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Scheepers M, Bragança PHN, Chakona A. Naming the other cousin: A new goldie barb (Cyprinidae: Smiliogastrininae) from the northeast escarpment in South Africa, with proposed taxonomic rearrangement of the goldie barb group in southern Africa. JOURNAL OF FISH BIOLOGY 2024. [PMID: 39021263 DOI: 10.1111/jfb.15870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 06/20/2024] [Accepted: 06/25/2024] [Indexed: 07/20/2024]
Abstract
A growing body of evidence indicates that the global diversity of freshwater fishes has not been fully documented. Studies of freshwater fishes that were previously thought to be morphologically variable have revealed the existence of deeply divergent lineages, with many distinct species. In southern Africa a number of Enteromius species exhibit either exceedingly wide or divided distribution patterns that should be rare for freshwater fishes with limited dispersal opportunities between river systems. One such species is the sidespot barb, Enteromius neefi. As currently defined, E. neefi has a disjunct distribution that is divided between rivers in the northeast escarpment in South Africa and Eswatini, and tributaries of the Upper Zambezi in Zambia and southern Congo in the Democratic Republic of Congo, with a large geographic gap between these two populations. With the use of molecular and morphological methods, the level of divergence between the two populations was examined, and a new species was described from the Steelpoort River in the Limpopo River system of South Africa. Findings from this study provide further evidence for a number of taxonomic problems within the goldie barbs of southern Africa, and some taxonomic rearrangements are proposed for this group.
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Affiliation(s)
- Martinus Scheepers
- NRF-South African Institute for Aquatic Biodiversity (NRF-SAIAB), Makhanda, South Africa
- Department of Ichthyology and Fisheries Science, Rhodes University, Makhanda, South Africa
| | - Pedro H N Bragança
- NRF-South African Institute for Aquatic Biodiversity (NRF-SAIAB), Makhanda, South Africa
- Department of Ichthyology, American Museum of Natural History, New York, New York, USA
| | - Albert Chakona
- NRF-South African Institute for Aquatic Biodiversity (NRF-SAIAB), Makhanda, South Africa
- Department of Ichthyology and Fisheries Science, Rhodes University, Makhanda, South Africa
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2
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Ni X, Chen Y, Deng G, Fu C. Pleistocene Landscape Dynamics Drives Lineage Divergence of a Temperate Freshwater Fish Gobio rivuloides in Coastal Drainages of Northern China. Genes (Basel) 2023; 14:2146. [PMID: 38136969 PMCID: PMC10743038 DOI: 10.3390/genes14122146] [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: 10/26/2023] [Revised: 11/20/2023] [Accepted: 11/26/2023] [Indexed: 12/24/2023] Open
Abstract
Understanding historical processes underlying lineage distribution patterns is a primary goal of phylogeography. We selected Gobio rivuloides (Cypriniformes: Gobionidae) as a model to improve our knowledge about how intraspecific genetic divergence of freshwater fishes arises in coastal drainages of northern China via statistical analysis using cytochrome b gene. The time-calibrated phylogeny of G. rivuloides showed the divergence of two major lineages (I and II) at ~0.98 Ma (million years ago). Lineage I can be divided into two sub-lineages (I-A and I-B) with a divergence time of ~0.83 Ma. Sub-lineage I-A inhabits the Amur River, and sub-lineage I-B lives in the Luan River and Liao River. Lineage II is distributed in the Yellow River and Hai River, with close genetic relationships between the two drainages, and can be split into two sub-lineages (II-C and II-D) with a divergence time of ~0.60 Ma. Our findings indicate that the splitting of lineages and sub-lineages could be attributed to geographic isolation caused by the formation of the Bohai Sea, river capture, and the episodic hydrologic closing of a paleolake during the late Lower-Middle Pleistocene. It is also the first report we know of displaying a clear phylogeographic break for freshwater fishes across coastal drainages in northern China.
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Affiliation(s)
| | | | | | - Cuizhang Fu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200438, China; (X.N.); (Y.C.); (G.D.)
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3
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Hao C, Liu Y, Wei N, Arken K, Shi C, Yue C. The complete mitochondrial genomes of the Leuciscus baicalensis and Rutilus rutilus: a detailed genomic comparison among closely related species of the Leuciscinae subfamily. Gene 2023:147535. [PMID: 37328078 DOI: 10.1016/j.gene.2023.147535] [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: 01/09/2023] [Revised: 05/04/2023] [Accepted: 05/31/2023] [Indexed: 06/18/2023]
Abstract
Cyprinidae is the largest family in the order of freshwater fish Cypriniformes. Increased subfamily members of Cyprinidae have been suggested to be re-classified for decades. In this study, we sequenced the mitochondrial genomes (mitogenomes) of Leuciscus baicalensis and Rutilus rutilus collected from northwest China and compared with other closely related species to determine their associated family or subfamily. We used Illumina NovaSeq to sequence the entire mitochondrial genomes of Leuciscus baicalensis and Rutilus rutilus and characterized the mitogenomes by the gene structure, gene order, and the secondary structures of the 22 tRNA genes. We compared mitogenome features of Leuciscinae with other subfamilies in Cyprinidae. We used the analytic Bayesian Information and Maximum Likelihood methods to determine phylogenetic trees of 13 PCGs. The mitogenomes of Leuciscus baicalensis and Rutilus rutilus were 16,607 bp and 16,606 bp, respectively. Organization and location of these genes were consistent with already studied Leuciscinae fishes. Synonymous codon usage was conservative in Leuciscinae as compared with other subfamilies in Cyprinidae. Phylogenetic analysis indicated that Leuciscinae was a monophyletic group, and genus Leuciscus was a paraphyletic group. Our approach, for the first time, of studying comparative mitochondrial genomics and phylogenetics together provided a supportive platform to the analysis of population genetics and phylogeny for Leuciscinae. Our results indicated a promising potential of comparative mitochondrial genomics in the manifestation of phylogenetic relationships between fishes, leading us to a suggestion that mitogenomes should be routinely considered in clarifying phylogenetics of family and subfamily members of fish.
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Affiliation(s)
- Cuilan Hao
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China.
| | - Yanjun Liu
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Nianwen Wei
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Kadirden Arken
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Caixia Shi
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Cheng Yue
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
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4
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Vainutis KS, Voronova AN, Urabe M, Kazarin VM. Integrative approach for discovering of the new species within the genus Allocreadium Looss, 1900 (Trematoda: Allocreadiidae) and framing of biogeographical hypotheses for the genus. Syst Parasitol 2023; 100:189-213. [PMID: 36522565 DOI: 10.1007/s11230-022-10081-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 12/04/2022] [Indexed: 12/23/2022]
Abstract
In July 2012 new Allocreadium species was isolated from Carassius gibelio caught in the Arsenyevka River, Primorsky region, Russia. Analyses on the morphometrics and internal organs' topology revealed that these worms are morphologically closest with A. isoporum but both species are independent according to high genetic distances based on the 28S gene fragment (5.434±0.0073%). Unlike A. isoporum found earlier in Europe, the new species named A. pseudoisoporum sp. nov. has a shorter body length and the vitellarium not reaching the posterior end of the body at some distance and its anterior border is on the level of the ventral sucker. Allocreadium pseudoisoporum sp. nov. differs from seven species previously found in the Russian Far East with the following features: smaller size of the body, suckers' ratio, range values, and topology of internal structures. Newly localities in the Pavlovka River and the Artyomovka River were discovered for A. khankaiensis. Morphological variability of the worms from the Pavlovka River was observed in comparison with A. khankaiensis from the Komissarovka River. Using scanning electron microscope, we examined external surfaces of three species (A. pseudoisoporum sp. nov., A. khankaiensis, A. hemibarbi) and observed structures reminiscent sensory receptors. This study was aimed to describe species diversity of allocreadiids inhabiting the south of Primorsky region, and to clarify phylogenetic relationships between the species from the genus Allocreadium Looss, 1900 using molecular genetic methods. The phylogenetic Bayesian tree based on the 28S gene showed a clear separation of ten Allocreadium species and confirmed the validity of A. pseudoisoporum sp. nov. Allocreadium pseudoisoporum sp. nov. is most similar to A. gotoi (genetic distances - 3.578±0.0051% in 28S, and 18.777±0.0149% in cox1), and represented the earliest divergent lineage in Allocreadium clade on the phylogenetic tree based on the 28S gene, thereby indicating its proximity to the ancestral node. Also, dichotomous keys for 25 Palearctic species of Allocreadium were prepared based on the morphology of the adult worms.
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Affiliation(s)
- Konstantin S Vainutis
- Pacific Branch of the Federal State Budget Scientific Institution "Russian Federal Research Institute of Fisheries and Oceanography", 4 Alley Shevchenko, Vladivostok, Russian Federation, 690091. .,The Far Eastern State Technical Fisheries University (FESTFU), 52B Lugovaya Street, Vladivostok, Russian Federation, 690087. .,Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, pr. 100-letija, 159, Vladivostok, Russian Federation, 690022.
| | - Anastasia N Voronova
- Pacific Branch of the Federal State Budget Scientific Institution "Russian Federal Research Institute of Fisheries and Oceanography", 4 Alley Shevchenko, Vladivostok, Russian Federation, 690091
| | - Misako Urabe
- Department of Ecosystem Studies, Faculty of Environmental Science, The University of Shiga Prefecture, Shiga, 522-8533, Japan
| | - Vitaly M Kazarin
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, pr. 100-letija, 159, Vladivostok, Russian Federation, 690022
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Chen XJ, Song L, Cao YW, Wang Q. Phylogenetic relationship and characterization of the complete mitochondrial genome sequence of Opsarius caudiocellatus (Cypriniformes: Danionidae: Chedrinae). Mitochondrial DNA B Resour 2022; 7:2051-2055. [DOI: 10.1080/23802359.2022.2151324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Xiao Jiang Chen
- College of Fisheries Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, China
| | - Lin Song
- College of Fisheries Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, China
| | - You Wen Cao
- College of Fisheries Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, China
| | - Quan Wang
- College of Fisheries Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, China
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Chen XJ, Song L, Song Y, Wang Q. Determination and analysis of the complete mitochondrial genome of Barilius barila (Cypriniformes: Danionidae: Chedrinae). MITOCHONDRIAL DNA PART B 2022; 7:2002-2005. [PMID: 36451966 PMCID: PMC9704074 DOI: 10.1080/23802359.2022.2148824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Cyprinid fish Barilius barila found in the Irrawaddy water system is a valuable fishery resource and has been listed as Least Concern by the IUCN. This study determined the complete mitochondrial genome of B. barila from Yunnan, China, for the first time. Circular molecule of B. barila mitogenome was sequenced to be 16,560 bp in length, with the typical gene structure of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and two noncoding areas (control region and the origin of L-strand replication). Overall nucleotides composition appeared to be 27.5% A, 24.8% T, 19.2% G, and 28.6% C, with a slight AT (52.3%) bias. The topology of the phylogenetic tree showed that B. barila was well grouped with Opsarius caudiocellatus, and clustered together with the genus Opsarius instead of Barilius, revealing that it was more reasonable for Barilius barila to belong to Opsarius rather than Barilius.
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Affiliation(s)
- Xiao Jiang Chen
- College of Fisheries Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, P.R. China
| | - Lin Song
- College of Fisheries Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, P.R. China
| | - Yang Song
- College of Fisheries Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, P.R. China
| | - Quan Wang
- College of Fisheries Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, P.R. China
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7
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Reier S, Kruckenhauser L, Snoj A, Trontelj P, Palandačić A. The minnow Phoxinus lumaireul (Leuciscidae) shifts the Adriatic-Black Sea basin divide in the north-western Dinaric Karst region. ECOHYDROLOGY : ECOSYSTEMS, LAND AND WATER PROCESS INTERACTIONS, ECOHYDROGEOMORPHOLOGY 2022; 15:e2449. [PMID: 36245897 PMCID: PMC9539529 DOI: 10.1002/eco.2449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 05/25/2022] [Accepted: 06/26/2022] [Indexed: 06/16/2023]
Abstract
Karst landscapes are characterized by intermittent and sinking streams. The most common method used to study underground hydrological connections in karst is tracing tests. However, a more biologically oriented approach has been suggested: analysis of the genetic structure of aquatic organisms. Biological tracers can be sought among trogloxenes, that is, surface species that occasionally enter caves and groundwater. One such example is the fish genus Phoxinus, which exhibits high genetic diversity and complex phylogeography in the Balkan Peninsula. In the north-western Dinaric Karst, the complex hydrological network was digitalized in 2020. Contemporaneously, Phoxinus lumaireul populations in the Slovenian Dinaric Karst were intensively sampled and analysed for fragments of two mitochondrial genes and one nuclear gene. The derived phylogeographic structure and data on hydrological connections were compared to evaluate support for three alternative scenarios: The genetic structure (1) is a consequence of the ongoing geneflow through underground connections, (2) reflects a previous hydrological network or (3) is an outcome of anthropogenic translocations. The results suggest that the first two scenarios seem to have played a major role, while the third has not had profound effects on the genetic composition. Comparison between the genetic structure of Slovenian Dinaric Karst sampling sites and that of hydrologically isolated reference sampling sites indicated a greater genetic connectivity in the former. Moreover, the range of Adriatic (1a) and Black Sea (1c) haplotypes does not correspond to the Adriatic-Black Sea basin divide but is shifted northwards.
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Affiliation(s)
- Susanne Reier
- First Zoological DepartmentNatural History Museum ViennaViennaAustria
- Department of Evolutionary BiologyUniversity of ViennaViennaAustria
| | - Luise Kruckenhauser
- Department of Evolutionary BiologyUniversity of ViennaViennaAustria
- Central Research LaboratoriesNatural History Museum ViennaViennaAustria
| | - Aleš Snoj
- Department of Animal Science, Biotechnical FacultyUniversity of LjubljanaDomžaleSlovenia
| | - Peter Trontelj
- Department of Biology, Biotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
| | - Anja Palandačić
- First Zoological DepartmentNatural History Museum ViennaViennaAustria
- Department of Biology, Biotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
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8
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Unauthorized Stocking of an Endangered Bitterling Acheilognathus typus in an Irrigation Pond Detected and Substantiated by Biological and Human Lines of Evidence. FISHES 2022. [DOI: 10.3390/fishes7040150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Acheilognathus typus, an endangered bitterling, was captured in an irrigation pond in the northern part of Niigata prefecture, Japan, in 2019. This bitterling species had once occupied that region. Its absence for years indicated the possible extinction of the bitterling there. We expected that the recently captured individuals are an unknown remnant stock of that endangered species found through an extensive survey. Mitochondrial genotyping, however, revealed that the recently captured individuals had a common haplotype with those from Kashimadai, Miyagi prefecture, Japan. The uniqueness of the haplotype to these two ponds indicates a stock identity between them. In the pond in Kashimadai, the illegal activity of catching the bitterlings by a person from the northern Niigata prefecture was detected in 2015. We conclude that the bitterling from the northern Niigata prefecture was stocked from a pond in Kashimadai. Our report is the first example of unauthorized bitterling stocking substantiated from both biological and human lines of evidence.
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9
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Canales-Aguirre CB, Ritchie PA, Hernández S, Herrera-Yañez V, Ferrada Fuentes S, Oyarzún FX, Hernández CE, Galleguillos R, Arratia G. Phylogenetic relationships, origin and historical biogeography of the genus Sprattus (Clupeiformes: Clupeidae). PeerJ 2021; 9:e11737. [PMID: 34466280 PMCID: PMC8380030 DOI: 10.7717/peerj.11737] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 06/17/2021] [Indexed: 12/04/2022] Open
Abstract
The genus Sprattus comprises five species of marine pelagic fishes distributed worldwide in antitropical, temperate waters. Their distribution suggests an ancient origin during a cold period of the earth’s history. In this study, we evaluated this hypothesis and corroborated the non-monophyly of the genus Sprattus, using a phylogenetic approach based on DNA sequences of five mitochondrial genome regions. Sprattus sprattus is more closely related to members of the genus Clupea than to other Sprattus species. We also investigated the historical biogeography of the genus, with the phylogenetic tree showing two well-supported clades corresponding to the species distribution in each hemisphere. Time-calibrated phylogenetic analyses showed that an ancient divergence between Northern and Southern Hemispheres occurred at 55.8 MYBP, followed by a diversification in the Oligocene epoch in the Northern Hemisphere clade (33.8 MYBP) and a more recent diversification in the Southern Hemisphere clade (34.2 MYBP). Historical biogeography analyses indicated that the most recent common ancestor (MRCA) likely inhabited the Atlantic Ocean in the Southern Hemisphere. These results suggest that the ancestral population of the MRCA diverged in two populations, one was dispersed to the Northern Hemisphere and the other across the Southern Hemisphere. Given that the Eocene was the warmest epoch since the Paleogene, the ancestral populations would have crossed the tropics through deeper cooler waters, as proposed by the isothermal submergence hypothesis. The non-monophyly confirmed for the genus Sprattus indicates that its systematics should be re-evaluated.
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Affiliation(s)
| | - Peter A Ritchie
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Sebastián Hernández
- Biomolecular Laboratory, Center for International Programs, Universidad Veritas, San José, Costa Rica.,Sala de Colecciones Biológicas, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile
| | - Victoria Herrera-Yañez
- Laboratorio de Genética y Acuicultura, Departamento de Oceanografía, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Sandra Ferrada Fuentes
- Laboratorio de Genética y Acuicultura, Departamento de Oceanografía, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Fernanda X Oyarzún
- Centro i∼mar, Universidad de Los Lagos, Puerto Montt, Chile.,Centro de Investigación en Biodiversidad y Ambientes Sustentables (CIBAS), Universidad Católica de la Santísima Concepción, Concepción, Chile.,Instituto Milenio en Socioecología Costera, Santiago, Chile
| | - Cristián E Hernández
- Laboratorio de Ecología Evolutiva y Filoinformática, Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile.,Universidad Católica de Santa María, Arequipa, Perú
| | - Ricardo Galleguillos
- Laboratorio de Genética y Acuicultura, Departamento de Oceanografía, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Gloria Arratia
- Biodiversity Institute and Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, United States of America
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10
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Rocha S, Azevedo C, Alves Â, Antunes C, Casal G. Morphological and molecular characterization of myxobolids (Cnidaria, Myxozoa) infecting cypriniforms (Actinopterygii, Teleostei) endemic to the Iberian Peninsula. Parasite 2019; 26:48. [PMID: 31414983 PMCID: PMC6694745 DOI: 10.1051/parasite/2019049] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 07/30/2019] [Indexed: 11/21/2022] Open
Abstract
The Iberian Peninsula provides a unique freshwater ecosystem for native and endemic cypriniforms to thrive. Despite cypriniforms being hosts to multiple myxobolids worldwide, little research has been performed in this geographic location. In this study, the examination of three Iberian endemic cypriniforms showed that myxosporean richness in the Iberian Peninsula is underestimated, with three new and one known myxobolid species being reported based on morphological and molecular data (SSU). Myxobolus arcasii n. sp. is described from the kidney and gonads of the "bermejuela" Achondrostoma arcasii, M. duriensis n. sp. from the gills of the Northern straight-mouth nase Pseudochondrostoma duriense, and Thelohanellus paludicus n. sp. from the intestine of the Southern Iberian spined-loach Cobitis paludica. Myxobolus pseudodispar Gorbunova, 1936 is further reported from several organs of P. duriense, and from the spleen of A. arcasii. The occurrence of M. pseudodispar in endemic Iberian species reveals that host-shift followed its co-introduction with central European leuciscids into this geographic location. Several other myxobolids originally described from barbels in central Europe have also been reported from the Iberian endemic cypriniform Luciobarbus bocagei. Nonetheless, except for M. musculi, the identification of these myxobolids in L. bocagei is here shown to be dubious and require molecular confirmation. Phylogenetic analyses reveal M. arcasii n. sp. and M. duriensis n. sp. clustering within different lineages of leuciscid-infecting species, showing that myxobolids entered Leuciscidae as hosts multiple times during their evolution. Constituting the first myxobolid reported from the subfamily Cobitinae, Thelohanellus paludicus n. sp. stands alone in the tree topology.
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Affiliation(s)
- Sónia Rocha
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Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS/UP) Rua Jorge Viterbo Ferreira No. 228 4050-313 Porto Portugal
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Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Terminal de Cruzeiros de Leixões Av. General Norton de Matos s/n 4450-208 Matosinhos Portugal
| | - Carlos Azevedo
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Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS/UP) Rua Jorge Viterbo Ferreira No. 228 4050-313 Porto Portugal
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Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Terminal de Cruzeiros de Leixões Av. General Norton de Matos s/n 4450-208 Matosinhos Portugal
| | - Ângela Alves
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Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS/UP) Rua Jorge Viterbo Ferreira No. 228 4050-313 Porto Portugal
| | - Carlos Antunes
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Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Terminal de Cruzeiros de Leixões Av. General Norton de Matos s/n 4450-208 Matosinhos Portugal
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Aquamuseu do Rio Minho Parque do Castelinho 4920-290 Vila Nova de Cerveira Portugal
| | - Graça Casal
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University Institute of Health Sciences & Institute of Research and Advanced Training in Health Sciences and Technologies, CESPU Rua Central da Gandra No. 1317 4585-116 Gandra Portugal
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11
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Phylogenetic relationships of Cypriniformes and plasticity of pharyngeal teeth in the adaptive radiation of cyprinids. SCIENCE CHINA-LIFE SCIENCES 2019; 62:553-565. [DOI: 10.1007/s11427-019-9480-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 11/01/2018] [Indexed: 12/23/2022]
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12
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Schönhuth S, Vukić J, Šanda R, Yang L, Mayden RL. Phylogenetic relationships and classification of the Holarctic family Leuciscidae (Cypriniformes: Cyprinoidei). Mol Phylogenet Evol 2018; 127:781-799. [PMID: 29913311 DOI: 10.1016/j.ympev.2018.06.026] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 06/12/2018] [Accepted: 06/15/2018] [Indexed: 12/15/2022]
Abstract
The phylogenetic relationships and classification of the freshwater fish order Cypriniformes, like many other species-rich groups of vertebrates, has evolved over time with some consistency and inconsistencies of relationships across various studies. Within Cypriniformes, the Holarctic family Leuciscidae is one of the most widely distributed and highly diverse monophyletic groups of cyprinoids. Despite several studies conducted on this group, alternative hypotheses exist as to the composition and relationships within Leuciscidae. Here we assess the extent, composition, phylogenetic relationships, and taxonomy of this highly diverse group of fishes, using multiple mitochondrial and nuclear loci and a comprehensive and dense taxonomic sampling. Analyses of 418 specimens (410 species) resolve a well-supported Leuciscidae including 362 specimens (358 taxa) in six well-supported subfamilies/major clades: Pseudaspininae/Far East Asian clade (FEA); Laviniinae/North American Western clade (WC); Plagopterinae/North American Creek Chub-Plagopterin clade (CC-P); Leuciscinae/Eurasian Old World clade (OW) (minus Phoxinus) plus North American Notemigonus; Phoxininae/Eurasian Phoxinus clade (PHX); and Pogonichthyinae/North American clade (NA) including all remaining leuciscids. Within Leuciscidae, neither the traditional phoxinins (Phoxinus, FEA, Nearctic genera) nor all Nearctic genera (minus Notemigonus) are resolved as monophyletic; whereas the WC and CC-P form two independent lineages from remaining North American cyprinoids. A close relationship exists between Eurasian Phoxinus, NA, and OW clades, while FEA is the sister group to all remaining Leuciscidae. Major lineages resolved within these six subfamilies are mostly congruent with some previous studies. Our results suggests a complex evolutionary history of this diverse and widespread group of fishes.
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Affiliation(s)
- Susana Schönhuth
- Biology Department, Saint Louis University, 3507 Laclede Avenue, St. Louis, MO 63103, USA.
| | - Jasna Vukić
- Department of Ecology, Faculty of Science, Charles University, Vinicna 7, 128 44 Prague, Czech Republic
| | - Radek Šanda
- Department of Zoology, National Museum, Vaclavske namesti 68, 115 79 Prague, Czech Republic
| | - Lei Yang
- Florida Museum of Natural History, University of Florida, 1659 Museum Rd., Gainesville, FL 32611, USA
| | - Richard L Mayden
- Biology Department, Saint Louis University, 3507 Laclede Avenue, St. Louis, MO 63103, USA
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13
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Reconciling the biogeography of an invader through recent and historic genetic patterns: the case of topmouth gudgeon Pseudorasbora parva. Biol Invasions 2018. [DOI: 10.1007/s10530-018-1693-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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14
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Krabbenhoft TJ, Turner TF. Comparative transcriptomics of cyprinid minnows and carp in a common wild setting: a resource for ecological genomics in freshwater communities. DNA Res 2018; 25:11-23. [PMID: 28985264 PMCID: PMC5824830 DOI: 10.1093/dnares/dsx034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 08/12/2017] [Indexed: 12/30/2022] Open
Abstract
Comparative transcriptomics can now be conducted on organisms in natural settings, which has greatly enhanced understanding of genome–environment interactions. Here, we demonstrate the utility and potential pitfalls of comparative transcriptomics of wild organisms, with an example from three cyprinid fish species (Teleostei:Cypriniformes). We present extensively filtered and annotated transcriptome assemblies that provide a valuable resource for studies of genome evolution (e.g. polyploidy), ecological and morphological diversification, speciation, and shared and unique responses to environmental variation in cyprinid fishes. Our results and analyses address the following points: (i) ‘essential developmental genes’ are shown to be ubiquitously expressed in a diverse suite of tissues across later ontogenetic stages (i.e. juveniles and adults), making these genes are useful for assessing the quality of transcriptome assemblies, (ii) the influence of microbiomes and other exogenous DNA, (iii) potentially novel, species-specific genes, and (iv) genomic rearrangements (e.g. whole genome duplication). The data we present provide a resource for future comparative work in cypriniform fishes and other taxa across a variety of sub-disciplines, including stress response, morphological diversification, community ecology, ecotoxicology, and climate change.
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Affiliation(s)
- Trevor J Krabbenhoft
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Thomas F Turner
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA
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15
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Dai W, Zou M, Yang L, Du K, Chen W, Shen Y, Mayden RL, He S. Phylogenomic Perspective on the Relationships and Evolutionary History of the Major Otocephalan Lineages. Sci Rep 2018; 8:205. [PMID: 29317769 PMCID: PMC5760653 DOI: 10.1038/s41598-017-18432-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 12/11/2017] [Indexed: 12/21/2022] Open
Abstract
The phylogeny of otocephalan fishes is the subject of broad controversy based on morphological and molecular evidence. The primary unresolved issue pertaining to this lineage relates to the origin of Characiphysi, especially the paraphyly of Characiformes. The considerable uncertainty associated with this lineage has precluded a greater understanding of the origin and evolution of the clade. Herein, a phylogenomic approach was applied to resolve this debate. By analyzing 10 sets of transcriptomic data generated in this study and 12 sets of high-throughput data available in public databases, we obtained 1,110 single-copy orthologous genes (935,265 sites for analysis) from 22 actinopterygians, including 14 otocephalan fishes from six orders: Clupeiformes, Gonorynchiformes, Cypriniformes, Siluriformes, Characiformes, and Gymnotiformes. Based on a selection of 125 nuclear genes screened from single-gene maximum likelihood (ML) analyses and sequence bias testing, well-established relationships among Otocephala were reconstructed. We suggested that Gymnotiformes are more closely related to Characiformes than to Siluriformes and Characiformes are possibly paraphyletic. We also estimated that Otocephala originated in the Early-Late Jurassic, which postdates most previous estimations, and hypothesized scenarios of the early historical biogeographies of major otocephalan lineages.
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Affiliation(s)
- Wei Dai
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Ming Zou
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Beijing, 430070, People's Republic of China
| | - Liandong Yang
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Kang Du
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Weitao Chen
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Yanjun Shen
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Richard L Mayden
- Department of Biology, Saint Louis University, Saint Louis, MO, 63103, USA
| | - Shunping He
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China.
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16
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Ito T, Fukuda T, Morimune T, Hosoya K. Evolution of the connection patterns of the cephalic lateral line canal system and its use to diagnose opsariichthyin cyprinid fishes (Teleostei, Cyprinidae). Zookeys 2017:115-131. [PMID: 29290716 PMCID: PMC5740415 DOI: 10.3897/zookeys.718.13574] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 10/28/2017] [Indexed: 11/12/2022] Open
Abstract
The cephalic lateral line canal systems were compared among 12 species of the cyprinid tribe Opsariichthyini. All species were characterized by the separation of the supraorbital canal from both the infraorbital and the temporal canals, and the left side of the supratemporal canal from the right side of the canal. In species of Candidia, Opsariichthys, Parazacco, and Zacco, and Nipponocyprissieboldii the temporal canal was separated from the preoperculomandibular canal. In Nipponocypristemminckii and N.koreanus, the temporal canal was connected to the preoperculomandibular canal. Separation of the left and right sides of the supratemporal canal is a possible synapomorphy of the opsariichthyin cyprinids. Opsariichthysuncirostris and O.bidens are unique among the opsariichthyins in that the connection between the infraorbital and temporal canals is retarded. The variation in arrangement of the cephalic lateral line canal system can be used as diagnostic characters for the opsariichthyin species.
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Affiliation(s)
- Taiki Ito
- Wetlands International Japan, 2F Jono Building II 17-1, Odenma-cho, Nihonbashi, Chuo-ku, Tokyo, 103-0011, Japan
| | - Toyoaki Fukuda
- Tezukayama Junior & Senior High School, Gakuen-minami 3-1-3, Nara 631-0034, Japan
| | - Toshihiko Morimune
- Department of Environmental Management, Faculty of Agriculture, Kindai University, Nakamachi 3327-204, Nara 631-8505, Japan
| | - Kazumi Hosoya
- Department of Environmental Management, Faculty of Agriculture, Kindai University, Nakamachi 3327-204, Nara 631-8505, Japan
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17
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Nakamura Y, Yasuike M, Mekuchi M, Iwasaki Y, Ojima N, Fujiwara A, Chow S, Saitoh K. Rhodopsin gene copies in Japanese eel originated in a teleost-specific genome duplication. ZOOLOGICAL LETTERS 2017; 3:18. [PMID: 29075512 PMCID: PMC5645911 DOI: 10.1186/s40851-017-0079-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/11/2017] [Indexed: 06/16/2023]
Abstract
BACKGROUND Gene duplication is considered important to increasing the genetic diversity in animals. In fish, visual pigment genes are often independently duplicated, and the evolutionary significance of such duplications has long been of interest. Eels have two rhodopsin genes (rho), one of which (freshwater type, fw-rho) functions in freshwater and the other (deep-sea type, ds-rho) in marine environments. Hence, switching of rho expression in retinal cells is tightly linked with eels' unique life cycle, in which they migrate from rivers or lakes to the sea. These rho genes are apparently paralogous, but the timing of their duplication is unclear due to the deep-branching phylogeny. The aim of the present study is to elucidate the evolutionary origin of the two rho copies in eels using comparative genomics methods. RESULTS In the present study, we sequenced the genome of Japanese eel Anguilla japonica and reconstructed two regions containing rho by de novo assembly. We found a single corresponding region in a non-teleostean primitive ray-finned fish (spotted gar) and two regions in a primitive teleost (Asian arowana). The order of ds-rho and the neighboring genes was highly conserved among the three species. With respect to fw-rho, which was lost in Asian arowana, the neighboring genes were also syntenic between Japanese eel and Asian arowana. In particular, the pattern of gene losses in ds-rho and fw-rho regions was the same as that in Asian arowana, and no discrepancy was found in any of the teleost genomes examined. Phylogenetic analysis supports mutual monophyly of these two teleostean synteny groups, which correspond to the ds-rho and fw-rho regions. CONCLUSIONS Syntenic and phylogenetic analyses suggest that the duplication of rhodopsin gene in Japanese eel predated the divergence of eel (Elopomorpha) and arowana (Osteoglossomorpha). Thus, based on the principle of parsimony, it is most likely that the rhodopsin paralogs were generated through a whole genome duplication in the ancestor of teleosts, and have remained till the present in eels with distinct functional roles. Our result indicates, for the first time, that teleost-specific genome duplication may have contributed to a gene innovation involved in eel-specific migratory life cycle.
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Affiliation(s)
- Yoji Nakamura
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
| | - Motoshige Yasuike
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
| | - Miyuki Mekuchi
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
| | - Yuki Iwasaki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
- Present address: National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540 Japan
| | - Nobuhiko Ojima
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
- Present address: Japan Fisheries Research and Education Agency, 2-3-3 Minatomirai, Nishi, Yokohama, Kanagawa 220-6115 Japan
| | - Atushi Fujiwara
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
| | - Seinen Chow
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
| | - Kenji Saitoh
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
- Present address: Tohoku National Fisheries Research Institute, Japan Fisheries Research and Education Agency, 3-27-5 Shinhama, Shiogama, Miyagi 985-0001 Japan
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18
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Lin M, Mu X, Yan X. The complete mitochondrial genome of Cichla ocellaris. MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:620-622. [PMID: 33473921 PMCID: PMC7800511 DOI: 10.1080/23802359.2017.1372713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
In this study, the complete mitochondrial (mt) genome of Cichlao cellaris was determined. The mt genome has a length of 16,526 bp and encodes 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and one AT-rich non-coding region (D-loop). The gene arrangement was similar to those of typical fishes. The total base composition of the mt genome was 25.1% T, 30.8% C, 29.3% A, and 14.8% G. Of the 13 PCGs, 12 genes start with an ATG codon, except COX1 is with GTG. And among these 13 genes, seven (ND1, COX1, ATP8, ND4L, ND5, ND6, and Cytb) used TAA or TAG as the termination codon, whereas six (ND2, COX2, ATP6, COX3, ND3, and ND4) have incomplete stop codon T. Its control region is atypical in being short at 850 bp. This mt genome sequence data will be useful for phylogenetic and systematic analyses within the family Cichlaidae.
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Affiliation(s)
- Minghui Lin
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Xidong Mu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Xi Yan
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
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19
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Kwan YS, Kim D, Ko MH, Lee WO, Won YJ. Multi-locus phylogenetic analyses support the monophyly and the Miocene diversification of Iksookimia (Teleostei: Cypriniformes: Cobitidae). SYST BIODIVERS 2017. [DOI: 10.1080/14772000.2017.1340912] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Ye-Seul Kwan
- Graduate Degree Program, Division of EcoScience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, South Korea
- Present Address: Nakdonggang National Institute of Biological Resources, Sangju-si, Gyeongsangbuk-do, 37242, South Korea
| | - Daemin Kim
- Division of EcoScience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, South Korea
- Present Address: Graduate Degree Program, Department of Ecology and Evolutionary Biology, Yale University, P.O.Box 208106, New Haven, Connecticut, 06520-8106, USA
| | - Myeong-Hun Ko
- Division of EcoScience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, South Korea
| | - Wan-Ok Lee
- Inland Fisheries Research Institute, National Fisheries Research and Development Institute, 65 Gangbyeon-ro, Gapyeong-gun, Gyeonggi-do, 12453, South Korea
| | - Yong-Jin Won
- Division of EcoScience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, South Korea
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20
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Kartavtsev YP. Barcode index number, taxonomic rank and modes of speciation: examples from fish. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:535-542. [PMID: 28481646 DOI: 10.1080/24701394.2017.1315570] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Species delimitation by DNA sequence data or DNA barcoding is successful, as confirmed by the vast BOLD data base. However, the theory that would explain this fact has not been developed yet. An approach based on Barcoding Index Number (BIN), suggested in the assignment, allows delimiting of taxa of three ranks (species, genera, and families) and statistical validation with a high precision of delimiting (over 80%), as well as shows for majority of Co-1-based single gene trees good correspondence between their topology and conventional taxa content for analyzed fish species (R2 ≈ 0.84-0.98). Knowledge of deviations from these data can help to find out new taxa and improve biodiversity description. It is concluded that delimiting is successful for bulk of cases because the geographic mode of speciation prevails in nature. It takes a long time for new taxa to form in isolation, which allows accumulation of random mutations and many different nucleotide substitutions between them that can be detected by molecular markers and give unique DNA barcodes. The use of BIN approach, described here, can aid greatly in making this important question clearer especially under wider examination of other organisms.
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Affiliation(s)
- Yuri Phedorovich Kartavtsev
- a Laboratory of Molecular Systematics, A.V. Zhirmunsky Institute of Marine Biology , National Scientific Center of Marine Biology, Russian Academy of Sciences , Vladivostok , Russia.,b Chair of Biodiversity and Marine Bioresources, Far Eastern Federal University , Vladivostok , Russia
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21
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Hirt MV, Arratia G, Chen WJ, Mayden RL, Tang KL, Wood RM, Simons AM. Effects of gene choice, base composition and rate heterogeneity on inference and estimates of divergence times in cypriniform fishes. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw045] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- M. Vincent Hirt
- University of Minnesota, Ecology, Evolution, and Behavior Graduate Program, St. Paul, MN 55108, USA
- University of Minnesota, Bell Museum of Natural History, Minneapolis, MN 55455, USA
| | - Gloria Arratia
- Biodiversity Research Center, University of Kansas, Lawrence, KS 66045, USA
| | - Wei-Jen Chen
- National Taiwan University, Institute of Oceanography, Taipei 10617, Taiwan
| | - Richard L. Mayden
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Kevin L. Tang
- Department of Biology, University of Michigan-Flint, Flint, MI 48502, USA
| | - Robert M. Wood
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Andrew M. Simons
- University of Minnesota, Bell Museum of Natural History, Minneapolis, MN 55455, USA
- Department of Fisheries, Wildlife, and Conservation Biology, University of Minnesota, St. Paul, MN 55108, USA
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22
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Wang Y, Sun S. Complete mitochondrial genome of the jellyfish, Nemopilema nomurai (Cnidaria: Scyphozoa) and the phylogenetic relationship in the related species. MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:165-166. [PMID: 33473754 PMCID: PMC7800497 DOI: 10.1080/23802359.2017.1298417] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The complete mitochondrial genome of giant jellyfish Nemopilema nomurai collected from East China Sea was determined by next-generation sequencing. The mitogenome is a circular molecule 17,024 bp in length, including 13 protein-coding genes (including Cox 1, Cox2, Atp 8, Atp 6, ND5, ND 6, ND3, ND41, ND1,ND4, Cytb), 6 tRNAs (tRNA-Trp, tRNA-Met, tRNA-Val, tRNA-Arg, tRNA-Glu, tRNA-Asn), 2 rRNA genes (small subunit RNA and large subunit RNA), and 1 putative control region. The phylogenetic tree in the related species showed that giant jellyfish is close to Hydraoligaclis.
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Affiliation(s)
- Yantao Wang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Song Sun
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Jiaozhou Bay Marine Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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23
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Mohanta SK, Swain SK, Das SP, Bit A, Das G, Pradhan S, Sundaray JK, Jayasankar P, Ninawe AS, Das P. Complete mitochondrial genome sequence of E. suratensis revealed by next generation sequencing. MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:746-747. [PMID: 33473612 PMCID: PMC7800130 DOI: 10.1080/23802359.2016.1176877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The complete mitochondrial genome of Etroplus suratensis, the Green chromide cichlid, was determined for the first time through NGS method. The genome is 16,467 bp (Accession no. KU301747) in length and consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and one control region. Organization of genes and their order are in accordance with other vertebrates. The overall base composition on plus strand was A: 28.3%, G: 15.2%, C: 30.9%, T: 25.6%, and the A + T content 53.9%. The control region contains a putative termination-associated sequence and three conserved sequence blocks. This mitogenome sequence data would play an important role in population genetics and phylogenetics of cichlid fish of India.
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Affiliation(s)
- Sudip K Mohanta
- Department of Zoology, Banabhumi (Degree) Mahavidyalaya, Rangamatia, Odisha, India
| | - Subrat K Swain
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - Sofia P Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - Amrita Bit
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - Gargee Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - Sanghamitra Pradhan
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - Jitendra K Sundaray
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - P Jayasankar
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - A S Ninawe
- Department of Biotechnology, Goverment of India, New Delhi, India
| | - Paramananda Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
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24
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Stout CC, Tan M, Lemmon AR, Lemmon EM, Armbruster JW. Resolving Cypriniformes relationships using an anchored enrichment approach. BMC Evol Biol 2016; 16:244. [PMID: 27829363 PMCID: PMC5103605 DOI: 10.1186/s12862-016-0819-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 10/28/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cypriniformes (minnows, carps, loaches, and suckers) is the largest group of freshwater fishes in the world (~4300 described species). Despite much attention, previous attempts to elucidate relationships using molecular and morphological characters have been incongruent. In this study we present the first phylogenomic analysis using anchored hybrid enrichment for 172 taxa to represent the order (plus three out-group taxa), which is the largest dataset for the order to date (219 loci, 315,288 bp, average locus length of 1011 bp). RESULTS Concatenation analysis establishes a robust tree with 97 % of nodes at 100 % bootstrap support. Species tree analysis was highly congruent with the concatenation analysis with only two major differences: monophyly of Cobitoidei and placement of Danionidae. CONCLUSIONS Most major clades obtained in prior molecular studies were validated as monophyletic, and we provide robust resolution for the relationships among these clades for the first time. These relationships can be used as a framework for addressing a variety of evolutionary questions (e.g. phylogeography, polyploidization, diversification, trait evolution, comparative genomics) for which Cypriniformes is ideally suited.
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Affiliation(s)
- Carla C. Stout
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL 36849 USA
| | - Milton Tan
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL 36849 USA
| | - Alan R. Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32306 USA
| | - Emily Moriarty Lemmon
- Department of Biological Sciences, Florida State University, Tallahassee, FL 32306 USA
| | - Jonathan W. Armbruster
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL 36849 USA
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25
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Wang Y, Shen Y, Feng C, Zhao K, Song Z, Zhang Y, Yang L, He S. Mitogenomic perspectives on the origin of Tibetan loaches and their adaptation to high altitude. Sci Rep 2016; 6:29690. [PMID: 27417983 PMCID: PMC4945904 DOI: 10.1038/srep29690] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 06/23/2016] [Indexed: 01/11/2023] Open
Abstract
Tibetan loaches are the largest group of Tibetan fishes and are well adapted to the Tibetan Plateau. To investigate the origin of Tibetan loaches and their adaptations to the Tibetan Plateau, we determined 32 complete mitochondrial genomes that included 29 Tibetan loach species, two Barbatula species and Schistura longus. By combining these newly determined sequences with other previously published mitochondrial genomes, we assembled a large mitogenomic data set (11,433 bp) of 96 species in the superfamily Cobitoidea, to investigate the phylogenetic status of the genus Triplophysa. The resulting phylogeny strongly supported that the genus Triplophysa forms a monophyletic group within Nemacheilidae. Our molecular dating time suggests that the lineage leading to the Tibetan loaches and other loaches diverged approximately 23.5 Ma, which falls within the period of recent major uplifts of the Tibetan Plateau in the Early Miocene. Selection analyses revealed that the mitochondrial protein-coding genes of Tibetan loaches have larger ratios of nonsynonymous to synonymous substitutions than do those of non-Tibetan loaches, indicating that Tibetan loaches accumulated more nonsynonymous mutations than non-Tibetan loaches and exhibited rapid evolution. Two positively selected sites were identified in the ATP8 and ND1 genes.
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Affiliation(s)
- Ying Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China.,University of the Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yanjun Shen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China.,University of the Chinese Academy of Sciences, Beijing 100049, PR China
| | - Chenguang Feng
- University of the Chinese Academy of Sciences, Beijing 100049, PR China.,Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, China
| | - Kai Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, China
| | - Zhaobin Song
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Yanping Zhang
- Gansu Key Laboratory of Cold Water Fishes Germplasm Resources and Genetics Breeding, Gansu Fishers Research Institute, Lanzhou 730030, PR China
| | - Liandong Yang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
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Kartavtsev YP, Batischeva NM, Bogutskaya NG, Katugina AO, Hanzawa N. Molecular systematics and DNA barcoding of Altai osmans, oreoleuciscus (pisces, cyprinidae, and leuciscinae), and their nearest relatives, inferred from sequences of cytochrome b (Cyt-b), cytochrome oxidase c (Co-1), and complete mitochondrial genome. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:502-517. [PMID: 27159700 DOI: 10.3109/24701394.2016.1149822] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Mitochondrial DNA (mtDNA) at the protein-coding Cyt-b gene along with data retrieved from GenBank for Co-1 gene fragments and complete mitochondrial genome (mitogenome) of Altai osmans and the nearest relatives of Leuciscinae fish species were compared for the estimation of variability and phylogenetic tree building. Phylogenetic trees were built by four techniques: Bayesian (BA), maximum likelihood (ML), maximum parsimony (MP), and neighbor-joining (NJ). Resolution of Cyt-b trees for species of two genera (Oreoleuciscus and Phoxinus) was quite distinct at all the approaches. For Tribolodon, the single gene trees were not well resolved; however, the mitogenome tree was resolved. Species identification on per individual basis (DNA barcoding) was high for both Cyt-b and Co-1 genes. The trees built using the data for 13 protein mitochondrial genes revealed a complicated phylogenetic pattern within the subfamily Leuciscinae. Scores of the average p-distances at three taxonomic levels were considerably different: (1) 1.16 ± 0.96, (2) 8.21 ± 1.01, and (3) 16.41 ± 0.85 for Cyt-b and (1) 1.04 ± 0.78, (2) 8.30 ± 0.92, and (3) 10.74 ± 0.79 for 13 protein genes of mitogenome, where (1) is intraspecies, (2) is intragenus, and (3) is intrasubfamily levels. Data on mitogenome distances were summarized for the taxonomic hierarchy for the first time. A concordant increase in distance score with growth of the rank of taxa (having the minimum score at the intraspecies level), both for a single gene and the whole mitogenome, substantiates the concept that speciation in the subfamily Leuciscinae in most cases follows the geographic mode. The distinct clustering of Altai osmans, Oreoleuciscus potanini and O. humilis, in the Cyt-b and Co-1 gene trees with small overall genetic distances, obtained for both genes, allows us to consider these taxa as separate but genetically sister species.
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Affiliation(s)
- Yuri Phedorovich Kartavtsev
- a A.V. Zhirmunsky Institute of Marine Biology FEB RAS , Vladivostok , Russian Federation.,b Far Eastern Federal University, School of Natural Sciences , Vladivostok , Russian Federation
| | - Natalia M Batischeva
- a A.V. Zhirmunsky Institute of Marine Biology FEB RAS , Vladivostok , Russian Federation
| | | | - Anna O Katugina
- a A.V. Zhirmunsky Institute of Marine Biology FEB RAS , Vladivostok , Russian Federation.,b Far Eastern Federal University, School of Natural Sciences , Vladivostok , Russian Federation
| | - Naoto Hanzawa
- d Yamagata University, Graduate school of Science and Engineering , Yamagata , Japan
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27
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Bar I, Smith A, Bubner E, Yoshizaki G, Takeuchi Y, Yazawa R, Chen BN, Cummins S, Elizur A. Assessment of yellowtail kingfish (Seriola lalandi) as a surrogate host for the production of southern bluefin tuna (Thunnus maccoyii) seed via spermatogonial germ cell transplantation. Reprod Fertil Dev 2016. [DOI: 10.1071/rd15136] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Germ cell transplantation is an innovative technology for the production of interspecies surrogates, capable of facilitating easier and more economical management of large-bodied broodstock, such as the bluefin tuna. The present study explored the suitability of yellowtail kingfish (Seriola lalandi) as a surrogate host for transplanted southern bluefin tuna (Thunnus maccoyii) spermatogonial cells to produce tuna donor-derived gametes upon sexual maturity. Germ cell populations in testes of donor T. maccoyii males were described using basic histology and the molecular markers vasa and dead-end genes. The peripheral area of the testis was found to contain the highest proportions of dead-end-expressing transplantable Type A spermatogonia. T. maccoyii Type A spermatogonia-enriched preparations were transplanted into the coelomic cavity of 6–10-day-old post-hatch S. lalandi larvae. Fluorescence microscopy and polymerase chain reaction analysis detected the presence of tuna cells in the gonads of the transplanted kingfish fingerlings at 18, 28, 39 and 75 days after transplantation, indicating that the transplanted cells migrated to the genital ridge and had colonised the developing gonad. T. maccoyii germ cell-derived DNA or RNA was not detected at later stages, suggesting that the donor cells were not maintained in the hosts’ gonads.
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28
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Biogeography and divergent patterns of body size disparification in North American minnows. Mol Phylogenet Evol 2015. [DOI: 10.1016/j.ympev.2015.07.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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29
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Sember A, Bohlen J, Šlechtová V, Altmanová M, Symonová R, Ráb P. Karyotype differentiation in 19 species of river loach fishes (Nemacheilidae, Teleostei): extensive variability associated with rDNA and heterochromatin distribution and its phylogenetic and ecological interpretation. BMC Evol Biol 2015; 15:251. [PMID: 26573692 PMCID: PMC4647339 DOI: 10.1186/s12862-015-0532-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 11/04/2015] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Loaches of the family Nemacheilidae are one of the most speciose elements of Palearctic freshwater ichthyofauna and have undergone rapid ecological adaptations and colonizations. Their cytotaxonomy is largely unexplored; with the impact of cytogenetical changes on this evolutionary diversification still unknown. An extensive cytogenetical survey was performed in 19 nemacheilid species using both conventional (Giemsa staining, C- banding, Ag- and Chromomycin A3/DAPI stainings) and molecular (fluorescence in situ hybridization with 5S rDNA, 45S rDNA, and telomeric (TTAGGG)n probes) methods. A phylogenetic tree of the analysed specimens was constructed based on one mitochondrial (cytochrome b) and two nuclear (RAG1, IRBP) genes. RESULTS Seventeen species showed karyotypes composed of 2n = 50 chromosomes but differentiated by fundamental chromosome number (NF = 68-90). Nemachilichthys ruppelli (2n = 38) and Schistura notostigma (2n = 44-48) displayed reduced 2n with an elevated number of large metacentric chromosomes. Only Schistura fasciolata showed morphologically differentiated sex chromosomes with a multiple system of the XY1Y2 type. Chromomycin A3 (CMA3)- fluorescence revealed interspecific heterogeneity in the distribution of GC-rich heterochromatin including its otherwise very rare association with 5S rDNA sites. The 45S rDNA sites were mostly located on a single chromosome pair contrasting markedly with a pattern of two (Barbatula barbatula, Nemacheilus binotatus, N. ruppelli) to 20 sites (Physoschistura sp.) of 5S rDNA. The cytogenetic changes did not follow the phylogenetic relationships between the samples. A high number of 5S rDNA sites was present in species with small effective population sizes. CONCLUSION Despite a prevailing conservatism of 2n, Nemacheilidae exhibited a remarkable cytogenetic variability on microstructural level. We suggest an important role for pericentric inversions, tandem and centric fusions in nemacheilid karyotype differentiation. Short repetitive sequences, genetic drift, founder effect, as well as the involvement of transposable elements in the dispersion of ribosomal DNA sites, might also have played a role in evolutionary processes such as reproductive isolation. These remarkable dynamics of their genomes qualify river loaches as a model for the study of the cytogenetic background of major evolutionary processes such as radiation, endemism and colonization of a wide range of habitats.
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Affiliation(s)
- Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, 277 21, Czech Republic.
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Viničná 5, 128 44, Prague 2, Czech Republic.
| | - Jörg Bohlen
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, 277 21, Czech Republic.
| | - Vendula Šlechtová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, 277 21, Czech Republic.
| | - Marie Altmanová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, 277 21, Czech Republic.
- Department of Ecology, Faculty of Science, Charles University in Prague, Viničná 7, 128 44, Prague 2, Czech Republic.
| | - Radka Symonová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, 277 21, Czech Republic.
- Research Institute for Limnology, University of Innsbruck, Mondseestraße 9, A-5310, Mondsee, Austria.
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, 277 21, Czech Republic.
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Mu X, Wang X, Liu Y, Song H, Liu C, Gu D, Wei H, Luo J, Hu Y. An unusual mitochondrial genome structure of the tonguefish, Cynoglossus trigrammus: Control region translocation and a long additional non-coding region inversion. Gene 2015; 573:216-24. [PMID: 26187073 DOI: 10.1016/j.gene.2015.07.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/06/2015] [Accepted: 07/13/2015] [Indexed: 10/23/2022]
Abstract
Flatfishes (Pleuronectiformes) exhibit different types of large-scale gene rearrangements. In the present study, the mitochondrial (mt) genome (18,369bp) of a tonguefish, Cynoglossus trigrammus, was determined using de novo mitochondrion genome sequencing. Compared with other flatfishes, the mt genome of C. trigrammus revealed distinct mitogenome architectures that primarily included two striking findings: 1) insertion of an additional long non-coding region (1647bp) making it the second largest genome length among Pleuronectiformes and 2) the translocation of the control region. The reconstructed phylogenetic tree based on 13 mt protein-coding gene sequences recovered the monophyletic suborder Pleuronectoidei and the family Cynoglossidae. These data provide useful information for a better understanding of the mitogenomic diversities and evolution in fish as well as novel genetic markers for studying population genetics and species identification.
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Affiliation(s)
- Xidong Mu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Xuejie Wang
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Yi Liu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Hongmei Song
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Chao Liu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Dangen Gu
- Key Laboratory of the Conservation and Ecological Restoration of Fishery Resource in Pearl River, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Hui Wei
- Key Laboratory of the Conservation and Ecological Restoration of Fishery Resource in Pearl River, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Jianren Luo
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; Key Laboratory of the Conservation and Ecological Restoration of Fishery Resource in Pearl River, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Yinchang Hu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; Key Laboratory of the Conservation and Ecological Restoration of Fishery Resource in Pearl River, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
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Guinot G, Cavin L. 'Fish' (Actinopterygii and Elasmobranchii) diversification patterns through deep time. Biol Rev Camb Philos Soc 2015; 91:950-981. [PMID: 26105527 DOI: 10.1111/brv.12203] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 05/20/2015] [Accepted: 05/27/2015] [Indexed: 11/30/2022]
Abstract
Actinopterygii (ray-finned fishes) and Elasmobranchii (sharks, skates and rays) represent more than half of today's vertebrate taxic diversity (approximately 33000 species) and form the largest component of vertebrate diversity in extant aquatic ecosystems. Yet, patterns of 'fish' evolutionary history remain insufficiently understood and previous studies generally treated each group independently mainly because of their contrasting fossil record composition and corresponding sampling strategies. Because direct reading of palaeodiversity curves is affected by several biases affecting the fossil record, analytical approaches are needed to correct for these biases. In this review, we propose a comprehensive analysis based on comparison of large data sets related to competing phylogenies (including all Recent and fossil taxa) and the fossil record for both groups during the Mesozoic-Cainozoic interval. This approach provides information on the 'fish' fossil record quality and on the corrected 'fish' deep-time phylogenetic palaeodiversity signals, with special emphasis on diversification events. Because taxonomic information is preserved after analytical treatment, identified palaeodiversity events are considered both quantitatively and qualitatively and put within corresponding palaeoenvironmental and biological settings. Results indicate a better fossil record quality for elasmobranchs due to their microfossil-like fossil distribution and their very low diversity in freshwater systems, whereas freshwater actinopterygians are diverse in this realm with lower preservation potential. Several important diversification events are identified at familial and generic levels for elasmobranchs, and marine and freshwater actinopterygians, namely in the Early-Middle Jurassic (elasmobranchs), Late Jurassic (actinopterygians), Early Cretaceous (elasmobranchs, freshwater actinopterygians), Cenomanian (all groups) and the Paleocene-Eocene interval (all groups), the latter two representing the two most exceptional radiations among vertebrates. For each of these events along with the Cretaceous-Paleogene extinction, we provide an in-depth review of the taxa involved and factors that may have influenced the diversity patterns observed. Among these, palaeotemperatures, sea-levels, ocean circulation and productivity as well as continent fragmentation and environment heterogeneity (reef environments) are parameters that largely impacted on 'fish' evolutionary history, along with other biotic constraints.
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Affiliation(s)
- Guillaume Guinot
- Department of Geology and Palaeontology, Natural History Museum of Geneva, Route de Malagnou 1, CP 6434, CH-1211, Geneva 6, Switzerland.
| | - Lionel Cavin
- Department of Geology and Palaeontology, Natural History Museum of Geneva, Route de Malagnou 1, CP 6434, CH-1211, Geneva 6, Switzerland
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Wu J, He Y, Ren H, Zhang Y, Du Z, Xie M, Zhu G, Wang Q, Jiang Y, He T, Wen A. The complete mitochondrial genome sequence of Beaufortia szechuanensis (Cypriniformes, Balitoridae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2535-6. [PMID: 25922961 DOI: 10.3109/19401736.2015.1038792] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The Beaufortia szechuanensis is endemic to the upper reaches of Yangtze River in China. In this study, we successfully sequenced the mitochondrial genome of the B. szechuanensis, collected from the Qingyi River. The complete mitochondrial genome of B. szechuanensis was a circular molecule of 16,559 bp in length, containing 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes, 22 transfer RNA (tRNA) genes, an origin of light-strand replication (OL) and a control region (D-loop). It is the first complete mitochondrial DNA data in the genus Beaufortia. The cytochrome c oxidase subunit I (COI) sequence of 14 species in Balitoridae was used for phylogenetic analysis. The topology demonstrated that the Balitoridae can be classified into two subfamilies, and the B. szechuanensis belongs to the subfamily Gastromyzoninae.
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Affiliation(s)
- Jiayun Wu
- a College of Life Sciences, Sichuan Agricultural University , Ya'an , P.R. China
| | - Yuxiao He
- a College of Life Sciences, Sichuan Agricultural University , Ya'an , P.R. China
| | - Hongmei Ren
- b School of Animal Science, Xichang College , Xichang , P.R. China , and
| | - Yi Zhang
- b School of Animal Science, Xichang College , Xichang , P.R. China , and
| | - Zongjun Du
- c College of Animal Science and Technology, Sichuan Agricultural University , Ya'an , P.R. China
| | - Meng Xie
- a College of Life Sciences, Sichuan Agricultural University , Ya'an , P.R. China
| | - Guangxiang Zhu
- a College of Life Sciences, Sichuan Agricultural University , Ya'an , P.R. China
| | - Qin Wang
- a College of Life Sciences, Sichuan Agricultural University , Ya'an , P.R. China
| | - Yanzhi Jiang
- a College of Life Sciences, Sichuan Agricultural University , Ya'an , P.R. China
| | - Tao He
- a College of Life Sciences, Sichuan Agricultural University , Ya'an , P.R. China
| | - Anxiang Wen
- a College of Life Sciences, Sichuan Agricultural University , Ya'an , P.R. China
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Yang L, Sado T, Vincent Hirt M, Pasco-Viel E, Arunachalam M, Li J, Wang X, Freyhof J, Saitoh K, Simons AM, Miya M, He S, Mayden RL. Phylogeny and polyploidy: Resolving the classification of cyprinine fishes (Teleostei: Cypriniformes). Mol Phylogenet Evol 2015; 85:97-116. [DOI: 10.1016/j.ympev.2015.01.014] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Revised: 01/29/2015] [Accepted: 01/30/2015] [Indexed: 01/30/2023]
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34
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Liu X, Du H, Wu C, Xiao K, Qu H, Zhang X, Gao Y, Chen L. Complete mitochondrial genome of the Ictiobus cyprinellus (Actinopterygii: Ostariophysi). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3242-3. [PMID: 25630730 DOI: 10.3109/19401736.2015.1007365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of Ictiobus cyprinellus was first determined by a polymerase chain reaction-based sequencing method in this study. The mitochondria was 16,611 bp in length, including 13 protein genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and 1 control region. All genes were encoded on the heavy strain except for ND6 and eight tRNA genes. The gene arrangement of I. cyprinellus was similar to those found in the other Catostomidae species. Base composition of the heavy strain was A (29.40%), T (24.86%), C (27.96%), G (17.78%) and with A + T bias of 54.26%.
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Affiliation(s)
- Xueqing Liu
- a Institute of Chinese Sturgeon, China Three Gorges Corporation , Yichang , China and
| | - Hejun Du
- a Institute of Chinese Sturgeon, China Three Gorges Corporation , Yichang , China and.,b Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes , Institute of Chinese Sturgeon, China Three Gorges Corporation , Yichang , China
| | - Chuan Wu
- a Institute of Chinese Sturgeon, China Three Gorges Corporation , Yichang , China and
| | - Kan Xiao
- a Institute of Chinese Sturgeon, China Three Gorges Corporation , Yichang , China and
| | - Huantao Qu
- a Institute of Chinese Sturgeon, China Three Gorges Corporation , Yichang , China and
| | - Xu Zhang
- a Institute of Chinese Sturgeon, China Three Gorges Corporation , Yichang , China and.,b Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes , Institute of Chinese Sturgeon, China Three Gorges Corporation , Yichang , China
| | - Yong Gao
- a Institute of Chinese Sturgeon, China Three Gorges Corporation , Yichang , China and.,b Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes , Institute of Chinese Sturgeon, China Three Gorges Corporation , Yichang , China
| | - Lei Chen
- a Institute of Chinese Sturgeon, China Three Gorges Corporation , Yichang , China and.,b Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes , Institute of Chinese Sturgeon, China Three Gorges Corporation , Yichang , China
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Sahoo L, Swain SK, Bej D, Das SP, Jayasankar P, Das P. Complete mitochondrial genome sequence of Labeo fimbriatus (Bloch, 1975). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4019-4020. [PMID: 25629503 DOI: 10.3109/19401736.2014.1003824] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of Labeo fimbriatus, the fringe-lipped carp, was determined for the first time. The genome was 16,614 bp in length and consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and one control region. Organization of genes and their order are in accordance with other vertebrates. The overall base composition on the plus strand was A: 32.35%, G: 15.46%, C: 27.54%, T: 24.647%, and the A + T content 57%. The control region contains a microsatellite, (TA)12, a putative termination-associated sequence and three conserved sequence blocks. This mitogenome sequence data would play an important role in population genetics and phylogenetics of cultivable carps of India.
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Affiliation(s)
- Lakshman Sahoo
- a Fish Genetics and Biotechnology Division , ICAR - Central Institute of Freshwater Aquaculture , Kausalyaganga , Odisha , India
| | - Subrat K Swain
- a Fish Genetics and Biotechnology Division , ICAR - Central Institute of Freshwater Aquaculture , Kausalyaganga , Odisha , India
| | - Dillip Bej
- a Fish Genetics and Biotechnology Division , ICAR - Central Institute of Freshwater Aquaculture , Kausalyaganga , Odisha , India
| | - Sofia P Das
- a Fish Genetics and Biotechnology Division , ICAR - Central Institute of Freshwater Aquaculture , Kausalyaganga , Odisha , India
| | - P Jayasankar
- a Fish Genetics and Biotechnology Division , ICAR - Central Institute of Freshwater Aquaculture , Kausalyaganga , Odisha , India
| | - Paramananda Das
- a Fish Genetics and Biotechnology Division , ICAR - Central Institute of Freshwater Aquaculture , Kausalyaganga , Odisha , India
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Conway KW, Britz R, Shrestha J, Manimekalan A, Rüber L. Molecular systematics of the Asian torrent minnows (Ostariophysi: Psilorhynchidae) inferred from nuclear and mitochondrial DNA sequence data. J ZOOL SYST EVOL RES 2014. [DOI: 10.1111/jzs.12090] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kevin W. Conway
- Department of Wildlife and Fisheries Sciences and Biodiversity Research and Teaching Collections; Texas A&M University; College Station TX USA
| | - Ralf Britz
- Department of Zoology; The Natural History Museum; London UK
| | - Jiwan Shrestha
- Nepal Academy for Science and Technology (NAST); Khumaltar; Lalitpur Kathmandu Nepal
| | | | - Lukas Rüber
- Naturhistorisches Museum der Burgergemeinde Bern; Bern Switzerland
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Abstract
Sex determination can be robustly genetic, strongly environmental, or genetic subject to environmental perturbation. The genetic basis of sex determination is unknown for zebrafish (Danio rerio), a model for development and human health. We used RAD-tag population genomics to identify sex-linked polymorphisms. After verifying this "RAD-sex" method on medaka (Oryzias latipes), we studied two domesticated zebrafish strains (AB and TU), two natural laboratory strains (WIK and EKW), and two recent isolates from nature (NA and CB). All four natural strains had a single sex-linked region at the right tip of chromosome 4, enabling sex genotyping by PCR. Genotypes for the single nucleotide polymorphism (SNP) with the strongest statistical association to sex suggested that wild zebrafish have WZ/ZZ sex chromosomes. In natural strains, "male genotypes" became males and some "female genotypes" also became males, suggesting that the environment or genetic background can cause female-to-male sex reversal. Surprisingly, TU and AB lacked detectable sex-linked loci. Phylogenomics rooted on D. nigrofasciatus verified that all strains are monophyletic. Because AB and TU branched as a monophyletic clade, we could not rule out shared loss of the wild sex locus in a common ancestor despite their independent domestication. Mitochondrial DNA sequences showed that investigated strains represent only one of the three identified zebrafish haplogroups. Results suggest that zebrafish in nature possess a WZ/ZZ sex-determination mechanism with a major determinant lying near the right telomere of chromosome 4 that was modified during domestication. Strains providing the zebrafish reference genome lack key components of the natural sex-determination system but may have evolved variant sex-determining mechanisms during two decades in laboratory culture.
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Characterization of the mitochondrial genome and phylogeny of the black arowana (Osteoglossum ferreirai). Biologia (Bratisl) 2014. [DOI: 10.2478/s11756-014-0426-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Norfatimah M, Teh L, Salleh M, Mat Isa M, SitiAzizah M. Complete mitochondrial genome of Malaysian Mahseer (Tor tambroides). Gene 2014; 548:263-9. [DOI: 10.1016/j.gene.2014.07.044] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 07/08/2014] [Accepted: 07/14/2014] [Indexed: 10/25/2022]
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40
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Kawamura K, Ueda T, Arai R, Smith C. Phylogenetic relationships of bitterling fishes (Teleostei: Cypriniformes: Acheilognathinae), inferred from mitochondrial cytochrome B sequences. Zoolog Sci 2014; 31:321-9. [PMID: 24832905 DOI: 10.2108/zs130233] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Bitterling (Teleostei: Acheilognathinae) are small cyprinid fishes with a discrete distribution in East Asia and Europe. We used a complete mitochondrial cytochrome b sequence (1141 bp) from 49 species or subspecies in three genera (Tanakia, Rhodeus, and Acheilognathus), sampled across the major part of their distribution, to elucidate their phylogeny and biogeography, focusing particularly on their origin and dispersal. Based on high support value, the monophyletic Acheilognathinae separated into two major clades, Acheilognathus and Tanakia-Rhodeus. In the latter clade, the monophyly of Rhodeus was poorly supported, though it was topologically nested in Tanakia. On the basis of molecular-clock calibration, both clades diverged in the middle Miocene, with Tanakia-Rhodeus diverging slightly earlier than Acheilognathus. The Tanakia-Rhodeus clade expanded its distribution westward from the Far East, eventually reaching Europe, while Acheilognathus dispersed in the temperate regions of East Asia. A feature common to both clades is that most extant species, including Japanese endemics, appeared by the end of the Pliocene, corresponding with the present delineation of the Japanese archipelago. Autumn-spawning species with an embryonic diapause, unique to bitterling among cyprinid fishes, formed two distinct lineages (barbatulusrhombeus and longipinnis-typus) within Acheilognathus. The estimated time of divergence of the two lineages was approximately from the late Pliocene, a period characterized by glaciations. The timing of divergence suggests that the shift of spawning from spring to autumn, coupled with embryonic diapause, convergently emerged twice in the evolution of bitterling, possibly as an adaptation to the climate of the late Pliocene.
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Affiliation(s)
- Kouichi Kawamura
- 1 Faculty of Bioresources, Mie University, Kurimamachiya 1577, Tsu, Mie 514-8507, Japan
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Li XY, Zhang XJ, Li Z, Hong W, Liu W, Zhang J, Gui JF. Evolutionary history of two divergent Dmrt1 genes reveals two rounds of polyploidy origins in gibel carp. Mol Phylogenet Evol 2014; 78:96-104. [PMID: 24859683 DOI: 10.1016/j.ympev.2014.05.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 04/30/2014] [Accepted: 05/03/2014] [Indexed: 11/27/2022]
Abstract
Polyploidy lineages, despite very rare in vertebrates, have been proposed to play significant role in speciation and evolutionary success, but the occurrence history and consequences are still largely unknown. In this study, we used the conserved Dmrt1 to analyze polyploidy occurrence and evolutionary process in polyploid gibel carp. We identified two divergent Dmrt1 genes and respectively localized the two genes on three homologous chromosomes. Subsequently, the corresponding full-length cDNAs and genomic sequences of Dmrt1 genes were also characterized from the closely related species including Carassius auratus auratus and Cyprinus carpio, and their two Dmrt1 genes were respectively localized on two homologous chromosomes. Significantly, the evolutionary relationship analyses among cDNA and genomic DNA sequences of these Dmrt1 genes revealed two rounds of polyploidy origins in the gibel carp: an early polyploidy might result in an common tetraploid ancestor of Carassius auratus gibelio, Carassius auratus auratus and Cyprinus carpio before 18.49 million years ago (Mya), and an late polyploidy might occur from evolutionary branch of Carassius auratus at around 0.51 Mya, which lead to the occurrence of the hexaploid gibel carp. Therefore, this study provides clear genetic evidence for understanding occurrence time and historical process of polyploidy in polyploid vertebrates.
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Affiliation(s)
- Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Graduate University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Graduate University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Graduate University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Wei Hong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Graduate University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Wei Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Graduate University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Jun Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Graduate University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Graduate University of the Chinese Academy of Sciences, Wuhan 430072, China.
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Krabbenhoft TJ, Turner TF. Clock gene evolution: seasonal timing, phylogenetic signal, or functional constraint? J Hered 2014; 105:407-15. [PMID: 24558102 PMCID: PMC3984439 DOI: 10.1093/jhered/esu008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 10/21/2013] [Accepted: 01/17/2014] [Indexed: 01/22/2023] Open
Abstract
Genetic determinants of seasonal reproduction are not fully understood but may be important predictors of organism responses to climate change. We used a comparative approach to study the evolution of seasonal timing within a fish community in a natural common garden setting. We tested the hypothesis that allelic length variation in the PolyQ domain of a circadian rhythm gene, Clock1a, corresponded to interspecific differences in seasonal reproductive timing across 5 native and 1 introduced cyprinid fishes (n = 425 individuals) that co-occur in the Rio Grande, NM, USA. Most common allele lengths were longer in native species that initiated reproduction earlier (Spearman's r = -0.70, P = 0.23). Clock1a allele length exhibited strong phylogenetic signal and earlier spawners were evolutionarily derived. Aside from length variation in Clock1a, all other amino acids were identical across native species, suggesting functional constraint over evolutionary time. Interestingly, the endangered Rio Grande silvery minnow (Hybognathus amarus) exhibited less allelic variation in Clock1a and observed heterozygosity was 2- to 6-fold lower than the 5 other (nonimperiled) species. Reduced genetic variation in this functionally important gene may impede this species' capacity to respond to ongoing environmental change.
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Affiliation(s)
- Trevor J Krabbenhoft
- the Museum of Southwestern Biology, Department of Biology, MSC03-2020, University of New Mexico, Albuquerque, NM 87131-0001
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Sallan LC. Major issues in the origins of ray-finned fish (Actinopterygii) biodiversity. Biol Rev Camb Philos Soc 2014; 89:950-71. [DOI: 10.1111/brv.12086] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 01/02/2014] [Accepted: 01/16/2014] [Indexed: 10/25/2022]
Affiliation(s)
- Lauren C. Sallan
- Department of Organismal Biology and Anatomy; University of Chicago; Chicago IL 60637 U.S.A
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor MI 48109 U.S.A
- Michigan Society of Fellows; University of Michigan; Ann Arbor MI 48109 U.S.A
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Pasco-Viel E, Yang L, Veran M, Balter V, Mayden RL, Laudet V, Viriot L. Stability versus diversity of the dentition during evolutionary radiation in cyprinine fish. Proc Biol Sci 2014; 281:20132688. [PMID: 24523268 DOI: 10.1098/rspb.2013.2688] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Evolutionary radiations, especially adaptive radiations, have been widely studied but mainly for recent events such as in cichlid fish or Anolis lizards. Here, we investigate the radiation of the subfamily Cyprininae, which includes more than 1300 species and is estimated to have originated from Southeast Asia around 55 Ma. In order to decipher a potential adaptive radiation, within a solid phylogenetic framework, we investigated the trophic apparatus, and especially the pharyngeal dentition, as teeth have proved to be important markers of ecological specialization. We compared two tribes within Cyprininae, Poropuntiini and Labeonini, displaying divergent dental patterns, as well as other characters related to their trophic apparatus. Our results suggest that the anatomy of the trophic apparatus and diet are clearly correlated and this explains the difference in dental patterns observed between these two tribes. Our results illustrate the diversity of mechanisms that account for species diversity in this very diverse clade: diversification of dental characters from an ancestral pattern on the one hand, conservation of a basal synapomorphy leading to ecological specialization on the other hand. By integrating morphological, ecological and phylogenetic analyses, it becomes possible to investigate ancient radiation events that have shaped the present diversity of species.
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Affiliation(s)
- Emmanuel Pasco-Viel
- Evo-devo of Vertebrate Dentition, Institut de Génomique Fonctionnelle de Lyon (IGFL), UMR CNRS 5242, Université de Lyon, Université Claude Bernard Lyon 1, , Ecole Normale Supérieure de Lyon, Lyon, France, Molecular Zoology, Institut de Génomique Fonctionnelle de Lyon (IGFL), UMR CNRS 5242, Université de Lyon, Université Claude Bernard Lyon 1, , Ecole Normale Supérieure de Lyon, Lyon, France, Department of Biology, Saint Louis University, , St Louis, MO 63103, USA, Centre de Recherches sur la Paléobiodiversité et les Paléoenvironnements (CRP2), Département Histoire de la Terre, UMR CNRS 7207, Muséum National d'Histoire Naturelle, , Paris, France, Laboratoire de Géologie de Lyon (LGLTPE), UMR CNRS 5276, Université de Lyon, Université Claude Bernard Lyon 1, , Ecole Normale Supérieure de Lyon, Lyon, France
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Wang J, Wu X, Chen Z, Yue Z, Ma W, Chen S, Xiao H, Murphy RW, Zhang Y, Zan R, Luo J. Molecular phylogeny of European and African Barbus and their West Asian relatives in the Cyprininae (Teleostei: Cypriniformes) and orogenesis of the Qinghai-Tibetan Plateau. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s11434-013-5878-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Nikaido M, Noguchi H, Nishihara H, Toyoda A, Suzuki Y, Kajitani R, Suzuki H, Okuno M, Aibara M, Ngatunga BP, Mzighani SI, Kalombo HWJ, Masengi KWA, Tuda J, Nogami S, Maeda R, Iwata M, Abe Y, Fujimura K, Okabe M, Amano T, Maeno A, Shiroishi T, Itoh T, Sugano S, Kohara Y, Fujiyama A, Okada N. Coelacanth genomes reveal signatures for evolutionary transition from water to land. Genome Res 2013; 23:1740-8. [PMID: 23878157 PMCID: PMC3787270 DOI: 10.1101/gr.158105.113] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Coelacanths are known as “living fossils,” as they show remarkable morphological resemblance to the fossil record and belong to the most primitive lineage of living Sarcopterygii (lobe-finned fishes and tetrapods). Coelacanths may be key to elucidating the tempo and mode of evolution from fish to tetrapods. Here, we report the genome sequences of five coelacanths, including four Latimeria chalumnae individuals (three specimens from Tanzania and one from Comoros) and one L. menadoensis individual from Indonesia. These sequences cover two African breeding populations and two known extant coelacanth species. The genome is ∼2.74 Gbp and contains a high proportion (∼60%) of repetitive elements. The genetic diversity among the individuals was extremely low, suggesting a small population size and/or a slow rate of evolution. We found a substantial number of genes that encode olfactory and pheromone receptors with features characteristic of tetrapod receptors for the detection of airborne ligands. We also found that limb enhancers of bmp7 and gli3, both of which are essential for limb formation, are conserved between coelacanth and tetrapods, but not ray-finned fishes. We expect that some tetrapod-like genes may have existed early in the evolution of primitive Sarcopterygii and were later co-opted to adapt to terrestrial environments. These coelacanth genomes will provide a cornerstone for studies to elucidate how ancestral aquatic vertebrates evolved into terrestrial animals.
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Affiliation(s)
- Masato Nikaido
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
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John L, Philip S, Dahanukar N, Anvar Ali PH, Tharian J, Raghavan R, Antunes A. Morphological and genetic evidence for multiple evolutionary distinct lineages in the endangered and commercially exploited red lined torpedo barbs endemic to the Western Ghats of India. PLoS One 2013; 8:e69741. [PMID: 23894533 PMCID: PMC3718778 DOI: 10.1371/journal.pone.0069741] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Accepted: 06/16/2013] [Indexed: 11/19/2022] Open
Abstract
Red lined torpedo barbs (RLTBS) (Cyprinidae: Puntius) endemic to the Western Ghats Hotspot of India, are popular and highly priced freshwater aquarium fishes. Two decades of indiscriminate exploitation for the pet trade, restricted range, fragmented populations and continuing decline in quality of habitats has resulted in their 'Endangered' listing. Here, we tested whether the isolated RLTB populations demonstrated considerable variation qualifying to be considered as distinct conservation targets. Multivariate morphometric analysis using 24 size-adjusted characters delineated all allopatric populations. Similarly, the species-tree highlighted a phylogeny with 12 distinct RLTB lineages corresponding to each of the different riverine populations. However, coalescence-based methods using mitochondrial DNA markers identified only eight evolutionarily distinct lineages. Divergence time analysis points to recent separation of the populations, owing to the geographical isolation, more than 5 million years ago, after the lineages were split into two ancestral stocks in the Paleocene, on north and south of a major geographical gap in the Western Ghats. Our results revealing the existence of eight evolutionarily distinct RLTB lineages calls for the re-determination of conservation targets for these cryptic and endangered taxa.
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Affiliation(s)
- Lijo John
- Marine Biotechnology Division, Central Marine Fisheries Research Institute (CMFRI), Kochi, India
- Export Inspection Agency (EIA), Kochi, India
| | - Siby Philip
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Rua dos Bragas, Porto, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Porto, Portugal
- Conservation Research Group (CRG), St. Albert’s College, Kochi, India
| | - Neelesh Dahanukar
- Indian Institute of Science Education and Research (IISER), Pune, India
- Zoo Outreach Organization (ZOO), Coimbatore, India
| | | | - Josin Tharian
- Department of Zoology, St. John’s College, Anchal, Kerala, India
| | - Rajeev Raghavan
- Conservation Research Group (CRG), St. Albert’s College, Kochi, India
- Zoo Outreach Organization (ZOO), Coimbatore, India
- Durrell Institute of Conservation and Ecology (DICE), University of Kent, Canterbury, United Kingdom
- Research Group Zoology: Biodiversity & Toxicology, Center for Environmental Sciences, University of Hasselt, Diepenbeek, Belgium
| | - Agostinho Antunes
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Rua dos Bragas, Porto, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Porto, Portugal
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Haponski AE, Stepien CA. Phylogenetic and biogeographical relationships of theSanderpikeperches (Percidae: Perciformes): patterns across North America and Eurasia. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12114] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amanda E. Haponski
- The Great Lakes Genetics/Genomics Laboratory; Lake Erie Center and the Department of Environmental Sciences; The University of Toledo; 6200 Bayshore Road; Toledo; OH; 43616; USA
| | - Carol A. Stepien
- The Great Lakes Genetics/Genomics Laboratory; Lake Erie Center and the Department of Environmental Sciences; The University of Toledo; 6200 Bayshore Road; Toledo; OH; 43616; USA
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Chen WJ, Lavoué S, Mayden RL. Evolutionary origin and early biogeography of otophysan fishes (Ostariophysi: Teleostei). Evolution 2013; 67:2218-39. [PMID: 23888847 DOI: 10.1111/evo.12104] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 02/15/2013] [Indexed: 11/26/2022]
Abstract
The biogeography of the mega-diverse, freshwater, and globally distributed Otophysi has received considerable attention. This attraction largely stems from assumptions as to their ancient origin, the clade being almost exclusively freshwater, and their suitability as to explanations of trans-oceanic distributions. Despite multiple hypotheses explaining present-day distributions, problems remain, precluding more parsimonious explanations. Underlying previous hypotheses are alternative phylogenies for Otophysi, uncertainties as to temporal diversification and assumptions integral to various explanations. We reexamine the origin and early diversification of this clade based on a comprehensive time-calibrated, molecular-based phylogenetic analysis and event-based approaches for ancestral range inference of lineages. Our results do not corroborate current phylogenetic classifications of otophysans. We demonstrate Siluriformes are never sister to Gymnotiformes and Characiformes are most likely nonmonophyletic. Divergence time estimates specify a split between Cypriniformes and Characiphysi with the fragmentation of Pangea. The early diversification of characiphysans either predated, or was contemporary with, the separation of Africa and South America, and involved a combination of within- and between-continental divergence events for these lineages. The intercontinental diversification of siluroids and characoids postdated major intercontinental tectonic fragmentations (<90 Mya). Post-tectonic drift dispersal events are hypothesized to account for their current distribution patterns.
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Affiliation(s)
- Wei-Jen Chen
- Institute of Oceanography, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, 10617, Taiwan.
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Bej D, Sahoo L, Das SP, Swain S, Jayasankar P, Das P. Complete mitochondrial genome sequence of Cirrhinus mrigala (Hamilton, 1822). MITOCHONDRIAL DNA 2013; 24:91-93. [PMID: 22994312 DOI: 10.3109/19401736.2012.722998] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The complete mitochondrial genome of Cirrhinus mrigala was determined using the polymerase chain reaction. The mitogenome (16,594 bp) has the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one control region. The overall base composition on the heavy strand was as follows: A: 32.0%, G: 15.5%, C: 28.0%, T: 24.55% and the A+T content: 56.5%. The control region contains a dinucleotide repeat motif, (TA)14, a termination-associated sequence and three conserved sequence blocks. These mitogenome sequence data would play an important role in population genetics and the molecular taxonomy of cultivable cyprinids in India.
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Affiliation(s)
- Dillip Bej
- Fish Genetics and Biotechnology Division, Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha 751002, India
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