Successive cycles of allopatric differentiation and secondary contact shape phylogeographical structure in an Indo-West Pacific reef fish

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Abstract Geographical barriers and sea-level fluctuations have significantly influenced the population genetic structure and evolutionary history of Indo-West Pacific (IWP) reef species. This study examines these effects in Abudefduf septemfasciatus (banded sergeant), a widely distributed egg-brooding IWP damselfish. Using 4700 genome-wide single nucleotide polymorphisms obtained from double-digest restriction site-associated DNA sequencing and a 1638-bp mitochondrial gene fragment from 106 samples across six IWP locations, we identified two main genetic clusters: one in the Indian Ocean and another in the Pacific Ocean. Within the Pacific, two distinct subclusters were detected, with overlapping ranges in Taiwan. Demographic analysis of the dataset using two-population genetic models in ∂a∂I, based on diffusion approximation, revealed asymmetric gene flow, with stronger migration from the Indian Ocean to the Pacific. Recurrent episodes of isolation and secondary contact during Pleistocene glacial cycles further shaped these genetic patterns. Our findings provide new insights into the complex phylogeography and evolutionary dynamics of banded sergeants, contributing to a broader understanding of how historical environmental changes have driven the diversification of IWP reef fishes.

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