Genome-wide SNPs reveal complex fine scale population structure in the California market squid fishery (Doryteuthis opalescens)

Abstract

Understanding the extent and distribution of population structure and genetic connectivity of fisheries targets are crucial for informing management. This study uses population genomics to examine patterns of genetic structure of the market squid (Doryteuthis opalescens), one of the most important commercially harvested species in California. Data from 662 single nucleotide polymorphism (SNP) loci from a total of 149 individuals representing five monthly sampling groups (May–September 2014) in the Northern (Monterey) and Southern (Southern California) regions of the fishery (n = 8) revealed no significant genetic differentiation between regions (FST = 0.008, p > 0.05, FCT = − 0.006, p > 0.05). However, discriminant analysis of principal components and pairwise comparisons of genetic differentiation revealed unexpected complex patterns of fine-scale population structure over time. These results suggest the existence of smaller potentially genetically varied micro-cohorts that continually spawn in California, as opposed to the prevailing notion that spawning occurs in two asynchronous peaks in the Northern and Southern regions of the fishery, with important implications for fisheries management.