Bayesian analyses of Pacific swordfish (Xiphias gladius L.) genetic differentiation using multilocus single nucleotide polymorphism (SNP) data

There is no consensus on the population structure of Pacific swordfish, and current-working hypotheses based on genetic and fisheries data include variations of two, three, and four stocks. In this study the hypothesis of panmixia for Pacific swordfish was tested using multilocus analyses of single-copy nuclear DNA loci on 891 swordfish collected in 16 localities. Sampling coverage differs from all previous genetic studies by offering a more comprehensive representation of tropical areas and by including early life history stages (ELS). Accordingly, samples of larvae, juveniles, and adults were characterized at 10 loci containing 20 informative SNPs, 19 of which were genotyped using high resolution melting analysis (HRMA) and one as a restriction fragment length polymorphism (RFLP). Additionally, two short sequence repeat (SSR) loci were characterized. Exact tests of genetic differentiation, analyses of molecular variance (AMOVA), principal coordinates analysis (PCoA), Bayesian analyses using STRUCTURE and GENELAND conducted on these data all rejected the hypothesis of panmixia for Pacific swordfish, and identified Taiwan as the most highly differentiated sample. Samples from temperate areas differed from most tropical samples (SST > 24 °C), but genetic heterogeneity was also detected among several tropical samples. By contrast, no differences were detected among temperate samples despite the considerable geographic distances (up to 18,000 km) separating them. Further, Bayesian analyses using both STRUCTURE and GENELAND suggested a pattern of genetic differentiation in Pacific swordfish more complex than a simple separation of tropical and temperate regions, with no clear delineation of geographic boundaries as those displayed by Atlantic swordfish. AMOVAs conducted to test models of population structure based on fisheries data failed to yield significant proportions of among-group variance. The observed patterns of genetic differentiation of Pacific swordfish are discussed in reference to studies of reproductive biology, tagging experiments, and previous genetic studies conducted on this species.