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Mesophotic reefs are found at depths of the ocean defined by the amount of incident light (1%–10% of light found at the surface). These ecosystems remain unexplored in many regions, including the Pacific region along the coast of Mexico, given the difficulty of accessing them using traditional methods, such as scuba. Using a remotely operated vehicle, we characterized fish assemblages across rock and sand habitat at mesophotic depths around continental islands in the Gulf of California and oceanic islands in the Revillagigedo Archipelago in Mexico. We conducted 78 video-transect surveys and identified observed fish to the lowest taxonomic level possible. Using species’ presence per video-transect, we calculated traditional diversity indices (species richness, taxonomic distinctness, and trophic level) and functional indices (number of functional entities, functional richness, and functional volume) for each island group and habitat type. The model results indicated that habitat type was the most important factor for predicting mesophotic fish diversity. The functional indices showed higher values for the rocky reefs of oceanic islands than for the sandy habitats, driven primarily by the presence of elasmobranchs and commercially important transpacific species. While the values of taxonomic distinctness and functional diversity could indicate that the mesophotic reefs in the oceanic island group are more ecologically intact than those around the continental islands, it will require more exploration to determine if this condition persists over time and if these ecosystems could serve as refuges for commercial fish species against the increasing number of disturbances impacting shallow reefs.
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