Genetic Diversity and Population Structure of Squalus cf. mitsukurii (Chondrichthyes: Squalidae) Revealed by ddRAD Sequencing

Abstract

Assessing genetic structure across ocean basins is essential to understand connectivity and guide conservation in data-deficient open-water sharks. In this study, we examined the population genomics of Squalus cf. mitsukurii by analyzing tissue samples collected from two distant regions: California, USA (Pacific Ocean) and Pernambuco, Brazil (Southwestern Atlantic Ocean). Using double-digestrestriction site-associated DNA sequencing (ddRADseq), we generated 33 480 939 raw reads across 28 individuals and retained 1118 high-quality single nucleotide polymorphisms (SNPs) after stringent filtering. Genetic diversity was moderate (He = 0.211–0.244), with low inbreeding levels (Fis = −0.005–0.106). DAPC and pairwise Fst analyses revealed moderate genetic structure, indicating limited gene flow between the sampled populations. This study provides the first genomic evidence of populationdifferentiation in S. cf. mitsukurii across these regions. Our findings underscore the importance of genome-wide data and informing regionally conservation strategies, especially for exploited species commonly misidentified in commercial landings and lacking population management.