Population structure of Chilean blue mussel (Mytilus chilensis) in Southern Chile assessed by neutral and adaptive genetic variation

Like many marine invertebrates, Chilean blue mussel (Mytilus chilensis) populations have been thought to be panmictic with limited genetic structure due to pelagic larvae. However, advances in genotyping-by-sequencing technology have enabled investigation of adaptive genetic variation that may identify outlier loci that better distinguish populations that have evolved in different environments.  We studied 190 mussels sampled in 6 locations from southern Chile: 4 from Reloncaví Gulf and estuary, one from southern Chiloe Island and one from Magallanes with 2,165 SNP loci obtained with RAD-seq. Differentiation among collections with 891 neutral loci was very low as expected (F_ST = 0.0072). On the other hand, differentiation among all six collections was much higher with putative outlier loci 58 (F_ST = 0.1139) and indicated potential for local adaptation. DAPC results with these 58 outlier loci demonstrated that much of the differentiation could be attributed to the three major regions and environments that M. chilensis occupy: extreme conditions in Patagonia (Magallanes) influenced by Cape Horn current, inner bay collections influenced by freshwater (four locations from Reloncaví), and outer bay saltwater collection (Chiloe Island) influenced by Humboldt current. The southern Patagonia collection from Magallanes was most distinct, but additional outlier tests with this collection excluded revealed that adaptive divergence remained between inner and outer bay collections (34 candidate loci, F_ST= 0.0886). The four locations from the inner bay area of Reloncaví were largely panmictic with all panels of markers, likely due to similar environments and high gene flow from aquaculture activities and low geographic distance. However, our results show that it is possible to separate inner and outer bay populations in the culture area, with individual assignment of 100% to Magallanes, 84% to Chiloe Island and 35% to Reloncaví area, providing the opportunity for traceability of aquaculture production. Overall, this study demonstrates how adaptive genetic variation can be utilized for applications related to human propagation and distribution of species with high gene flow.