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Generating genomic data for 19 tropical reef fish species of the Western Indian Ocean, we investigate how species ecology influences genetic diversity patterns from local to regional scales. We distinguish between the α , β and γ components of genetic diversity, which we subsequently link to six ecological traits. We find that the α and γ components of genetic diversity are strongly correlated so that species with a high total regional genetic diversity display systematically high local diversity. The α and γ diversity components are negatively associated with species abundance recorded using underwater visual surveys and positively associated with body size. Pelagic larval duration is found to be negatively related to genetic β diversity supporting its role as a dispersal trait in marine fishes. Deviation from the neutral theory of molecular evolution motivates further effort to understand the processes shaping genetic diversity and ultimately the diversification of the exceptional diversity of tropical reef fishes.

Coral reef ecosystems are among the first to fundamentally change in structure due to climate change, which leads to questioning of whether decades of knowledge regarding reef management is still applicable. Here we assess ecological responses to no-take marine reserves over two decades, spanning a major climate-driven coral bleaching event. Pre-bleaching reserve responses were consistent with a large literature, with higher coral cover, more species of fish, and greater fish biomass, particularly of upper trophic levels. However, in the 16 years following coral mortality, reserve effects were absent for the reef benthos, and greatly diminished for fish species richness. Positive fish biomass effects persisted, but the groups of fish benefiting from marine reserves profoundly changed, with low trophic level herbivores dominating the responses. These findings highlight that while marine reserves still have important roles on coral reefs in the face of climate change, the species and functional groups they benefit will be substantially altered.

Tropical coastal communities are highly reliant on coral reefs, which provide nutrition and employment for millions of people. Climate-driven coral bleaching events are fundamentally changing coral reef ecosystems and are predicted to reduce productivity of coral reef fish and fisheries, with significant implications for food security and livelihoods. Yet evidence of long-term bleaching impacts on coral reef fishery productivity is lacking. Here, we analyse over 20 years of fish abundance, catch and habitat data to assess long-term impacts of climate-driven coral mass mortality and regime shifts on nearshore artisanal coral reef fisheries in the Seychelles. Contrary to expectations, total catch and mean catch rates were maintained or increased after coral bleaching, consistent with increasing abundance of herbivorous target species in underwater surveys, particularly on macroalgal-dominated reefs. Catch instability increased as habitats followed divergent post-disturbance trajectories and the distribution of target species became more spatially variable, potentially impacting fisher incomes and local market supply chains. Although coral bleaching increased fishery dependence on herbivore species, our results show that climate-impacted reefs can still provide livelihoods and fish protein for coastal communities.