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Anti Vasemägi has always been interested in fish. Even as a child, he was fascinated by aquatic life, particularly fishes. He acknowledges that such an interest is not uncommon among children, but he has made a career of it. He is currently a professor in the department of aquatic resources at the Swedish University of Agricultural Sciences (SLU), and is also a professor of aquaculture at the Estonian University of Life Sciences (EMÜ) in Tartu. His research is in evolutionary biology, genomics, population genetics, and ecology. Recent work has focused on humic substance-driven adaptation in fish, and freshwater perch in particular. “I’ve always been a fish freak,” he says.
Vasemägi and colleagues at SLU and EMÜ recently authored a paper in Molecular Ecology that sheds light on how the genomes of freshwater perch have changed in response to humic environments. Humic substances originate from degrading organic materials, such as leaves and peat that make lake water turn yellowish, brown or even black.
This process, called brownification, has been increasing in recent decades, as irrigation ditches dug in forests filter into lakes, changing their composition. While clear water allows for sunlight to reach lake bottoms, supporting photosynthesis, dark waters do not allow sunlight to penetrate, and support rich bacterial communities which subsist on humic substances. In this way, the entire ecosystems of lakes are being altered, creating highly acidic environments where most fish species are not able to reproduce and survive.
“It’s a totally different ecosystem,” says Anti. “We are interested in how a key species adapts to these extreme conditions.”
Both sides of the Baltic
The samples, obtained from eight freshwater wild perch and eight living in humic environments, were all collected from lakes in Estonia. Whole-genome sequencing was then performed within Sweden’s Science for Life Laboratory (SciLifeLab), its national research infrastructure for the advancement of molecular biosciences.
The researchers obtained sequencing data from different tissues of perch, including gill, spleen, olfactory rosette, whole eye, and liver tissue samples. They integrated this data with previously identified markers associated with selection, and were able to identify tissues, candidate genes, and SNP-gene expression associations that could be involved in the adaptation of freshwater perch to humic lakes. The researchers also found a preponderance of outlier SNPs in differentially expressed genes in gill and spleen tissues, indicating an important role in adaptation.
They also identified 2,640 cis-acting expression quantitative trait loci (eQTLs), known as cis-eQTLs, and observed an enrichment of these outliers among expression-associated SNPs in spleen and olfactory rosette tissues. Several of these eQTLs were found in the regions that showed the strongest selection signals, suggesting that natural selection has shaped the frequency of the discovered associations.
cis-eQTLs introduce heritable changes in gene expression that can enhance an organism’s fitness in specific environments. Such regulatory variations provide a substrate for natural selection to act upon, enabling populations to adapt to different environments through regulatory changes rather than alterations in protein-coding sequences.
The research presented in the new paper had various funding sources, Anti says. The scientists were supported in part by a €935,000 Estonian Research Grant awarded to paper co-author Riho Gross, a professor of aquaculture at EMÜ, and a SEK 3.7 million Swedish Research Council grant to Vasemägi. “We had people working on both sides of the Baltic,” he notes.
An integrative approach
All together, this integrative approach pointed toward specific organs that likely play an important role in adaptation, and allowed the researchers to develop a list of candidate genes under divergent selection based on their expression patterns. They were also able to identify links between SNPs in the perch genomes and variation in transcript abundance.
According to Anti, the value of the new Molecular Ecology paper is not just in the data it produced, but also in the way the researchers combined different datasets. By taking selection signals in the genome, overlaying them with multi-tissue gene expression, adding functional information layers, and identifying eQTLs linked to expression-associated SNPs, the researchers were able to discover many functional genomic links that would otherwise be unknown.
“The novel approach enabled us to combine multiple omics information layers in a more systematic way,” Anti commented. “We linked the functional genomics and evolutionary genomics perspectives,” he said.
Such approaches could also be applied in future studies, Anti notes. “Hopefully, this can be used in wide range of species,” he says. “It doesn’t have to be in perch. It doesn’t even have to be fish.”
Future uses
But what real-world value does such knowledge have? By better understanding how selection works, scientists can understand the population structuring of perch in different environments. They can also understand how different fish populations are connected to each other, Anti says.
“Understanding how selection shapes genome variation can be useful in perch aquaculture,” Anti says.
Anti notes that lakes have become increasingly humic over the past half century because of forest management. “It’s a global trend, the trend of waters getting more humic. Freshwaters are getting browner,” he says. “Digging ditches for draining forests has affected our lakes.”
This article is written by Justin Petrone. This article was funded by the European Regional Development Fund through Estonian Research Council.
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