Repeated selection of alternatively adapted haplotypes creates sweeping genomic remodeling in stickleback

Heterogeneous genetic divergence can accumulate across the genome when populations adapt to different habitats while still exchanging alleles. How long does diversification take and how much of the genome is affected? When divergence occurs in parallel from standing genetic variation, how often are the same haplotypes involved? We explore these questions using RAD-seq genotyping data, and show that broad-scale genomic re-patterning, fueled by copious standing variation, can emerge in just dozens of generations in replicate natural populations of threespine stickleback fish (Gasterosteus aculeatus). After the catastrophic 1964 Alaskan earthquake, marine stickleback colonized newly created ponds on seismically uplifted islands. We find that freshwater fish in these young ponds differ from their marine ancestors across the same genomic segments previously shown to have diverged in much older lake populations. Outside of these core divergent regions the genome shows no population structure across the ocean-freshwater divide, consistent with strong local selection acting in alternative environments on stickleback populations still connected by significant gene flow. Reinforcing this inference, a majority of divergent haplotypes that are at high frequency in ponds are detectable in the sea – even across great geographic distances. Building upon previous population genomics work in this model species, our data suggest that a long history of divergent selection and gene flow among stickleback populations in oceanic and freshwater habitats has maintained polymorphisms of alternatively adapted DNA sequences that facilitate parallel evolution.

Identifier
Source https://data.blue-cloud.org/search-details?step=~0128634E882536904C1664A33C9D24A65F51B37F837
Metadata Access https://data.blue-cloud.org/api/collections/8634E882536904C1664A33C9D24A65F51B37F837
Provenance
Instrument Illumina HiSeq 2500; ILLUMINA
Publisher Blue-Cloud Data Discovery & Access service; ELIXIR-ENA
Publication Year 2024
OpenAccess true
Contact blue-cloud-support(at)maris.nl
Representation
Discipline Marine Science
Spatial Coverage (-149.536W, 59.412S, -146.296E, 61.349N)
Temporal Coverage Begin 2005-07-01T00:00:00Z
Temporal Coverage End 2012-05-01T00:00:00Z