Ice ages and butterflyfishes: Phylogenomics elucidates the ecological and evolutionary history of reef fishes in an endemism hotspot

Joseph DiBattista, Michael E. Alfaro, Laurie Sorenson, John H. Choat, Jean-Paul A. Hobbs, Tane Sinclair-Taylor, Luiz A. Rocha, Jonathan Chang, Osmar J. Luiz, Peter F. Cowman, Matt Friedman, Michael L. Berumen

Research output: Contribution to journalArticlepeer-review

10 Scopus citations


For tropical marine species, hotspots of endemism occur in peripheral areas furthest from the center of diversity, but the evolutionary processes that lead to their origin remain elusive. We test several hypotheses related to the evolution of peripheral endemics by sequencing ultraconserved element (UCE) loci to produce a genome-scale phylogeny of 47 butterflyfish species (family Chaetodontidae) that includes all shallow water butterflyfish from the coastal waters of the Arabian Peninsula (i.e., Red Sea to Arabian Gulf) and their close relatives. Bayesian tree building methods produced a well-resolved phylogeny that elucidated the origins of butterflyfishes in this hotspots of endemism. We show that UCEs, often used to resolve deep evolutionary relationships, represent an important tool to assess the mechanisms underlying recently diverged taxa. Our analyses indicate that unique environmental conditions in the coastal waters of the Arabian Peninsula probably contributed to the formation of endemic butterflyfishes. Older endemic species are also associated with narrow versus broad depth ranges, suggesting that adaptation to deeper coral reefs in this region occurred only recently (
Original languageEnglish (US)
Pages (from-to)10989-11008
Number of pages20
JournalEcology and Evolution
Issue number22
StatePublished - Oct 23 2018

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledged KAUST grant number(s): CRG-1-2012-BER-002
Acknowledgements: This work was supported by the KAUST Office of Competitive Research Funds under Award No. CRG-1-2012-BER-002 and baseline research funds to M.L.B.; National Geographic Society Grant 9024-11 to J.D.D.; National Science Foundation grant DEB-0842397 to M.E.A.; California Academy of Sciences funding to L.A.R; Australia Research Council Discovery ECR Award DE170100516 to P.F.C. For support in Socotra, we kindly thank the Ministry of Water and Environment of Yemen, staff at the Environment Protection Authority Socotra, and especially Salah Saeed Ahmed, Fouad Naseeb and Thabet Abdullah Khamis, as well as Ahmed Issa Ali Affrar from Socotra Specialist Tour for handling general logistics. For logistic support elsewhere, we thank Eric Mason at Dream Divers, Nicolas Prévot at Dolphin Divers and the crew of the M/V Deli in Djibouti, David Pence, the KAUST Coastal and Marine Resources Core Lab and Amr Gusti, the Administration of the British Indian Ocean Territory and Chagos Conservation Trust, the Ministry of Agriculture and Fisheries in Oman including Abdul Karim, the Ministère de la Pêche et des Résources Halieutiques – Madagascar, the Western Australia Department of Fisheries, Parks Australia, as well as the University of Milano-Bicocca Marine Research and High Education Centre in Magoodhoo, the Ministry of Fisheries and Agriculture, Republic of Maldives, and the community of Maghoodhoo, Faafu Atoll. For specimen collections, we thank David Bellwood, Brian Bowen, John Burns, Darren Coker, Richard Coleman, Joshua Copus, Joshua Drew, Iria Fernandez-Silva, Michelle Gaither, Brian Greene, Elliott Jessup, Randy Kosaki, Jason Leonard, Keo Lopes, Sarah Longo, Cassie Lyons, Jennifer McIlwain, Gerrit Nanninga, David Pence, Mark Priest, Richard Pyle, Frédéric Ramahatratra, Mark Royer, Pablo Saenz-Agudelo, Anne Sheppard, Charles Sheppard, Jacqueline Troller, Daniel Wagner, Robert Whitton, and members of the Reef Ecology Lab at KAUST. For assistance with bench work at KAUST we thank Craig Michell. We also acknowledge important contributions from Robert J. Toonen, John E. Randall, Jo-Ann C. Leong, and David Catania for assistance with specimen archiving, and the KAUST Bioscience Core Laboratory with Sivakumar Neelamegam and Hicham Mansour for their assistance with Illumina sequencing. Special thanks to Scott Partridge for the use of his illustrations of the Chaetodontidae family.


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