Although population genomics approaches have been successful in identifying regions of the genome shaped by natural selection, the progress in dissecting the molecular mechanisms of adaptive variants and traits has been slow. By integrating multi-tissue (gill, spleen, olfactory rosette, whole eye and liver) transcriptomes from 16 wild Eurasian perch (Perca fluviatilis) populations and previously identified footprints of selection based on whole genome scan, we prioritize tissues, candidate genes and putative SNP-gene expression associations involved in humic adaptation of this keystone freshwater fish. Over 5,000 differentially expressed genes (DEGs) were discovered across the five tissues. A significant excess of outlier SNPs among DEGs found in the gill and spleen tissues indicated their involvement in humic adaptation. Further, 3,617 cis-eQTLs that associate with gene expression variation in perch were identified, with approximately 9% of genes harbouring cis-eQTLs showing differential expression between humic and clear-water habitats. Several cis-eQTLs were found in the regions showing most consistent signals of selection also harbouring DEGs (chr. 5: PLAGL2, chr. 7: PPP1R8, TCHH, chr. 8: IFITM3). Thus, our integrative analyses enabled to pinpoint specific organs that play a key role in adaptation, prioritize candidate genes under divergent selection based on their expression patterns, and identify links between SNPs and transcript abundance variation. We expect that the multi-omics strategy outlined in this work provides a practical framework for understanding the genetic basis of phenotypic diversification and adaptation for wide range of species.

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 extremely 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 involves 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 highlights the next challenge moving from high-throughput outlier identification towards functional validation of causal mutations underlying phenotypic traits of ecological and evolutionary importance.