New genetic method reveals how perch adapt to different aquatic environments

Focusing on the Eurasian perch (Perca fluviatilis), the study, recently published in Molecular Ecology, identified genetic signatures of adaptation to drastically different aquatic environments, namely dark water (acidic, nutrient-poor) and clear water lakes. This research provides insights into the molecular mechanisms that help species thrive in dark water environment, with the new method offering broad potential applications across a wide range of species.

A more complete understanding of effects of natural selection

In population genetic research, "outlier loci" are genetic variants that stand out due to their unusual frequency or strong association with environmental factors. However, deciding how to define these outliers has long been a challenge among evolutionary biologists. The dynamic outlier slicing approach allows researchers to adjust the stringency of their analysis dynamically, enabling a more nuanced exploration of how genetic variants contribute to key biological processes.

By integrating this method with genome annotation and gene ontology (GO) analysis, which groups genes by their biological function, the researchers uncovered robust patterns of genetic enrichment across regulatory regions of the genome.

“Our method provides a more detailed understanding of how genes and their functions evolve under natural selection. It gives scientists a flexible tool to evaluate the robustness of their findings and detect most consistent patterns that might otherwise be missed, ”explained María Eugenia López, researcher at SLU and lead author of the study.

Slicing through the data to find key functions

By sequencing a large number of perch genomes collected across northern Europe, the study identified around 3,000 genetic outliers across hundreds of genomic regions linked to adaptation. By meticulously slicing through those outliers, the new method revealed the importance of regulatory DNA regions in adaptation. Furthermore, dynamic outlier slicing highlighted processes vital for adaptation and survival in dark water environments, including ion channels for osmotic balance, molecular transport, and gated channels for cell stability.

“Our work shows that refining how we assess genetic outliers allows us to gain a clearer and more comprehensive understanding of adaptation,” said Anti Vasemägi, professor at SLU and senior author of the study.

Impact beyond fish

Although the study focused on Eurasian perch, the method and its findings have far-reaching implications beyond the world of fish. Dynamic outlier slicing can be applied to a wide range of species, offering deeper insights into how organisms adapt to climate change, pollution, and shifting ecosystems.

Read the article: Dynamic Outlier Slicing Allows Broader Exploration of Adaptive Divergence: A Comparison of Individual Genome and Pool-Seq Data Linked to Humic Adaptation in Perch