Data from: Adaptive genetic variation distinguishes Chilean blue mussels (Mytilus chilensis) from different marine environments

Chilean mussel populations have been thought to be panmictic with limited
genetic structure. Genotyping-by-sequencing approaches have enabled
investigation of genome-wide variation that may better distinguish
populations that have evolved in different environments. We investigated
neutral and adaptive genetic variation in Mytilus from six locations in
southern Chile with 1,240 SNP obtained with RAD-seq. Differentiation among
locations with 891 neutral SNPs was low (FST = 0.005). Higher
differentiation was obtained with a panel of 58 putative outlier SNPs (FST
= 0.114) indicating the potential for local adaptation. This panel
identified clusters of genetically related individuals and demonstrated
that much of the differentiation (~92%) could be attributed to the three
major regions and environments: extreme conditions in Patagonia, inner bay
influenced by aquaculture (Reloncaví́), and outer bay (Chiloé Island).
Patagonia samples were most distinct, but additional analysis carried out
excluding this collection also revealed adaptive divergence between inner
and outer bay samples. The four locations within Reloncaví́ area were most
similar with all panels of markers, likely due to similar environments,
high gene flow by aquaculture practices and low geographic distance.
However, fine scale structure could be detected when analyses included
only this zone. Our results and the SNP markers developed will be a
powerful tool supporting management and programs of this harvested
species.