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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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Hoban ML, Whitney J, Collins AG, Meyer C, Murphy KR, Reft AJ, Bemis KE. Skimming for barcodes: rapid production of mitochondrial genome and nuclear ribosomal repeat reference markers through shallow shotgun sequencing. PeerJ 2022; 10:e13790. [PMID: 35959477 PMCID: PMC9359134 DOI: 10.7717/peerj.13790] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/05/2022] [Indexed: 01/17/2023] Open
Abstract
DNA barcoding is critical to conservation and biodiversity research, yet public reference databases are incomplete. Existing barcode databases are biased toward cytochrome oxidase subunit I (COI) and frequently lack associated voucher specimens or geospatial metadata, which can hinder reliable species assignments. The emergence of metabarcoding approaches such as environmental DNA (eDNA) has necessitated multiple marker techniques combined with barcode reference databases backed by voucher specimens. Reference barcodes have traditionally been generated by Sanger sequencing, however sequencing multiple markers is costly for large numbers of specimens, requires multiple separate PCR reactions, and limits resulting sequences to targeted regions. High-throughput sequencing techniques such as genome skimming enable assembly of complete mitogenomes, which contain the most commonly used barcoding loci (e.g., COI, 12S, 16S), as well as nuclear ribosomal repeat regions (e.g., ITS1&2, 18S). We evaluated the feasibility of genome skimming to generate barcode references databases for marine fishes by assembling complete mitogenomes and nuclear ribosomal repeats. We tested genome skimming across a taxonomically diverse selection of 12 marine fish species from the collections of the National Museum of Natural History, Smithsonian Institution. We generated two sequencing libraries per species to test the impact of shearing method (enzymatic or mechanical), extraction method (kit-based or automated), and input DNA concentration. We produced complete mitogenomes for all non-chondrichthyans (11/12 species) and assembled nuclear ribosomal repeats (18S-ITS1-5.8S-ITS2-28S) for all taxa. The quality and completeness of mitogenome assemblies was not impacted by shearing method, extraction method or input DNA concentration. Our results reaffirm that genome skimming is an efficient and (at scale) cost-effective method to generate all mitochondrial and common nuclear DNA barcoding loci for multiple species simultaneously, which has great potential to scale for future projects and facilitate completing barcode reference databases for marine fishes.
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Affiliation(s)
- Mykle L. Hoban
- Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa, Kāne‘ohe, Hawai‘i, United States of America
| | - Jonathan Whitney
- Pacific Islands Fisheries Science Center, National Oceanic and Atmospheric Administration, Honolulu, Hawai‘i, United States of America
| | - Allen G. Collins
- NOAA National Systematics Laboratory, Natural Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Christopher Meyer
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Katherine R. Murphy
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Abigail J. Reft
- NOAA National Systematics Laboratory, Natural Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Katherine E. Bemis
- NOAA National Systematics Laboratory, Natural Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
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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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Wagner M, Kovačić M, Koblmüller S. Unravelling the taxonomy of an interstitial fish radiation: Three new species of Gouania (Teleostei: Gobiesocidae) from the Mediterranean Sea and redescriptions of G. willdenowi and G. pigra. JOURNAL OF FISH BIOLOGY 2021; 98:64-88. [PMID: 32985685 PMCID: PMC7821206 DOI: 10.1111/jfb.14558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 06/11/2023]
Abstract
The clingfish (Gobiesocidae) genus Gouania Nardo, 1833 is endemic to the Mediterranean Sea and inhabits, unlike any other vertebrate species in Europe, the harsh intertidal environment of gravel beaches. Following up on a previous phylogenetic study, we revise the diversity and taxonomy of this genus by analysing a comprehensive set of morphological (meristics, morphometrics, microcomputed tomography imaging), geographical and genetic (DNA-barcoding) data. We provide descriptions of three new species, G. adriatica sp. nov., G. orientalis sp. nov. and G. hofrichteri sp. nov., as well as redescriptions of G. willdenowi (Risso, 1810) and G. pigra (Nardo, 1827) and assign neotypes for the latter two species. In addition to elucidating the complex taxonomic situation of Gouania, we discuss the potential of this enigmatic clingfish genus for further ecological, evolutionary and biodiversity studies that might unravel even more diversity in this unique Mediterranean fish radiation.
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Affiliation(s)
- Maximilian Wagner
- Institute of BiologyUniversity of GrazGrazAustria
- Department of BiologyUniversity of AntwerpAntwerpBelgium
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