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The impact of selection, gene flow and demographic history on heterogeneous genomic divergence: three‐spine sticklebacks in divergent environments
Author(s) -
Ferchaud AnneLaure,
Hansen Michael M.
Publication year - 2016
Publication title -
molecular ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.619
H-Index - 225
eISSN - 1365-294X
pISSN - 0962-1083
DOI - 10.1111/mec.13399
Subject(s) - biology , stickleback , gasterosteus , gene flow , freshwater fish , population , parallel evolution , selection (genetic algorithm) , ecology , ecological selection , freshwater ecosystem , evolutionary biology , gene , fishery , phylogenetic tree , genetic variation , genetics , ecosystem , demography , artificial intelligence , sociology , fish <actinopterygii> , computer science
Heterogeneous genomic divergence between populations may reflect selection, but should also be seen in conjunction with gene flow and drift, particularly population bottlenecks. Marine and freshwater three‐spine stickleback ( Gasterosteus aculeatus ) populations often exhibit different lateral armour plate morphs. Moreover, strikingly parallel genomic footprints across different marine–freshwater population pairs are interpreted as parallel evolution and gene reuse. Nevertheless, in some geographic regions like the North Sea and Baltic Sea, different patterns are observed. Freshwater populations in coastal regions are often dominated by marine morphs, suggesting that gene flow overwhelms selection, and genomic parallelism may also be less pronounced. We used RAD sequencing for analysing 28 888 SNP s in two marine and seven freshwater populations in Denmark, Europe. Freshwater populations represented a variety of environments: river populations accessible to gene flow from marine sticklebacks and large and small isolated lakes with and without fish predators. Sticklebacks in an accessible river environment showed minimal morphological and genomewide divergence from marine populations, supporting the hypothesis of gene flow overriding selection. Allele frequency spectra suggested bottlenecks in all freshwater populations, and particularly two small lake populations. However, genomic footprints ascribed to selection could nevertheless be identified. No genomic regions were consistent freshwater–marine outliers, and parallelism was much lower than in other comparable studies. Two genomic regions previously described to be under divergent selection in freshwater and marine populations were outliers between different freshwater populations. We ascribe these patterns to stronger environmental heterogeneity among freshwater populations in our study as compared to most other studies, although the demographic history involving bottlenecks should also be considered in the interpretation of results.