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Yatsuyanagi T, Kanbe T, Fujii K, Inoue S, Araki H. Environmental DNA unveils deep phylogeographic structure of a freshwater fish. Mol Ecol 2024; 33:e17337. [PMID: 38558465 DOI: 10.1111/mec.17337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 03/14/2024] [Accepted: 03/21/2024] [Indexed: 04/04/2024]
Abstract
Phylogeography bears an important part in ecology and evolution. However, current phylogeographic studies are largely constrained by limited numbers of individual samples. Using an environmental DNA (eDNA) assay for phylogeographic analyses, this study provides detailed information regarding the history of Siberian stone loach Barbatula toni, a primary freshwater fish across the whole range of Hokkaido, Japan. Based on an eDNA metabarcoding on 293 river water samples, we detected eDNA from B. toni in 189 rivers. A total of 51 samples, representing the entire island, were then selected from the B. toni eDNA-positive sample set for the subsequent analyses. To elucidate the phylogeographic structure of B. toni, newly developed eDNA metabarcoding primers (Barba-cytb-F/R) were applied to these samples, specifically targeting their haplotypic variation in cytochrome b. After a bioinformatic processing to mitigate haplotypic false positives, a total of 50 eDNA haplotypes were identified. Two regionally restricted, genetically distinct lineages of the species were revealed as a result of phylogeographic analyses on the haplotypes and tissue-derived DNA from B. toni. According to a molecular clock analysis, they have been genetically isolated for at least 1.5 million years, suggesting their ancient origin and colonisation of Hokkaido, presumably in the glacial periods. These results demonstrate how freshwater fishes can alter their distributions over evolutionary timescales and how eDNA assay can deepen our understanding of phylogeography.
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Affiliation(s)
| | - Takashi Kanbe
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Kazuya Fujii
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
- Fukuda Hydrologic Center, Sapporo, Japan
| | - Shouko Inoue
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Hitoshi Araki
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
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Dey A, Choudhury H, Mazumder A, Thaosen S, Sarma D. Psilorhynchus nahlongthai, a new fish species (Teleostei: Psilorhynchidae) from the Brahmaputra drainage, northeast India. J Fish Biol 2020; 96:642-650. [PMID: 31900922 DOI: 10.1111/jfb.14251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/03/2020] [Indexed: 06/10/2023]
Abstract
Psilorhynchus nahlongthai, a new psilorhynchid fish, is described from the Diyung River, a tributary to the Kopili River (itself a southern tributary of the Brahmaputra drainage) in Assam, northeast India. It is placed in the Psilorhynchus balitora species group and can be easily distinguished from all other members of this group by a combination of the following characters: dense and prominent tuberculation on the head region; thick and long pre- and post-epiphyseal fontanelles on the neurocranium; 9 + 8 caudal-fin rays; and 34 (24 + 10) vertebrae. Genetic divergence between P. nahlongthai and members of the P. balitora species group from the Brahmaputra and neighbouring drainages, with K2P distances ranging 3.7%-14.7% and 7.4%-20.7% in the mitochondrial COI and cyt b gene datasets respectively, support its report as a new species.
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Affiliation(s)
- Abhinit Dey
- Department of Zoology, Gauhati University, Guwahati, Assam, India
| | | | | | - Sarbojit Thaosen
- Department of Zoology, Haflong Government College, Haflong, Assam, India
| | - Dandadhar Sarma
- Department of Zoology, Gauhati University, Guwahati, Assam, India
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Huang JQ, Yang J, Wu ZQ, Zhao YH. Oreonectes guilinensis (Teleostei, Cypriniformes, Nemacheilidae), a new loach species from Guangxi, China. J Fish Biol 2020; 96:111-119. [PMID: 31782180 DOI: 10.1111/jfb.14191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 11/04/2019] [Indexed: 06/10/2023]
Abstract
A new loach Oreonectes guilinensis sp. nov. is described from Guangxi Zhuang Autonomous Region, China. It is the second surface-dwelling fish identified in the genus Oreonectes after the type species Oreonectes platycephalus. This new species can be distinguished from other species within the genus by the combination of the following features: a round caudal fin, 13-14 branched rays, an incomplete lateral line with 4-6 pores, a short pelvic fin located some distance from the anus, a scale-covered body, a stout build (body width 14.0%-16.7% of standard length), a posterior chamber of well-developed airbladder and a yellowish-brown body with a lateral dark brown strip. The maximum likelihood phylogenetic analysis based on cytb gene recovered this new species in a well-supported clade with the type species O. platycephalus, sister to the Lefua clade. Morphological comparisons as well as our phylogenetic tree support Oreonectes shuilongensis, Oreonectes daqikongensis, Oreonectes jiarongensis as species of Troglonectes. Based on our results there are 6 valid species in the genus Oreonectes.
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Affiliation(s)
- Jin-Qing Huang
- College of Life Science and Technology, Guangxi University, Nanning, China
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jian Yang
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Nanning Normal University, Nanning, China
| | - Zhi-Qiang Wu
- College of Life Science and Technology, Guangxi University, Nanning, China
| | - Ya-Hui Zhao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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Turan D, Kaya C, Kalayci G, Bayçelebi E, Aksu İ. Oxynoemacheilus cemali, a new species of stone loach (Teleostei: Nemacheilidae) from the Çoruh River drainage, Turkey. J Fish Biol 2019; 94:458-468. [PMID: 30671971 DOI: 10.1111/jfb.13909] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 12/23/2018] [Indexed: 06/09/2023]
Abstract
Oxynoemacheilus cemali sp. nov. is described from the Çoruh River drainage in the eastern Black Sea basin. One molecular marker (coI), 25 morphometric and four meristic characters were analysed. Oxynoemacheilus cemali is distinguished from O. kosswigi, O. banarescui, O. samanticus and O. angorae in the Black Sea basin by having a suborbital groove in males, an axillary lobe at the pelvic-fin base, no dorsal adipose crest on the caudal peduncle, a slightly-forked caudal fin and 7-15 dark grey dorsal saddles. Morever, Oxynoemacheilus cemali is distinguished by commonly having 9-15 irregularly-shaped dark-grey bars on the flank posterior to the dorsal-fin origin or, rarely having a mottled pattern or 4-6 irregularly shaped dark-grey bars on the flank posterior to the dorsal-fin origin. Oxynoemacheilus cemali is also distinguished from the closely related species O. araxensis and O. cyri, distributed outside the Black Sea basin, by having 15 and 31 diagnostic nucleotide substitutions in the coI barcode region, respectively.
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Affiliation(s)
- Davut Turan
- Faculty of Fisheries and Aquatic Sciences, Recep Tayyip Erdoğan University, Rize, Turkey
| | - Cüneyt Kaya
- Faculty of Fisheries and Aquatic Sciences, Recep Tayyip Erdoğan University, Rize, Turkey
| | - Gökhan Kalayci
- Faculty of Fisheries and Aquatic Sciences, Recep Tayyip Erdoğan University, Rize, Turkey
| | - Esra Bayçelebi
- Faculty of Fisheries and Aquatic Sciences, Recep Tayyip Erdoğan University, Rize, Turkey
| | - İsmail Aksu
- Faculty of Fisheries and Aquatic Sciences, Recep Tayyip Erdoğan University, Rize, Turkey
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Corona-Santiago DK, Domínguez-Domínguez O, Tovar-Mora L, Pardons-Blas JR, Herrerías-Diego Y, Pérez-Rodríguez R, Doadrio I. Historical biogeography reveals new independent evolutionary lineages in the Pantosteus plebeius-nebuliferus species-group (Actinopterygii: Catostomidae). BMC Evol Biol 2018; 18:173. [PMID: 30453887 PMCID: PMC6245702 DOI: 10.1186/s12862-018-1286-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 10/31/2018] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND The Pantosteus plebeius-nebuliferus species-group is a group of freshwater fishes distributed in endo- and exorheic drainage basins in the Mexican Sierra Madre Occidental mountain range system and central North Mexico. The geological history of this region is considered an important factor in explaining the evolutionary history of low vagility animals like freshwaters fishes. The aim of this study was to examine the phylogenetic relationships and describe the evolutionary history of the species-group. We hypothesized that the genetic structure and distribution of the main clades of Pantosteus plebeius-nebuliferus are associated with the geological history of Northern Mexico. To this end, we obtained DNA sequences of mitochondrial and nuclear genes and performed phylogenetic and phylogeographic analyses. Divergence time estimation and ancestral area reconstruction were also carried out to propose a biogeographical hypothesis, and species boundaries within the species-group were also tested. RESULTS We identified four clades within the Pantosteus plebeius-nebuliferus species-group in both markers. Divergence ranged from 5.9% to 9.2% for cytb and 0.1% to 0.9% for GHI. We observed significant genetic structure and no shared haplotypes between clades. We estimated that the clades diverged during the last 5.1 Myr, with a biogeographic scenario suggesting eight vicariant and four dispersal events through the historic range of the species-group. We found that the best species-delimitation model is when four species are assumed, which correspond to the main clades. We identified nine evolutionary significance units (ESUs), pertinent to the conservation of the group, each representing populations present in distinct drainage basins. CONCLUSIONS The evolutionary history of the Pantosteus plebeius-nebuliferus species-group is characterized by vicariant post-dispersal processes, linked to geological changes in the Sierra Madre Occidental and central Northern Mexico since the Pliocene. This is congruent with biogeographic patterns described for other co-distributed fish species. We propose a new phylogenetic hypothesis for the species-group, clarifying the taxonomy of this evolutionarily complex group. Our results suggest that the species-group consists of at least four clades with independent evolutionary histories, two of which may represent new undescribed species. Our identification of ESUs provides a basis upon which conservation measures can be developed for the species-group.
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Affiliation(s)
- Diushi Keri Corona-Santiago
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC. c/José Gutiérrez Abascal, 2, 28006 Madrid, Spain
| | - Omar Domínguez-Domínguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán Mexico
- Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán Mexico
| | - Llanet Tovar-Mora
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán Mexico
| | - José Ramón Pardons-Blas
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC. c/José Gutiérrez Abascal, 2, 28006 Madrid, Spain
| | - Yvonne Herrerías-Diego
- Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán Mexico
| | - Rodolfo Pérez-Rodríguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán Mexico
| | - Ignacio Doadrio
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC. c/José Gutiérrez Abascal, 2, 28006 Madrid, Spain
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Wu WJ, He AY, Yang JX, Du LN. Description of a new species of Triplophysa (Teleostei: Nemacheilidae) from Guizhou Province, China. J Fish Biol 2018; 93:88-94. [PMID: 29882375 DOI: 10.1111/jfb.13670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 04/23/2018] [Indexed: 06/08/2023]
Abstract
A new cave-dwelling fish species Triplophysa guizhouensis is described based on specimens collected from Guizhou, China, in a subterranean system interconnected with the Hongshui River drainage. The species can be distinguished from its congeners by a combination of characters: eyes present; caudal fin with 14 branched rays; inner gill rakers of first gill arch 8-10; posterior chamber of air bladder developed; and body posterior of dorsal fin scaled. A key to species of Triplophysa in the Pearl River basin is provided.
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Affiliation(s)
- Wei-Jun Wu
- China Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Nanning, China
| | - An-You He
- China Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Nanning, China
| | - Jun-Xing Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Li-Na Du
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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Sember A, Bohlen J, Šlechtová V, Altmanová M, Pelikánová Š, Ráb P. Dynamics of tandemly repeated DNA sequences during evolution of diploid and tetraploid botiid loaches (Teleostei: Cobitoidea: Botiidae). PLoS One 2018; 13:e0195054. [PMID: 29590207 PMCID: PMC5874072 DOI: 10.1371/journal.pone.0195054] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/15/2018] [Indexed: 12/16/2022] Open
Abstract
Polyploidization has played an important role in the evolution of vertebrates, particularly at the base of Teleostei-an enormously successful ray-finned fish group with additional genome doublings on lower taxonomic levels. The investigation of post-polyploid genome dynamics might provide important clues about the evolution and ecology of respective species and can help to decipher the role of polyploidy per se on speciation. Few studies have attempted to investigate the dynamics of repetitive DNA sequences in the post-polyploid genome using molecular cytogenetic tools in fishes, though recent efforts demonstrated their usefulness. The demonstrably monophyletic freshwater loach family Botiidae, branching to evolutionary diploid and tetraploid lineages separated >25 Mya, offers a suited model group for comparing the long-term repetitive DNA evolution. For this, we integrated phylogenetic analyses with cytogenetical survey involving Giemsa- and Chromomycin A3 (CMA3)/DAPI stainings and fluorescence in situ hybridization with 5S/45S rDNA, U2 snDNA and telomeric probes in representative sample of 12 botiid species. The karyotypes of all diploids were composed of 2n = 50 chromosomes, while majority of tetraploids had 2n = 4x = 100, with only subtle interspecific karyotype differences. The exceptional karyotype of Botia dario (2n = 4x = 96) suggested centric fusions behind the 2n reduction. Variable patterns of FISH signals revealed cases of intraspecific polymorphisms, rDNA amplification, variable degree of correspondence with CMA3+ sites and almost no phylogenetic signal. In tetraploids, either additivity or loci gain/loss was recorded. Despite absence of classical interstitial telomeric sites, large blocks of interspersed rDNA/telomeric regions were found in diploids only. We uncovered different molecular drives of studied repetitive DNA classes within botiid genomes as well as the advanced stage of the re-diploidization process in tetraploids. Our results may contribute to link genomic approach with molecular cytogenetic analyses in addressing the origin and mechanism of this polyploidization event.
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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, Czech Republic
| | - Jörg Bohlen
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
| | - Vendula Šlechtová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
| | - Marie Altmanová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2, Czech Republic
| | - Šárka Pelikánová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
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Li J, Lan JH, Chen XY, Du LN. Description of Triplophysa luochengensis sp. nov. (Teleostei: Nemacheilidae) from a karst cave in Guangxi, China. J Fish Biol 2017; 91:1009-1017. [PMID: 28853143 DOI: 10.1111/jfb.13364] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 05/31/2017] [Indexed: 06/07/2023]
Abstract
A new cave-dwelling fish Triplophysa luochengensis is described based on specimens collected from a karst cave in Guangxi Zhuang Autonomous Region, China, that is interconnected to the Hongshui River drainage. The species can be distinguished from its congeners by a combination of characters: eyes degenerated, anal fin with six branched rays, caudal fin with 16-17 branched rays, pectoral-fin length 72·4-95·8% of the distance between pectoral-fin origin and pelvic-fin origin, lateral head length 26·2-28·2% of standard length (LS ), eye diameter 7·5-8·6 of LS , body covered by sparse scales, lateral line complete and 7-8 pre-operculo-mandibular pores. Dark pigments irregularly present on dorsum of head, dorsum and flank.
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Affiliation(s)
- J Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510380, China
| | - J H Lan
- Du'an Fishery Technique Popularization Station, Du'an 530700, China
| | - X Y Chen
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw 05282, Myanmar
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - L N Du
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
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9
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Liu SW, Pan XF, Yang JX, Chen XY. A new cave-dwelling loach, Triplophysa xichouensis sp. nov. (Teleostei Nemacheilidae) from Yunnan, China. J Fish Biol 2017; 90:834-846. [PMID: 28155227 DOI: 10.1111/jfb.13201] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 09/29/2016] [Indexed: 06/06/2023]
Abstract
A new cave-dwelling loach of the genus Triplophysa, T. xichouensis, is described from an outlet of a subterranean river in Xisa Town, Xichou County, Yunnan Province, China. It can be distinguished from its congeners by the following characters: dorsal-fin rays iii, 8; anal-fin rays ii, 6; pectoral-fin rays i, 9 or 10; pelvic-fin rays i, 5 or 6; branched caudal-fin rays 16(8+8); eyes highly degenerated to a very tiny black dot; dorsal-fin origin closer to snout tip than to caudal-fin base and anterior to vertical line of pelvic-fin origin; pectoral fin length about two-thirds the distance between pectoral-fin origin to pelvic-fin origin; caudal peduncle slender, its length about three times its depth; caudal fin emarginate; body smooth and scaleless; lateral line complete and straight; anterior chamber of air bladder wrapped in dumbbell-shaped bony capsule and the posterior one well developed, long, oval; intestine short, bending in zigzag shape behind stomach. A key for the cave-dwelling species of Triplophysa is provided. urn:lsid:zoobank.org:pub:9162FFB1-7911-47C3-AE50-6A00E9590327.
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Affiliation(s)
- S W Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - X F Pan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - J X Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - X Y Chen
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, 05282, Myanmar
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10
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Kappas I, Vittas S, Pantzartzi CN, Drosopoulou E, Scouras ZG. A Time-Calibrated Mitogenome Phylogeny of Catfish (Teleostei: Siluriformes). PLoS One 2016; 11:e0166988. [PMID: 27907107 PMCID: PMC5132296 DOI: 10.1371/journal.pone.0166988] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 11/07/2016] [Indexed: 11/18/2022] Open
Abstract
A very significant part of the world's freshwater ichthyofauna is represented by ancient, exceptionally diverse and cosmopolitan ray-finned teleosts of the order Siluriformes. Over the years, catfish have been established as an exemplary model for probing historical biogeography at various scales. Yet, several tantalizing gaps still exist in their phylogenetic history, timeline and mode of diversification. Here, we re-examine the phylogeny of catfish by assembling and analyzing almost all publicly available mitogenome data. We constructed an ingroup matrix of 62 full-length mitogenome sequences from 20 catfish families together with four cypriniform outgroups, spanning 15,557 positions in total. Partitioned maximum likelihood analyses and Bayesian relaxed clock dating using fossil age constraints provide some useful and novel insights into the evolutionary history of this group. Loricarioidei are recovered as the first siluriform group to diversify, rendering Neotropics the cradle of the order. The next deepest clade is the South American Diplomystoidei placed as a sister group to all the remaining Siluroidei. The two multifamilial clades of "Big Asia" and "Big Africa" are also recovered, albeit nodal support for the latter is poor. Within "Big Asia", Bagridae are clearly polyphyletic. Other interfamilial relationships, including Clariidae + Heteropneustidae, Doradidae + Auchenipteridae and Ictaluridae + Cranoglanididae are robustly resolved. Our chronogram shows that siluriforms have a Pangaean origin, at least as far back as the Early Cretaceous. The inferred timeline of the basal splits corroborates the "Out-of-South America" hypothesis and accords well with the fossil record. The divergence of Siluroidei most likely postdated the final separation of Africa and South America. An appealing case of phylogenetic affinity elaborated by biogeographic dispersal is exemplified by the Early Paleogene split between the Southeast Asian Cranoglanididae and Ictaluridae, with the latter radiating into North America's freshwater realm by Eocene. The end of Cretaceous probably concludes the major bout of diversification at the family level while with the dawn of the Cenozoic a prolific radiation is evident at the generic level.
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Affiliation(s)
- Ilias Kappas
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Spiros Vittas
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Chrysoula N. Pantzartzi
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Elena Drosopoulou
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Zacharias G. Scouras
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- * E-mail:
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11
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Yi S, Wang S, Zhong J, Wang W. Comprehensive Transcriptome Analysis Provides Evidence of Local Thermal Adaptation in Three Loaches (Genus: Misgurnus). Int J Mol Sci 2016; 17:ijms17121943. [PMID: 27886141 PMCID: PMC5187763 DOI: 10.3390/ijms17121943] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/27/2016] [Accepted: 11/14/2016] [Indexed: 02/07/2023] Open
Abstract
The geographic distribution of three Misgurnus species, M. anguillicaudatus, M. bipartitus, and M. mohoity, displays a specific pattern in China, coincident with temperature zones. In this study, we sequenced the transcriptomes of these three species and used the sequences to investigate the lineage-specific adaptations within the genus Misgurnus. In total, 51 orphan genes (19 in M. anguillicaudatus, 18 in M. bipartitus, and 14 in M. mohoity) that may contribute to the species-specific adaptations were identified. An analysis of 1392 one-to-one orthologous genes revealed significantly higher ratios of nonsynonymous-to-synonymous substitutions in the M. mohoity lineage than in M. anguillicaudatus. The genes displaying signatures of positive selection and rapid evolution in Misgurnus were involved in four function categories, (1) energy metabolism; (2) signal transduction; (3) membrane; and (4) cell proliferation or apoptosis, implying that these candidate genes play critical roles in the thermal adaptation of the fish to their living environments. We also detected more than five positively selected sites in cldn15lb and isca1, which function as important factors in paracellular Na+ transport and Fe/S cluster assembly, respectively. Overall, our study provides valuable insights into the adaptive evolution of loaches from different temperature zones in China and is a foundation for future studies to clarify the genetic basis of temperature adaptation in fishes.
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Affiliation(s)
- Shaokui Yi
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
- Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
| | - Sai Wang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
- Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jia Zhong
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
- Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
| | - Weimin Wang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
- Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
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Wu YY, Sun ZY, Guo YS. A new species of the genus Triplophysa (Cypriniformes: Nemacheilidae), Triplophysa daochengensis, from Sichuan Province, China. Zool Res 2016; 37:290-296. [PMID: 27686788 PMCID: PMC5071342 DOI: 10.13918/j.issn.2095-8137.2016.5.290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 06/20/2016] [Indexed: 06/06/2023] Open
Abstract
Triplophysa daochengensis sp. nov. is described from the Daocheng River, a northern tributary of the Jinsha River in Sichuan Province, China. The new species can be distinguished from its congeners by the following characters: body smooth and scales absent; lateral line complete; caudal peduncle compressed, depth unchanging; head length equal to caudal-peduncle length; lower jaw shovel-shaped; dorsal-fin origin anterior to pelvic-fin origin and closer to the tip of the snout than to the caudal-fin base, last unbranched ray hard; pelvic-fin tip not reaching anus; posterior chamber of gas bladder absent; intestine of spiral type with three winding coils.
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Affiliation(s)
- Yu-Yi Wu
- College of Life Sciences, China West Normal University, Nanchong Sichuan 637009, China
| | - Zhi-Yu Sun
- Sichuan Academy of Forestry, Chengdu Sichuan 610081, China.
| | - Yan-Shu Guo
- College of Life Sciences, China West Normal University, Nanchong Sichuan 637009, China.
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13
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Perdices A, Bohlen J, Šlechtová V, Doadrio I. Molecular Evidence for Multiple Origins of the European Spined Loaches (Teleostei, Cobitidae). PLoS One 2016; 11:e0144628. [PMID: 26727121 PMCID: PMC4699775 DOI: 10.1371/journal.pone.0144628] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 11/21/2015] [Indexed: 11/19/2022] Open
Abstract
We present a phylogenetic investigation of the Northern Clade, the major monophyletic clade within the freshwater fish family Cobitidae, one of the most prominent families of freshwater fishes found in Asian and European waters. Phylogenetic reconstructions based on the cytochrome b and RAG-1 genes show the genera Microcobitis, Sabanejewia, Koreocobitis and Kichulchoia as monophyletic groups. These reconstructions also show a Cobitis sensu lato and a Misgurnus sensu lato group. The Cobitis sensu lato group includes all species of Cobitis, Iksookimia, Niwaella and Kichulchoia, while the Misgurnus sensu lato group includes Misgurnus, Paramisgurnus and Koreocobitis. Although the monophyly of both the Cobitis sensu lato and Misgurnus sensu lato groups is supported, relationships within the groups are incongruent with current generic definitions. The absence of monophyly of most genera included in the Cobitis sensu lato group (Cobitis, Iksookimia and Niwaella) or their low genetic differentiation (Kichuchoia) supports their consideration as synonyms of Cobitis. Molecular phylogenies indicate that the Asian species of Misgurnus experienced a mitochondrial introgression from a lineage of Cobitis. We also find two nuclear haplotypes in the same Cobitis species from the Adriatic area that, in the absence of morphological differentiation, may indicate molecular introgression. Most lineages within the Northern Clade consist of species found in East Asia. However, some lineages also contain species from Europe and Asia Minor. The phylogenetic relationships presented here are consistent with previous studies suggesting an East Asian origin of the Northern Clade. According to the current distributions and phylogenetic relationships of the Misgurnus sensu lato and Cobitis clade lineages, particularly of M. fossilis and C. melanoleuca, the range expansion of East Asian species into Europe was most likely via Siberia into Northern and Central Europe. Phylogenetic analyses also show that the Cobitis sensu lato group consists of two clear subgroups (I and II), each presenting geographical differences. Subgroup I is distributed exclusively in East Asian drainages with an Eastern European offshoot (C. melanoleuca), whereas Subgroup II includes species widespread throughout Europe (including the Mediterranean), Asia Minor, the Black Sea and the Caucasus, with some lineages related to species restricted to East Asia.
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Affiliation(s)
- Anabel Perdices
- Department of Biodiversity and Evolutionary Biology, Museo Nacional Ciencias Naturales, CSIC, Madrid, Spain
- * E-mail:
| | - Joerg Bohlen
- Laboratory of Fish Genetics Institute of Animal Physiology and Genetics, Libechov, Czech Republic
| | - Vendula Šlechtová
- Laboratory of Fish Genetics Institute of Animal Physiology and Genetics, Libechov, Czech Republic
| | - Ignacio Doadrio
- Department of Biodiversity and Evolutionary Biology, Museo Nacional Ciencias Naturales, CSIC, Madrid, Spain
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14
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Zhou X, Yu Y, Li Y, Wu J, Zhang X, Guo X, Wang W. Comparative analysis of mitochondrial genomes in distinct nuclear ploidy loach Misgurnus anguillicaudatus and its implications for polyploidy evolution. PLoS One 2014; 9:e92033. [PMID: 24643051 PMCID: PMC3958399 DOI: 10.1371/journal.pone.0092033] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 02/17/2014] [Indexed: 01/23/2023] Open
Abstract
Misgurnus anguillicaudatus has several natural ploidy types. To investigate whether nuclear polyploidy have an impact on mitochondrial DNA (mtDNA), the complete mitochondrial genomes (mitogenomes) of five distinct ploidy M. anguillicaudatus (natural diploid, triploid, tetraploid, pentaploid and hexaploid), which were collected in central China, were sequenced and analyzed. The five mitogenomes share the same gene arrangement and have similar gene size, base composition and codon usage pattern. The most variable regions of the mitogenome were the protein-coding genes, especially the ND4L (5.39% mutation rate). Most variations occurred in tetraploids. The phylogenetic tree showed that the tetraploid M. anguillicaudatus separated early from other ploidy loaches. Meanwhile, the mitogenomes from pentaploids, and hexaploids have the closest phylogenetic relations, but far from that of tetraploids, implying that pentaploids and hexaploids could not be formed from tetraploids, possibly from the diploids and triploids. The genus Misgurnus species were divided into two divergent inter-genus clades, and the five ploidy M. anguillicaudatus were monophyletic, which support the hypotheses about the mitochondrial introgression in loach species.
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Affiliation(s)
- Xiaoyun Zhou
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, P.R. China
| | - Yongyao Yu
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, P.R. China
| | - Yanhe Li
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, P.R. China
| | - Junjie Wu
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, P.R. China
| | - Xiujie Zhang
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, P.R. China
| | - Xianwu Guo
- Laboratorio de Biomedicina Molecular, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Boulevard del Maestro esquina Elías Piña, Colonia Narciso Mendoza, Tamaulipas, Mexico
| | - Weimin Wang
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, P.R. China
- * E-mail:
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16
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Unmack PJ, Dowling TE, Laitinen NJ, Secor CL, Mayden RL, Shiozawa DK, Smith GR. Influence of introgression and geological processes on phylogenetic relationships of Western North American mountain suckers (Pantosteus, Catostomidae). PLoS One 2014; 9:e90061. [PMID: 24619087 PMCID: PMC3949674 DOI: 10.1371/journal.pone.0090061] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 01/29/2014] [Indexed: 12/04/2022] Open
Abstract
Intense geological activity caused major topographic changes in Western North America over the past 15 million years. Major rivers here are composites of different ancient rivers, resulting in isolation and mixing episodes between river basins over time. This history influenced the diversification of most of the aquatic fauna. The genus Pantosteus is one of several clades centered in this tectonically active region. The eight recognized Pantosteus species are widespread and common across southwestern Canada, western USA and into northern Mexico. They are typically found in medium gradient, middle-elevation reaches of rivers over rocky substrates. This study (1) compares molecular data with morphological and paleontological data for proposed species of Pantosteus, (2) tests hypotheses of their monophyly, (3) uses these data for phylogenetic inferences of sister-group relationships, and (4) estimates timing of divergence events of identified lineages. Using 8055 base pairs from mitochondrial DNA protein coding genes, Pantosteus and Catostomus are reciprocally monophyletic, in contrast with morphological data. The only exception to a monophyletic Pantosteus is P. columbianus whose mtDNA is closely aligned with C. tahoensis because of introgression. Within Pantosteus, several species have deep genetic divergences among allopatric sister lineages, several of which are diagnosed and elevated to species, bringing the total diversity in the group to 11 species. Conflicting molecular and morphological data may be resolved when patterns of divergence are shown to be correlated with sympatry and evidence of introgression.
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Affiliation(s)
- Peter J. Unmack
- WIDB 401, Department of Biology, Brigham Young University, Provo, Utah, United States of America
- National Evolutionary Synthesis Center, Durham, North Carolina, United States of America
- * E-mail:
| | - Thomas E. Dowling
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, United States of America
| | - Nina J. Laitinen
- WIDB 401, Department of Biology, Brigham Young University, Provo, Utah, United States of America
| | - Carol L. Secor
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Richard L. Mayden
- Department of Biology, Saint Louis University, St. Louis, Missouri, United States of America
| | - Dennis K. Shiozawa
- WIDB 401, Department of Biology, Brigham Young University, Provo, Utah, United States of America
| | - Gerald R. Smith
- Museum of Zoology, The University of Michigan, Ann Arbor, Michigan, United States of America
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17
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Xue X, Wang L, Chen Y, Zhang X, Luo H, Li Z, Zhao H, Yao B. Identification and molecular characterization of an Akirin2 homolog in Chinese loach (Paramisgurnus dabryanus). Fish Shellfish Immunol 2014; 36:435-443. [PMID: 24389387 DOI: 10.1016/j.fsi.2013.12.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 12/21/2013] [Accepted: 12/23/2013] [Indexed: 06/03/2023]
Abstract
Akirin is a nuclear factor involved in innate immune responses of arthropods and mammals. In this study we have cloned an Akirin2 gene, pdakirin2, from freshwater Chinese loach (Paramisgurnus dabryanus) and characterized its biological functions. Phylogenetic analysis revealed deduced PdAkirin2 had high sequence identities to Akirin2 homologs from fish and mammals (70-91%), it contained two conserved nuclear localization signals (NLSs) with verified sub-cellular localization. Quantitative real-time (qRT)-PCR analysis indicated that PdAkirin2 was present in a wide range of loach tissues and showed up-regulation with challenges of Aeromonas hydrophila NJ-1, LPS and poly I:C. PdAkirin2 as an immune factor had significant effects on the expression of cytokines (TNFα, IFN-α, IFN-γ, IL-4 and IL-1β) and transcription factor NF-κB. This study provides insights into the potential role of PdAkirin2 in the innate immune system.
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Affiliation(s)
- Xianli Xue
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12, Zhongguancun South Street, Beijing 100081, PR China
| | - Liwen Wang
- National Animal Husbandry Extension Service, Beijing 100125, PR China
| | - Yeyu Chen
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12, Zhongguancun South Street, Beijing 100081, PR China
| | - Xinshang Zhang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12, Zhongguancun South Street, Beijing 100081, PR China
| | - Huiying Luo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12, Zhongguancun South Street, Beijing 100081, PR China
| | - Zhongyuan Li
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12, Zhongguancun South Street, Beijing 100081, PR China
| | - Heng Zhao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12, Zhongguancun South Street, Beijing 100081, PR China.
| | - Bin Yao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12, Zhongguancun South Street, Beijing 100081, PR China.
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18
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Bineesh KK, Akhilesh KV, Gomon MF, Abdussamad EM, Pillai NGK, Gopalakrishnan A. Redescription of Chlorophthalmus corniger, a senior synonym of Chlorophthalmus bicornis (Family: Chlorophthalmidae). J Fish Biol 2014; 84:513-522. [PMID: 24490937 DOI: 10.1111/jfb.12305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 11/18/2013] [Indexed: 06/03/2023]
Abstract
Chlorophthalmus corniger is redescribed on the basis of recently collected specimens. The species is redefined as a species of Chlorophthalmus with the lower jaw terminating in a distinctly projecting horizontal plate with strong, spine-like processes directed forward from the plate's corners; body silvery grey, with numerous minute black spots and traces of broad darker crossbars; base of anterior dorsal fin spines and distal parts of dorsal fins black; adipose fin tiny with numerous black spots; caudal fin black; 3·5 scales above lateral line; three rows of cheek scales; head very large, 34·3-40·1% standard length (LS ); eye large, 29·8-40·8% head length (LH ); pectoral fin long, extending to beyond dorsal fin base, 21·7-26·2% LS . Chlorophthalmus bicornis is a junior synonym of C. corniger based on the examination of the type series of both species. It is confined to the northern half of the Indian Ocean, reliably recorded from Somalia and the Gulf of Aden to southern Java, Indonesia, at depths between 200 and 500 m. A lectotype and three paralectotypes were designated for C. corniger. DNA barcodes for Indian species of Chlorophthalmus were generated.
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Affiliation(s)
- K K Bineesh
- Central Marine Fisheries Research Institute, P. B. No.1603, Ernakulam North, P. O., Kochi-682 018, Kerala, India
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19
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Li L, Zhai S, Wang L, Si S, Wu H, Chang Z. Hsp60 in caudal fin regeneration from Paramisgurnus dabryanus: molecular cloning and expression characterization. Fish Shellfish Immunol 2014; 36:401-408. [PMID: 24380831 DOI: 10.1016/j.fsi.2013.12.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 12/13/2013] [Accepted: 12/19/2013] [Indexed: 06/03/2023]
Abstract
Heat shock protein 60 (Hsp60) is a kind of highly conserved immunogenic molecule involved in a wide range of biochemical processes in response to external stressors. Its multifunction in regulating immune responses and modulating signal pathway interests us in investigating its role in fin regeneration that has become an excellent and interesting model for studying the molecular basis of morphogenesis. We firstly clarified basical process and crucial period of caudal fins regeneration in Paramisgurnus dabryanus by histological analysis. Then we cloned full-length cDNA of hsp60 from P. dabryanus (designated as PdHsp60) by RACE method. The cDNA contains a 124 bp 5'UTR, a 1731 bp open reading frame (ORF) encoding 576 amino acids and a 510 bp 3'UTR (Accession no.: KF544774). The phylogenetic tree shows that the PdHsp60 fits within the hsp60 clade. And quantitative RT-PCR detected the PdHsp60 began to increase rapidly its expression at 1 dpa and reached its peak at 2 dpa. Next, spatial distribution analysis of PdHsp60 in fins showed that PdHsp60 located mainly in the deeper lay of regenerated epidermis when PdHsp60 expressed most. After the PdHsp60 had been cloned into the pET-32a vector, SDS-PAGE and Western blotting analysis confirmed that the PdHsp60 protein was efficiently expressed in Escherichia coli BL21. These findings have revealed that PdHsp60, a highly conserved gene related to the innate immune system and stress response during vertebrate evolution, is involved in response to wounding stimulation--in the formation of wound epidermis which occurs as the first phase of fin regeneration after fin amputation in caudal fin regeneration.
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Affiliation(s)
- Li Li
- Molecular and Genetic Laboratory, College of Life Science, Henan Normal University, 46# East of Construction Road, Xinxiang, Henan 453007, China
| | - Shengna Zhai
- Molecular and Genetic Laboratory, College of Life Science, Henan Normal University, 46# East of Construction Road, Xinxiang, Henan 453007, China
| | - Lele Wang
- Molecular and Genetic Laboratory, College of Life Science, Henan Normal University, 46# East of Construction Road, Xinxiang, Henan 453007, China
| | - Songbo Si
- Molecular and Genetic Laboratory, College of Life Science, Henan Normal University, 46# East of Construction Road, Xinxiang, Henan 453007, China
| | - Hailan Wu
- Molecular and Genetic Laboratory, College of Life Science, Henan Normal University, 46# East of Construction Road, Xinxiang, Henan 453007, China
| | - Zhongjie Chang
- Molecular and Genetic Laboratory, College of Life Science, Henan Normal University, 46# East of Construction Road, Xinxiang, Henan 453007, China.
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Abstract
In this study, the complete mitogenome sequence of Chinese sucker Myxocyprinus asiaticus (Cypriniformes, Catostomidae) has been amplified and sequenced by employing long polymerase chain reaction method. The mitogenome, consisting of 16,636 base pairs (bp), had the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs genes, and a noncoding control region (CR). CR of 944 bp length is located between tRNA(Pro) and tRNA(Phe). The overall base composition of M. asiaticus is 28.62% for A, 27.90% for C, 24.8% for T, and 18.70% for G, with a slight AT bias of 53.40%. The complete mitogenome may provide important DNA molecular data for further phylogenetic analyses for higher taxa of teleost fishes especially for the members of Cypriniformes.
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Affiliation(s)
- I-Shiung Chen
- Institute of Marine Biology, National Taiwan Ocean University , Keelung 202, Taiwan , Republic of China
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21
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Liu SW, Yang JX, Chen XY. [Discovery and its significance of spawning grounds of Jinshaiasinensis from upper and middle Jinshajiang River]. Dongwuxue Yanjiu 2013; 34:626-630. [PMID: 24415696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
During April, July to August and November of 2012,three surveys were conducted to estimate the early-stage fish resources in the area of Liyuan power station on Jinshajiang River of Yunnan Province. During the survey conducted at the crossing of Daju Town, Yulong County, Yunnan Province, from July to August, 2012, two egg-tides of Jinshaia sinensis were detected. One was from 8:00 of August 1(st) to 10:00 of August 4(th) and the other one was from 23:00 of August 9(th) to 6:00 of August 13(th). The average egg diameter was 3.89 mm, ranging from 3.37 to 4.41 mm. Natural fertilization and hatching rate as well as abnormality rate in mimic wild environment were 91.5%, 97.1% and 2.2%, respectively. Meanwhile, three spawning grounds had been conjectured, which were Longpan Town, Liming Town and Judian Town of Yulong County, Yunnan Province. Moreover, the total number of eggs from those three spawning grounds during the two egg-tides was approximately 1.49×10(7) ind.. The discovery of the three spawing grounds is of importance in fullfilling the study of Jinshaia sinensis, and in protecting fish resources under the influences of power stations.
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Affiliation(s)
- Shu-Wei Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
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22
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Liu SW, Chen XY. [Two new Cypriniformes fish records from Yunnan Province-Carassioides acuminatus and Hemimyzon pumilicorpora]. Dongwuxue Yanjiu 2013; 34:504-506. [PMID: 24115664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Two new Cypriniformes fish records from Yunnan Province, Carassioides acuminatus (collected from mainstream of Red River in Hekou County) and Hemimyzon pumilicorpora (collected from Gula River, Gula Town, Funing County, upper stream of the Pearl River drainage), were identified during fish specimen sorting at Kunming Institute of Zoology, Chinese Academy of Sciences. These two new records not only clarify the distribution patterns of the two species, but also enrich the knowledge of native fishes of Yunnan Province.
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Affiliation(s)
- Shu-Wei Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
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Flerova EA, Balabanova LV. [Ultrastructure of granulocytes of bony fishes (orders Salmoniformes, Cypriniformes, Perciformes)]. Zh Evol Biokhim Fiziol 2013; 49:162-171. [PMID: 23789402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Analysis of data on utrastructure of granulocytes of freshwater and marine bony fish of orders Salmoniformes, Cypriniformes, and Perciformes showed that in all studied species there were revealed two types of granulocytes - neutrophils and eosinophils. The exception was the bluefish Pomatomus saltatrix L. whose pronephros hemopoietic tissue was found to contain one type of the granulocytic line - neutrophils. The identification parameters of granular leukocytes are specific granules filling the cytoplasm. The main form of specific granules in neutrophils of bony fish of various phylogenetic groups is an elongated granule with different distribution of fibrils or a granule that has crystalloid formed from fibrils. The main form of eosinophil granules - large, electron-dense, homogenous.
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Hwang DY, Koim SK, Ryu SH, Hwang UW. Complete mitochondrial genome of Acheilognathus signifer (Cypriniformes, Cyprinidae): comparison of light-strand replication origins from six Acheilognathus species. Mitochondrial DNA 2012; 23:306-307. [PMID: 22591207 DOI: 10.3109/19401736.2012.683180] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Acheilognathus signifer (Cypriniformes, Cyprinidae) is an endemic, endangered fresh water fish species in the Korean peninsula. In this study, the mitochondrial genome of A. signifer was completely sequenced, which is 16,566 bp in length. The characteristics of the complete mitochondrial genome were described in detail.
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Pandey A, Lakra WS, Thapliyal RP, Goswami M, Singh M, Malakar AK. Morphological taxonomy and molecular divergence of four balitorid species (subfamily: Nemachelinae) from Central Himalaya, India. Mitochondrial DNA 2012; 23:239-249. [PMID: 22651235 DOI: 10.3109/19401736.2012.674117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The fishes in this study belong to the difficult group. It is difficult to identify about more than 50 nemacheilid loach species in India, mainly due to the poor quality of the original descriptions, the lack of good reviews, and the similarity of a number of the banded species. In view of this, a morphometric and genetic study was conducted on four species that have been documented in Central Himalayan region of India. Using comparative methods, a contribution to the knowledge about the variability of four Himalayan hillstream loaches, a molted loach Acanthocobitis botia (Hamilton, 1822), Nemacheilus corica (Hamilton, 1822), a creek loach Schistura beavani (Gunther, 1868), and Schistura montana (McClelland, 1838), was accomplished. Morphometric data were analyzed by univariate (CV and analysis of variance) and multivariate analyses (discriminant function analysis and cluster analysis). Based on the results of these statistical analyses, generally all four species grouped into their own species cluster with minimal overlap between two species of genus Schistura. Mitochondrial DNA cytochrome b (Cyt b) gene analysis revealed 7.7-17.6% genetic distances among the four species. Molecular phylogenetic relationship among these species and other Balitoridae species was investigated using published mitochondrial Cyt b sequences. Dendrograms obtained by the maximum likelihood and maximum parsimony method analyses exhibited the same topology. According to this topology, all the four species represented distinct species group and A. botia form the most distinct species while S. beavani and S. montana are clustered together with Nemacheilus species to form a single group. This work may build the base for the revision of taxonomic identity of fishes of the family Balitoridae. The results may further help to enhance the knowledge of the ichthyologists in understanding the fish fauna of India and assist them in planning conservation and management strategies for the propagation of these less studied small indigenous species along their natural range of distribution.
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Affiliation(s)
- Ajay Pandey
- Department of Zoology and Biotechnology, HNB Garhwal Central University , Srinagar, Garhwal, Uttarakhand, India.
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Abstract
A new species, Triplophysa huapingensis, is described from the Hongshuihe River, Guangxi, China. The new species is distinguished from other species of Triplophysa by the following combination of characters: body covered with scales, lateral line complete, eyes not degenerate, dorsal fin truncate, caudal fin forked, tip of pelvic fin not reaching anus, eight branched rays of dorsal fin, six branched rays of pelvic fin, 16 branched rays of caudal fin, grey and black diffused blotches on dorsal and lateral head and body. A key to all recorded species of Triplophysa in the Xijiang River system is provided.
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Affiliation(s)
- L P Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming 650223, China
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27
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Yang Q, Zhou W, Yang LP, Lan JH. [Morphologic differentiation analysis for rounded caudal fin group of Oreonectes (Balitoridae) from China]. Dongwuxue Yanjiu 2011; 32:343-347. [PMID: 21698803 DOI: 10.3724/sp.j.1141.2011.03343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Morphological characteristics were compared between three recorded species of rounded caudal fin Oreonectes and specimens collected from Guan'an of Guangxi. The results showed the Oreonectes sp. from Guan'an was distinguished from O. anphthalmus. Although some morphologic differentiations existed among Oreonectes sp., O. polystigmus, and O. platycephalus, their differentiations were not enough to distinguish between them. Consequently, we used multivariate morphometrics to determine their morphologic differentiation. Twenty-six frame characteristics and 20 general characteristics of 63 specimens were measured. The results of the Principal Component Analysis showed that Oreonectes sp. and O. polystigmus, and Oreonectes sp. and O. platycephalus occupied obviously different areas in the scatter plot. It is suggested that the specimens collected from Guan'an may be a cryptic new species of Oreonectes. However, its taxonomic status should be decided by evidence from anatomical and molecular biological studies.
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Affiliation(s)
- Qin Yang
- Faculty of Conservation Biology in Southwest Forestry University, Key Laboratory of Forest Disaster Warning and Control in Yunnan Province, Kunming 650224, China
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28
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Harant R, Bohlen J. Enobarbus is a synonym of Lepidocephalichthys (Osteichthyes, Cobitidae). J Fish Biol 2010; 77:2443-2453. [PMID: 21155793 DOI: 10.1111/j.1095-8649.2010.02836.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
External and internal morphological characters of the holotype of Enobarbus maculatus were examined and compared with those of other cobitid species to verify whether Enobarbus is a distinct genus. Analyses of radiographs demonstrated that the neural spines and the pterygiophores of the dorsal fin are of irregular shape, often doubled, reduced or bent. The holotype of E. maculatus bears an ossified structure on the last pectoral-fin ray, a structure otherwise known only from males of the genus Lepidocephalichthys. In Lepidocephalichthys, the shape of the ossified structure is species-specific, and the structure of Enobarbus is very similar to that of Lepidocephalichthys thermalis, the only other known species of the family Cobitidae occurring at the type locality of Enobarbus. Furthermore, the cranial and the axial skeleton of E. maculatus is similar to that of L. thermalis, except for the pterygiophores and the neural spines, that are strongly malformed in Enobarbus. In general, the results presented here show that the genus Enobarbus shares the most important characters (thickening of last two pectoral-fin rays in males, structure of swimbladder capsule, shape of neurocranium and suborbital spine) with Lepidocephalichthys and that its long dorsal fin is correlated with strong malformations of the vertebral column and the fin ray insertions. Consequently, the only known specimen of Enobarbus is most likely a teratological male of L. thermalis, and Enobarbus is a junior synonym of Lepidocephalichthys.
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Affiliation(s)
- R Harant
- Department of Zoology, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
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29
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Abstract
A new species of hillstream loach Balitora eddsi is described from the Karnali River drainage in south-western Nepal. The new species is distinguished from all its congeners by possessing the following combination of characters: six to seven unbranched pectoral-fin rays, pelvic-fin length 12-14% standard length (L(S)), dorsal surface without circular or irregular shaped dark blotches, snout pointed, median lobe between anterior rostral barbels pointed posteriorly, dorsal-fin origin posterior to pelvic-fin origin, lateral line scales 66-67, caudal peduncle length 22-23.2% L(S), caudal peduncle depth 4.1-4.2 times its length.
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Affiliation(s)
- K W Conway
- Department of Biology, Saint Louis University, 3507 Laclede Avenue, St Louis, MO 63109, USA.
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Sedivá A, Apostolou A, Kohout J, Bohlen J. Molecular phylogeographic analyses of the loach Oxynoemacheilus bureschi reveal post-glacial range extensions across the Balkans. J Fish Biol 2010; 76:357-368. [PMID: 20738712 DOI: 10.1111/j.1095-8649.2009.02492.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Rivers on the Balkan Peninsula can be separated into ichthyofaunistic areas with different endemic fish species. The Vardar River contains a particularly large number of endemics, indicating its complete and long-term isolation from neighbouring river systems. One of the few species shared with other rivers is the loach species Oxynoemacheilus bureschi. In this study, the genetic analyses of 175 individuals of O. bureschi from 17 sites, covering the entire distribution of the species, including the Rivers Vardar (= Axios), Struma (= Strymon), Mesta (= Nestos) and Danube, were performed using one mitochondrial and one nuclear marker. Genetic differentiation among populations was in general low. Shared haplotypes were common and occurred even between distant localities and different river systems. This points to a high degree of gene flow among populations and rejects the hypothesis that the population in the Vardar River represents a relict from an early colonization of the Balkan Peninsula. In contrast, the results suggest that populations in the Vardar River, as well as those in the Danube River, are of recent origin, and a human-mediated introduction cannot be excluded. On the other hand, the populations in the Aggitis River, a left tributary of the lower Struma River, were clearly separated from the rest of the species and represent a long-term isolated lineage. Demographic analyses suggest a recent population expansion for O. bureschi, in which the population in the Aggitis River was not involved.
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Affiliation(s)
- A Sedivá
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Rumburská 89, 277 21 Libechov, Czech Republic.
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31
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Chen WJ, Lheknim V, Mayden RL. Molecular phylogeny of the Cobitoidea (Teleostei: Cypriniformes) revisited: position of enigmatic loach Ellopostoma resolved with six nuclear genes. J Fish Biol 2009; 75:2197-2208. [PMID: 20738682 DOI: 10.1111/j.1095-8649.2009.02398.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Molecular variation in six nuclear genes provides substantive phylogenetic evidence for the recognition of a new cypriniform family, the Ellopostomatidae, to include the enigmatic Southern Asia loach genus Ellopostoma. The current six loach families form a monophyletic group, with the Nemacheilidae as the sister group to Ellopostomatidae; Vaillantellidae forms the sister group to all families exclusive of Botiidae. While the superfamily Cobitoidea includes eight families, the monophyly of this large clade within the Cypriniformes remains a vexing problem despite extensive molecular analyses and is in need of further investigation.
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Affiliation(s)
- W-J Chen
- Department of Biology, Saint Louis University, 3507 Laclede Ave, St. Louis, MO 63103, USA.
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32
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Conway KW, Mayden RL. Gill-filament ossifications: a possible morphological synapomorphy uniting the families Balitoridae and Cobitidae (Ostariophysi: Cypriniformes). J Fish Biol 2009; 75:2839-2844. [PMID: 20738528 DOI: 10.1111/j.1095-8649.2009.02469.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Ossifications associated with the gill filaments of members of the Balitoridae and Cobitidae are described for the first time. Although gill-filament ossifications are common in teleosts, similar ossifications were not observed in other members of the order Cypriniformes. Their presence is interpreted as a shared and derived character uniting the families Balitoridae and Cobitidae as a monophyletic group.
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Affiliation(s)
- K W Conway
- Department of Biology, Saint Louis University, 3507 Laclede Avenue, St Louis, MO 63103-2010, USA.
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Shed'ko SV, Miroshnichenko IL, Nemkova GA. [On the systematics and phylogeography of eight-barbel loaches the genus Lefua (Cobitoidea: Nemacheilidae): mtDNA typing of L. pleskei]. Genetika 2008; 44:938-947. [PMID: 18767542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Comparative analysis of personal sequence data for the mtDNA control region (926 to 928 bp) from eight-barbel loaches inhabiting eight localities in the Amur River basin (4) and the Sea of Japan (4) and the GeneBank/NCBI data for the Lefua individuals from the other regions of the world showed that eight-barbel loaches from Primorskii krai water basins were marked by a specific group of mtDNA haplotypes. This finding is considered as supporting the species status of L. pleskei. Genetic distances within L. pleskei are small (on average 0.355) and close to those within L. nikkonis (on average 0.48%). The distances between this species pair are the least (on average 2.15%) among all other pairs compared. In MP, ML, and Bayesian trees, L. pleskei and L. nikkonis haplotypes formed a common clade with high statistically significant support. In all tree variants, L. costata mtDNA haplotypes were located out of the group of interest. A clade consisting of highly diverged lineages of Lefua sp. and L. echigonia haplotypes occupied even more independent position. The mtDNA haplotypes of L. pleskei and L. costata from the Amur River basin were evolutionary young and derived from the haplotypes found in these species from the Sea of Japan (L. pleskei) or the Yellow Sea (L. costata) basins. It is thereby suggested that both species rather recently migrated into the Amur River system. According to the molecular clock data, basal diversification of the eight-barbel loach lineages took place at the end of middle Miocene (about 11 to 12 Myr ago), while divergence of L. pleskei and L. costata ancestral forms probably occurred approximately, 5 Myr ago. Since all main lineages of eight-barbel loaches were found in the Sea of Japan basin (continental coastline and the islands), the divergence order and dispersal patterns of the Lafua species might have been largely determined by the geological development pattern of this water body and the adjacent territories.
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Perdices A, Bohlen J, Doadrio I. The molecular diversity of adriatic spined loaches (Teleostei, Cobitidae). Mol Phylogenet Evol 2008; 46:382-90. [PMID: 17625922 DOI: 10.1016/j.ympev.2007.05.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2007] [Accepted: 05/08/2007] [Indexed: 10/23/2022]
Affiliation(s)
- Anabel Perdices
- National Museum of Natural History, Department of Biodiversity and Evolutionary Biology, C/José Gutiérrez Abascal 2, 28006 Madrid, Spain.
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35
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Abstract
Studies of the zebrafish (Danio rerio) promise to contribute much to an understanding of the developmental genetic mechanisms underlying diversification of the vertebrate dentition. Tooth development, structure, and replacement in the zebrafish largely reflect the primitive condition of jawed vertebrates, providing a basis for comparison with features of the more extensively studied mammalian dentition. A distinctive derived feature of the zebrafish dentition is restriction of teeth to a single pair of pharyngeal bones. Such reduction of the dentition, characteristic of the order Cypriniformes, has never been reversed, despite subsequent and extensive diversification of the group in numbers of species and variety of feeding modes. Studies of the developmental genetic mechanism of dentition reduction in the zebrafish suggest a potential explanation for irreversibility in that tooth loss seems to be associated with loss of developmental activators rather than gain of repressors. The zebrafish and other members of the family Cyprinidae exhibit species-specific numbers and arrangements of pharyngeal teeth, and extensive variation in tooth shape also occurs within the family. Mutant screens and experimental alteration of gene expression in the zebrafish are likely to yield variant tooth number and shape phenotypes that can be compared with those occurring naturally within the Cyprinidae. Such studies may reveal the relative contribution to trends in dental evolution of biases in the generation of variation and sorting of this variation by selection or drift.
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Affiliation(s)
- David W Stock
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309-0334, USA.
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36
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Patricia Hernandez L, Bird NC, Staab KL. Using zebrafish to investigate cypriniform evolutionary novelties: functional development and evolutionary diversification of the kinethmoid. J Exp Zool B Mol Dev Evol 2007; 308:625-41. [PMID: 17358013 DOI: 10.1002/jez.b.21166] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Although the zebrafish has become a popular model organism for biomedical studies, we propose that the wealth of morphological novelties that characterize this cypriniform fish makes it well suited for investigating the development of evolutionary innovations. Morphological novelties associated with feeding in cypriniform fishes include: a unique structure of the pharyngeal jaws in which the lower pharyngeal jaws are enlarged and opposed to a pad on the basioccipital process; a palatal organ found on the roof of the buccal chamber that is thought to help process detrital food within the buccal chamber; and, the kinethmoid, a novel ossification that effects a unique means of premaxillary protrusion. We present new morphological and developmental data and review functional data regarding the role of the kinethmoid in premaxillary protrusion in the zebrafish. Premaxillary protrusion plays an important role in effective prey acquisition in teleosts and the evolution of a unique means of premaxillary protrusion within Cypriniformes may have led to a number of trophic radiations within this clade. Ontogenetic data from zebrafish show that substantial premaxillary protrusion is not seen until these fish have undergone metamorphosis at which point the adductor mandibulae musculature becomes divided and all ligamentous attachments become established. A comparative study of families within Cypriniformes shows diverse morphologies of the kinethmoid. The morphological diversification that characterizes the kinethmoid suggests that this feeding structure has played a role in trophic radiations within Cypriniformes, since the morphology of this feature is correlated with feeding habits.
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Affiliation(s)
- L Patricia Hernandez
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA.
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37
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Mayden RL, Tang KL, Conway KW, Freyhof J, Chamberlain S, Haskins M, Schneider L, Sudkamp M, Wood RM, Agnew M, Bufalino A, Sulaiman Z, Miya M, Saitoh K, He S. Phylogenetic relationships of Danio within the order Cypriniformes: a framework for comparative and evolutionary studies of a model species. J Exp Zool B Mol Dev Evol 2007; 308:642-54. [PMID: 17554749 DOI: 10.1002/jez.b.21175] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The evolutionary relationships of species of Danio and the monophyly and phylogenetic placement of the genus within the family Cyprinidae and subfamily Rasborinae provide fundamentally important phyloinformatics necessary for direct evaluations of an array of pertinent questions in modern comparative biology. Although the genus Danio is not one of the most diverse within the family, Danio rerio is one of the most important model species in biology. Many investigations have used this species or presumed close relatives to address specific questions that have lasting impact on the hypothesis and theory of development in vertebrates. Largely lacking from this approach has been a holistic picture of the exact phylogenetic or evolutionary relationships of this species and its close relatives. One thing that has been learned over the previous century is that many organismal attributes (e.g., developmental pathways, ecologies, behaviors, speciation) are historically constrained and their origins and functions are best explained via a phylogenetic approach. Herein, we provide a molecular evaluation of the phylogenetic placement of the model species Danio rerio within the genus Danio and among hypothesized closely related species and genera. Our analysis is derived from data using two nuclear genes (RAG1, rhodopsin) and five mitochondrial genes (ND4, ND4L, ND5, COI, cyt b) evaluated using parsimony, maximum likelihood, and Bayesian analyses. The family Cyprinidae is resolved as monophyletic but the subfamily Rasborinae (priority over Danioinae) is an unnatural assemblage. Danio is identified as a monophyletic group sister to a clade inclusive of the genera Chela, Microrasbora, Devario, and Inlecypris, not Devario nor Esomus as hypothesized in previous studies. Danio rerio is sister to D. kyathit among the species of Danio evaluated in this analysis. Microrasbora and Rasbora are non-monophyletic assemblages; however, Boraras is monophyletic.
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Affiliation(s)
- Richard L Mayden
- Department of Biology, 3507 Laclede Avenue, Saint Louis University, St. Louis, Missouri 63103, USA.
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38
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Miyazaki JI, Nakao K, Mihara M, Sakai T, Gunji Y, Tojo K, Muraoka K, Hosoya K. Incongruence between mtDNA phylogeny and morphologial and ecological characters in loaches of the genus Lefua (Balitoridae, Cypriniformes). Zoolog Sci 2007; 24:666-75. [PMID: 17824774 DOI: 10.2108/zsj.24.666] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2006] [Accepted: 02/19/2007] [Indexed: 11/17/2022]
Abstract
To elucidate the phylogenetic position of Lefua loaches from Aichi and Shizuoka Prefectures of Honshu Island, Japan, we determined their nucleotide sequences for the mitochondrial D-loop region and compared these to sequences from four other Lefua species: L. costata, L. nikkonis, L. echigonia, and L. sp. Loaches identified as L. sp. on the basis of morphology comprised a clade (the L. sp. Tokai population) that grouped together with L. echigonia; hence, the processes involved in evolution within the genus Lefua were unclear. We performed randomly amplified polymorphic DNA (RAPD) analyses to obtain genetic information on nuclear DNA. The RAPD patterns of the L. sp. Tokai population differed from those of the local L. echigonia and L. sp. populations. The L. sp. Tokai population was similar to L. echigonia with regard to mitochondrial DNA but differed from L. echigonia and L. sp. with respect to nuclear DNA; this indicated that the evolutionary background of the L. sp. Tokai population was unique. We suggest that introgression of mitochondria occurred from L. echigonia to the L. sp. Tokai population, and speculate on the process of evolution of the latter population of Lefua. As with six L. echigonia populations and two L. sp. populations, we regard the L. sp. Tokai population as an evolutionary significant unit (ESU) that qualifies for protection as an endangered loach.
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Affiliation(s)
- Jun-Ichi Miyazaki
- Faculty of Education and Human Sciences, University of Yamanashi, Kofu, Yamanashi, Japan.
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39
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Slechtová V, Bohlen J, Tan HH. Families of Cobitoidea (Teleostei; Cypriniformes) as revealed from nuclear genetic data and the position of the mysterious genera Barbucca, Psilorhynchus, Serpenticobitis and Vaillantella. Mol Phylogenet Evol 2007; 44:1358-65. [PMID: 17433724 DOI: 10.1016/j.ympev.2007.02.019] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Revised: 02/13/2007] [Accepted: 02/21/2007] [Indexed: 10/23/2022]
Affiliation(s)
- Vendula Slechtová
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, Rumburská 89, 27 721 Libechov, Czech Republic.
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40
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Janko K, Bohlen J, Lamatsch D, Flajshans M, Epplen JT, Ráb P, Kotlík P, Slechtová V. The gynogenetic reproduction of diploid and triploid hybrid spined loaches (Cobitis: Teleostei), and their ability to establish successful clonal lineages—on the evolution of polyploidy in asexual vertebrates. Genetica 2007; 131:185-94. [PMID: 17216551 DOI: 10.1007/s10709-006-9130-5] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2006] [Accepted: 12/06/2006] [Indexed: 11/30/2022]
Abstract
Polyploidisation is assumed to have played a significant role in the evolution of hybrid asexual lineages. The virtual absence of natural asexual systems in which more than a single ploidy level successfully establishes successful independent clonal lineages is generally explained by the strong effects of polyploidisation on fitness. Experimental crosses were made between diploid and triploid asexual Cobitis elongatoides x C. taenia hybrids (female) and both parental spined loach species (male). Genotyping of the progeny using allozymes and multilocus DNA fingerprinting, along with flow cytometric measurement of ploidy level, demonstrated the occurrence of gynogenetic reproduction in both female biotypes. The incorporation of the sperm genome occurred in some progeny, giving rise to a higher ploidy level, but the rate of polyploidisation differed significantly between the diploid and triploid females. These outcomes are consistent with the existence of developmental constraints on tetraploidy, which determine the rarity of tetraploids in natural populations. No cases of ploidy level reduction were observed. Since diploid and triploid hybrid populations occur where the lack of potential progenitor excludes the possibility of de novo origin, it is probable that both diploid and triploid females can establish successful clonal lineages. Spined loaches represent a unique example, among asexual vertebrates, where more than one ploidy level can establish persistent clonal lineages, which are reproductively independent of one another.
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Affiliation(s)
- Karel Janko
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Rumburská 89, 27721, Libechov, Czech Republic.
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41
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Abstract
Cypriniformes (which includes the minnows, carps, loaches, algae-eaters, stone loaches, and suckers) is a morphologically diverse and incredibly speciose order of teleosts. It has been suggested that a number of evolutionary innovations, key to improved hearing and feeding, have played an important role in cypriniform fishes' success. One such innovation, the Weberian apparatus, is a novel assemblage of vertebral elements and modified ribs that relay and amplify sound pressure changes from the gas bladder to the inner ear. The Weberian apparatus unites Cypriniformes with other major orders into an extremely species-rich group of fishes, the Otophysi. Together, otophysan fishes comprise one of the largest groups of fishes in the world, as well as the majority of freshwater fishes. Here we present a detailed comparison of the Weberian apparatus in a number of cypriniform families using cleared and stained specimens. We present data regarding inter- and intrafamilial morphological variation within Cypriniformes. With few, but evolutionarily important, exceptions we find that diagnostic features of the Weberian apparatus characterize each family. Interspecific variation within each of the families Balitoridae, Gyrinocheilidae, and Catostomidae is only slight, whereas variation among subfamilies within Cyprinidae and Cobitidae is far more significant. This comparative study identifies a number of distinct morphologies, some of which appear highly correlated with ecological niche. For example, inhabiting swift-moving waters appears to be a key factor in the encapsulation of the anterior gas bladder in some cobitids, balitorids, and gobionin cyprinids.
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Affiliation(s)
- Nathan C Bird
- Department of Biological Sciences, The George Washington University, Washington, District of Columbia 20052, USA.
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42
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Wang X, Li J, He S. Molecular evidence for the monophyly of East Asian groups of Cyprinidae (Teleostei: Cypriniformes) derived from the nuclear recombination activating gene 2 sequences. Mol Phylogenet Evol 2007; 42:157-70. [PMID: 16919973 DOI: 10.1016/j.ympev.2006.06.014] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2006] [Revised: 06/14/2006] [Accepted: 06/16/2006] [Indexed: 11/16/2022]
Abstract
The family Cyprinidae is one of the largest families of fishes in the world and a well-known component of the East Asian freshwater fish fauna. However, the phylogenetic relationships among cyprinids are still poorly understood despite much effort paid on the cyprinid molecular phylogenetics. Original nucleotide sequence data of the nuclear recombination activating gene 2 were collected from 109 cyprinid species and four non-cyprinid cypriniform outgroup taxa and used to infer the cyprinid phylogenetic relationships and to estimate node divergence times. Phylogenetic reconstructions using maximum parsimony, maximum likelihood, and Bayesian analysis retrieved the same clades, only branching order within these clades varied slightly between trees. Although the morphological diversity is remarkable, the endemic cyprinid taxa in East Asia emerged as a monophyletic clade referred to as Xenocypridini. The monophyly for the subfamilies including Cyprininae and Leuciscinae, as well as the tribes including Labeonini, Gobionini, Acheilognathini, and Leuciscini, was also well resolved with high nodal support. Analysis of the RAG2 gene supported the following cyprinid molecular phylogeny: the Danioninae is the most basal subfamily within the family Cyprinidae and the Cyprininae is the sister group of the Leuciscinae. The divergence times were estimated for the nodes corresponding to the principal clades within the Cyprinidae. The family Cyprinidae appears to have originated in the mid-Eocene in Asia, with the cladogenic event of the key basal group Danioninae occurring in the early Oligocene (about 31-30 MYA), and the origins of the two subfamilies, Cyprininae and Leuciscinae, occurring in the mid-Oligocene (around 26 MYA).
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Affiliation(s)
- Xuzhen Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, 7 Donghu Nanlu, Wuhan, Hubei 430072, PR China
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Slechtová V, Bohlen J, Freyhof J, Ráb P. Molecular phylogeny of the Southeast Asian freshwater fish family Botiidae (Teleostei: Cobitoidea) and the origin of polyploidy in their evolution. Mol Phylogenet Evol 2006; 39:529-41. [PMID: 16337410 DOI: 10.1016/j.ympev.2005.09.018] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2005] [Accepted: 09/12/2005] [Indexed: 10/25/2022]
Abstract
The freshwater fish family Botiidae is represented by seven genera on the Indian subcontinent and in East and Southeast Asia and includes diploid as well as evolutionary tetraploid species. We present a phylogeny of Botiidae including 33 species representing all described genera using the mitochondrial cytochrome b and 12s rRNA genes to reconstruct the phylogenetic relationships among the genera and to estimate the number of polyploidisation events during their evolution. Our results show two major lineages, the subfamilies Leptobotiinae with the genera Leptobotia and Parabotia and Botiinae with the genera Botia, Chromobotia, Sinibotia, Syncrossus, and Yasuhikotakia. Our results suggest that two species that were traditionally placed into the genus Yasuhikotakia form a monophyletic lineage with the species of Sinibotia. A review of the data on the ploidy level of the included species shows all diploid species to belong to Leptobotiinae and all tetraploid species to Botiinae. A single polyploidisation event can therefore be hypothesised to have occurred in the ancestral lineage leading to the Botiinae.
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Affiliation(s)
- Vendula Slechtová
- Institute of Animal Physiology and Genetics of the Academy of Sciences of the Czech Republic, Rumburská 89, 277 21 Libechov, Czech Republic.
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Bohlen J, Perdices A, Doadrio I, Economidis PS. Vicariance, colonisation, and fast local speciation in Asia Minor and the Balkans as revealed from the phylogeny of spined loaches (Osteichthyes; Cobitidae). Mol Phylogenet Evol 2006; 39:552-61. [PMID: 16439160 DOI: 10.1016/j.ympev.2005.12.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2005] [Revised: 12/12/2005] [Accepted: 12/13/2005] [Indexed: 11/16/2022]
Abstract
We reconstruct the phylogeny of the morphologically diagnosable subgenera Bicanestrinia, Beysehiria, and Cobitis sensu stricto of the genus Cobitis from Asia Minor and the Balkans. We used the complete cytochrome b gene of 65 specimens in order to infer their evolutionary history in this zoogeographically interesting area. Our phylogeographic analysis did not evidence the previously suggested monophyly of the Bicanestrinia subgenus but revealed five monophyletic lineages in the area: the lineages Bicanestrinia I-IV including all species of Bicanestrinia plus the lineage Cobitis s. str. The monotypic subgenus Beysehiria from Lake Beysehir in Anatolia was closely related to the syntopic population of C. turcica and nested inside the lineage Bicanestrinia III. The strictly allopatric distribution of the four lineages of Bicanestrinia suggests that vicariance has played a major role in the diversification of Bicanestrinia. All analysed species of Cobitis s. str. from Asia Minor and Balkans were closely related to Cobitis s. str. from Central Europe, the Danube basin and the Caucasus, indicating at least two colonisation events into Asia Minor and the Balkans. A third, recent colonisation event led to the presence of C. strumicae, generally restricted to the Aegean Sea drainage, in the Danube basin. Besides the evidences of vicariance and colonisation events in the phylogenetic history of the genus Cobitis in Asia Minor and the Balkans, our analysis suggested also a rapid morphological evolution of C. bilseli in a lacustrine environment. Application of Cobitis mitochondrial cytochrome b clocks of 0.68% sequence divergence per million years (MY) suggest that the split between the five major lineages happened approximately 12.4-17.6 MYA, and according to the lack of basal resolution of this monophyletic group probably the split of all lineages happened within a narrow time window.
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Affiliation(s)
- Jörg Bohlen
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, Rumburská 89, 27 721 Libechov, Czech Republic.
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Tang Q, Liu H, Mayden R, Xiong B. Comparison of evolutionary rates in the mitochondrial DNA cytochrome b gene and control region and their implications for phylogeny of the Cobitoidea (Teleostei: Cypriniformes). Mol Phylogenet Evol 2006; 39:347-57. [PMID: 16213167 DOI: 10.1016/j.ympev.2005.08.007] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2005] [Revised: 08/15/2005] [Accepted: 08/18/2005] [Indexed: 10/25/2022]
Abstract
It is widely accepted that mitochondrial DNA (mtDNA) control region evolves faster than protein encoding genes with few exceptions. In the present study, we sequenced the mitochondrial cytochrome b gene (cyt b) and control region (CR) and compared their rates in 93 specimens representing 67 species of loaches and some related taxa in the Cobitoidea (Order Cypriniformes). The results showed that sequence divergences of the CR were broadly higher than those of the cyt b (about 1.83 times). However, in considering only closely related species, CR sequence evolution was slower than that of cyt b gene (ratio of CR/cyt b is 0.78), a pattern that is found to be very common in Cypriniformes. Combined data of the cyt b and CR were used to estimate the phylogenetic relationship of the Cobitoidea by maximum parsimony, neighbor-joining, and Bayesian methods. With Cyprinus carpio and Danio rerio as outgroups, three analyses identified the same four lineages representing four subfamilies of loaches, with Botiinae on the basal-most clade. The phylogenetic relationship of the Cobitoidea was ((Catostomidae+Gyrinocheilidae)+(Botiinae+(Balitorinae+(Cobitinae+Nemacheilinae)))), which indicated that Sawada's Cobitidae (including Cobitinae and Botiinae) was not monophyletic. Our molecular phylogenetic analyses are in very close agreement with the phylogenetic results based on the morphological data proposed by Nalbant and Bianco, wherein these four subfamilies were elevated to the family level as Botiidae, Balitoridae, Cobitidae, and Nemacheilidae.
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Affiliation(s)
- Qiongying Tang
- Institute of Hydrobiology, Chinese Academy of Sciences, Hubei, Wuhan 430072, PR China
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46
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Doadrio I, Perdices A. Phylogenetic relationships among the Ibero-African cobitids (Cobitis, cobitidae) based on cytochrome b sequence data. Mol Phylogenet Evol 2005; 37:484-93. [PMID: 16150615 DOI: 10.1016/j.ympev.2005.07.009] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2004] [Revised: 07/01/2005] [Accepted: 07/06/2005] [Indexed: 10/25/2022]
Abstract
We estimated the phylogenetic relationships of all Ibero-African spined loaches of the genus Cobitis using the complete mitochondrial cytochrome b gene (1140bp). We analysed 93 individuals of seven cobitid species found in all the principal drainages of the Iberian Peninsula and North Africa. A molecular phylogeny was used to revise current systematics of the Ibero-African Cobitis species and to infer a biogeographical model for Cobitis in the Western Mediterranean area during the Cenozoic period. Phylogenetic analysis provided support for the monophyly of two mtDNA clades: Clade A or Italian Clade with the Italian species (C. bilineata, C. zanandreai), and Clade B or the Ibero-African Clade. The Ibero-African Clade included all species endemic for the Iberian Peninsula (C. vettonica, C. calderoni, and C. paludica) and North Africa (C. maroccana). The species C. paludica does not constitute a natural group, and could be divided into at least four monophyletic mtDNA lineages with moderate to high bootstrap values and posterior probability support. Phylogenetic relationships of the Ibero-African species were not resolved satisfactorily, but in all analyses C. calderoni from Northern Iberian Peninsula was basal. We have re-calibrated a molecular clock for the genus Cobitis (0.68% per million year by pairwise) using populations inhabiting both sides of the Gibraltar Strait. Application of this Cobitis mtDNA clock provides evidence that the Messinian salinity crisis played a primary role in the diversification of some Ibero-African cobitid species. The basal polytomies of the Ibero-African Clade might suggest that all mtDNA lineages diversified rapidly.
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Affiliation(s)
- Ignacio Doadrio
- Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006 Madrid, Spain
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Dowling TE, Marsh PC, Kelsen AT, Tibbets CA. Genetic monitoring of wild and repatriated populations of endangered razorback sucker (Xyrauchen texanus, Catostomidae, Teleostei) in Lake Mohave, Arizona-Nevada. Mol Ecol 2005; 14:123-35. [PMID: 15643956 DOI: 10.1111/j.1365-294x.2004.02408.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Native Fishes Work Group, formed in 1991, developed and implemented a protocol to enhance the dwindling razorback sucker population in Lake Mohave, Arizona-Nevada. This large, genetically diverse population is severely reduced in size as a result of recruitment failure associated with predation on larvae. To circumvent this problem, wild larvae are captured, reared in protective custody until they are large enough to escape predation, and then released back into the lake. We present results of a monitoring program designed to assess the effectiveness of the sampling design in transmitting the high genetic diversity found in wild adults. Variation in a fragment from the mitochondrial DNA gene cytochrome b was examined by analysis of single-stranded polymorphisms and direct sequencing. Samples were characterized from three life history stages. Characterization of wild adults verified previous results that identified considerable diversity and provided baseline data. Samples of larvae from several temporal collections from throughout the spawning season and four geographical areas were characterized for 7 years (1997-2003) to assess the transmission of genetic variation from wild adults to larvae. Several analyses identified significant differences among temporal collections, resulting from sampling errors associated with finite number of females spawning at a given time and place. Comparisons among areas and years failed to identify significant variation, indicating that pooled collections for each year possess the same levels and patterns of genetic variation. Examination of repatriates representing 11 years (1992-2002) also failed to identify significant differences among cohorts; however, some sample sizes were small and the amova may lack sufficient power to detect differences. Contrasts of wild adults, larvae, and repatriates identified statistically significant differences among collections within these three groups; however, levels of variation are small and not biologically meaningful. More importantly, this analysis failed to detect significant differences among adults, larvae, and repatriates indicating that the program has been achieving its goal of transmitting variation from adults through the larvae and into the repatriate population. The reproductive capability of repatriates has not been examined, so it is unknown if the program will maintain genetic variation found in the original adult population. This will be most easily achieved by periodic monitoring of genetic variation in larval samples. If levels of variation become reduced in repatriates, levels and patterns of diversity in larvae are also expected to become reduced, and deviations in estimates of genetic diversity may become larger and more frequent. If this is the case, intervention may be necessary to ensure that certain individuals are not over-represented in the repatriate population.
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Affiliation(s)
- T E Dowling
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe AZ 85287-4501, USA.
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Irie-Kushiyama S, Asano-Miyoshi M, Suda T, Abe K, Emori Y. Identification of 24 genes and two pseudogenes coding for olfactory receptors in Japanese loach, classified into four subfamilies: a putative evolutionary process for fish olfactory receptor genes by comprehensive phylogenetic analysis. Gene 2004; 325:123-35. [PMID: 14697517 DOI: 10.1016/j.gene.2003.10.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Twenty-four olfactory receptor (OR) genes and two pseudogenes have been identified in the genome of Japanese loach (Misgurnus anguillicaudatus). The genes were classified into four subfamilies according to the similarity of the amino acid sequences. In each subfamily, members showed high sequence similarity not only to each other but also to orthologues of other fish species. The number of members in each OR subfamily was roughly estimated to be from 3 to 10 by genomic Southern blot analysis. The genes of all four OR subfamilies were shown to express on olfactory neurons of the olfactory epithelium by in situ hybridization analysis. Two major features of fish OR genes were found by comprehensive and comparative analyses on OR genes of Japanese loach and other fish species including catfish, zebrafish and pufferfish. First, the phylogenetic tree comprising of representative subfamily members suggests the existence of several prototype genes common to the genomes of many fish species. Second, when all members of orthologous subfamilies identified in each clade of the tree are integrated, the members of a single species comprise a monophyletic group. This means that 'intraspecies' sequence homology, that is, homology among paralogous genes of the same subfamily in a species, is higher than 'interspecies' homology, that is, homology between orthologous genes of different species. This suggests that the subfamily members of a species have evolved recently. Taken together, fish OR genes have evolved from a limited number of prototype genes common to most fish species, and several genes in a subfamily have diversely evolved in each species from each prototype.
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Affiliation(s)
- Sakura Irie-Kushiyama
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan
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Liu HZ. Phylogenetic relationships of the cypriniformes tested by mtDNA 12S rRNA sequence variations. Yi Chuan Xue Bao 2004; 31:137-42. [PMID: 15473303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Cypriniformes is the largest order of freshwater fishes. The phylogenetic relationships of the Cypriniformes have been studied by many investigators based on morphological characters, but no agreement has been reached. In the present paper, complete mitochondrial 12S rRNA sequences of five families of the Cypriniformes were determined and analyzed to test the present morphological hypotheses. After alignment, there are 1000 sites, among which 467 sites are in stems and 533 sites in loops. 395 sites are variable, and of which 267 are informative. Neighbor-joining and Maximum Parsimony methods were employed for phylogenetic analysis. The results indicate that the cyprinids form a monophyletic group while the non-cyprinid cypriniforms form another one, which is in accordance with the hypothesis proposed by Siebert. The Cyprinidae consists of three main clades, the Danionini, the Cyprinini, and the Leuciscini. However, in the non-cyprinid cypriniforms, the relationships could not be resolved clearly. The Cobitidae is polyphyletic. Homalopteridae, Noemacheilinae and Cobitinae may have closer relationships.
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Affiliation(s)
- Huan-Zhang Liu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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Mezhzherin SV, Lisetskaia TI. [Genetic structure of species complex of the spined loach Cobitis auc. (Cypriniformes: Cobitidae) in Severskiĭ Donets river basin]. Tsitol Genet 2004; 38:36-43. [PMID: 15098446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Biochemical, genetic, cytometric and morphological analyses of spined loaches of the middle stream of Severskiy Donetz river revealed 3 bisexual species: Cobitis taenia s.l. (68% of the sample); C. melanoleuca (11%); Sabanejewia aurata (9%) and 2 hybrid forms: triploid C. taenia(2)-sp. (9%) and diploid C. taenia-melanoleuca (3%). Distinctive features of genetic structure of polyploid hybrids C. taenia(2)-sp. as well as taxonomic identity of diploid C. taenia s.l. of Severskiy Donetz river were discussed in regard to the Dnieper population ones.
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