Mesophotic coral ecosystems (MCEs; reefs 30–150 m depth) are poorly studied, with existing research heavily geographically biased away from the most species-rich reef regions. Yet, MCEs are of high interest because of their unique species and potential to act as refuges from the impacts of fishing. Using baited remote underwater video systems, we surveyed reef fish communities from 2 to 85 m depths throughout the Raja Ampat archipelago in West Papua, Indonesia—an area considered the heart of the Coral Triangle where coral reef biodiversity is greatest. We sought to provide the first assessment of fish communities across this depth gradient in the region and identify whether human population density and market access differently affected fish abundance based on depth. Here we show that—similar to shallow reefs—Raja Ampat MCEs are exceptionally diverse, with 152 fish species recorded at depths greater than 40 m. We found that fish community structures were highly depth driven, with declines in fish abundance at increased depth. In contrast to previous studies elsewhere in the world, we found that the proportion of planktivores declined across the shallow reef to MCE depth gradient. While greater human population density correlated with lower Epinephelidae and Lutjanidae abundance (two key fisheries families), we did not find evidence that MCEs provide a depth refuge from fishing. Surprisingly, we also found that fish abundance declined at greater distances from the major regional market—likely caused by historical fisheries pressure in more remote areas. These results both expand upon and contrast some previously established MCE-depth patterns and human impact patterns on fish communities, suggesting that regional context and historical pressures matters. Our findings highlight the need for future MCE studies within the Coral Triangle region.

21Mesophotic coral ecosystems (MCEs; reefs 30-150 m depth) are poorly studied, with 22 existing research heavily geographically biased away from the most species-rich reef 23regions. Yet, MCEs are of high interest because of their unique species and potential to act 24 as refuges from the impacts of fishing. Using baited remote underwater video systems, we 25 surveyed reef fish communities from depths of 2 to 85 m throughout the Raja Ampat 26 archipelago in West Papua, Indonesia -an area considered the heart of the Coral Triangle 27where coral reef biodiversity is greatest. Here we show-similar to shallow reefs-Raja 28Ampat MCEs are exceptionally diverse, with 152 fish species recorded at depths greater 29 than 40 m. We found that fish communities were highly depth driven, with declines in fish 30 abundance at increased depth. In contrast to previous studies elsewhere in the world, we 31 found that the proportion of planktivores declined across the shallow reef to MCE depth 32 gradient. While greater human population density correlated with lower reef fish biomass, 33we did not observe differential impacts based on depth, and so found no evidence that 34MCEs provide a depth refuge from fishing. Our results expand and contrast some previously 35 established MCE-depth patterns in fish communities, highlighting the need for future MCE 36

We present the first mitochondrial genomes from Chagos Archipelago, Indian Ocean, of three putative species of reef forming Acropora (Acropora aff. tenuis, Acropora aff. cytherea and Acropora aff. orbicularis). The circular genome consists respectively of 18,334 bp, 18,353 bp and 18,584 bp. All mitochondrial genomes recovered comprise 13 protein-coding genes, two transfer RNA genes and two ribosomal RNA genes, with an overall GC content ranging from 37.9% to 38.0%. These new genomic data contribute to our increased understanding of genus Acropora and its species boundaries, ultimately aiding species monitoring and conservation efforts.