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Remarkable phylogenetic resolution of the most complex clade of Cyprinidae (Teleostei: Cypriniformes): A proof of concept of homology assessment and partitioning sequence data integrated with mixed model Bayesian analyses
Tao, Wenjing1,2; Mayden, Richard L.3; He, Shunping1; Mayden, RL (reprint author), St Louis Univ, Dept Biol, 3507 Laclede Ave, St Louis, MO 63103 USA.
2013-03-01
Source PublicationMOLECULAR PHYLOGENETICS AND EVOLUTION
ISSN1055-7903
Volume66Issue:3Pages:603-616
AbstractDespite many efforts to resolve evolutionary relationships among major clades of Cyprinidae, some nodes have been especially problematic and remain unresolved. In this study, we employ four nuclear gene fragments (3.3 kb) to infer interrelationships of the Cyprinidae. A reconstruction of the phylogenetic relationships within the family using maximum parsimony, maximum likelihood, and Bayesian analyses is presented. Among the taxa within the monophyletic Cyprinidae, Rasborinae is the basal-most lineage; Cyprinine is sister to Leuciscine. The monophyly for the subfamilies Gobioninae, Leuciscinae and Acheilognathinae were resolved with high nodal support. Although our results do not completely resolve relationships within Cyprinidae, this study presents novel and significant findings having major implications for a highly diverse and enigmatic clade of East-Asian cyprinids. Within this monophyletic group five closely-related subgroups are identified. Tinca tinca, one of the most phylogenetically enigmatic genera in the family, is strongly supported as having evolutionary affinities with this East-Asian clade; an established yet remarkable association because of the natural variation in phenotypes and generalized ecological niches occupied by these taxa. Our results clearly argue that the choice of partitioning strategies has significant impacts on the phylogenetic reconstructions, especially when multiple genes are being considered. The most highly partitioned model (partitioned by codon positions within genes) extracts the strongest phylogenetic signals and performs better than any other partitioning schemes supported by the strongest 2 Delta ln Bayes factor. Future studies should include higher levels of taxon sampling and partitioned, model-based analyses. (C) 2012 Elsevier Inc. All rights reserved.; Despite many efforts to resolve evolutionary relationships among major clades of Cyprinidae, some nodes have been especially problematic and remain unresolved. In this study, we employ four nuclear gene fragments (3.3 kb) to infer interrelationships of the Cyprinidae.
SubtypeArticle
KeywordCyprinidae Nuclear Genes Phylogeny Mixed Model Bayesian Analyses
Department[Tao, Wenjing; He, Shunping] Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan 430072, Peoples R China; [Tao, Wenjing] Chinese Acad Sci, Grad Univ, Beijing 100039, Peoples R China; [Mayden, Richard L.] St Louis Univ, Dept Biol, St Louis, MO 63103 USA
DOI10.1016/j.ympev.2012.09.024
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine
Funding OrganizationNational Basic Research Program of China (973 Program) [2010CB126302]; National Natural Science Foundation of China [31090254, U1036603]; Chinese Academy of Sciences [KSCX2-EW-Q-12]; USA NSF EF [0431326, DEB-1021840, DBI-0956370] ; National Basic Research Program of China (973 Program) [2010CB126302]; National Natural Science Foundation of China [31090254, U1036603]; Chinese Academy of Sciences [KSCX2-EW-Q-12]; USA NSF EF [0431326, DEB-1021840, DBI-0956370] ; National Basic Research Program of China (973 Program) [2010CB126302]; National Natural Science Foundation of China [31090254, U1036603]; Chinese Academy of Sciences [KSCX2-EW-Q-12]; USA NSF EF [0431326, DEB-1021840, DBI-0956370] ; National Basic Research Program of China (973 Program) [2010CB126302]; National Natural Science Foundation of China [31090254, U1036603]; Chinese Academy of Sciences [KSCX2-EW-Q-12]; USA NSF EF [0431326, DEB-1021840, DBI-0956370]
Indexed BySCI
Language英语
WOS Research AreaBiochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
WOS SubjectBiochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
WOS IDWOS:000315553400003
WOS KeywordSITE RATE VARIATION ; RAY-FINNED FISHES ; EUROPEAN CYPRINIDS ; POSTERIOR PROBABILITIES ; MOLECULAR SYSTEMATICS ; MULTIGENE PHYLOGENY ; LIKELIHOOD ANALYSIS ; CONTROL REGION ; NUCLEAR LOCI ; MITOCHONDRIAL
Funding OrganizationNational Basic Research Program of China (973 Program) [2010CB126302]; National Natural Science Foundation of China [31090254, U1036603]; Chinese Academy of Sciences [KSCX2-EW-Q-12]; USA NSF EF [0431326, DEB-1021840, DBI-0956370] ; National Basic Research Program of China (973 Program) [2010CB126302]; National Natural Science Foundation of China [31090254, U1036603]; Chinese Academy of Sciences [KSCX2-EW-Q-12]; USA NSF EF [0431326, DEB-1021840, DBI-0956370] ; National Basic Research Program of China (973 Program) [2010CB126302]; National Natural Science Foundation of China [31090254, U1036603]; Chinese Academy of Sciences [KSCX2-EW-Q-12]; USA NSF EF [0431326, DEB-1021840, DBI-0956370] ; National Basic Research Program of China (973 Program) [2010CB126302]; National Natural Science Foundation of China [31090254, U1036603]; Chinese Academy of Sciences [KSCX2-EW-Q-12]; USA NSF EF [0431326, DEB-1021840, DBI-0956370]
Citation statistics
Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/19264
Collection水生生物多样性与资源保护研究中心_期刊论文
Corresponding AuthorMayden, RL (reprint author), St Louis Univ, Dept Biol, 3507 Laclede Ave, St Louis, MO 63103 USA.
Affiliation1.Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan 430072, Peoples R China
2.Chinese Acad Sci, Grad Univ, Beijing 100039, Peoples R China
3.St Louis Univ, Dept Biol, St Louis, MO 63103 USA
Recommended Citation
GB/T 7714
Tao, Wenjing,Mayden, Richard L.,He, Shunping,et al. Remarkable phylogenetic resolution of the most complex clade of Cyprinidae (Teleostei: Cypriniformes): A proof of concept of homology assessment and partitioning sequence data integrated with mixed model Bayesian analyses[J]. MOLECULAR PHYLOGENETICS AND EVOLUTION,2013,66(3):603-616.
APA Tao, Wenjing,Mayden, Richard L.,He, Shunping,&Mayden, RL .(2013).Remarkable phylogenetic resolution of the most complex clade of Cyprinidae (Teleostei: Cypriniformes): A proof of concept of homology assessment and partitioning sequence data integrated with mixed model Bayesian analyses.MOLECULAR PHYLOGENETICS AND EVOLUTION,66(3),603-616.
MLA Tao, Wenjing,et al."Remarkable phylogenetic resolution of the most complex clade of Cyprinidae (Teleostei: Cypriniformes): A proof of concept of homology assessment and partitioning sequence data integrated with mixed model Bayesian analyses".MOLECULAR PHYLOGENETICS AND EVOLUTION 66.3(2013):603-616.
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