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

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.

Shared and distinct patterns of genetic structure in two sympatric large decapods

“…Our study aimed to assess and compare the extent of genetic structure in lobsters and crawfish across most of their geographical range, using thousands of SNP markers derived from restriction-siteassociated DNA (RAD) sequencing. This genotyping-by-sequencing (GBS) approach provides a powerful method for interrogating sufficient genome-wide variation to discern even weakly differentiated sub-groups (Andrews et al, 2016) and has recently improved the identification of population structuring and its evolutionary drivers in other wide-ranging, large decapods (i.e., American lobster, H. americanus- Benestan et al, 2015Benestan et al, , 2016; Ornate spiny lobster, Panulirus ornatus- Farhadi et al, 2022). We hypothesised that GBS of geographically extensive samples could reveal levels of spatial genetic heterogeneity beyond that detected to date, and that correlations with environmental and spatial gradients could identify potential drivers of differentiation.…”