Ancient DNA reveals how farming, wildlife and human activity transformed a Canadian lake's ecosystem over 1,000 years

A lake in Canada has yielded an unusually detailed record of how people, plants and wildlife reshaped the environment over the course of a millennium.

Scientists have reconstructed roughly 1,000 years of ecological history around Crawford Lake by examining tiny traces of ancient DNA preserved in layers of sediment at the bottom of the lake.

The material has allowed researchers to follow changes involving plants, animals, insects, fungi and microorganisms, while also identifying signs of human activity.


The study, published in Molecular Ecology, offers a detailed look at how the ecosystem changed from the period before local agriculture through Indigenous farming, later settlement and eventually industrialisation.

Researchers say the approach provides information that traditional methods of studying ancient environments can sometimes miss.

DNA preserved in layers tells a story

Crawford Lake is unusual because its water does not fully mix with the sediment at the bottom. This condition allows successive layers of material to accumulate and remain remarkably well preserved.

Scientists compare the process to tree rings. Each sediment layer corresponds to a particular period, creating a chronological record of environmental change.

Instead of relying only on pollen, fossils or other physical remains, researchers examined sedimentary ancient DNA, or sedaDNA.

These microscopic genetic traces are left behind by organisms living in or around the lake and can remain trapped in the sediment for centuries.

By analysing the samples, the team was able to reconstruct a much broader picture of the ecosystem.

The data included evidence from plants and animals as well as bacteria and fungi, allowing researchers to examine several parts of the environment at the same time.

The resulting record stretches from periods before intensive agriculture to the arrival of European settlers and the environmental changes associated with modern industry.

Indigenous farming left a genetic footprint

One of the most significant findings concerns Indigenous agriculture around Crawford Lake.

The DNA evidence supports earlier research showing that Indigenous communities cultivated maize and sunflower in the area between roughly the 1200s and 1500s.

These crops were part of the agricultural traditions commonly associated with the Three Sisters system, in which maize, beans and squash were cultivated together. When sunflower was added, the combination became known as the Four Sisters.

The new research provides the first sedaDNA evidence from Crawford Lake for maize and sunflower, offering another way to identify farming activity that took place centuries ago.

The researchers also found an intriguing change in Canada goose DNA during periods associated with Indigenous agriculture.

Scientists suggest that geese may have fed in cultivated fields before returning to the lake. Their droppings could have carried nutrients into the water, while traces of the crops they consumed may also have entered the lake's sediment.

That could help explain evidence of recurring algal blooms, which occur when excess nutrients enter an aquatic ecosystem.

Wildlife changes reveal the impact of people

The DNA record also shows how the surrounding ecosystem changed after agricultural activity declined.

Following the abandonment of the site in the 1500s, researchers found evidence pointing toward a return of several species associated with a less disturbed landscape, including pine trees, rabbits, deer, beavers and loons.

Maize, meanwhile, disappeared from the record.

The contrast provides scientists with an opportunity to observe how ecosystems respond when human activity changes or stops.

Rather than presenting environmental history as a straight line, the sediment reveals periods of disturbance, recovery and renewed transformation.

The study also produced evidence that traditional paleoecological techniques may not always capture every species present in a landscape.

For example, DNA from cattle appears in sediment dating to the early 1800s. That provides evidence of cattle in the area that was not apparent from the conventional record examined by researchers.

Scientists were able to detect these changes because sedaDNA captures genetic fragments left behind by organisms, even when their physical remains are no longer visible.

A new way to read the Anthropocene debate

Crawford Lake became internationally known during the scientific debate over the proposed Anthropocene, a geological epoch intended to represent the period in which human activity became a dominant force shaping Earth's environment.

Its sediments contain several markers associated with industrialisation and modern human activity, including fossil-fuel residues, plastics, artificial fertilisers, acid rain and plutonium.

Although the proposal to formally recognise the Anthropocene as a new geological epoch was ultimately rejected, Crawford Lake remains an important site for understanding the scale and history of human environmental impact.

The new sedaDNA research adds another layer to that story.

Rather than focusing solely on the industrial era, the study traces ecological changes across a much longer period. It shows that humans were influencing the environment long before modern industrialisation, while also demonstrating that the nature and intensity of that influence changed over time.

Researchers used a technique called capture enrichment to find specific genetic material within the sediment. Scientists prepare RNA-based genetic probes that can bind to DNA from selected organisms.

Magnetic beads are then used to pull the targeted material from the sample.

This makes it possible to search for genetic evidence from hundreds or even thousands of species without relying entirely on random sequencing.

The team also found that DNA age alone does not determine how well genetic material survives. Some roughly 500-year-old DNA recovered from Crawford Lake was more damaged than DNA tens or hundreds of thousands of years old preserved in Arctic permafrost.

That finding highlights the importance of environmental conditions in preserving ancient DNA.

Researchers say future work could use improved genetic panels designed specifically for the Eastern Woodland region. Such tools may make it easier to detect crops such as beans and squash that were not identified in the current analysis.

For scientists, the broader promise is clear: sedimentary DNA can turn a lake bottom into a detailed biological archive, revealing changes that might otherwise remain invisible.

At Crawford Lake, a thousand years of environmental history has effectively been stored beneath the water—and modern genetic technology is allowing researchers to read it one fragment at a time.

Frequently asked questions

What did scientists discover at Crawford Lake?

Researchers reconstructed around 1,000 years of ecological change by analysing ancient DNA preserved in the lake's sediment. The evidence tracks plants, animals, insects, fungi, bacteria and human activity.

What is sedimentary ancient DNA?

Sedimentary ancient DNA, or sedaDNA, consists of genetic fragments left behind by organisms and preserved in layers of sediment. Scientists can analyse these traces to identify species that lived in or around an environment in the past.

What does the DNA reveal about Indigenous farming?

The study detected DNA from maize and sunflower in sediment associated with Indigenous farming between approximately the 1200s and 1500s, providing new genetic evidence of agriculture around Crawford Lake.

Why is Crawford Lake important to climate and environmental research?

Crawford Lake contains exceptionally well-preserved sediment layers that record environmental changes over centuries. Its sediments also contain evidence of industrial pollution and other human impacts, making it an important site for studying the long-term relationship between people and ecosystems.