Data and code associated with: Genomic responses to parallel selection in the eelgrass Zostera marina in adjacent bays

The extent of parallel genomic responses to similar selective pressures
depends on a complex array of environmental, demographic, and evolutionary
forces. Laboratory experiments with replicated selective pressures yield
mixed outcomes under controlled conditions and our understanding of
genomic parallelism in the wild is limited to a few well-established
systems. Here, we examine genomic signals of selection in the eelgrass
Zostera marina across temperature gradients in adjacent embayments.
Although we find many genomic regions with signals of selection within
each bay, there is little overlap at the SNP level across bays. We do find
overlap at the gene level, potentially suggesting multiple mutational
pathways to the same phenotype. Using polygenic models we find that some
sets of candidate SNPs are able to predict temperature across both bays,
suggesting that small but parallel shifts in allele frequencies may be
missed by independent genome scans. Together, these results highlight the
continuous rather than binary nature of parallel evolution in polygenic
traits and the complexity of evolutionary predictability.