Genome-wide SNPs reveal fine-scale genetic structure in ornate spiny lobster Panulirus ornatus throughout Indo-West Pacific Ocean

Abstract

Abstract Genome-wide, single nucleotide polymorphism (SNP) typing can improve the management of valuable marine species by delineating finer scale population structure compared with traditional markers. This approach was applied to the spiny lobster, Panulirus ornatus distributed in the Indo-West Pacific and is one of the most highly valuable seafood products in the world. A total of 3008 SNPs was generated from DArTseq sequencing of 224 lobsters sampled at 13 locations across the Indo-Pacific. SNPs revealed a highly significant genetic structure among samples (analysis of molecular variance FST = 0.046). Pairwise genetic comparison showed significant differences among the majority of sampling locations. Outlier loci (including an outlier SNP mapped to the CASc gene with different allele frequencies among sampling locations) revealed highly significant pairwise differentiation, especially a genetic break between regional populations in northern Australia and South East Asia. Significant pairwise differences in outliers among sampling locations, even over small geographic scales, suggest a possible role of local adaptation on the population structure. Genetic differences identified among samples from northern Australia and South East Asia are sufficient to refute the single-stock hypothesis proposed using conventional genetic markers. The results of genome-level SNPs identify five management units across the species’ range, with significant implications for the future fisheries management and aquaculture development of this species.