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Abstract Many countries with tropical reef systems face hard choices preserving coral reefs in the face of climate change on limited budgets. One approach to maximising regional reef resilience is targeting management efforts and resources at reefs that export large numbers of larvae to other reefs. However, this requires reef connectivity to be quantified. To map coral connectivity in the Seychelles reef system we carried out a population genomic study of the Porites lutea species complex using 241 sequenced colonies from multiple islands. To identify oceanographic drivers of this connectivity and quantify variability, we further used a 2 km resolution regional ocean simulation coupled with a larval dispersal model to predict the flow of coral larvae between reef sites. Patterns of admixture and gene flow are broadly supported by model predictions, but the realised connectivity is greater than that predicted from model simulations. Both methods detected a biogeographic dispersal barrier between the Inner and Outer Islands of Seychelles. However, this barrier is permeable and substantial larval transport is possible across Seychelles, particularly for one of two putative species found in our genomic study. The broad agreement between predicted connectivity and observed genetic patterns supports the use of such larval dispersal simulations in reef system management in Seychelles and the wider region.

Marine protected areas can be designated for a number of reasons, but exactly how they provide benefits is only recently being understood. We assessed the effect of protection on the size and distribution of six common species of grouper in a coral reef ecosystem. Data on live coral cover, coral genus diversity, and coral colony structure type were also compared to give an indication of reef quality between sites. A significant interaction was found for Aethaloperca rogaa and Cephalopholis nigripinnis, indicating that protected areas held greater numbers of smaller and median sized fish of these species than unprotected areas. Similar but nonsignificant trends were found for Cephalopholis miniata and Cephalopholis argus. For Anyperodon leucogrammicus, MPAs held significantly more fish than unprotected sites, but as the increase was equal between size categories there was no interaction. The last species Epinephelus fasciatus, which was one of the smallest species, had no significant interaction, similar mean counts between protected and unprotected areas, and no obvious strong favouritism for particular sites with values indicating better reef quality, indicating intraspecies competition. The results of this study indicate that while the MPAs in this study are likely too small to benefit large groupers, the improvements to habitat quality have indirect benefits to groupers, especially at their earlier life stages.