DNA time machine: Insights into a century of loss

The approach could help regulators to protect the planet’s existing biodiversity levels.

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Scientists and regulators are working hard, but biodiversity is disappearing at a startling rate. These changes can occur slowly, their effects take years, and there are few historical records, making it difficult to understand their impact.

Future generations might not be able to benefit from the services provided by nature if we can’t find revolutionary ways to protect biodiversity. Analyzing the DNA traces that organisms shed is one method of tracking changes in biodiversity across time.

Researchers from the University of Birmingham, in collaboration with Goethe University in Frankfurt, have developed a conceptual framework that establishes the links between biodiversity dynamics and abiotic change through time and space using artificial intelligence. They ran the first proof of concept of their DNA’ time machine’ to shed light on a century of environmental change in a freshwater lake.

Their framework mainly relies on AI applied to DNA-based biodiversity, climate variables, and pollution. It is expected to help regulators to protect the planet’s existing biodiversity levels or even improve them.

Researchers recreated a 100-year-old library of biodiversity, chemical pollution, and climate change levels using sediment from the bottom of a lake in Denmark. This lake is an ideal natural experiment to test the biodiversity time machine because of its well-documented history of changes in water quality.

The continuous record of biological and environmental signals found in the sediment dates back to the beginning of the Industrial Revolution. It includes settings that were either relatively pristine or heavily altered.

Principal investigator Luisa Orsini, Professor of Evolutionary Systems Biology and Environmental Omics at the University of Birmingham and Fellow of the Alan Turing Institute explained: “We took a sediment core from the bottom of the lake and used biological data within that sediment like a time machine – looking back in time to build a detailed picture of biodiversity over the last century at yearly resolution. By analyzing biological data with climate change data and pollution levels, we can identify the factors having the biggest impact on biodiversity.”

Utilizing environmental DNA—genetic material deposited by bacteria, plants, and animals—researchers were able to create an in-depth picture of the freshwater ecosystem. With the aid of artificial intelligence, they examined the data along with pollution and climatic statistics to determine what would account for the lake’s historical loss of species.

They found that pollutants such as insecticides and fungicides, alongside increases in minimum temperature (a 1.2-1.5-degree increase), caused the most damage to biodiversity levels. These changes had yet to be identified before using traditional techniques.

The functional roles microorganisms played in the ecosystem (such as degradation and nitrogen metabolism) were also altered, suggesting that biodiversity loss may lead to loss of ecosystem functions.

Nevertheless, the DNA found in the sediment also indicated that the lake had started to heal during the previous 20 years. The area around the lake saw decreased agricultural land use, which enhanced the water quality. However, although there was an increase in biodiversity overall, the communities had changed from the (semi)pristine phase. This is problematic because different species can provide other ecosystem services, and if they cannot return to a specific location, it may be impossible to restore those services.

Niamh Eastwood, lead author and PhD student at the University of Birmingham, said: “The biodiversity loss caused by this pollution and the warming water temperature is potentially irreversible. The species found in the lake 100 years ago that have been lost will not all be able to return. It is not possible to restore the lake to its original pristine state, even though the lake is recovering. This research shows that if we fail to protect biodiversity, much of it could be lost forever.”

Dr. Jiarui Zhou, co-lead author and Assistant Professor in Environmental Bioinformatics at the University of Birmingham said“We have demonstrated the value of AI-based approaches for understanding historical drivers of biodiversity loss. As new data becomes available, more sophisticated AI models can be used further to improve our predictions of the causes of biodiversity loss.”

Environmental regulators can use the findings to identify species or ecosystems at risk from environmental change and prioritize them for intervention. The approach can also be used to determine which chemicals pose the greatest threat to biodiversity.

Journal Reference:

  1. Niamh Eastwood, Jiarui Zhou, Romain Derelle, et al. 100 years of anthropogenic impact causes changes in freshwater functional biodiversity. eLife. DOI: 10.7554/eLife.86576.3
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