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Yin D, Chen C, Lin D, Hua Z, Ying C, Zhang J, Zhao C, Liu Y, Cao Z, Zhang H, Wang C, Liang L, Xu P, Jian J, Liu K. Telomere-to-telomere gap-free genome assembly of the endangered Yangtze finless porpoise and East Asian finless porpoise. Gigascience 2024; 13:giae067. [PMID: 39283687 PMCID: PMC11403816 DOI: 10.1093/gigascience/giae067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 04/27/2024] [Accepted: 08/16/2024] [Indexed: 09/22/2024] Open
Abstract
BACKGROUND The Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis, YFP) and the East Asian finless porpoise (Neophocaena asiaeorientalis sunameri, EFP) are 2 subspecies of the narrow-ridged finless porpoise that live in freshwater and saltwater, respectively. The main objective of this study was to provide contiguous chromosome-level genome assemblies for YFP and EFP. RESULTS Here, we generated and upgraded the genomes of YFP and EFP at the telomere-to-telomere level through the integration of PacBio HiFi long reads, ultra-long ONT reads, and Hi-C sequencing data with a total size of 2.48 Gb and 2.50 Gb, respectively. The scaffold N50 of 2 genomes was 125.12 Mb (YFP) and 128 Mb (EFP) with 1 contig for 1 chromosome. The telomere repeat and centromere position were clearly identified in both YFP and EFP genomes. In total, 5,480 newfound genes were detected in the YFP genome, including 56 genes located in the newly identified centromere regions. Additionally, synteny blocks, structural similarities, phylogenetic relationships, gene family expansion, and inference of selection were studied in connection with the genomes of other related mammals. CONCLUSIONS Our research findings provide evidence for the gradual adaptation of EFP in a marine environment and the potential sensitivity of YFP to genetic damage. Compared to the 34 cetacean genomes sourced from public databases, the 2 new assemblies demonstrate superior continuity with the longest contig N50 and scaffold N50 values, as well as the lowest number of contigs. The improvement of telomere-to-telomere gap-free reference genome resources supports conservation genetics and population management for finless porpoises.
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Affiliation(s)
- Denghua Yin
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | | | - Danqing Lin
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Zhong Hua
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Congping Ying
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Jialu Zhang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | | | - Yan Liu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Zhichen Cao
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | - Han Zhang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | | | | | - Pao Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Jianbo Jian
- BGI Genomics, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
| | - Kai Liu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
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2
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Ramos E, Selleghin-Veiga G, Magpali L, Daros B, Silva F, Picorelli A, Freitas L, Nery MF. Molecular Footprints on Osmoregulation-Related Genes Associated with Freshwater Colonization by Cetaceans and Sirenians. J Mol Evol 2023; 91:865-881. [PMID: 38010516 DOI: 10.1007/s00239-023-10141-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 10/29/2023] [Indexed: 11/29/2023]
Abstract
The genetic basis underlying adaptive physiological mechanisms has been extensively explored in mammals after colonizing the seas. However, independent lineages of aquatic mammals exhibit complex patterns of secondary colonization in freshwater environments. This change in habitat represents new osmotic challenges, and additional changes in key systems, such as the osmoregulatory system, are expected. Here, we studied the selective regime on coding and regulatory regions of 20 genes related to the osmoregulation system in strict aquatic mammals from independent evolutionary lineages, cetaceans, and sirenians, with representatives in marine and freshwater aquatic environments. We identified positive selection signals in genes encoding the protein vasopressin (AVP) in mammalian lineages with secondary colonization in the fluvial environment and in aquaporins for lineages inhabiting the marine and fluvial environments. A greater number of sites with positive selection signals were found for the dolphin species compared to the Amazonian manatee. Only the AQP5 and AVP genes showed selection signals in more than one independent lineage of these mammals. Furthermore, the vasopressin gene tree indicates greater similarity in river dolphin sequences despite the independence of their lineages based on the species tree. Patterns of distribution and enrichment of Transcription Factors in the promoter regions of target genes were analyzed and appear to be phylogenetically conserved among sister species. We found accelerated evolution signs in genes ACE, AQP1, AQP5, AQP7, AVP, NPP4, and NPR1 for the fluvial mammals. Together, these results allow a greater understanding of the molecular bases of the evolution of genes responsible for osmotic control in aquatic mammals.
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Affiliation(s)
- Elisa Ramos
- Laboratório de Genômica Evolutiva., Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas, Cidade Universitária, Campinas, SP, 13083970, Brazil
| | - Giovanna Selleghin-Veiga
- Laboratório de Genômica Evolutiva., Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas, Cidade Universitária, Campinas, SP, 13083970, Brazil
| | - Letícia Magpali
- Laboratório de Genômica Evolutiva., Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas, Cidade Universitária, Campinas, SP, 13083970, Brazil
| | - Beatriz Daros
- Laboratório de Genômica Evolutiva., Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas, Cidade Universitária, Campinas, SP, 13083970, Brazil
| | - Felipe Silva
- Laboratório de Genômica Evolutiva., Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas, Cidade Universitária, Campinas, SP, 13083970, Brazil
| | - Agnello Picorelli
- Laboratório de Genômica Evolutiva., Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas, Cidade Universitária, Campinas, SP, 13083970, Brazil
| | - Lucas Freitas
- Laboratório de Genômica Evolutiva., Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas, Cidade Universitária, Campinas, SP, 13083970, Brazil
| | - Mariana F Nery
- Laboratório de Genômica Evolutiva., Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas, Cidade Universitária, Campinas, SP, 13083970, Brazil.
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3
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Piboon P, Kriengsakpichit N, Poommouang A, Buddhachat K, Brown JL, Kampuansai J, Chomdej S, Kaewmong P, Kittiwattanawong K, Nganvongpanit K. Relationship of stranded cetaceans in Thai territorial waters to global populations: Mitochondrial DNA diversity of Cuvier's beaked whale, Indo Pacific finless porpoise, pygmy sperm whale, and dwarf sperm whale. Sci Prog 2022; 105:368504221103776. [PMID: 35635263 PMCID: PMC10450302 DOI: 10.1177/00368504221103776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2023]
Abstract
Cetaceans inhabit oceans throughout the world. Four specific odontocetes, namely Cuvier's beaked whale (Ziphius cavirostris), Indo Pacific finless porpoise (Neophocaena phocaenoides), pygmy sperm whale (Kogia breviceps), and dwarf sperm whale (Kogia sima), have occasionally been found stranded along Thailand's coastal waters (the Andaman Sea and the Gulf of Thailand). Although shared haplotypes of each species for many locations have been found, and some species have revealed genetic structure through haplotype networks, cetaceans in Thai waters have never been investigated in terms of comparing haplotypes to those that have existed before. Herein, we have illustrated the matrilineally phylogeographic relationships among worldwide populations through Bayesian Phylogenetic tree computations using Markov Chain Monte Carlo (MCMC) and Median-Joining Networks (MJNs). Unique haplotypes of the control region mitochondrial DNA of Thai odontocetes were found for all species. Moreover, a high degree of worldwide haplotype diversity (hd) above 0.8 among the four species was detected, while the lowest degree of nucleotide diversity (π) was observed in the Indo Pacific finless porpoise (1.12% ± 0.184%). An expansion of the effective female population size worldwide of three odontocete species was detected using Bayesian Skyline Reconstruction, but this did not include the Indo Pacific finless porpoise. Because Thai seas are located within the Indo Polynesian province, where this biodiversity hotspot exists, we speculate that these odontocetes may also inhabit specific habitats within the Malay Peninsula and Thailand's territorial waters. Therefore, closer attention and monitoring of these cetacean populations will be necessary for future conservation efforts.
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Affiliation(s)
- Promporn Piboon
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Napat Kriengsakpichit
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Anocha Poommouang
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Kittisak Buddhachat
- Excellence Center in Veterinary Bioscience, Chiang Mai, Thailand
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, Thailand
| | - Janine L. Brown
- Center for Species Survival, Smithsonian Conservation Biology Institute, Front Royal, VA, USA
| | - Jatupol Kampuansai
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Siriwadee Chomdej
- Excellence Center in Veterinary Bioscience, Chiang Mai, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | | | | | - Korakot Nganvongpanit
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
- Excellence Center in Veterinary Bioscience, Chiang Mai, Thailand
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4
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Zhao L, Sakornwimon W, Lin W, Zhang P, Chantra R, Dai Y, Aierken R, Wu F, Li S, Kittiwattanawong K, Wang X. Early divergence and differential population histories of the Indo-Pacific humpback dolphin in the Pacific and Indian Oceans. Integr Zool 2021; 16:612-625. [PMID: 33560551 DOI: 10.1111/1749-4877.12527] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The currently recognized Indo-Pacific humpback dolphin occurs in estuaries and surrounding shallow waters from the South China Sea to the Asian coast of the Indian Ocean. However, a recent study suggested that the humpback dolphin from the Bay of Bengal may represent a distinct phylogenetic species. In this study, we sequenced 915-bp mtDNA segments from five geographic populations in both Chinese and Thai waters; together with previously published sequences, these data revealed that the ancestral Indo-Pacific humpback dolphin might have split during the transition from the Oligocene to Miocene (23.45 Mya, 95% HPD: 16.65-26.55 Mya), and then dispersed along the Pacific and Indian Ocean coasts of Asia. Genetic differentiation was detected between most of the examined populations, except for only a few pairwise populations in the northern South China Sea. Genetic differentiation/distance between the humpback dolphins from the northern and southern South China Sea met the sub-species threshold value proposed for marine mammals, whereas that between the humpback dolphins in the Pacific and the Indian Ocean was above the species threshold. Bayesian inference of historic gene flow indicated low but constant northward gene flow along the Indian Ocean coast; however, there was a recent abrupt increase in gene flow in the Pacific region, likely due to the shortening coastline at the low stand of sea level. Our results revealed that the current taxonomic classification of Indo-Pacific humpback dolphins may not reflect their phylogeography.
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Affiliation(s)
- Liyuan Zhao
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration, Xiamen, China
| | - Watchara Sakornwimon
- Marine and Coastal Resources Research Center, The Middle Gulf of Thailand, Chumphon, Thailand
| | - Wenzhi Lin
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Peijun Zhang
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Rachawadee Chantra
- Marine and Coastal Resources Research Center, The Upper Gulf of Thailand, Samut Sakhon, Thailand
| | - Yufei Dai
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration, Xiamen, China
| | - Reyilamu Aierken
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration, Xiamen, China
| | - Fuxing Wu
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration, Xiamen, China
| | - Songhai Li
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | | | - Xianyan Wang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration, Xiamen, China
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5
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Ben Chehida Y, Thumloup J, Schumacher C, Harkins T, Aguilar A, Borrell A, Ferreira M, Rojas-Bracho L, Robertson KM, Taylor BL, Víkingsson GA, Weyna A, Romiguier J, Morin PA, Fontaine MC. Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum. Sci Rep 2020; 10:15190. [PMID: 32938978 PMCID: PMC7494866 DOI: 10.1038/s41598-020-71603-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 08/17/2020] [Indexed: 01/30/2023] Open
Abstract
Historical variation in food resources is expected to be a major driver of cetacean evolution, especially for the smallest species like porpoises. Despite major conservation issues among porpoise species (e.g., vaquita and finless), their evolutionary history remains understudied. Here, we reconstructed their evolutionary history across the speciation continuum. Phylogenetic analyses of 63 mitochondrial genomes suggest that porpoises radiated during the deep environmental changes of the Pliocene. However, all intra-specific subdivisions were shaped during the Quaternary glaciations. We observed analogous evolutionary patterns in both hemispheres associated with convergent evolution to coastal versus oceanic environments. This suggests that similar mechanisms are driving species diversification in northern (harbor and Dall's) and southern species (spectacled and Burmeister's). In contrast to previous studies, spectacled and Burmeister's porpoises shared a more recent common ancestor than with the vaquita that diverged from southern species during the Pliocene. The low genetic diversity observed in the vaquita carried signatures of a very low population size since the last 5,000 years. Cryptic lineages within Dall's, spectacled and Pacific harbor porpoises suggest a richer evolutionary history than previously suspected. These results provide a new perspective on the mechanisms driving diversification in porpoises and an evolutionary framework for their conservation.
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Affiliation(s)
- Yacine Ben Chehida
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands
| | - Julie Thumloup
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands
| | - Cassie Schumacher
- Swift Biosciences, 674 S. Wagner Rd., Suite 100, Ann Arbor, MI, 48103, USA
| | - Timothy Harkins
- Swift Biosciences, 674 S. Wagner Rd., Suite 100, Ann Arbor, MI, 48103, USA
| | - Alex Aguilar
- IRBIO and Department of Evolutive Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Diagonal 643, 08071, Barcelona, Spain
| | - Asunción Borrell
- IRBIO and Department of Evolutive Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Diagonal 643, 08071, Barcelona, Spain
| | - Marisa Ferreira
- MATB-Sociedade Portuguesa de Vida Selvagem, Estação de Campo de Quiaios, Apartado EC Quiaios, 3080-530, Figueira da Foz, Portugal.,CPRAM-Ecomare, Estrada Do Porto de Pesca Costeira, 3830-565, Gafanha da Nazaré, Portugal
| | - Lorenzo Rojas-Bracho
- Comisión Nacional de Áreas Naturales Protegidas (CONANP), C/o Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana 3918, Fraccionamiento Zona Playitas, 22860, Ensenada, BC, Mexico
| | - Kelly M Robertson
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - Barbara L Taylor
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - Gísli A Víkingsson
- Marine and Freshwater Research Institute, Fornubúðum 5, 220, Hafnarfjörður, Iceland
| | - Arthur Weyna
- Institut Des Sciences de L'Évolution (Université de Montpellier, CNRS UMR 5554), Montpellier, France
| | - Jonathan Romiguier
- Institut Des Sciences de L'Évolution (Université de Montpellier, CNRS UMR 5554), Montpellier, France
| | - Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - Michael C Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands. .,Laboratoire MIVEGEC (Université de Montpellier, CNRS 5290, IRD 229) et Centre de Recherche en Écologie et Évolution de la Santé (CREES), Institut de Recherche Pour Le Développement (IRD), 911 Avenue Agropolis, BP 64501, 34394, Montpellier Cedex 5, France.
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6
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Chen M, Fontaine MC, Ben Chehida Y, Zheng J, Labbé F, Mei Z, Hao Y, Wang K, Wu M, Zhao Q, Wang D. Genetic footprint of population fragmentation and contemporary collapse in a freshwater cetacean. Sci Rep 2017; 7:14449. [PMID: 29089536 PMCID: PMC5663847 DOI: 10.1038/s41598-017-14812-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 10/16/2017] [Indexed: 02/07/2023] Open
Abstract
Understanding demographic trends and patterns of gene flow in an endangered species is crucial for devising conservation strategies. Here, we examined the extent of population structure and recent evolution of the critically endangered Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis). By analysing genetic variation at the mitochondrial and nuclear microsatellite loci for 148 individuals, we identified three populations along the Yangtze River, each one connected to a group of admixed ancestry. Each population displayed extremely low genetic diversity, consistent with extremely small effective size (≤92 individuals). Habitat degradation and distribution gaps correlated with highly asymmetric gene-flow that was inefficient in maintaining connectivity between populations. Genetic inferences of historical demography revealed that the populations in the Yangtze descended from a small number of founders colonizing the river from the sea during the last Ice Age. The colonization was followed by a rapid population split during the last millennium predating the Chinese Modern Economy Development. However, genetic diversity showed a clear footprint of population contraction over the last 50 years leaving only ~2% of the pre-collapsed size, consistent with the population collapses reported from field studies. This genetic perspective provides background information for devising mitigation strategies to prevent this species from extinction.
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Affiliation(s)
- Minmin Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology of Chinese Academy of Sciences, Wuhan, 430072, China.,Research Center of Aquatic Organism Conservation and Water Ecosystem Restoration in Anhui Province, College of Life Science, Anqing Normal University, Anqing, 246133, China
| | - Michael C Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands.
| | - Yacine Ben Chehida
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands
| | - Jinsong Zheng
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology of Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Frédéric Labbé
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands.,Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Biological Sciences, University of Notre Dame, Galvin Life Sciences Center, Notre Dame, IN, 46556, USA
| | - Zhigang Mei
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology of Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yujiang Hao
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology of Chinese Academy of Sciences, Wuhan, 430072, China
| | - Kexiong Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology of Chinese Academy of Sciences, Wuhan, 430072, China
| | - Min Wu
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology of Chinese Academy of Sciences, Wuhan, 430072, China
| | - Qingzhong Zhao
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology of Chinese Academy of Sciences, Wuhan, 430072, China
| | - Ding Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology of Chinese Academy of Sciences, Wuhan, 430072, China.
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7
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Lin W, Karczmarski L, Wu Y. Phylogeography of the finless porpoise and potential implications for the taxonomy of Neophocaena spp. Mamm Biol 2017. [DOI: 10.1016/j.mambio.2017.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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8
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Cheng J, Sha ZL. Cryptic diversity in the Japanese mantis shrimp Oratosquilla oratoria (Crustacea: Squillidae): Allopatric diversification, secondary contact and hybridization. Sci Rep 2017; 7:1972. [PMID: 28512346 PMCID: PMC5434036 DOI: 10.1038/s41598-017-02059-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/04/2017] [Indexed: 11/20/2022] Open
Abstract
Mounting evidence of cryptic species in the marine realm emphasizes the necessity to thoroughly revise our current perceptions of marine biodiversity and species distributions. Here, we used mitochondrial cytochrome oxidase subunit I (mtDNA COI) and nuclear ribosomal internal transcribed spacer (nrDNA ITS) to investigate cryptic diversity and potential hybridization in the Japanese mantis shrimp Oratosquilla oratoria in the Northwestern (NW) Pacific. Both mitochondrial and nuclear gene genealogies revealed two cryptic species in this morphotaxon, which was further confirmed by extensive population-level analyses. One cryptic species is restricted to cold waters with a distribution range corresponding to temperate affinities, while the other dwelled warm waters influenced by the Kuroshio Current. Their divergence was postulated to be attributable to the vicariant event which resulted from the isolation of the Sea of Japan during the middle Pliocene (c. 3.85 Mya, 95% HPD 2.23–6.07 Mya). Allopatric speciation was maintained by limited genetic exchange due to their habitat preferences. Furthermore, the observation of recombinant nrDNA ITS sequence and intra-individual ITS polymorphism suggested recent hybridization event of the two cryptic species occurred in sympatric areas. Our study also illustrated that the Changjiang River outflow might act as an oceanic barrier to gene flow and promoted allopatric diversification in O. oratoria species complex.
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Affiliation(s)
- Jiao Cheng
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Zhong-Li Sha
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
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9
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Lu Z, Xu S, Song N, Gao T, Tian J, Han J. Analysis of the diet of finless porpoise (Neophocaena asiaeorientalis sunameri) based on prey morphological characters and DNA barcoding. CONSERV GENET RESOUR 2016. [DOI: 10.1007/s12686-016-0575-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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10
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Viet Tran TT, Ke Phan L, Durand JD. Diversity and distribution of cryptic species within the Mugil cephalus species complex in Vietnam. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:493-501. [PMID: 27159692 DOI: 10.3109/24701394.2016.1143467] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Mugil cephalus sensu lato is a globally distributed complex of cryptic species whose distribution range and evolutionary history remains largely unknown. In the North West (NW) Pacific three species have been identified genetically among fish described morphologically as M. cephalus. Their distribution ranges are largely parapatric and has been proposed to mirror different thermal preferences. To date, few samples have been analyzed from South China Sea, which limits inferences on the evolutionary history of the species complex. We sampled fish identified morphologically as M. cephalus along Vietnamese shores and characterized them using the sequence polymorphism of two mitochondrial genes, the cytochrome oxidase I and cytochrome b. This demonstrated that all three species described in the NW Pacific are present in both northern and southern Vietnamese waters. Although the difference in species abundance reflects those observed in the NW Pacific, no phylogeographic pattern was revealed. In addition, no population structure was observed whatever the species or the distribution range considered, which indicates a significant level of gene flow that maintains genetic homogeneity of the three species. It is also conceivable that each species experienced a recent population expansion from a single ancestral population. Finally we suggest that if the cold waters of the NW Pacific present a physiologic challenge leading to the almost parapatric distribution of the three species, then it is likely that the warm surface temperatures of the South China Sea negate this barrier.
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Affiliation(s)
- Thanh Thi Viet Tran
- a Vietnam National Museum of Nature, Vietnam Academy of Science and Technology , Caugiay , Hanoi , Vietnam
| | - Long Ke Phan
- a Vietnam National Museum of Nature, Vietnam Academy of Science and Technology , Caugiay , Hanoi , Vietnam
| | - Jean-Dominique Durand
- b Institut de Recherche pour le Développement (IRD), UMR MARBEC, Laboratory of Zoology, Department of Ecology and Evolutionary Biology , University of Science, VNUHCM , Chi Minh City , Vietnam
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Liu X, Chen R, Li G, Li J. Mitochondrial genome of the Neophocaena asiaeorientalis asiaeorientalis (Phocaenidae: Neophocaena). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3145-6. [DOI: 10.3109/19401736.2015.1007305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Xinyang Liu
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, People’s Republic of China,
| | - Ran Chen
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, People’s Republic of China,
- Tongling Freshwater Dolphins National Natural Reserve, Tongling, Anhui, People’s Republic of China, and
| | - Gang Li
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, People’s Republic of China,
| | - Jinhua Li
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, People’s Republic of China,
- The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, People’s Republic of China
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