Abstract
Marine Protected Areas (MPAs) are widely considered to be one of the best strategies available for protecting species diversity and ecosystem processes in marine environments, particularly in developing, tropical nations. While data on connectivity and genetic structure of marine populations are critical to designing appropriately sized and spaced networks of MPAs, such data are rarely available. Here we present an assessment of genetic structure in reef-building corals from Papua and West Papua, Indonesia, among the most biologically diverse and least disturbed coral reef regions in the world, and the focus of the multi-institutional Birds Head Seascape initiative to design and implement a functional network of MPAs. Microsatellite variation was assessed within and among populations of Pocillopora damicornis (Linnaeus , 1758) and Seriatopora hystrix (Dana 1846) (family: Pocilloporidae) from three regions, each currently under a different conservation regime: Teluk Cenderawasih, Raja Ampat, and southwest Papua. Analyses of molecular variance, assignment tests, and genetical bandwidth mapping revealed significant local-scale structure in both species, and a lack of regional filters to gene flow. Overall, P. damicornis populations were less structured ( F ST = 0.139, p < 0.00001) than those of S. hystrix ( F ST = 0.357, p < 0.00001). In order to maintain connectivity within and among regions, coral reef conservation on the local scale is needed. These data have been directly applied to the design of a MPA network in the Bird’s Head Seascape.