Data from: Region-wide and ecotype-specific differences in demographic histories of threespine stickleback populations, estimated from whole genome sequences

We analysed 81 whole genome sequences of threespine sticklebacks from
Pacific North America, Greenland and Northern Europe, representing 16
populations. Principal component analysis of nuclear SNPs grouped
populations according to geographical location, with Pacific populations
being more divergent from each other relative to European and Greenlandic
populations. Analysis of mitogenome sequences showed Northern European
populations to represent a single phylogeographical lineage, whereas
Greenlandic and particularly Pacific populations showed admixture between
lineages. We estimated demographic history using a genomewide coalescence
with recombination approach. The Pacific populations showed gradual
population expansion starting >100 Kya, possibly reflecting
persistence in cryptic refuges near the present distributional range,
although we do not rule out possible influence of ancient admixture. Sharp
population declines ca. 14–15 Kya were suggested to reflect founding of
freshwater populations by marine ancestors. In Greenland and Northern
Europe, demographic expansion started ca. 20–25 Kya coinciding with the
end of the Last Glacial Maximum. In both regions, marine and freshwater
populations started to show different demographic trajectories ca. 8–9
Kya, suggesting that this was the time of recolonization. In Northern
Europe, this estimate was surprisingly late, but found support in
subfossil evidence for presence of several freshwater fish species but not
sticklebacks 12 Kya. The results demonstrate distinctly different
demographic histories across geographical regions with potential
consequences for adaptive processes. They also provide empirical support
for previous assumptions about freshwater populations being founded
independently from large, coherent marine populations, a key element in
the Transporter Hypothesis invoked to explain the widespread occurrence of
parallel evolution across freshwater stickleback populations.