Genomic data resolve long-standing uncertainty by distinguishing white marlin (Kajikia albida) and striped marlin (K. audax) as separate species

Large pelagic fishes are often broadly distributed and capable of long-distance movements. These factors can promote gene flow that makes it difficult to disentangle intra- vs. inter-specific levels of genetic differentiation. Here, we assess the relationship of two istiophorid billfishes, white marlin (Kajikia albida) and striped marlin (K. audax), presently considered sister species inhabiting separate ocean basins. Previous studies report levels of genetic differentiation between these species that are smaller than those observed among populations of other istiophorid species. To determine whether white marlin and striped marlin comprise separate species or populations of a single globally distributed species, we surveyed 2520 single nucleotide polymorphisms (SNPs) in 62 white marlin and 242 striped marlin across the Atlantic, Pacific, and Indian oceans. Multivariate analyses resolved white marlin and striped marlin as distinct groups, and a species tree composed of separate lineages was strongly supported over a single lineage tree. Genetic differentiation between white marlin and striped marlin (F-ST = 0.5384) was also substantially larger than between populations of striped marlin (F-ST = 0.0192-0.0840), and we identified SNPs that allow unambiguous species identification. Our findings indicate that white marlin and striped marlin comprise separate species, which we estimate diverged at approximately 2.38 Mya.