Population genomics and molecular evolution in salmonids

Salmonid fishes are characterised by a very high level of variation in trophic, ecological, physiological, and life history adaptations to diverse environments. Some salmonid taxa show exceptional potential for fast, within-lake diversification into morphologically and ecologically distinct variants, often in parallel; these are the lake-resident charr and whitefish (several species in the genera Salvelinus and Coregonus). Such rapid diversifications can offer clues about the genetic drivers of ecological speciation by natural selection. The often high parallelism in the ecological adaptations and diversifications in Salvelinus and Coregonus species also makes it possible to assess what genetic factors are shared in lake divergences as well as amongst species of these two highly diversifying salmonids. Such sharing is often assessed by examining the overlap of signatures of natural selection across populations or species. Moreover, recent advances in ecological genomics have shown a role of introgression in distributing these shared adaptive genetic variants amongst populations. First, to infer similarities of selection signals and shared selected genes and gene functions that potentially promote the diversification potential of species, I compared the signatures of selection in the sequences of transcriptomes of the diversifying salmonids Salvelinus and Coregonus against non-diversifying salmonids. Second, I analysed the influence the often complex demographic history of diverging species has on signals of positive selection at the population level using computer simulations. Third, informed by step two, I examined the sharing of selection across five divergences of Salvelinus into benthic and pelagic ecomorphs using whole-genome resequencing. Fourth, I analysed the role of adaptive introgression in promoting diversification and local adaptation in one exemplary population of Salvelinus based on whole-genome sequences. I found evidence for limited but putatively ecologically significant sharing of genes under selection and higher sharing of gene functions and large-scale genomic regions under selection, both at the interspecies level in transcriptomes and at the interpopulation, whole-genome level in Salvelinus. The shared targets of selection in Salvelinus matched known quantitative trait loci of ecological importance in salmonids, with a predominance of genetic variants in putative regulatory regions. In an exemplary population of Salvelinus, putative adaptive introgression was shown to play a potential role in rapid diversifications. The results of this thesis support the notion that parallelism at the genetic level does not have to be pervasive in order for pronounced phenotypic parallelism to occur, implying a highly polygenic basis of most ecological adaptations