Phylogeography of commercial tuna and mackerel in the Indonesian Archipelago

While numerous population genetics studies have investigated phylogeographic patterns of coral reef organisms in the Coral Triangle, few have addressed whether fishes in the pelagic environment exhibit concordant patterns of genetic subdivision. We analyzed approximately 400 base pairs of the mitochondrial control region to compare population structure and phylogeography of five pelagic tuna and mackerel within a subset of their geographic ranges (i.e., the Indonesian Archipelago). Focal species include frigate tuna [Auxis thazard (Lacepede, 1800)], kawakawa [Euthynnus affinis (Cantor, 1849)], skipjack tuna [Katsuwonus pelamis (Linnaeus, 1758)], Indian mackerel [Rastrelliger kanagurta (Cuvier, 1816)], and narrow-barred Spanish mackerel [Scomberomorus commerson (Lacepede, 1800)]. Observed patterns of regional genetic subdivision were consistent with the role of Pleistocene vicariance in structuring populations. Divergence dates of all pelagic fish lineages dated to the Pleistocene epoch. Concordant barriers to larval dispersal found near Sumatra, Sulawesi, and Papua suggested that the Halmahera and Mindanao eddies and the Indonesian flowthrough may be contemporary forces maintaining genetic divergence between demes of pelagic fishes. Given the economic importance of these species, we suggest that the scale of management for pelagics in Indonesia be re-evaluated to reflect regional differences in the genetic composition of fishes.