Abstract
Describing patterns of spatially‐explicit population genetic structure and connectivity is vital for well‐designed conservation or management policies for marine species. However, for species having high dispersal capabilities and large population sizes, describing significant genetic structure may be difficult. Perna canaliculus , the endemic New Zealand green‐lipped mussel, is the cornerstone species of this country's aquaculture industry. Several studies performed with various genetic marker types have revealed two distinct genetic groups (northern and southern), but no further genetic differentiation. Here, we describe the first use of ddRAD‐seq‐derived SNPs to examine the genetic structuring of P. canaliculus . Using 185 neutral and 28 outlier SNPs from 32 sampling sites, two major genetic groups (northern and south‐west—with a genetic break at ~42° S, below the Cook Strait/Raukawa Moana region) were confirmed. The use of the outlier panel revealed stronger genetic differences in allelic frequencies than markers under neutral expectations. Moreover, the SNP data provided, for the first time, evidence of substructure over the extensive range of the population that was sampled: six further genetic subgroups were identified within the two main groups. Seascape analysis revealed that genetic variation correlates strongly with variables related to food availability, habitat composition and current speed, reflecting selective pressure and genetic signals of local adaptation, suggesting these processes play a key role modulating the genetic structure of the green‐lipped mussel. Gene flow networks suggest migration from the south‐west group into the northern group. This pattern of migration is also revealed in contemporary oceanographic models of larval dispersal, which indicate high historical gene flow between the two groups, and a minor influence of genetic drift. These results offer valuable insights into the genetic structure and factors influencing genetic divergence in P. canaliculus and how genetic stocks may be managed.