Data from: Conservation genetics of the scalloped hammerhead shark in Pacific coastal waters of Colombia

Previous investigations on the population genetics of scalloped hammerhead sharks (Sphyrna lewini) in the Eastern Tropical Pacific have lacked information about possible nursery areas. Identifying such areas is key to conservation prioritization since it clarifies distribution areas and promotes conservation initiatives that can protect young animals from threats such as overfishing. We investigated the genetic diversity, phylogeography, and connectivity of S. lewini found in three areas of Colombia’s Pacific coast: around Malpelo Island and in two National Natural Parks on the mainland, PNN Sanquianga and PNN Utría. We analyzed one mitochondrial marker (control region-CR) and genotyped 15 microsatellite loci in 137 samples; CR analyses showed haplotypes shared between the Colombian Pacific areas and areas previously sampled in the Eastern Tropical Pacific and Indo-Pacific regions, but four were unique to the Colombian Pacific. Genetic diversity at the mitochondrial level was similar to that from other Indo-Pacific regions. Population assignment and paternity analyses detected three parent–offspring pairs (POPs) between Malpelo Island and PNN Sanquianga, and one between Malpelo Island and PNN Utría. These results support genetic connectivity between Malpelo Island and the Colombian Pacific coast, suggesting that these two coastal areas are nurseries for S. lewini and require conservation planning to protect this endangered shark species.