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Abstract:
Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age,
providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in
nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the
genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a
genome-wide set of loci that are consistently associated with marine–freshwater divergence. Our results indicate
that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in
repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during
early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine–
freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive
evolution in nature.
