The genomic basis of adaptive evolution in threespine sticklebacks

TLDR

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. The study develops a high‑quality reference genome assembly for threespine sticklebacks. The authors sequenced genomes from twenty additional individuals across global marine and freshwater populations to identify loci consistently linked to marine‑freshwater divergence. The study shows that globally shared standing genetic variation, including chromosomal inversions, drives repeated marine‑freshwater divergence, with both coding and regulatory changes present but regulatory changes predominating.

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.