First evidence of fine-scale adaptive genetic structure in farmed populations of Mytilus mussels

In Chile, the world's second-largest mussel producer, farming of the edible Mytilus mussels relies on the collection of wild larvae and its subsequent transfer to high-density grow-out areas, primarily in northern Patagonia. Previous studies have described the species as a highly diverse panmictic unit with low spatial genetic differentiation. The genetic diversity of farmed populations and the influence of environmental heterogeneity, however, remain unexplored. This study examines the genetic structure of cultivated and wild populations in Chaparano and Bahía Ilque, two nearby locations (<50 km apart) in northern Patagonia, a region characterized by strong vertical and horizontal environmental gradients. We obtained 97,722 SNPs using Genotyping-by-Sequencing (GBS) from 91 individuals. Our results confirm low spatial genetic structure in neutral loci, suggesting high connectivity among wild populations. However, we identified 18 putatively adaptive SNPs, indicating subtle local adaptation. Notably, the farmed population in Chaparano exhibited high genetic differentiation from the adjacent wild population, likely linked to differences in maximum temperature and salinity range. These findings suggest that aquaculture conditions can impose selective pressures, even when farmed populations experience similar oceanographic conditions to wild populations. This study provides the first evidence of fine-scale adaptive differentiation in Mytilus mussels, highlighting the role of environmental variability in shaping genetic structure. Understanding these dynamics is crucial for the sustainability of mussel aquaculture as a social-ecological system, ensuring the conservation of genetic diversity and long-term resilience.