Genomics of humic adaptation in Eurasian perch (Perca fluviatilis): SNP genotypes of 32 perch individuals, supplementary figures and tables

Extreme environments are inhospitable to the majority of species, but some
organisms are able to survive in such hostile conditions due to
evolutionary adaptations. For example, modern bony fishes have colonized
various aquatic environments, including perpetually dark, hypoxic,
hypersaline and toxic habitats. Eurasian perch (Perca fluviatilis) is
among the few fish species of northern latitudes that is able to live in
very acidic humic lakes. Such lakes represent almost “nocturnal”
environments; they contain high levels of dissolved organic matter, which
in addition to creating a challenging visual environment, also affects a
large number of other habitat parameters and biotic interactions. To
reveal the genomic targets of humic-associated selection, we performed
whole-genome sequencing of perch originating from 16 humic and 16
clear-water lakes in northern Europe. We identified over 800,000 SNPs, of
which >10,000 were identified as potential candidates under
selection (associated with >3,000 genes) using multiple outlier
approaches. Our findings suggest that adaptation to the humic environment
may involve hundreds of regions scattered across the genome. Putative
signals of adaptation were detected in genes and gene families with
diverse functions, including organism development and ion transportation.
The observed excess of variants under selection in regulatory regions
highlights the importance of adaptive evolution via regulatory elements,
rather than via protein sequence modification. Our study demonstrates the
power of whole-genome analysis to illuminate multifaceted nature of humic
adaptation and provides the foundation for further investigation of causal
mutations underlying phenotypic traits of ecological and evolutionary
importance.