Data from: The genomic signature of ecological divergence along the benthic-limnetic axis in allopatric and sympatric threespine stickleback

The repeated occurrence of similar phenotypes in independent lineages
(i.e., parallel evolution) in response to similar ecological conditions
can provide compelling insights into the process of adaptive evolution. An
intriguing question is to what extent repeated phenotypic changes are
underlain by repeated changes at the genomic level and whether patterns of
genomic divergence differ with the geographic context in which populations
evolve. Here, we combine genomic, morphological and ecological datasets to
investigate the genomic signatures of divergence across populations of
threespine stickleback (Gasterosteus aculeatus) that adapted to
contrasting ecological niches (benthic or limnetic) in either sympatry or
allopatry. We found that genome-wide differentiation (FST) was an order of
magnitude higher and substantially more repeatable for sympatric benthic
and limnetic specialists compared to allopatric populations with similar
levels of ecological divergence. We identified genomic regions
consistently differentiated between sympatric ecotypes that were also
differentiated between or associated with benthic vs. limnetic niche in
allopatric populations. These candidate regions were enriched on three
chromosomes known to be involved in the benthic-limnetic divergence of
threespine stickleback. Some candidate regions overlapped with QTL for
body shape and trophic traits such as gill raker number, traits that
strongly differ between benthic and limnetic ecotypes. In sum, our study
shows that magnitude and repeatability of genomic signatures of ecological
divergence in threespine stickleback highly depend on the geographic
context. The identified candidate regions provide starting points to
identify functionally important genes for the adaptation to benthic and
limnetic niches.