Phylogeography of Indo-Pacific Coral Reef Fishe

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 FST 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