Population connectivity of the European squid Loligo vulgaris along the West Iberian Peninsula coast: comparing mtDNA and SNPs

Abstract Understanding genetic diversity and population connectivity in marine organisms is essential for fisheries management. In the present study, we examined the population genetics of the European squid, Loligo vulgaris , along the western Iberian Peninsula at two genetic resolutions using the mitochondrial cytochrome oxidase subunit I gene (COI) and genomic markers obtained via double digest restriction-site associated DNA sequencing (ddRADseq). The results obtained revealed 79 haplotypes out of 160 COI sequences, while the SNP data set included 86,431 loci after filtering for 38 individuals with 86,319 neutral data. Mitochondrial COI analyses revealed high haplotype (0.961) and nucleotide (0.010) diversities, and the haplotype network reveals complex sub-structure in Turkish waters within a panmictic population. Both Tajima’s D and Fu’s Fs tests suggest that the population of L. vulgaris analysed is evolving neutrally. Pairwise F st for neutral SNPs were low (0 < F st <0.002) and not significant showing high homogeneity among populations, while pairwise comparations for candidate adaptive SNPs (112 loci) showed F st values ranging from 0.026 to 0.234. While neutral SNPs showed admixture, the candidate adaptive SNPs showed a moderate significant structure with a latitudinal discrimination. Overall, both genetic approaches showed homogeneity and strong genetic flux identifying a unique population along the Western Iberian Peninsula.