Data from: Population genomics reveals multiple drivers of population differentiation in a sex-role-reversed pipefish

A major goal of molecular ecology is to identify the causes of genetic and
phenotypic differentiation among populations. Population genomics is
suitably poised to tackle these key questions by diagnosing the
evolutionary mechanisms driving divergence in nature. Here, we set out to
investigate the evolutionary processes underlying population
differentiation in the Gulf pipefish, Syngnathus scovelli. We sampled
approximately 50 fish from each of 12 populations distributed from the
Gulf coast of Texas to the Atlantic coast of Florida and performed
restriction-site-associated DNA sequencing to identify SNPs throughout the
genome. After imposing quality and stringency filters, we selected a panel
of 6348 SNPs present in all 12 populations, 1753 of which were not
physically linked. We identified a genome-wide pattern of isolation by
distance, in addition to a more substantial genetic break separating
populations in the Gulf of Mexico from those in the Atlantic. We also used
several divergence outlier approaches and tests for genotype–environment
correlations to identify 400 SNPs putatively involved in local adaptation.
Patterns of phenotypic differentiation and variation diverged from the
overall genomic pattern, suggesting that selection, phenotypic plasticity
or demographic factors may be shaping phenotypes in distinct populations.
Overall, our results suggest that population divergence is driven by a
variety of factors in S. scovelli, including neutral processes and
selection on multiple traits.