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Analysis of American Eels Finds Genetic Component to Fresh, Brackish Water Habitat Survival

NEW YORK (GenomeWeb) – A genetic analysis of American eels by a team of Canadian researchers has shown that there is a genetic basis for whether they thrive in brackish or fresh water.

Brackish or fresh water-dwelling American eels belong to the same, random-mating species, Anguilla rostrada, and travel to the same spot in the Sargasso Sea in the North Atlantic Ocean to spawn, but settle in different environments. Freshwater eels tend to grow and mature more slowly, and are more likely to be female. Phenotypic plasticity, it was thought, accounted for these differences.

But as the University of Laval's Scott Pavey and his colleagues reported in Current Biology today, that doesn't appear to be the case. Instead, through a genome-wide association study, they found more than 300 loci that consistently co-vary with eel ecotype.

"People have considered these differences in growth and age to be 100 percent due to phenotypic plasticity, independent of the genotype," first author Pavey said in a statement. "But what we found is that genes affect whether an eel can survive freshwater or brackish environments."

Pavey and his colleagues collected genetic samples from yellow and silver eels living in eight different freshwater and brackish water locations in the Atlantic Canada and St. Lawrence River regions. Through a GWAS using restriction-site-associated DNA markers, or RAD tags, they searched for genetic variations linked to these ecotypes.

Some 331 SNPs, they reported, were associated with whether an eel lived in brackish or freshwater. Of these, more than half are nearly fixed in one ecotype — 137 markers in freshwater-living eels and 45 in brackish water-living eels.

Of these 331 SNPs, 99 were associated with 101 annotated protein-coding genes from the still-unpublished eel genome. Seven SNPs could be traced to exonic regions, one to a 3' UTR, and the others to interior introns. Five of the seven exonic mutations were non-synonymous, the researchers found. The 91 divergent SNPs in interior introns are likely involved somehow in cis regulation, they added.

The protein-coding regions near these 331 SNPs were enriched for development-related Gene Ontology terms, especially respiratory, cardiac, and limb bud development.

In particular, the freshwater module is enriched for genes involved in transcription factor and calcium ion binding. The Ut2 gene, which is a urinary transporter, could represent an adaptation that the freshwater fish need for their journey through saltwater to return to their spawning grounds, the researchers said, noting the SNP they recovered in this gene was fixed in the freshwater ecotype.

Meanwhile, the brackish/saltwater module is enriched for genes involved in growth factor receptor binding, positive regulation of chemotaxis, and respiratory system development.

Pavey and his colleagues suggested that one of two mechanisms could result in consistent genetic differences between habitat ecotypes, despite random mating: genotype-dependent habitat choice or intra-generational spatially variable selection.

Previous work, they noted, supports both of these possibilities. When given the choice, some eels will move toward saltier water while others prefer freshwater, and if those groups are similar genetically, that could support the former mechanism. Similarly, modeling has suggested that within-generation selection can lead to differences in quantitative traits.

"Although we cannot rule out or definitively support either of the two hypotheses regarding the mechanism (or their interaction), we do demonstrate that there are polygenic genetic differences between the ecotypes that are sufficient enough to correctly reassign them blindly to their habitat of origin," Pavey and his colleagues wrote in their paper.

That these eel populations differ genetically could also inform strategies aimed at their conservation, the researchers added.

While the American eel has failed to receive protection under the US Endangered Species Act, its numbers are dwindling. Efforts to move eels from abundant rearing areas to freshwater areas have failed, and the researchers suggested that their finding of a genetic aspect behind the divergent ecotypes could help explain that failure and inform strategies to protect genetic diversity in eels.