Population structure and adaptation in fishes: Insights from clupeid and salmonid species

Abstract

Marine fishes represent a valuable resource for the global economy and food consumption. Accordingly, many species experience high levels of exploitation necessitating effective management plans. However, long term sustainability may be jeopardized from insufficient knowledge about intra-specific population structure and adaptive divergence. The large population sizes and high migration rates common to most marine fishes impede the differentiating effect of genetic drift, having led to expectations of no population structure and that the occurrence of local adaptation should be rare in these species. Comprehensive genetic analyses on the small pelagic fish European sprat (Sprattus sprattus) revealed significant population structure throughout its distribution with an overall pattern of reduced connectivity across environmental transition zones. Population structure reflected both historical separations over glacial time scales and more recent colonisation of new habitats. Further, strong genetic divergence at several regional scales demonstrated limited connectivity among sea-going and local fjord populations along the Norwegian coast as well as indications for the potential of locally adapted populations in the brackish Baltic Sea. If forces of natural selection are able to override the homogenizing effects of high gene flow, the detection of adaptive signatures has often been constrained by a general lack of genomic resources. However, advances in sequencing technologies now enable cost-effective developments of gene-associated markers facilitating detection of adaptive divergence. To further address the potential existence of locally adapted populations in small pelagic fishes, we developed hundreds of transcriptome derived markers to identify genes affected by natural selection in Atlantic herring (Clupea harengus). Comprehensive sampling throughout the northeastern Atlantic revealed clear genetic structure among regions, and coupled with environmental inference strong signatures of divergent selection at a range of candidate genes suggested adaptation to local temperature and salinity conditions. A similar genome-scan based investigation of local adaptation was conducted in the salmonid Oncorhynchus mykiss. Despite profound socio economic importance many populations have experienced strong declines and future conservation can be improved from identification of key environmental parameters and genes expected to maintain genetic diversity among populations. In contrast to marine fishes, salmonids are characterised by low gene flow, and together with the highly diverse habitats and phenotypes found among populations this suggest amble potential for local adaptation to evolve. However, the genetic architecture and spatial scale of local adaptation is poorly known, and evidence has often been restricted to one or few genes at local scales. We found divergent selection for several genes often relating to local habitat conditions. Inference from known gene functions provided further evidence for adaptively important roles played by immune response genes. Overall, results from this PhD revealed complex patterns of population structure and evidence for locally adapted populations in small pelagic fishes as well as interesting patterns of adaptively important candidate genes in a salmonid. These results contribute to our understanding of the evolutionary processes shaping biodiversity in the wild and findings may be extended from the actual species studied to assist managing fish resources under an evolutionarily sustainable framework in the future.