Cryptic diversity and phylogeography of the spotted scat Scatophagus argus (Acanthuriformes, Scatophagidae) across the Indo-West Pacific

The spotted scat, Scatophagus argus , is a commercially important euryhaline fish widely distributed in the Indo-West Pacific, yet the systematics and evolutionary history of this species remain poorly understood. We investigated the genetic diversity, phylogeography, and demographic history of S. argus using 239 mitochondrial COI sequences (129 newly determined for this study) from across its range. Haplotype network analysis identified four major haplogroups: two predominantly distributed in the Indian Ocean, one in the West Pacific, and one in Australia. Mean K2P distances among haplogroups (5.08–7.72%) greatly exceeded those within haplogroups (0.45–0.91%), indicating deeply divergent mitochondrial lineages and possible species-level cryptic diversity. The distributions of the West Pacific and Indian haplogroups overlap in the Thai-Malay Peninsula region. Whereas Pleistocene exposure of the Sunda Shelf may have driven the divergence of these haplogroups by restricting gene flow between the Indian and Pacific Oceans, their secondary contact appears to have been facilitated by the recent inundation of the Sunda Shelf, enabling range expansion and lineage admixture. Demographic analyses indicated late Pleistocene population expansion in Haplogroup I, whereas Haplogroups II and IV showed no clear expansion signal. The coexistence of three lineages of S. argus within Thai waters highlights this region as a critical zone of genetic diversity for future research. These findings underscore the need to uncover hidden diversity for effective fisheries management and conservation.