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Xuzhen Wang - One of the best experts on this subject based on the ideXlab platform.
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Cyprinid phylogeny based on bayesian and maximum likelihood analyses of partitioned data implications for Cyprinidae systematics
Science China-life Sciences, 2012Co-Authors: Xuzhen Wang, Xiaoni Gan, Richard L. MaydenAbstract:Cyprinidae is the biggest family of freshwater fish, but the phylogenetic relationships among its higher-level taxa are not yet fully resolved. In this study, we used the nuclear recombination activating gene 2 and the mitochondrial 16S ribosomal RNA and cytochrome b genes to reconstruct Cyprinid phylogeny. Our aims were to (i) demonstrate the effects of partitioned phylogenetic analyses on phylogeny reconstruction of Cyprinid fishes; (ii) provide new insights into the phylogeny of Cyprinids. Our study indicated that unpartitioned strategy was optimal for our analyses; partitioned analyses did not provide better-resolved or -supported estimates of Cyprinid phylogeny. Bayesian analyses support the following relationships among the major monophyletic groups within Cyprinidae: (Cyprininae, Labeoninae), ((Acheilognathinae, ((Leuciscinae, Tincinae), Gobioninae)), Xenocyprininae). The placement of Danioninae was poorly resolved. Estimates of divergence dates within the family showed that radiation of the major Cyprinid groups occurred during the Late Oligocene through the Late Miocene. Our phylogenetic analyses improved our understanding of the evolutionary history of this important fish family.
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phylogenomic analysis resolves the formerly intractable adaptive diversification of the endemic clade of east asian Cyprinidae cypriniformes
PLOS ONE, 2010Co-Authors: Wenjing Tao, Xiaoni Gan, Xuzhen Wang, Mingming Zou, Richard L. MaydenAbstract:Despite their great diversity and biological importance, evolutionary relationships among the endemic clade of East Asian Cyprinidae remain ambiguous. Understanding the phylogenetic history of this group involves many challenges. For instance, ecomorphological convergence may confound morphology-based phylogenetic inferences, and previous molecular phylogenetic studies based on single genes have often yielded contradictory and poorly supported trees. We assembled a comprehensive data matrix of 100 nuclear gene segments (similar to 71132 base pairs) for representative species of the endemic East Asian Cyprinid fauna and recovered a robust phylogeny from this genome-wide signal supported by multiple analytical methods, including maximum parsimony, maximum likelihood and Bayesian inference. Relaxed molecular clock analyses indicated species radiations of this clade concentrated at approximately 1.9-7.6 MYA. We provide evidence that the bursts of diversification in this fauna are directly linked to major paleoenvironmental events associated with monsoon evolution occurring from late Miocene to Pliocene. Ancestral state reconstruction reveals convergent morphological characters are hypothesized to be independent products of similar selective pressures in ecosystems. Our study is the first comprehensive phylogenetic study of the enigmatic East-Asian Cyprinids. The explicit molecular phylogeny provides a valuable framework for future research in genome evolution, adaptation and speciation of Cyprinids.
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molecular evidence for the monophyly of east asian groups of Cyprinidae teleostei cypriniformes derived from the nuclear recombination activating gene 2 sequences
Molecular Phylogenetics and Evolution, 2007Co-Authors: Xuzhen Wang, Junbing Li, Shunping HeAbstract: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). (c) 2006 Elsevier Inc. All rights reserved.
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molecular evidence for the monophyly of east asian groups of Cyprinidae teleostei cypriniformes derived from the nuclear recombination activating gene 2 sequences
Molecular Phylogenetics and Evolution, 2007Co-Authors: Xuzhen WangAbstract: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).
Ian A. Johnston - One of the best experts on this subject based on the ideXlab platform.
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Duplication of a Single myhz1.1 Gene Facilitated the Ability of Goldfish (Carassius auratus) to Alter Fast Muscle Contractile Properties With Seasonal Temperature Change.
Frontiers in physiology, 2018Co-Authors: Daniel Garcia De La Serrana, Kristin M. Wreggelsworth, Ian A. JohnstonAbstract:Seasonal temperature changes markedly effect the swimming performance of some Cyprinid fish acutely tested at different temperatures, involving a restructuring of skeletal muscle phenotype including changes in contractile properties and myosin heavy chain expression. We analyzed the transcriptome of fast myotomal muscle from goldfish (Carassius auratus L.) acclimated to either 8 or 25°C for 4 weeks (12 h light: 12 h dark) and identified 10 myosin heavy chains (myh) and 13 myosin light chain (myl) transcripts. Goldfish orthologs were classified based on zebrafish nomenclature as myhz1.1α, myhz1.1β, myhz1.1γ, myha, myhb, embryo_myh1, myh9b, smyh2, symh3, and myh11 (myosin heavy chains) and myl1a, myl1b, myl2, myl9a, myl9b, myl3, myl13, myl6, myl12.1a, myl12.1b, myl12.2a, myl12.2b, and myl10 (myosin light chains). The most abundantly expressed transcripts myhz1.1α, myhz1.1β, myhz1.1γ, myha, myl1a, myl1b, myl2, and myl3) were further investigated in fast skeletal muscle of goldfish acclimated to either 4, 8, 15, or 30°C for 12 weeks (12 h light:12 h dark). Total copy number for the myosin heavy chains showed a distinct optimum at 15°C (P < 0.01). Together myhz1.1α and myhz1.1β comprised 90 to 97% of myhc transcripts below 15°C, but only 62% at 30°C. Whereas myhz1.1α and myhz1.1β were equally abundant at 4 and 8°C, myhz1.1β transcripts were 17 and 12 times higher than myhz1.1α at 15 and 30°C, respectively, (P < 0.01). Myhz1.1γ expression was at least nine-fold higher at 30°C than at cooler temperatures (P < 0.01). In contrast, the expression of myha and myosin light chains showed no consistent pattern with acclimation temperature. A phylogenetic analysis indicated that the previously reported ability of goldfish and common carp to alter contractile properties and myofibrillar ATPase activity with temperature acclimation was related to the duplication of a single myhz1.1 fast muscle myosin heavy chain found in basal Cyprinids such as the zebrafish (Danio rerio).
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Table_4_Duplication of a Single myhz1.1 Gene Facilitated the Ability of Goldfish (Carassius auratus) to Alter Fast Muscle Contractile Properties With Seasonal Temperature Change.DOCX
2018Co-Authors: Daniel Garcia De La Serrana, Kristin M. Wreggelsworth, Ian A. JohnstonAbstract:Seasonal temperature changes markedly effect the swimming performance of some Cyprinid fish acutely tested at different temperatures, involving a restructuring of skeletal muscle phenotype including changes in contractile properties and myosin heavy chain expression. We analyzed the transcriptome of fast myotomal muscle from goldfish (Carassius auratus L.) acclimated to either 8 or 25°C for 4 weeks (12 h light: 12 h dark) and identified 10 myosin heavy chains (myh) and 13 myosin light chain (myl) transcripts. Goldfish orthologs were classified based on zebrafish nomenclature as myhz1.1α, myhz1.1β, myhz1.1γ, myha, myhb, embryo_myh1, myh9b, smyh2, symh3, and myh11 (myosin heavy chains) and myl1a, myl1b, myl2, myl9a, myl9b, myl3, myl13, myl6, myl12.1a, myl12.1b, myl12.2a, myl12.2b, and myl10 (myosin light chains). The most abundantly expressed transcripts myhz1.1α, myhz1.1β, myhz1.1γ, myha, myl1a, myl1b, myl2, and myl3) were further investigated in fast skeletal muscle of goldfish acclimated to either 4, 8, 15, or 30°C for 12 weeks (12 h light:12 h dark). Total copy number for the myosin heavy chains showed a distinct optimum at 15°C (P < 0.01). Together myhz1.1α and myhz1.1β comprised 90 to 97% of myhc transcripts below 15°C, but only 62% at 30°C. Whereas myhz1.1α and myhz1.1β were equally abundant at 4 and 8°C, myhz1.1β transcripts were 17 and 12 times higher than myhz1.1α at 15 and 30°C, respectively, (P < 0.01). Myhz1.1γ expression was at least nine-fold higher at 30°C than at cooler temperatures (P < 0.01). In contrast, the expression of myha and myosin light chains showed no consistent pattern with acclimation temperature. A phylogenetic analysis indicated that the previously reported ability of goldfish and common carp to alter contractile properties and myofibrillar ATPase activity with temperature acclimation was related to the duplication of a single myhz1.1 fast muscle myosin heavy chain found in basal Cyprinids such as the zebrafish (Danio rerio).
Jeanfrancois Martin - One of the best experts on this subject based on the ideXlab platform.
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variability structure and selection of mhciib genes inchondrostoma toxostoma and chondrostoma nasus in hybrid zones
2012Co-Authors: Kristina Civaňova, Caroline Costedoat, Andrea Vetešníková Šimková, André Gilles, Jeanfrancois MartinAbstract:To characterise the overall genetic diversity, population structure and selection processes in Cyprinid fish, MHC genes of IIB class have been analyzed. As the model organism in this study, two congeneric Cyprinids, the introduced Chondrostoma nasus and native, protected and endemic C. toxostoma that live in sympatry and form a hybrid zone in the Durance River (South France, Mediterranean Sea drainage) were studied. For the individual determination (pure species versus hybrid) all fish were genotyped for mtDNA (cyt b) and 41 microsatellite loci. The allelic variability in exon 2 of two MHCIIB genes (DAB1-like and DAB3-like) representing the most variable region with the nonsynonymous sites specifying the peptide binding region was analysed. The results reveal the non uniform allele expression within individuals, duplication of both studied loci (previously showed in several Cyprinid species) and that the exon 2 of DAB genes is subjected to positive selection. The difference in the MHCIIB profiles was found between allopatric and sympatric populations. Based on the hypothesis of parasite-mediated selection maintaining MHC polymorphism it could suggest the difference in parasite load between chondrostomes living in allopatric area and those living in hybrid zone.
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Cross-species amplification of 41 microsatellites in European Cyprinids: A tool for evolutionary, population genetics and hybridization studies
BMC Research Notes, 2010Co-Authors: Vincent Dubut, Jeanfrancois Martin, André Gilles, Rémi Chappaz, Melthide Sinama, Emese Meglecz, Juliette Fernandez, Caroline CostedoatAbstract:Background: Cyprinids display the most abundant and widespread species among the European freshwater Teleostei and are known to hybridize quite commonly. Nevertheless, a limited number of markers for conducting comparative differentiation, evolutionary and hybridization dynamics studies are available to date. Findings: Five multiplex PCR sets were optimized in order to assay 41 Cyprinid-specific polymorphic microsatellite loci (including 10 novel loci isolated from Chondrostoma nasus nasus, Chondrostoma toxostoma toxostoma and Leuciscus leuciscus) for 503 individuals (440 purebred specimens and 63 hybrids) from 15 European Cyprinid species. The level of genetic diversity was assessed in Alburnus alburnus, Alburnoides bipunctatus, C. genei, C. n. nasus, C. soetta, C. t. toxostoma, L. idus, L. leuciscus, Pachychilon pictum, Rutilus rutilus, Squalius cephalus and Telestes souffia. The applicability of the markers was also tested on Abramis brama, Blicca bjoerkna and Scardinius erythrophtalmus specimens. Overall, between 24 and 37 of these markers revealed polymorphic for the investigated species and 23 markers amplified for all the 15 European Cyprinid species. Conclusions: The developed set of markers demonstrated its performance in discriminating European Cyprinid species. Furthermore, it allowed detecting and characterizing hybrid individuals. These microsatellites will therefore be useful to perform comparative evolutionary and population genetics studies dealing with European Cyprinids, what is of particular interest in conservation issues and constitutes a tool of choice to conduct hybridization studies.
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Isolation and characterization of polymorphic microsatellite loci for the dace complex: Leuciscus leuciscus (Teleostei: Cyprinidae)
Molecular Ecology Resources, 2009Co-Authors: Vincent Dubut, Jeanfrancois Martin, André Gilles, Rémi Chappaz, Jeroen Van Houdt, Caroline CostedoatAbstract:Ten novel polymorphic microsatellites were isolated from the dace complex (Leuciscus leuciscus), which is a European Cyprinid species. Four multiplex polymerase chain reaction sets were optimized in order to genotype 26 polymorphic loci in all, including 16 previously published Cyprinid-specific loci. The level of genetic diversity was assessed in 142 dace individuals. We also successfully applied 26 of the microsatellites to 10 related species. These primers thus will be useful to assess population structure of the dace and other Cyprinid species, with application for conservation issues and phylogeographical approaches.
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isolation and characterization of microsatellites in leuciscus cephalus cypriniformes Cyprinidae and cross species amplification within the family Cyprinidae
Molecular Ecology Notes, 2007Co-Authors: Martina Vyskocilova, Andrea Vetešníková Šimková, Jeanfrancois MartinAbstract:Thirteen polymorphic microsatellites were isolated from Leuciscus cephalus, a widespread Cyprinid species with great ecological tolerance. Together with the cross-species amplification of six additional loci originally published for three Cyprinid fish species, we optimized a multiplex panel for L. cephalus allowing the genotyping of 19 polymorphic loci. Number of alleles and heterozygosity per locus in a sample of 20 fish individuals ranged from two to 16 and from 0.05 to 0.90, respectively. These primers will be useful in determining the population structure of L. cephalus. In addition, successful cross-amplification was obtained for several species of Cyprinidae.
Martina Vyskocilova - One of the best experts on this subject based on the ideXlab platform.
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isolation and characterization of microsatellites in leuciscus cephalus cypriniformes Cyprinidae and cross species amplification within the family Cyprinidae
Molecular Ecology Notes, 2007Co-Authors: Martina Vyskocilova, Andrea Vetešníková Šimková, Jeanfrancois MartinAbstract:Thirteen polymorphic microsatellites were isolated from Leuciscus cephalus, a widespread Cyprinid species with great ecological tolerance. Together with the cross-species amplification of six additional loci originally published for three Cyprinid fish species, we optimized a multiplex panel for L. cephalus allowing the genotyping of 19 polymorphic loci. Number of alleles and heterozygosity per locus in a sample of 20 fish individuals ranged from two to 16 and from 0.05 to 0.90, respectively. These primers will be useful in determining the population structure of L. cephalus. In addition, successful cross-amplification was obtained for several species of Cyprinidae.
Yaping Zhang - One of the best experts on this subject based on the ideXlab platform.
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the complete mitochondrial genomes of two species from sinocyclocheilus cypriniformes Cyprinidae and a phylogenetic analysis within cyprininae
Molecular Biology Reports, 2010Co-Authors: Lin Wang, Shanyuan Chen, Ruiguang Zan, Heng Xiao, Yaping ZhangAbstract:We determined the complete mitochondrial DNA sequences for two species of surface- and cave-dwelling-Cyprinid fishes, Sinocyclocheilus grahami and S. altishoulderus. Sequence comparison of 13 protein-coding genes shows that the mutation pattern of each single gene is quite similar to those of other vertebrate animal species. Analysis of the ratios of Ka/Ks at these loci between Sinocyclocheilus and two other Cyprinid species (Cyprinus carpio and Procypris rabaudi) show that Ka/Ks ratios are differed, consistent with purifying selection and variation in functional constraint among genes. Bayesian analysis and maximum likelihood analysis of the concatenated mitochondrial protein sequences for 14 Cyprinid taxa support the monophyly of the family Cyprininae, and further confirm the monophyly of the genus Sinocyclocheilus. The two Sinocyclocheilus species fall within the Cyprinion-Onychostoma lineage, including Cyprinus, Carassius, and Procypris, rather than among the Barbinae, as previously suggested on morphological grounds.
