Extensive connectivity limits spatial and bathymetric genetic differentiation in the exploited deep-shelf shrimp Heterocarpus reedi

Understanding the population genetic structure of exploited marine species is essential for informing effective management and conservation strategies. The Chilean nylon shrimp, Heterocarpus reedi, is the most commercially important demersal crustacean along the Chilean coast, yet its population connectivity across broad spatial and bathymetric gradients remains poorly resolved. Here, we use genome-wide single nucleotide polymorphisms (SNPs) to investigate patterns of genetic variation in H. reedi across approximately 1,100 km of coastline and a 140m of depth range. Analyses revealed low overall genetic differentiation and high connectivity across the species’ fishery range in the Chilean Coast, consistent with extensive gene flow in the marine environment. In 117,656 SNPs, no loci showed signals of diversifying selection across multiple independent runs, indicating limited evidence for spatially structured adaptive divergence. Accordingly, population structure was primarily evaluated using putatively neutral loci. These analyses uncovered subtle but statistically significant genetic structure, with both geographic distance (isolation by distance) and depth (isolation by depth) explaining comparable proportions of genetic differentiation. This suggests that horizontal and vertical gradients jointly influence connectivity, despite overall genetic homogeneity. Neutral processes dominate population genetic structure, while depth-related and spatial effects contribute weak but detectable deviations from panmixia. This study provides a genetic baseline for sustainable management of an intensively exploited deep-sea species and highlights the importance of considering both latitudinal and bathymetric dimensions in population genetic assessments, monitoring and management, of demersal marine taxa.