DOI: 10.5061/dryad.6djh9w0zc
title: Data from: The genomic signature of ecological divergence along the benthic-limnetic axis in allopatric and sympatric threespine stickleback

description: 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.
description: We
 reanalyzed previously collected morphological, ecological and genomic data
 of wild-caught stickleback from British Columbia, Canada, obtained from
 several independent datasets. The genotype data for the genome-wide
 association (GWA) mapping of lake size and the F<sub>ST</sub>
 analyses among small and large lakes were generated using ddRAD sequencing
 (Peterson, Weber, Kay, Fisher, & Hoekstra, 2012) for solitary
 stickleback populations from Vancouver Island. For 21 solitary
 populations, we obtained data on the proportion of benthic diet and gill
 raker numbers (a key trophic trait). Both of these datasets are from
 Bolnick and Ballare (2020); the genomic dataset was produced by Stuart et
 al. (2017). Genotype data used for F<sub>ST</sub> analyses
 from three sympatric benthic-limnetic species pairs (Paxton, Priest and
 Little Quarry Lakes) were generated by Samuk et al. (2017) using the
 genotyping-by-sequencing method. Diet and gill raker number data for the
 sympatric species pairs from Paxton and Priest Lakes were obtained from
 Schluter and McPhail (1992). QTL data on different sympatric species pairs
 were obtained from several previous studies (Arnegard et al., 2014; Conte
 et al., 2015; Malek, Boughman, Dworkin, & Peichel,
 2012).