Regional (south‐eastern Pacific Ocean) population genetics and global phylogeography of two endangered highly migratory pelagic sharks, the blue shark Prionace glauca and shortfin mako Isurus oxyrinchus

The blue shark Prionace glauca and the shortfin mako Isurus oxyrinchus are two large and highly migratory sharks inhabiting temperate and tropical waters worldwide that are heavily targeted by artisanal and industrial fisheries. The International Union for Nature Conservation classifies the blue shark and shortfin mako as ‘Near Threatened’ and ‘Vulnerable’, respectively, in the Nature Red List of Threatened Species v. 2019‐2. This study examined the population genetics of the shortfin mako and blue sharks at a regional (south‐eastern Pacific Ocean) and global scale. The null hypothesis of no genetic discontinuities among ocean basins and/or between hemispheres was tested using two mitochondrial markers suitable for population genetics inference in these species: the non‐coding control region and the protein‐coding gene cytochrome c oxidase I in I. oxyrinchus , and the control region and cytochrome b in P. glauca . Spatial genetic analyses suggested a single and two genetic clusters co‐occurring along the south‐eastern Pacific Ocean in the shortfin mako and blue shark, respectively. Phylogeographic analyses, migration estimates, haplotype networks and AMOVAs demonstrated that the two species exhibit an overall pattern of high genetic connectivity among hemispheres and across ocean basins with a signature of shallow genetic structuring worldwide. This study has generated valuable information for the management and conservation of heavily exploited sharks and highlights the need for additional inclusive research programmes assessing inter‐regional genomic discontinuities using more statistically powerful genetic markers to determine with precision population genetic discontinuities (if any) in these and other highly migratory sharks.