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Couëdel M, Dettai A, Guillaume MMM, Bruggemann F, Bureau S, Frattini B, Verde Ferreira A, Azie J, Bruggemann JH. New insights into the diversity of cryptobenthic Cirripectes blennies in the Mascarene Archipelago sampled using Autonomous Reef Monitoring Structures (ARMS). Ecol Evol 2023; 13:e9850. [PMID: 36937067 PMCID: PMC10019914 DOI: 10.1002/ece3.9850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/25/2023] [Accepted: 01/30/2023] [Indexed: 03/18/2023] Open
Abstract
Autonomous Reef Monitoring Structures (ARMS) are artificial mini-reefs designed for standardized sampling of sessile and small motile cryptobenthic organisms. ARMS are also effective for collecting small cryptobenthic fishes, such as the combtooth blennies of the genus Cirripectes. Recent studies discovered several Cirripectes species endemic to islands or archipelagos, in spite of the generally broad distributions of tropical and subtropical blennies. Thus, to evaluate the diversity and distribution of Cirripectes species in the Mascarene Archipelago, a little-studied region but an important biodiversity hotspot, complete mitochondrial genomes, and nuclear rhodopsin genes were sequenced for 39 specimens collected with ARMS deployed on outer reef slopes at Reunion and Rodrigues islands. Mitochondrial COI sequences were analyzed to integrate these specimens within the largest dataset of publicly available sequences. Three species were found in the Mascarene Archipelago, Cirripectes castaneus, Cirripectes randalli, and Cirripectes stigmaticus. C. castaneus and C. stigmaticus both have an Indo-Pacific distribution with several haplotypes shared among distant localities. In agreement with the literature, C. randalli shows a small-range endemism restricted to the Mascarenes. We confirmed the presence of C. castaneus, C. randalli, and C. stigmaticus in Rodrigues, and the presence of C. stigmaticus in Reunion. This study contributes to filling the gaps in taxonomic and molecular knowledge of the reef cryptobiome in the South-West Indian Ocean, and provides the first complete mitogenomes for the genus, a crucial step for future molecular-based inventories (e.g., eDNA).
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Affiliation(s)
- Marion Couëdel
- Université de La Réunion, UMR 9220 ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle‐Calédonie, CNRS)La RéunionSaint‐DenisFrance
| | - Agnes Dettai
- Muséum national d'Histoire naturelle (MNHN), UMR 7205 ISYEB (MNHN, CNRS, Sorbonne Université, EPHE, Université des Antilles)ParisFrance
| | - Mireille M. M. Guillaume
- Muséum national d'Histoire naturelle (MNHN)UMR 8067 BOrEA (MNHN, CNRS 2030, Sorbonne Université, IRD 207, Uni Caen‐Normandie, Université des Antilles)ParisFrance
- LabEx CORAILUniversité de PerpignanPerpignanFrance
| | - Fleur Bruggemann
- Université de La Réunion, UMR 9220 ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle‐Calédonie, CNRS)La RéunionSaint‐DenisFrance
| | - Sophie Bureau
- Université de La Réunion, UMR 9220 ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle‐Calédonie, CNRS)La RéunionSaint‐DenisFrance
| | - Baptiste Frattini
- Université de La Réunion, UMR 9220 ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle‐Calédonie, CNRS)La RéunionSaint‐DenisFrance
- Muséum national d'Histoire naturelle (MNHN)UMR 8067 BOrEA (MNHN, CNRS 2030, Sorbonne Université, IRD 207, Uni Caen‐Normandie, Université des Antilles)ParisFrance
| | - Amélie Verde Ferreira
- Muséum national d'Histoire naturelle (MNHN), UMR 7205 ISYEB (MNHN, CNRS, Sorbonne Université, EPHE, Université des Antilles)ParisFrance
| | | | - J. Henrich Bruggemann
- Université de La Réunion, UMR 9220 ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle‐Calédonie, CNRS)La RéunionSaint‐DenisFrance
- LabEx CORAILUniversité de PerpignanPerpignanFrance
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Samayoa AP, Struthers CD, Trnski T, Roberts CD, Liggins L. Molecular phylogenetics reveals the evolutionary history of marine fishes (Actinopterygii) endemic to the subtropical islands of the Southwest Pacific. Mol Phylogenet Evol 2022; 176:107584. [PMID: 35843570 DOI: 10.1016/j.ympev.2022.107584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/03/2022] [Accepted: 05/12/2022] [Indexed: 11/16/2022]
Abstract
Remote oceanic islands of the Pacific host elevated levels of actinopterygian (ray-finned fishes) endemism. Characterizing the evolutionary histories of these endemics has provided insight into the generation and maintenance of marine biodiversity in many regions. The subtropical islands of Lord Howe, Norfolk, and Rangitāhua (Kermadec) in the Southwest Pacific are yet to be comprehensively studied. Here, we characterize the spatio-temporal diversification of marine fishes endemic to these Southwest Pacific islands by combining molecular phylogenies and the geographic distribution of species. We built Bayesian ultrametric trees based on open-access and newly generated sequences for five mitochondrial and ten nuclear loci, and using fossil data for time calibration. We present the most comprehensive phylogenies to date for marine ray-finned fish genera, comprising 34 species endemic to the islands, including the first phylogenetic placements for 11 endemics. Overall, our topologies confirm the species status of all endemics, including three undescribed taxa. Our phylogenies highlight the predominant affinity of these endemics with the Australian fish fauna (53%), followed by the East Pacific (15%), and individual cases where the closest sister taxon of our endemic is found in the Northwest Pacific and wider Indo-Pacific. Nonetheless, for a quarter of our focal endemics, their geographic affinity remains unresolved due to sampling gaps within their genera. Our divergence time estimates reveal that the majority of endemic lineages (67.6%) diverged after the emergence of Lord Howe (6.92 Ma), the oldest subtropical island in the Southwest Pacific, suggesting that these islands have promoted diversification. However, divergence ages of some endemics pre-date the emergence of the islands, suggesting they may have originated outside of these islands, or, in some cases, ages may be overestimated due to unsampled taxa. To fully understand the role of the Southwest Pacific subtropical islands as a 'cradle' for diversification, our study advocates for further regional surveys focused on tissue collection for DNA analysis.
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Affiliation(s)
- André P Samayoa
- School of Natural Sciences, Massey University, Auckland 0745, New Zealand.
| | - Carl D Struthers
- Museum of New Zealand Te Papa Tongarewa, P.O. Box 467, Wellington, New Zealand.
| | - Thomas Trnski
- Natural Sciences, Auckland Museum Tāmaki Paenga Hira, Auckland 1010, New Zealand.
| | - Clive D Roberts
- Museum of New Zealand Te Papa Tongarewa, P.O. Box 467, Wellington, New Zealand.
| | - Libby Liggins
- School of Natural Sciences, Massey University, Auckland 0745, New Zealand; Natural Sciences, Auckland Museum Tāmaki Paenga Hira, Auckland 1010, New Zealand.
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Torres-Hernández E, Betancourt-Resendes I, Angulo A, Robertson DR, Barraza E, Espinoza E, Díaz-Jaimes P, Domínguez-Domínguez O. A multi-locus approach to elucidating the evolutionary history of the clingfish Tomicodon petersii (Gobiesocidae) in the Tropical Eastern Pacific. Mol Phylogenet Evol 2021; 166:107316. [PMID: 34537324 DOI: 10.1016/j.ympev.2021.107316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 09/07/2021] [Accepted: 09/14/2021] [Indexed: 10/20/2022]
Abstract
Marine species that are widely distributed in the Tropical Eastern Pacific (TEP) has served as a model for studying biogeographic patterns resulting from the effects of intraregional habitat discontinuities and oceanographic processes on the diversification and evolution of cryptobenthic reef fishes. Tomicodon petersii, a clingfish (Gobiesocidae) endemic to the TEP, is found on very shallow rocky reefs from central Mexico to northern Peru, and in the Cocos and Galapagos islands. We evaluated the effect of likely biogeographic barriers in different parts of the TEP on the diversification process of this species. We used one mitochondrial and three nuclear DNA markers from 112 individuals collected across the distribution range of T. petersii. Our phylogenetic results showed the samples constituted a monophyletic group, with three well-supported, allopatric subgroups: in the Mexican province, the Panamic province (from El Salvador to Ecuador), and the Galapagos Islands. The split between the Mexican and more southerly clades was estimated to occur at the end of the Miocene ca. 5.74 Mya, and the subsequent cladogenetic event separating the Galapagos population from the Panamic population at the junction of the Pliocene and Pleistocene, ca. 2.85 Mya. The species tree, Bayesian species delimitation tests (BPP), STACEY, and substantial genetic distances separating these three populations indicate that these three independent evolutionary units likely include two unnamed species. The cladogenetic events that promoted the formation of those genetically differentiated groups are consistent with disruptive effects on gene flow of habitat discontinuities and oceanographic processes along the mainland shoreline in the TEP and of ocean-island isolation, in conjunction with the species intrinsic life-history characteristics.
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Affiliation(s)
- Eloísa Torres-Hernández
- Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Av. Ciudad Universitaria 3000, C.P. 04510, Coyoacán, Ciudad de México, Mexico; Instituto Nacional de Biodiversidad (INABIO), Colección de Peces Calle Rumipamba 341, Av. De los Shyris, Parque "La Carolina", Quito, Ecuador.
| | - Isai Betancourt-Resendes
- CONACYT-Laboratorio de Zoología, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Av. De las Ciencias s/n, Juriquilla, C.P 76230, Delegación Santa Rosa Jáuregui, Santiago de Querétaro, Mexico.
| | - Arturo Angulo
- Museo de Zoología/ Centro de Investigación en Biodiversidad y Ecología Tropical (CIBET) y Centro de Investigación en Ciencias del Mar y Limnología (CIMAR), Universidad de Costa Rica, San Pedro de Montes de Oca, 11501-2060 San José, Costa Rica.
| | - D Ross Robertson
- Naos Marine Laboratory, Smithsonian Tropical Research Institute, Balboa, Panama.
| | - Enrique Barraza
- Universidad Francisco Gavidia, Instituto de Ciencia, Tecnología e Inovación, Segundo Nivel, Calle El Progreso N°2748, San Salvador, El Salvador.
| | - Eduardo Espinoza
- Dirección del Parque Nacional Galápagos, Puerto Ayora, Islas Galápagos, Ecuador.
| | - Píndaro Díaz-Jaimes
- Unidad de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Av. Ciudad Universitaria 3000, C.P. 04510, Coyoacán, Ciudad de México, Mexico.
| | - Omar Domínguez-Domínguez
- Instituto Nacional de Biodiversidad (INABIO), Colección de Peces Calle Rumipamba 341, Av. De los Shyris, Parque "La Carolina", Quito, Ecuador; Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Edificio "R" Planta Baja, Ciudad Universitaria, Morelia, Michoacán 58030, Mexico.
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Zhang L, Zhang J, Song P, Liu S, Liu P, Liu C, Lin L, Li Y. Reidentification of Decapterus macarellus and D. macrosoma (Carangidae) reveals inconsistencies with current morphological taxonomy in China. Zookeys 2020; 995:81-96. [PMID: 33281469 PMCID: PMC7688621 DOI: 10.3897/zookeys.995.58092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 11/03/2020] [Indexed: 12/03/2022] Open
Abstract
Decapterusmacarellus and D.macrosoma are economically important pelagic fish species that are widely distributed in tropical and subtropical seas. The two species are often mistakenly identified due to their morphological similarities as described in the Chinese literature on fish identification. In this study, D.macarellus and D.macrosoma samples were collected in the Eastern Indian Ocean and the South China Sea and reidentified using morphological and DNA barcoding techniques. The characteristics that distinguish the two species primarily include the scute coverage of the straight portion of the lateral line (the most indicative characteristic for classification), the shape of the predorsal scaled area and its location relative to the middle axis of the eye, and the shapes of the posterior margin of the maxilla and the posterior margin of the operculum. The results revealed a large number of misidentified sequences among the homologous cytochrome oxidase (COI) sequences of the two species in the NCBI database and that the genus Decapterus may include cryptic species. In terms of genetic structure, the Sundaland has not blocked genetic exchange between D.macarellus populations in the South China Sea and the Eastern Indian Ocean, giving rise to a high level of genetic diversity. In this study, we made corrections to the Chinese classification standards for D.macarellus and D.macrosoma and the erroneous reference sequences in the NCBI database, thereby providing accurate reference points for the future exploration of cryptic species in the genus Decapterus.
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Affiliation(s)
- Liyan Zhang
- College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China Shanghai Ocean University Shanghai China.,Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China Ministry of Natural Resources Xiamen China.,Fujian Institute of Oceanography, Xiamen 361013, China Fujian Institute of Oceanography Xiamen China
| | - Jing Zhang
- Fisheries College, Jimei University, Xiamen 361021, China Jimei University Xiamen China
| | - Puqing Song
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China Ministry of Natural Resources Xiamen China
| | - Shigang Liu
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China Ministry of Natural Resources Xiamen China
| | - Pan Liu
- College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China Shanghai Ocean University Shanghai China
| | - Cheng Liu
- College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China Shanghai Ocean University Shanghai China.,Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China Ministry of Natural Resources Xiamen China
| | - Longshan Lin
- College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China Shanghai Ocean University Shanghai China.,Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China Ministry of Natural Resources Xiamen China
| | - Yuan Li
- College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China Shanghai Ocean University Shanghai China.,Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China Ministry of Natural Resources Xiamen China
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Delrieu-Trottin E, Williams JT, Pitassy D, Driskell A, Hubert N, Viviani J, Cribb TH, Espiau B, Galzin R, Kulbicki M, Lison de Loma T, Meyer C, Mourier J, Mou-Tham G, Parravicini V, Plantard P, Sasal P, Siu G, Tolou N, Veuille M, Weigt L, Planes S. A DNA barcode reference library of French Polynesian shore fishes. Sci Data 2019; 6:114. [PMID: 31273217 PMCID: PMC6609690 DOI: 10.1038/s41597-019-0123-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/07/2019] [Indexed: 12/03/2022] Open
Abstract
The emergence of DNA barcoding and metabarcoding opened new ways to study biological diversity, however, the completion of DNA barcode libraries is fundamental for such approaches to succeed. This dataset is a DNA barcode reference library (fragment of Cytochrome Oxydase I gene) for 2,190 specimens representing at least 540 species of shore fishes collected over 10 years at 154 sites across the four volcanic archipelagos of French Polynesia; the Austral, Gambier, Marquesas and Society Islands, a 5,000,000 km2 area. At present, 65% of the known shore fish species of these archipelagoes possess a DNA barcode associated with preserved, photographed, tissue sampled and cataloged specimens, and extensive collection locality data. This dataset represents one of the most comprehensive DNA barcoding efforts for a vertebrate fauna to date. Considering the challenges associated with the conservation of coral reef fishes and the difficulties of accurately identifying species using morphological characters, this publicly available library is expected to be helpful for both authorities and academics in various fields.
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Affiliation(s)
- Erwan Delrieu-Trottin
- Institut de Recherche pour le Développement, UMR 226 ISEM (UM2-CNRS-IRD-EPHE), Université de Montpellier, Place Eugène Bataillon, CC 065, F-34095, Montpellier, cedex 05, France.
- Museum für Naturkunde, Leibniz-Institut für Evolutions-und Biodiversitätsforschung an der Humboldt-Universität zu Berlin, Invalidenstrasse 43, Berlin, 10115, Germany.
- PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 58 Avenue Paul Alduy, 66860, Perpignan, France.
- Laboratoire d'Excellence «CORAIL», Papetoai, Moorea, French Polynesia, France.
| | - Jeffrey T Williams
- Division of Fishes, Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD, 20746, USA.
| | - Diane Pitassy
- Division of Fishes, Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD, 20746, USA
| | - Amy Driskell
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., 20013, United States of America
| | - Nicolas Hubert
- Institut de Recherche pour le Développement, UMR 226 ISEM (UM2-CNRS-IRD-EPHE), Université de Montpellier, Place Eugène Bataillon, CC 065, F-34095, Montpellier, cedex 05, France
| | - Jérémie Viviani
- PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 58 Avenue Paul Alduy, 66860, Perpignan, France
- Département de Biologie, École Normale Supérieure de Lyon, Université de Lyon, UCB Lyon1, 46 Allée d'Italie, Lyon, France
- Team Evolution of Vertebrate Dentition, Institute of Functional Genomics of Lyon, ENS de Lyon, CNRS UMR 5242, Université de UCB Lyon1, 46 allée d'Italie, Lyon, France
| | - Thomas H Cribb
- School of Biological Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Benoit Espiau
- PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 58 Avenue Paul Alduy, 66860, Perpignan, France
- Laboratoire d'Excellence «CORAIL», Papetoai, Moorea, French Polynesia, France
| | - René Galzin
- PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 58 Avenue Paul Alduy, 66860, Perpignan, France
- Laboratoire d'Excellence «CORAIL», Papetoai, Moorea, French Polynesia, France
| | - Michel Kulbicki
- Institut de Recherche pour le Développement - UR 227 CoReUs, LABEX "CORAIL", UPVD, 66000, Perpignan, France
| | - Thierry Lison de Loma
- PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 58 Avenue Paul Alduy, 66860, Perpignan, France
- Laboratoire d'Excellence «CORAIL», Papetoai, Moorea, French Polynesia, France
| | - Christopher Meyer
- Department of Invertebrate Zoology, National Museum of Natural History, National Museum of Natural History, Smithsonian Institution, Washington, D.C., 20560-0163, United States of America
| | - Johann Mourier
- PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 58 Avenue Paul Alduy, 66860, Perpignan, France
- Laboratoire d'Excellence «CORAIL», Papetoai, Moorea, French Polynesia, France
- UMR 248 MARBEC (IRD, Ifremer, Univ. Montpellier, CNRS), Station Ifremer de Sète, Av Jean Monnet, CS 30171, 34203, Sète cedex, France
| | - Gérard Mou-Tham
- Institut de Recherche pour le Développement - UR 227 CoReUs, LABEX "CORAIL", UPVD, 66000, Perpignan, France
| | - Valeriano Parravicini
- PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 58 Avenue Paul Alduy, 66860, Perpignan, France
- Laboratoire d'Excellence «CORAIL», Papetoai, Moorea, French Polynesia, France
| | - Patrick Plantard
- PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 58 Avenue Paul Alduy, 66860, Perpignan, France
- Laboratoire d'Excellence «CORAIL», Papetoai, Moorea, French Polynesia, France
| | - Pierre Sasal
- PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 58 Avenue Paul Alduy, 66860, Perpignan, France
- Laboratoire d'Excellence «CORAIL», Papetoai, Moorea, French Polynesia, France
| | - Gilles Siu
- PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 58 Avenue Paul Alduy, 66860, Perpignan, France
- Laboratoire d'Excellence «CORAIL», Papetoai, Moorea, French Polynesia, France
| | - Nathalie Tolou
- PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 58 Avenue Paul Alduy, 66860, Perpignan, France
- Laboratoire d'Excellence «CORAIL», Papetoai, Moorea, French Polynesia, France
| | - Michel Veuille
- Laboratoire d'Excellence «CORAIL», Papetoai, Moorea, French Polynesia, France
- Institut Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, CNRS, MNHN, UPMC, EPHE. Ecole Pratique des Hautes Etudes, Paris Sciences Lettres (PSL), 57 rue Cuvier, CP39, F-75005, Paris, France
| | - Lee Weigt
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., 20013, United States of America
| | - Serge Planes
- PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 58 Avenue Paul Alduy, 66860, Perpignan, France.
- Laboratoire d'Excellence «CORAIL», Papetoai, Moorea, French Polynesia, France.
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