IHB OpenIR  > 水生生物多样性与资源保护研究中心  > 期刊论文
Phylogenetic relationships of the Cobitoidea (Teleostei: Cypriniformes) inferred from mitochondrial and nuclear genes with analyses of gene evolution
Liu, Si-qing1,2; Mayden, Richard L.3; Zhang, Jia-bo4; Yu, Dan1,2; Tang, Qiong-ying1; Deng, Xin5; Liu, Huan-zhang1; Tang, QY (reprint author), 7 S Donghu Rd, Wuhan 430072, Hubei, Peoples R China.
2012-10-15
Source PublicationGENE
ISSN0378-1119
Volume508Issue:1Pages:60-72
AbstractThe superfamily Cobitoidea of the order Cypriniformes is a diverse group of fishes, inhabiting freshwater ecosystems across Eurasia and North Africa. The phylogenetic relationships of this well-corroborated natural group and diverse clade are critical to not only informing scientific communities of the phylogeny of the order Cypriniformes, the world's largest freshwater fish order, but are key to every area of comparative biology examining the evolution of traits, functional structures, and breeding behaviors to their biogeographic histories, speciation, anagenetic divergence, and divergence time estimates. In the present study, two mitochondrial gene sequences (COI, ND4 + 5) and four single-copy nuclear gene segments (RH1, RAG1, EGR2B, IRBP) were used to infer the phylogenetic relationships of the Cobitoidea as reconstructed from maximum likelihood (ML) and partitioned Bayesian Analysis (BA). Analyses of the combined mitochondrial/nuclear gene datasets revealed five strongly supported monophyletic Cobitoidea families and their sister-group relationships: Botiidae + (Vaillantellidae + (Cobitidae + (Nemacheilidae + Balitoridae))). These recovered relationships are in agreement with previous systematic studies on the order Cypriniformes and/or those focusing on the superfamily Cobitoidea. Using these relationships, our analyses revealed pattern lineageor ecological-group-specific evolution of these genes for the Cobitoidea. These observations and results corroborate the hypothesis that these group-specific-ancestral ecological characters have contributed in the diversification and/or adaptations within these groups. Positive selections were detected in RH1 of nemacheilids and in RAG1 of nemacheilids and genus Vaillantella, which indicated that evolution of RH1 (related to eye's optic sense) and RAG1 (related to immunity) genes appeared to be important for the diversification of these groups. The balitorid lineage (those species inhabiting fast-flowing riverine habitats) had, as compared with other cobitoid lineages, significantly different dN/dS, dN and dS values for ND4 and IRBP genes. These significant differences are usually indicative of weaker selection pressure, and lineage-specific evolution on genes along the balitorid lineage. Furthermore, within Cobitoidea, excluding balitorids, species living in subtropics had significantly higher dN/dS values in RAG1 and IRBP genes than those living in temperate and tropical zones. Among tropical cobitoids, genes COI, ND5, EGR2B, IRBP and RH1, had a significantly higher mean dS value than those species in subtropical and temperate groups. These findings suggest that the evolution of these genes could also be ecological-group-specific and may have played an important role in the adaptive evolution and diversification of these groups. Thus, we hypothesize that the genes included in the present study were actively involved in lineage- and/or ecological-group-specific evolutionary processes of the highly diverse Cobitoidea. These two evolutionary patterns, both subject to further testing, are hypothesized as integral in the diversification with this major clade of the world's most diverse group of freshwater fishes. (C) 2012 Elsevier B.V. All rights reserved.; The superfamily Cobitoidea of the order Cypriniformes is a diverse group of fishes, inhabiting freshwater ecosystems across Eurasia and North Africa. The phylogenetic relationships of this well-corroborated natural group and diverse clade are critical to not only informing scientific communities of the phylogeny of the order Cypriniformes, the world's largest freshwater fish order, but are key to every area of comparative biology examining the evolution of traits, functional structures, and breeding behaviors to their biogeographic histories, speciation, anagenetic divergence, and divergence time estimates. In the present study, two mitochondrial gene sequences (COI, ND4 + 5) and four single-copy nuclear gene segments (RH1, RAG1, EGR2B, IRBP) were used to infer the phylogenetic relationships of the Cobitoidea as reconstructed from maximum likelihood (ML) and partitioned Bayesian Analysis (BA). Analyses of the combined mitochondrial/nuclear gene datasets revealed five strongly supported monophyletic Cobitoidea families and their sister-group relationships: Botiidae + (Vaillantellidae + (Cobitidae + (Nemacheilidae + Balitoridae))). These recovered relationships are in agreement with previous systematic studies on the order Cypriniformes and/or those focusing on the superfamily Cobitoidea. Using these relationships, our analyses revealed pattern lineageor ecological-group-specific evolution of these genes for the Cobitoidea. These observations and results corroborate the hypothesis that these group-specific-ancestral ecological characters have contributed in the diversification and/or adaptations within these groups. Positive selections were detected in RH1 of nemacheilids and in RAG1 of nemacheilids and genus Vaillantella, which indicated that evolution of RH1 (related to eye's optic sense) and RAG1 (related to immunity) genes appeared to be important for the diversification of these groups. The balitorid lineage (those species inhabiting fast-flowing riverine habitats) had, as compared with other cobitoid lineages, significantly different dN/dS, dN and dS values for ND4 and IRBP genes. These significant differences are usually indicative of weaker selection pressure, and lineage-specific evolution on genes along the balitorid lineage. Furthermore, within Cobitoidea, excluding balitorids, species living in subtropics had significantly higher dN/dS values in RAG1 and IRBP genes than those living in temperate and tropical zones. Among tropical cobitoids, genes COI, ND5, EGR2B, IRBP and RH1, had a significantly higher mean dS value than those species in subtropical and temperate groups. These findings suggest that the evolution of these genes could also be ecological-group-specific and may have played an important role in the adaptive evolution and diversification of these groups. Thus, we hypothesize that the genes included in the present study were actively involved in lineage- and/or ecological-group-specific evolutionary processes of the highly diverse Cobitoidea. These two evolutionary patterns, both subject to further testing, are hypothesized as integral in the diversification with this major clade of the world's most diverse group of freshwater fishes. (C) 2012 Elsevier B.V. All rights reserved.
SubtypeArticle
KeywordCobitoidea Phylogeny Gene Evolution Positive Selection Relaxed Selection
Department[Liu, Si-qing; Yu, Dan; Tang, Qiong-ying; Liu, Huan-zhang] Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan 430072, Hubei, Peoples R China; [Liu, Si-qing; Yu, Dan] Chinese Acad Sci, Grad Univ, Beijing 100049, Peoples R China; [Mayden, Richard L.] St Louis Univ, Dept Biol, St Louis, MO 63103 USA; [Zhang, Jia-bo] Huazhong Agr Univ, Coll Fisheries, Wuhan 430070, Hubei, Peoples R China; [Deng, Xin] Calif Environm Protect Agcy, Dept Pesticide Regulat, Sacramento, CA 95812 USA
DOI10.1016/j.gene.2012.07.040
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine
Funding OrganizationNational Natural Science Foundation of China [NSFC 30700072, 31061160185]; Knowledge Innovation Program of the Chinese Academy of Sciences [Y05E08]; Cypriniformes Tree of Life (CToL); U.S. National Science Foundation [NSF EF-0431326] ; National Natural Science Foundation of China [NSFC 30700072, 31061160185]; Knowledge Innovation Program of the Chinese Academy of Sciences [Y05E08]; Cypriniformes Tree of Life (CToL); U.S. National Science Foundation [NSF EF-0431326] ; National Natural Science Foundation of China [NSFC 30700072, 31061160185]; Knowledge Innovation Program of the Chinese Academy of Sciences [Y05E08]; Cypriniformes Tree of Life (CToL); U.S. National Science Foundation [NSF EF-0431326] ; National Natural Science Foundation of China [NSFC 30700072, 31061160185]; Knowledge Innovation Program of the Chinese Academy of Sciences [Y05E08]; Cypriniformes Tree of Life (CToL); U.S. National Science Foundation [NSF EF-0431326]
Indexed BySCI
Language英语
WOS Research AreaGenetics & Heredity
WOS SubjectGenetics & Heredity
WOS IDWOS:000309249600009
WOS KeywordSYNONYMOUS CODON USAGE ; AMINO-ACID SITES ; MOLECULAR PHYLOGENY ; MAXIMUM-LIKELIHOOD ; POSITIVE SELECTION ; TRANSLATIONAL SELECTION ; ORDER CYPRINIFORMES ; SUBSTITUTION MODELS ; SEQUENCE EVOLUTION ; NATURAL-SELECTION
Funding OrganizationNational Natural Science Foundation of China [NSFC 30700072, 31061160185]; Knowledge Innovation Program of the Chinese Academy of Sciences [Y05E08]; Cypriniformes Tree of Life (CToL); U.S. National Science Foundation [NSF EF-0431326] ; National Natural Science Foundation of China [NSFC 30700072, 31061160185]; Knowledge Innovation Program of the Chinese Academy of Sciences [Y05E08]; Cypriniformes Tree of Life (CToL); U.S. National Science Foundation [NSF EF-0431326] ; National Natural Science Foundation of China [NSFC 30700072, 31061160185]; Knowledge Innovation Program of the Chinese Academy of Sciences [Y05E08]; Cypriniformes Tree of Life (CToL); U.S. National Science Foundation [NSF EF-0431326] ; National Natural Science Foundation of China [NSFC 30700072, 31061160185]; Knowledge Innovation Program of the Chinese Academy of Sciences [Y05E08]; Cypriniformes Tree of Life (CToL); U.S. National Science Foundation [NSF EF-0431326]
Citation statistics
Cited Times:28[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/17156
Collection水生生物多样性与资源保护研究中心_期刊论文
Corresponding AuthorTang, QY (reprint author), 7 S Donghu Rd, Wuhan 430072, Hubei, Peoples R China.
Affiliation1.Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan 430072, Hubei, Peoples R China
2.Chinese Acad Sci, Grad Univ, Beijing 100049, Peoples R China
3.St Louis Univ, Dept Biol, St Louis, MO 63103 USA
4.Huazhong Agr Univ, Coll Fisheries, Wuhan 430070, Hubei, Peoples R China
5.Calif Environm Protect Agcy, Dept Pesticide Regulat, Sacramento, CA 95812 USA
Recommended Citation
GB/T 7714
Liu, Si-qing,Mayden, Richard L.,Zhang, Jia-bo,et al. Phylogenetic relationships of the Cobitoidea (Teleostei: Cypriniformes) inferred from mitochondrial and nuclear genes with analyses of gene evolution[J]. GENE,2012,508(1):60-72.
APA Liu, Si-qing.,Mayden, Richard L..,Zhang, Jia-bo.,Yu, Dan.,Tang, Qiong-ying.,...&Tang, QY .(2012).Phylogenetic relationships of the Cobitoidea (Teleostei: Cypriniformes) inferred from mitochondrial and nuclear genes with analyses of gene evolution.GENE,508(1),60-72.
MLA Liu, Si-qing,et al."Phylogenetic relationships of the Cobitoidea (Teleostei: Cypriniformes) inferred from mitochondrial and nuclear genes with analyses of gene evolution".GENE 508.1(2012):60-72.
Files in This Item:
File Name/Size DocType Version Access License
Phylogenetic relatio(1135KB) 开放获取--View Application Full Text
Related Services
Recommend this item
Bookmark
Usage statistics
Export to Endnote
Google Scholar
Similar articles in Google Scholar
[Liu, Si-qing]'s Articles
[Mayden, Richard L.]'s Articles
[Zhang, Jia-bo]'s Articles
Baidu academic
Similar articles in Baidu academic
[Liu, Si-qing]'s Articles
[Mayden, Richard L.]'s Articles
[Zhang, Jia-bo]'s Articles
Bing Scholar
Similar articles in Bing Scholar
[Liu, Si-qing]'s Articles
[Mayden, Richard L.]'s Articles
[Zhang, Jia-bo]'s Articles
Terms of Use
No data!
Social Bookmark/Share
File name: Phylogenetic relationships of the Cobitoidea (Teleostei Cypriniformes) inferred from mitochondrial and nuclear genes with analyses of gene evolution.pdf
Format: Adobe PDF
All comments (0)
No comment.
 

Items in the repository are protected by copyright, with all rights reserved, unless otherwise indicated.