This project aims to identify the molecular mechanisms and ecological consequences of adaptation in various fish species, such as Eurasian perch, European catfish and salmonids. In addition, intra-specific variation of fish parasites and parasite-host interactions will be evaluated using NGS approach. For perch, we will combine whole-genome sequencing, analysis of archival and contemporary samples, experiments measuring ecologically relevant phenotypic variation and whole organism performance to: 1) identify parallel humic substance-driven selective footprints in boreal lakes based on whole-genome SNP analysis; 2) detect genomic regions and genes affected by contemporary brownification (recent climate change-driven increase in coloured dissolved organic carbon) based on whole-genome SNP analysis of archived samples. In catfish, we are carrying out RNAseq differential expression analysis and genomic variant analysis from PoolSeq data. In salmonids, we are carrying out targeted SNP-chip analysis and dual RNAseq analysis.