Phylogeography of Indo-Pacific Coral Reef Fishes

Abstract

The Indo-Pacific represents the world’s most species-rich marine biogeographic realm, housing approximately 4,000 reef fish species whose distributional limits, population connectivity, and historical diversification patterns remain incompletely resolved. This study conducted a comprehensive phylogeographic analysis of eight broadly distributed Indo-Pacific coral reef fish species spanning five families — Acanthurus leucosternon, Chaetodon auriga, Amphiprion ocellaris, Thalassoma lunare, Lutjanus kasmira, Epinephelus merra, Pterois volitans, and Siganus javus —sampled from 36 reef sites across the Indian Ocean, Coral Triangle, and central Pacific (n = 1,248 individuals). Mitochondrial cytochrome b and control region sequences (combined 1,842 bp) were analysed using haplotype network, AMOVA, isolation-by-distance, and Bayesian skyline plot methods. Significant genetic structure was detected in six of eight species (AMOVA ΦST range: 0.08–0.42; all p < 0.001), with population differentiation generally increasing with pelagic larval duration (PLD) inversely (r= -0.74, p = 0.036). Species with PLD < 20 days showed strong oceanographic barrier effects at the Sunda Shelf and the Indo-Pacific Barrier, while species with PLD > 30 days showed near-panmixia across ocean basins. Bayesian skyline plots revealed Pleistocene population expansions in five species coinciding with the Last Glacial Maximum sea-level low-stand (18–12 ka), consistent with reef habitat recolonisation from glacial refugia. Isolation-by-distance patterns were significant for four species (Mantel r range: 0.42–0.68, all p < 0.05),indicating that larval dispersal along stepping-stone reef networks drives gene flow more strongly than direct oceanographic connectivity. These findings provide empirically grounded connectivity estimates for marine protected area network design in the Indo-Pacific biodiversity hotspot.