Dirt holds more secrets about biodiversity than you might think. At a glance, you may envision worms, bugs, and perhaps even bacteria and other single celled organisms that call it home, but there is something even smaller that contains a wealth of knowledge about biodiversity. Species that lived and died have left behind proof of their existence in the form of ancient environmental DNA (aeDNA). As residuals from past organisms, aeDNA are fragmented pieces of DNA that can be collected from ancient samples such as sediments, ice, or water. AeDNA allows scientists to look at evolutionary processes at different spatial and temporal scales than ever previously imagined.

AeDNA has applications in paleoecological studies, species identification, conservation biology, and in understanding evolutionary processes. Computational biology graduate students Maya Lemmon-Kishi and Fiona Callahan in Dr. Rasmus Nielsen’s lab are devoting their doctoral studies to harnessing the power available in aeDNA, specifically in understanding ecosystem dynamics to make informed conservation decisions for current species. But before the aeDNA data lands on Maya and Fiona’s desk, it must travel a long way. The aeDNA begins its journey in the Arctic Circle, where it is preserved within the ice. Scientists core massive sediment tubes from the ground, which are frozen and shipped to collaborators at the University of Copenhagen in a lab built specifically to handle ancient DNA and prevent contamination. Here, the “wet lab wizards” purify the aeDNA from the minerals that have been preserving it within the sediment. Scientists take the data from all the DNA fragments, or reads, and use incredible computational power to match the sequences to species in the National Center for Biotechnology Information (NCBI) database, which has genetic sequences from all branches of life: animals, plants, bacteria, viruses, and fungi. Finally, the data arrives at UC Berkeley, where Fiona and Maya get the report of all the species matches found.

AeDNA provides access to plant, animal, and microbial community data in a way that would be virtually impossible for ecologists to collect otherwise. Fiona describes it as an “unprecedented data source” and an ecologist’s “dream.” Part of the data’s power comes from its vast time scale. As Maya explains, “Most [fossil] samples end in the hundreds of thousands of years ago, [but] we can push past that [with aeDNA ].” These ancient samples could provide insights on current species, which could help scientists make better models and predictions on how to manage resources to protect biodiversity.

Although full of potential, aeDNA has its limitations, and this is where Maya and Fiona hope to fill in the gaps. Fiona is testing methods for piecing together which species may have existed in the same time frame and in the same area. Currently, many existing methods in the field are unable to provide accurate results. Fiona hopes to spend the next portion of their PhD developing better methods that could lead to a more accurate and holistic understanding of the ecological systems that existed in the past.

Maya works on another problem: the verification of aeDNA. Erosion and other methods of transfer sometimes mix soil and aeDNA that may not have truly existed in the same time frame. Since the age of soil is often used to estimate the age of aeDNA, mixing could lead to misclassification. Maya has developed an alternative method for identifying aeDNA age by mapping short DNA sequences onto the tree of life. The age of the sample can then be compared to the age of the sediment.

Even with all the challenges in working with aeDNA, Maya and Fiona are both optimistic about the potential this data offers to scientists. Fiona specifically highlights the insights that aeDNA could have for melting ice caps. They emphasize, “Understanding ecological dynamics is essential to mak[ing] management decisions in the future.” Some aeDNA data spans a time when the glaciers were receding, which allows scientists to generate models for how species changed over time as a result. These models can then be used to understand how melting ice caps will affect current species. Analyzing aeDNA from sediment cores has the potential to reveal historical biodiversity patterns, meaning the key to understanding the ecological future might just be buried in the past.

This article is part of the Spring 2024 issue.