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.
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- Supplementary Information (8.1M)
This file contains Supplementary Methods and Data, Supplementary Figures 1-10 and Supplementary Tables 1-10. The Supplementary Figures and Tables contain additional details on the genome assembly; gene annotation, sampled populations; morphometric analysis; number and details regarding the SOM/HMM and CSS methods; additional example loci; genome-wide summary of re-sequencing data; specific features of marine–freshwater divergent regions; and chromosome inversions.
- Supplementary Data (59K)
This file contains data supporting the conclusions in Figure 6, specifically genes located in the 81 regions jointly identified by both the SOM/HMM and the CSS methods. Annotations on protein coding changes and gene expression differences are also included.