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Zhang R, Fau M, Mah C, Eléaume M, Zhang D, Zhou Y, Lu B, Wang C. Systematics of deep-sea starfish order Brisingida (Echinodermata: Asteroidea), with a revised classification and assessments of morphological characters. Mol Phylogenet Evol 2024; 191:107993. [PMID: 38103706 DOI: 10.1016/j.ympev.2023.107993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 12/06/2023] [Accepted: 12/12/2023] [Indexed: 12/19/2023]
Abstract
Brisingida Fisher 1928 is one of the seven currently recognised starfish orders, and one of the least known taxa as being exclusive deep-sea inhabitants. Modern deep-sea expeditions revealed their common occurrences in various deep-sea settings including seamounts, basins and hydrothermal vent peripheral, underlining the necessity of clarifying their global diversity and phylogeny. In this study, we present a comprehensive molecular phylogeny of Brisingida which encompasses the highest taxonomic diversity to date. DNA sequences (COI, 16S, 12S and 28S) were obtained from 225 specimens collected in the global ocean, identified as 58 species spanning 15 of the 17 extant genera. Phylogenetic relationship was inferred using both maximum likelihood and Bayesian inference methods, revealing polyphyletic families and genera and indicating nonnegligible bias in prior morphology-based systematics. Based on the new phylogeny, a novel classification of the order, consisting of 5 families and 17 genera, is proposed. Families Odinellidae, Brisingasteridae and Novodiniidae (sensu Clark and Mah, 2001) were resurrected to encompass the genera Odinella, Brisingaster and Novodinia. Brisingidae and Freyellidae were revised to include 11 and 3 genera, respectively. A new genus and species, two new subgenera and seven new combinations are described and a key to each genus and family is provided. Transformations of morphological traits were evaluated under the present phylogenetic hypothesis. A series of paedomorphic characters were found in many genera and species, which led to a high degree of homoplasy across phylogenetically distant groups. Our results provide new insights in the phylogeny and ontogeny of the order, and highlight the necessity to evaluate character convergence under sound phylogenetic hypothesis.
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Affiliation(s)
- Ruiyan Zhang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China; School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Marine Fau
- Centre de Recherche en Paléontologie - Paris, Sorbonne Université, 4 place Jussieu, 75005 Paris, France; Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Christopher Mah
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Marc Eléaume
- Départment Origines et Évolution, Muséum National d'Histoire Naturelle, Paris, France
| | - Dongsheng Zhang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China; School of Oceanography, Shanghai Jiao Tong University, Shanghai, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Yadong Zhou
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Bo Lu
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Chunsheng Wang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China; School of Oceanography, Shanghai Jiao Tong University, Shanghai, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
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2
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González C, Ballesteros-Mejia L, Díaz-Díaz J, Toro-Vargas DM, Amarillo-Suarez AR, Gey D, León C, Tovar E, Arias M, Rivera N, Buitrago LS, Pinto-Moraes RH, Sano Martins IS, Decaëns T, González MA, Kitching IJ, Rougerie R. Deadly and venomous Lonomia caterpillars are more than the two usual suspects. PLoS Negl Trop Dis 2023; 17:e0011063. [PMID: 36821543 PMCID: PMC9949635 DOI: 10.1371/journal.pntd.0011063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/28/2022] [Indexed: 02/24/2023] Open
Abstract
Caterpillars of the Neotropical genus Lonomia (Lepidoptera: Saturniidae) are responsible for some fatal envenomation of humans in South America inducing hemostatic disturbances in patients upon skin contact with the caterpillars' spines. Currently, only two species have been reported to cause hemorrhagic syndromes in humans: Lonomia achelous and Lonomia obliqua. However, species identifications have remained largely unchallenged despite improved knowledge of venom diversity and growing evidence that the taxonomy used over past decades misrepresents and underestimates species diversity. Here, we revisit the taxonomic diversity and distribution of Lonomia species using the most extensive dataset assembled to date, combining DNA barcodes, morphological comparisons, and geographical information. Considering new evidence for seven undescribed species as well as three newly proposed nomenclatural changes, our integrative approach leads to the recognition of 60 species, of which seven are known or strongly suspected to cause severe envenomation in humans. From a newly compiled synthesis of epidemiological data, we also examine the consequences of our results for understanding Lonomia envenomation risks and call for further investigations of other species' venom activities. This is required and necessary to improve alertness in areas at risk, and to define adequate treatment strategies for envenomed patients, including performing species identification and assessing the efficacy of anti-Lonomia serums against a broader diversity of species.
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Affiliation(s)
- Camila González
- Centro de Investigaciones en Microbiología y Parasitología Tropical (CIMPAT), Facultad de Ciencias, Universidad de los Andes, Bogotá, Colombia, Bogotá, Colombia
- * E-mail: ;
| | - Liliana Ballesteros-Mejia
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, EPHE, Sorbonne Université, Université des Antilles, Paris, France
- CESAB, Centre de synthèse et d’Analyse sur la Biodiversité, Montpellier, France
| | - Juana Díaz-Díaz
- Centro de Investigaciones en Microbiología y Parasitología Tropical (CIMPAT), Facultad de Ciencias, Universidad de los Andes, Bogotá, Colombia, Bogotá, Colombia
| | - Diana M. Toro-Vargas
- Centro de Investigaciones en Microbiología y Parasitología Tropical (CIMPAT), Facultad de Ciencias, Universidad de los Andes, Bogotá, Colombia, Bogotá, Colombia
| | | | - Delphine Gey
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, EPHE, Sorbonne Université, Université des Antilles, Paris, France
| | - Cielo León
- Centro de Investigaciones en Microbiología y Parasitología Tropical (CIMPAT), Facultad de Ciencias, Universidad de los Andes, Bogotá, Colombia, Bogotá, Colombia
| | - Eduardo Tovar
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Bogotá, Colombia
| | - Mónica Arias
- CIRAD, UMR PHIM, Montpellier, France
- PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Nazario Rivera
- Secretaría de Salud de Casanare. Area de Salud Pública, Yopal, Colombia
| | | | | | | | - Thibaud Decaëns
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Mailyn A. González
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Bogotá, Colombia
| | | | - Rodolphe Rougerie
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, EPHE, Sorbonne Université, Université des Antilles, Paris, France
- * E-mail: ;
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3
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Meng W, Li L, Yuan X, Zhou Y. The complete mitochondrial genome of Leuciscus merzbacheri (Cypriniformes: Cyprinidae). Mitochondrial DNA B Resour 2023; 8:414-417. [PMID: 36969326 PMCID: PMC10035939 DOI: 10.1080/23802359.2023.2189496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Leuciscus merzbacheri (Zugmayer, 1912) is a cyprinid fish endemic to China, with a distribution range limited to Xinjiang Province. As a landmark species in the Junggar Basin, L. merzbacheri is of considerable significance regarding our understanding of the adaptive evolution of salt and alkali tolerance. In this study, the complete mitochondrial sequence of L. merzbacheri was obtained for the first time by high-throughput sequencing. The circular mitogenome is 16,609 bp in length and contains the standard 37 genes, including 13 protein-coding, 22 transfer RNA, and 2 ribosomal RNA genes, which is similar to that of other fish. The mitogenome contents of A, T, C, and G were 27.9, 26.3, 27.1, and 18.7%, respectively. Phylogenetically, L. merzbacheri was located on a new branch near the base of the phylogenetic tree, thereby suggesting an early origin.
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Affiliation(s)
- Wei Meng
- Zhejiang Marine Fisheries Research Institute, Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture, Zhoushan, China
| | - Lin Li
- Xinjiang Fisheries Research Institute, Urumqi, China
| | - Xiaoqian Yuan
- College of life Science and Technology, Xinjiang University, Urumqi, China
| | - Yongdong Zhou
- Zhejiang Marine Fisheries Research Institute, Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture, Zhoushan, China
- CONTACT Yongdong Zhou Zhejiang Marine Fisheries Research Institute, Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture, Zhoushan, China
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5
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Papetti C, Babbucci M, Dettai A, Basso A, Lucassen M, Harms L, Bonillo C, Heindler FM, Patarnello T, Negrisolo E. Not Frozen in the Ice: Large and Dynamic Rearrangements in the Mitochondrial Genomes of the Antarctic Fish. Genome Biol Evol 2021; 13:6133229. [PMID: 33570582 PMCID: PMC7936035 DOI: 10.1093/gbe/evab017] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2021] [Indexed: 12/21/2022] Open
Abstract
The vertebrate mitochondrial genomes generally present a typical gene order. Exceptions are uncommon and important to study the genetic mechanisms of gene order rearrangements and their consequences on phylogenetic output and mitochondrial function. Antarctic notothenioid fish carry some peculiar rearrangements of the mitochondrial gene order. In this first systematic study of 28 species, we analyzed known and undescribed mitochondrial genome rearrangements for a total of eight different gene orders within the notothenioid fish. Our reconstructions suggest that transpositions, duplications, and inversion of multiple genes are the most likely mechanisms of rearrangement in notothenioid mitochondrial genomes. In Trematominae, we documented an extremely rare inversion of a large genomic segment of 5,300 bp that partially affected the gene compositional bias but not the phylogenetic output. The genomic region delimited by nad5 and trnF, close to the area of the Control Region, was identified as the hot spot of variation in Antarctic fish mitochondrial genomes. Analyzing the sequence of several intergenic spacers and mapping the arrangements on a newly generated phylogeny showed that the entire history of the Antarctic notothenioids is characterized by multiple, relatively rapid, events of disruption of the gene order. We hypothesized that a pre-existing genomic flexibility of the ancestor of the Antarctic notothenioids may have generated a precondition for gene order rearrangement, and the pressure of purifying selection could have worked for a rapid restoration of the mitochondrial functionality and compactness after each event of rearrangement.
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Affiliation(s)
- Chiara Papetti
- Department of Biology, University of Padova, Padova 35121,Italy.,Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Roma 00196, Italy
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro 35020, Italy
| | - Agnes Dettai
- Institut de Systematique, Evolution, Biodiversité (ISYEB) Muséum national d'Histoire naturelle-CNRS-Sorbonne Université-EPHE, MNHN, Paris 75005, France
| | - Andrea Basso
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro 35020, Italy
| | - Magnus Lucassen
- Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Am Handelshafen 12, Bremerhaven 27570, Germany
| | - Lars Harms
- Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Am Handelshafen 12, Bremerhaven 27570, Germany.,Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg (HIFMB), Ammerlsity of Oldenburg (HIFMOldenburg 26129, Germany
| | - Celine Bonillo
- Service de Systématique Moléculaire, UMS2700 Acquisition et Analyse de Données (2AD), MNHN, Paris 75005, France
| | | | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro 35020, Italy
| | - Enrico Negrisolo
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro 35020, Italy.,CRIBI Interdepartmental Research Centre for Innovative Biotechnologies, University of Padova, viale G. Colombo 3, Padova 35121, Italy
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6
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Sanders MT, Merle D, Laurin M, Bonillo C, Puillandre N. Raising names from the dead: A time-calibrated phylogeny of frog shells (Bursidae, Tonnoidea, Gastropoda) using mitogenomic data. Mol Phylogenet Evol 2020; 156:107040. [PMID: 33310060 DOI: 10.1016/j.ympev.2020.107040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/04/2020] [Accepted: 12/08/2020] [Indexed: 12/23/2022]
Abstract
With 59 Recent species, Bursidae, known as «frog shells», are a small but widely distributed group of tropical and subtropical gastropods that are most diverse in the Indo-West Pacific. The present study is aimed at reconstructing phylogenetic relationships of bursid gastropods based on extensive and representative taxon sampling. Five genetic markers (cytochrome c oxidase subunit I (cox1), 16 s and 12 s rRNA mitochondrial genes, 28 s rRNA and Histone H3 nuclear gene) were sequenced for over 30 species in every known genus but Crossata. Furthermore, we sequenced the complete mt-genome of 9 species (10 specimens) (Aspa marginata, Marsupina bufo, Korrigania quirihorai, Korrigania fijiensis, Tutufa rubeta, Bursa lamarckii, Lampasopsis rhodostoma (twice), Bufonaria perelegans and Bursa aff. tuberosissima). Our analysis recovered Bursidae as a monophyletic group, whereas the genus Bursa was found to be polyphyletic. The genera Talisman and Dulcerana are resurrected and the genera Alanbeuella gen. nov. and Korrigania gen. nov. are described. Dating analysis using 21 extinct taxa for node and simplified tip calibrations was performed, showing a diversification of the group in two phases. Diversification may be linked to tectonic events leading to biodiversity relocation from the western Tethys toward the Indo-Pacific.
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Affiliation(s)
- Malcolm T Sanders
- Centre de Recherche en Paléontologie - Paris CR2P - UMR 7207 - CNRS, Muséum national d'Histoire naturelle, Sorbonne Université, 8 rue Buffon, CP 38, 75005 Paris, France; Institut de Systématique, Évolution, Biodiversité ISYEB - Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP26, F-75005 Paris, France.
| | - Didier Merle
- Centre de Recherche en Paléontologie - Paris CR2P - UMR 7207 - CNRS, Muséum national d'Histoire naturelle, Sorbonne Université, 8 rue Buffon, CP 38, 75005 Paris, France
| | - Michel Laurin
- Centre de Recherche en Paléontologie - Paris CR2P - UMR 7207 - CNRS, Muséum national d'Histoire naturelle, Sorbonne Université, 8 rue Buffon, CP 38, 75005 Paris, France
| | - Céline Bonillo
- Service de systématique moléculaire SSM - UMS 2700 - MNHN, CNRS, Muséum national d'Histoire naturelle, Sorbonne Université. 57 rue Cuvier, CP26, 75005 Paris, France
| | - Nicolas Puillandre
- Institut de Systématique, Évolution, Biodiversité ISYEB - Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP26, F-75005 Paris, France
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Hassanin A, Bonillo C, Tshikung D, Pongombo Shongo C, Pourrut X, Kadjo B, Nakouné E, Tu VT, Prié V, Goodman SM. Phylogeny of African fruit bats (Chiroptera, Pteropodidae) based on complete mitochondrial genomes. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12373] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Alexandre Hassanin
- Institut Systématique Evolution Biodiversité (ISYEB) Sorbonne Université MNHN CNRS EPHE Paris France
| | - Céline Bonillo
- Muséum National d'Histoire NaturelleUMS 2700 2AD Paris France
| | - Didier Tshikung
- Faculté de Médecine Vétérinaire Université de Lubumbashi Lubumbashi Democratic Republic of the Congo
| | - Célestin Pongombo Shongo
- Faculté de Médecine Vétérinaire Université de Lubumbashi Lubumbashi Democratic Republic of the Congo
| | - Xavier Pourrut
- Institut de Recherche pour le Développement UR 224 MIVEGEC Marseille France
| | - Blaise Kadjo
- UFR Biosciences Université Félix Houphouet‐Boigny Abidjan Côte d'Ivoire
| | | | - Vuong Tan Tu
- Institute of Ecology and Biological Resources Vietnam Academy of Science and Technology Hanoi Vietnam
| | - Vincent Prié
- Institut Systématique Evolution Biodiversité (ISYEB) Sorbonne Université MNHN CNRS EPHE Paris France
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Lord C, Bellec L, Dettaï A, Bonillo C, Keith P. Does your lip stick? Evolutionary aspects of the mouth morphology of the Indo‐Pacific clinging goby of the Sicyopterusgenus (Teleostei: Gobioidei: Sicydiinae) based on mitogenome phylogeny. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12291] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Clara Lord
- Unité Biologie des organismes et écosystèmes aquatiques (BOREA), Sorbonne Université, Muséum national d’Histoire naturelle, Université de Caen Normandie, CNRS, IRD, CP26 Université des Antilles Paris France
| | - Laure Bellec
- IFREMER, Centre Brest, REM/EEP/LEP ZI de la Pointe du Diable Plouzané France
| | - Agnès Dettaï
- Institut Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, École Pratique des Hautes Études, CNRS, CP30 Sorbonne Université Paris France
| | - Céline Bonillo
- Département Systématique et Évolution, UMS 2700 “Outils et Méthodes de la Systématique Intégrative” MNHN‐CNRS, Service de Systématique Moléculaire Muséum national d’Histoire naturelle, CP26 Paris cedex 05 France
| | - Philippe Keith
- Unité Biologie des organismes et écosystèmes aquatiques (BOREA), Sorbonne Université, Muséum national d’Histoire naturelle, Université de Caen Normandie, CNRS, IRD, CP26 Université des Antilles Paris France
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Mennesson MI, Maeda K, Keith P. Evolutionary aspects of cephalic sensory papillae of the Indo‐Pacific species of
Eleotris
(Teleostei: Eleotridae). ZOOL SCR 2019. [DOI: 10.1111/zsc.12366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marion I. Mennesson
- Unité Biologie des organismes et écosystèmes aquatiques (BOREA 7208), Muséum national d’Histoire naturelle, Sorbonne Université, Université de Caen Normandie Université des Antilles, CNRS, IRD, CP26 Paris France
| | - Ken Maeda
- Okinawa Institute of Science and Technology Graduate University (OIST) Onna Japan
| | - Philippe Keith
- Unité Biologie des organismes et écosystèmes aquatiques (BOREA 7208), Muséum national d’Histoire naturelle, Sorbonne Université, Université de Caen Normandie Université des Antilles, CNRS, IRD, CP26 Paris France
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Zhang Z, Cheng Q, Ge Y. The complete mitochondrial genome of Rhynchocypris oxycephalus (Teleostei: Cyprinidae) and its phylogenetic implications. Ecol Evol 2019; 9:7819-7837. [PMID: 31346443 PMCID: PMC6635945 DOI: 10.1002/ece3.5369] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/21/2019] [Accepted: 05/22/2019] [Indexed: 01/18/2023] Open
Abstract
Rhynchocypris oxycephalus (Teleostei: Cyprinidae) is a typical small cold water fish, which is distributed widely and mainly inhabits in East Asia. Here, we sequenced and determined the complete mitochondrial genome of R. oxycephalus and studied its phylogenetic implication. R. oxycephalus mitogenome is 16,609 bp in length (GenBank accession no.: MH885043), and it contains 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and two noncoding regions (the control region and the putative origin of light-strand replication). 12 PCGs started with ATG, while COI used GTG as the start codon. The secondary structure of tRNA-Ser (AGN) lacks the dihydrouracil (DHU) arm. The control region is 943bp in length, with a termination-associated sequence, six conserved sequence blocks (CSB-1, CSB-2, CSB-3, CSB-D, CSB-E, CSB-F), and a repetitive sequence. Phylogenetic analysis was performed with maximum likelihood and Bayesian methods based on the concatenated nucleotide sequence of 13 PCGs and the complete sequence without control region, and the result revealed that the relationship between R. oxycephalus and R. percnurus is closest, while the relationship with R. kumgangensis is farthest. The genus Rhynchocypris is revealed as a polyphyletic group, and R. kumgangensis had distant relationship with other Rhynchocypris species. In addition, COI and ND2 genes are considered as the fittest DNA barcoding gene in genus Rhynchocypris. This work provides additional molecular information for studying R. oxycephalus conservation genetics and evolutionary relationships.
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Affiliation(s)
- Zhichao Zhang
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research InstituteChinese Academy of Fishery SciencesShanghaiChina
- Wuxi Fisheries CollegeNanjing Agricultural UniversityWuxiChina
| | - Qiqun Cheng
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research InstituteChinese Academy of Fishery SciencesShanghaiChina
| | - Yushuang Ge
- Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research InstituteChinese Academy of Fishery SciencesShanghaiChina
- College of Marine SciencesShanghai Ocean UniversityShanghaiChina
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11
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de Mazancourt V, Klotz W, Marquet G, Mos B, Rogers DC, Keith P. The complex study of complexes: The first well-supported phylogeny of two species complexes within genus Caridina (Decapoda: Caridea: Atyidae) sheds light on evolution, biogeography, and habitat. Mol Phylogenet Evol 2018; 131:164-180. [PMID: 30423441 DOI: 10.1016/j.ympev.2018.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 11/08/2018] [Accepted: 11/08/2018] [Indexed: 02/02/2023]
Abstract
Atyid shrimps, a key component of tropical freshwater ecosystems, face multiple anthropogenic threats and thus need special attention. With more than 300 described species, the genus Caridina is the most speciose of all the Caridea infra-order. Caridina spp. occupy diverse habitats in tropical freshwaters of the Indo-West Pacific region. Several species complexes have been recognized, based on common morphological features, but little is known about how well these morphological characteristics align with phylogenetic characteristics. Furthermore, no phylogeny of the genus Caridina published so far has provided well-resolved and supported relationships among different species, thus impeding the possibility of proposing evolutionary hypotheses. In this study we used next generation sequencing (NGS) to provide new insights into the phylogenetic relationships among the genus Caridina, focusing on two complexes: 'Caridina nilotica' and 'Caridina weberi'. We collected 92 specimens belonging to these two groups from most of their known geographical range, representing 50 species, for which we sequenced seven mitochondrial genes and two nuclear markers using ion torrent NGS. We performed a phylogenetic analysis, which yielded the first well-supported tree for the genus Caridina. On this tree were mapped the geographic ranges and the habitats used by the different species, and a time calibration was tested. We found the driving factors that most likely account for separation of clades are differences in habitat and to a lesser extent geography. This work provides new insights into the taxonomy of this group and identifies opportunities for further studies in order to fill knowledge gaps that currently impede the management and conservation of atyid species.
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Affiliation(s)
- Valentin de Mazancourt
- Muséum national d'Histoire naturelle, Département Adaptations du Vivant, UMR 7208, CP026, 57, rue Cuvier, F-75231 Paris, Cedex 05, France.
| | | | - Gerard Marquet
- Muséum national d'Histoire naturelle, Département Adaptations du Vivant, UMR 7208, CP026, 57, rue Cuvier, F-75231 Paris, Cedex 05, France
| | - Benjamin Mos
- National Marine Science Centre, Southern Cross University, PO Box 4321, Coffs Harbour, NSW 2450, Australia
| | - D Christopher Rogers
- Kansas Biological Survey and the Natural History Museum (Biodiversity Institute), Kansas University, Higuchi Hall, 2101 Constant Avenue, Lawrence, KS 66047-3759, USA
| | - Philippe Keith
- Muséum national d'Histoire naturelle, Département Adaptations du Vivant, UMR 7208, CP026, 57, rue Cuvier, F-75231 Paris, Cedex 05, France
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12
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Mennesson MI, Bonillo C, Feunteun E, Keith P. Phylogeography of Eleotris fusca (Teleostei: Gobioidei: Eleotridae) in the Indo-Pacific area reveals a cryptic species in the Indian Ocean. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1063-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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13
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Denys GPJ, Persat H, Dettai A, Geiger MF, Freyhof J, Fesquet J, Keith P. Genetic and morphological discrimination of three species of ninespined stickleback Pungitius
spp. (Teleostei, Gasterosteidae) in France with the revalidation of Pungitius vulgaris
(Mauduyt, 1848). J ZOOL SYST EVOL RES 2017. [DOI: 10.1111/jzs.12178] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gaël P. J. Denys
- Unité Biologie des organismes et écosystèmes aquatiques (BOREA, UMR 7208); Sorbonne Universités; Muséum national d'Histoire naturelle; Université Pierre et Marie Curie; Université de Caen Basse-Normandie; CNRS; IRD; Paris France
| | - Henri Persat
- Écologie des Hydrosystèmes Naturels et Anthropisés; LEHNA UMR 5023; Bat. Forel; Université Claude Bernard Lyon 1; Villeurbanne Cedex France
| | - Agnès Dettai
- Institut de Systématique, Evolution, Biodiversité; ISYEB - UMR 7205 - CNRS; MNHN; UPMC; EPHE; Muséum national d'Histoire naturelle; Sorbonne Universités; Paris France
| | - Matthias F. Geiger
- Zoologisches Forschungsmuseum Alexander Koenig; Leibniz Institute for Animal Biodiversity; Bonn Germany
| | - Jörg Freyhof
- Leibniz Institute of Freshwater Ecology and Inland Fisheries; Berlin Germany
| | - Justine Fesquet
- Unité Biologie des organismes et écosystèmes aquatiques (BOREA, UMR 7208); Sorbonne Universités; Muséum national d'Histoire naturelle; Université Pierre et Marie Curie; Université de Caen Basse-Normandie; CNRS; IRD; Paris France
| | - Philippe Keith
- Unité Biologie des organismes et écosystèmes aquatiques (BOREA, UMR 7208); Sorbonne Universités; Muséum national d'Histoire naturelle; Université Pierre et Marie Curie; Université de Caen Basse-Normandie; CNRS; IRD; Paris France
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Mandon P, Aznar-Cormano L, Hourdez S, Samadi S. Assembly of the mitochondrial genome of the hydrothermal vent crab Segonzacia mesatlanticaand detection of potential nuclear pseudogenes. Mitochondrial DNA B Resour 2017; 2:291-293. [PMID: 33473801 PMCID: PMC7800491 DOI: 10.1080/23802359.2017.1318674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We assembled the mitogenome of the Bythograeid crab Segonzacia mesatlantica, using long-range amplification of the mitochondrial genome. The mitogenome is 15,521 base pair long (33.8% A, 21.7% C, 10.5% G, 34% T) with 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNAs, and a 624 bp AT-rich region. The gene arrangement is similar to other Brachyuran species. A whole genome shotgun sequencing approach revealed the presence of mitochondrial pseudogenes in the nuclear genome. This fifth mitogenome for a species of Bythograeidae should help resolve the puzzling question of the evolutionary origin of a family limited to deep-sea hydrothermal vents.
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Affiliation(s)
- Perrine Mandon
- Muséum National d’Histoire Naturelle, Sorbonne Universités, Institut de Systématique, Evolution, Biodiversité, (ISYEB – UMR 7205 – CNRS, MNHN, UPMC, EPHE), Paris, France
- Sorbonne Universités, UPMC Univ Paris 6, Station Biologique de Roscoff, Roscoff, France
- CNRS, UMR 7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - Laetitia Aznar-Cormano
- Muséum National d’Histoire Naturelle, Sorbonne Universités, Institut de Systématique, Evolution, Biodiversité, (ISYEB – UMR 7205 – CNRS, MNHN, UPMC, EPHE), Paris, France
| | - Stéphane Hourdez
- Sorbonne Universités, UPMC Univ Paris 6, Station Biologique de Roscoff, Roscoff, France
- CNRS, UMR 7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - Sarah Samadi
- Muséum National d’Histoire Naturelle, Sorbonne Universités, Institut de Systématique, Evolution, Biodiversité, (ISYEB – UMR 7205 – CNRS, MNHN, UPMC, EPHE), Paris, France
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