Data from: The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing

Understanding how genetic variation is partitioned across genomes within
and among populations is a fundamental problem in ecological and
evolutionary genetics. To address this problem, we studied the threespine
stickleback fish, which has repeatedly undergone parallel phenotypic and
genetic differentiation when oceanic fish have invaded freshwater
habitats. While significant evolutionary genetic research has been
performed using stickleback from geographic regions that have been
deglaciated in the last 20 000 years, less research has focused on
freshwater populations that predate the last glacial maximum. We performed
restriction-site associated DNA-sequencing (RAD-seq) based population
genomic analyses on stickleback from across Oregon, which was not
glaciated during the last maximum. We sampled stickleback from coastal,
Willamette Basin and central Oregon sites, analysed their genetic
diversity using RAD-seq, performed structure analyses, reconstructed their
phylogeographic history and tested the hypothesis of recent stickleback
introduction into central Oregon, where incidence of this species was only
recently documented. Our results showed a clear phylogeographic break
between coastal and inland populations, with oceanic populations
exhibiting the lowest levels of divergence from one another. Willamette
Basin and central Oregon populations formed a clade of closely related
populations, a finding consistent with a recent introduction of
stickleback into central Oregon. Finally, genome-wide analysis of genetic
diversity (π) and correlations of alleles within individuals in
subpopulations (FIS) supported a role for introgressive hybridization in
coastal populations and a recent expansion in central Oregon. Our results
exhibit the power of next-generation sequencing genomic approaches such as
RAD-seq to identify both historical population structure and recent
colonization history.