Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding

Mathon, Laetitia and Marques, Virginie and Mouillot, David and Albouy, Camille and Andrello, Marco and Baletaud, Florian and Borrero-Pérez, Giomar H. and Dejean, Tony and Edgar, Graham J. and Grondin, Jonathan and Guerin, Pierre-Edouard and Hocdé, Régis and Juhel, Jean-Baptiste and Kadarusman and Maire, Eva and Mariani, Gael and McLean, Matthew and Polanco F., Andrea and Pouyaud, Laurent and Stuart-Smith, Rick D. and Sugeha, Hagi Yulia and Valentini, Alice and Vigliola, Laurent and Vimono, Indra B. and Pellissier, Loïc and Manel, Stéphanie (2022) Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding. Proceedings of the Royal Society B: Biological Sciences, 289 (1973). ISSN 0962-8452

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Abstract

Increasing speed and magnitude of global change threaten the world's biodiversity and particularly coral reef fishes. A better understanding of large-scale patterns and processes on coral reefs is essential to prevent fish biodiversity decline but it requires new monitoring approaches. Here, we use environmental DNA metabarcoding to reconstruct well-known patterns of fish biodiversity on coral reefs and uncover hidden patterns on these highly diverse and threatened ecosystems. We analysed 226 environmental DNA (eDNA) seawater samples from 100 stations in five tropical regions (Caribbean, Central and Southwest Pacific, Coral Triangle and Western Indian Ocean) and compared those to 2047 underwater visual censuses from the Reef Life Survey in 1224 stations. Environmental DNA reveals a higher (16%) fish biodiversity, with 2650 taxa, and 25% more families than underwater visual surveys. By identifying more pelagic, reef-associated and crypto-benthic species, eDNA offers a fresh view on assembly rules across spatial scales. Nevertheless, the reef life survey identified more species than eDNA in 47 shared families, which can be due to incomplete sequence assignment, possibly combined with incomplete detection in the environment, for some species. Combining eDNA metabarcoding and extensive visual census offers novel insights on the spatial organization of the richest marine ecosystems.