Phylogeography of a pearl oyster ( P inctada maxima ) across the I ndo‐ A ustralian A rchipelago: evidence of strong regional structure and population expansions but no phylogenetic breaks

This study investigates the genetic structure and phylogeography of a broadcast spawning bivalve mollusc, P inctada maxima , throughout the I ndo‐ W est P acific and northern A ustralia. DNA sequence variation of the mitochondrial cytochrome oxidase subunit I ( COI ) gene was analysed in 367 individuals sampled from nine populations across the I ndo‐ W est P acific. Hierarchical AMOVA indicated strong genetic structuring amongst populations (Φ ST  = 0.372, P  < 0.001); however, sequence divergence between the 47 haplotypes detected was low (maximum 1.8% difference) and no deep phylogenetic divergence was observed. Results suggest the presence of genetic barriers isolating populations of the S outh C hina S ea and central I ndonesian regions, which, in turn, show patterns of historical separation from northern A ustralian regions. In P . maxima , historical vicariance during P leistocene low sea levels is likely to have restricted planktonic larval transport, causing genetic differentiation amongst populations. However, low genetic differentiation is observed where strong ocean currents are present and is most likely due to contemporary larval transport along these pathways. Geographical association with haplotype distributions may indicate signs of early lineage sorting arising from historical population separations, yet an absence of divergent phylogenetic clades related to geography could be the consequence of periodic pulses of high genetic exchange. We compare our results with previous microsatellite DNA analysis of these P . maxima populations, and discuss implications for future conservation management of this species. © 2012 The L innean S ociety of L ondon, B iological J ournal of the L innean S ociety , 2012, 107 , 632–646.