key to starting new fruitful research programs.

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