IHB OpenIR  > 期刊论文
Variation patterns of the mitochondrial 16S rRNA gene with secondary structure constraints and their application to phylogeny of cyprinine fishes (Teleostei : Cypriniformes)
Li, Junbing1,2; Wang, Xuzhen1; Kong, Xianghui3; Zhao, Kai4; He, Shunping1; Mayden, Richard L.5; He, SP, Chinese Acad Sci, Inst Hydrobiol, Lab Fish Phylogenet & Biogeog, Wuhan 430072, Hubei, Peoples R China
2008-05-01
Source PublicationMOLECULAR PHYLOGENETICS AND EVOLUTION
ISSN1055-7903
Volume47Issue:2Pages:472-487
AbstractThe mitochondrial 16S ribosomal RNA (rRNA) gene sequences from 93 cyprinid fishes were examined to reconstruct the phylogenetic relationships within the diverse and economically important subfamily Cyprininae. Within the subfamily a biased nucleotide composition (A > T, C > G) was observed in the loop regions of the gene, and in stem regions apparent selective pressures of base pairing showed a bias in favor of G over C and T over A. The bias may be associated with transition-transversion bias. Rates of nucleotide substitution were lower in stems than in loops. Analysis of compensatory substitutions across these taxa demonstrates 68% covariation in the gene and a logical weighting factor to account for dependence in mutations for phylogenetic inference should be 0.66. Comparisons of varied stem-loop weighting schemes indicate that the down-weightings for stem regions could improve the phylogenetic analysis and the degree of non-independence of stem substitutions was not as important as expected. Bayesian inference under four models of nucleotide substitution indicated that likelihood-based phylogenetic analyses were more effective in improving the phylogenetic performance than was weighted parsimony analysis. In Bayesian analyses, the resolution of phylogenies under the 16-state models for paired regions, incorporating GTR + G + I models for unpaired regions was better than those under other models. The subfamily Cyprininae was resolved as a monophyletic group, as well as tribe Labein and several genera. However, the monophyly of the currently recognized tribes, such as Schizothoracin, Barbin, Cyprinion + Onychostoma lineages, and some genera was rejected. Furthermore, comparisons of the parsimony and Bayesian analyses and results of variable length bootstrap analysis indicates that the mitochondrial 16S rRNA gene should contain important character variation to recover well-supported phylogeny of cyprinid taxa whose divergences occurred within the recent 8 MY, but could not provide resolution power for deep phylogenies spanning 10-19 MYA. (c) 2008 Published by Elsevier Inc.; The mitochondrial 16S ribosomal RNA (rRNA) gene sequences from 93 cyprinid fishes were examined to reconstruct the phylogenetic relationships within the diverse and economically important subfamily Cyprininae. Within the subfamily a biased nucleotide composition (A > T, C > G) was observed in the loop regions of the gene, and in stem regions apparent selective pressures of base pairing showed a bias in favor of G over C and T over A. The bias may be associated with transition-transversion bias. Rates of nucleotide substitution were lower in stems than in loops. Analysis of compensatory substitutions across these taxa demonstrates 68% covariation in the gene and a logical weighting factor to account for dependence in mutations for phylogenetic inference should be 0.66. Comparisons of varied stem-loop weighting schemes indicate that the down-weightings for stem regions could improve the phylogenetic analysis and the degree of non-independence of stem substitutions was not as important as expected. Bayesian inference under four models of nucleotide substitution indicated that likelihood-based phylogenetic analyses were more effective in improving the phylogenetic performance than was weighted parsimony analysis. In Bayesian analyses, the resolution of phylogenies under the 16-state models for paired regions, incorporating GTR + G + I models for unpaired regions was better than those under other models. The subfamily Cyprininae was resolved as a monophyletic group, as well as tribe Labein and several genera. However, the monophyly of the currently recognized tribes, such as Schizothoracin, Barbin, Cyprinion + Onychostoma lineages, and some genera was rejected. Furthermore, comparisons of the parsimony and Bayesian analyses and results of variable length bootstrap analysis indicates that the mitochondrial 16S rRNA gene should contain important character variation to recover well-supported phylogeny of cyprinid taxa whose divergences occurred within the recent 8 MY, but could not provide resolution power for deep phylogenies spanning 10-19 MYA. (c) 2008 Published by Elsevier Inc.
SubtypeArticle
KeywordMitochondrial 16s Rrna Gene Secondary Structure Constraints Phylogeny Cyprininae
Department[Li, Junbing; Wang, Xuzhen; He, Shunping] Chinese Acad Sci, Inst Hydrobiol, Lab Fish Phylogenet & Biogeog, Wuhan 430072, Hubei, Peoples R China; [Li, Junbing] Chinese Acad Sci, Grad Sch, Beijing 100039, Peoples R China; [Kong, Xianghui] Henan Normal Univ, Coll Life Sci, Xinxiang 453007, Peoples R China; [Zhao, Kai] Qinghai Univ, Agr & Anim Husb Coll, Xining 810003, Peoples R China; [Mayden, Richard L.] St Louis Univ, Dept Biol, St Louis, MO 63103 USA
Subject AreaBiochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
DOI10.1016/j.ympev.2007.09.012
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine
Indexed BySCI
Language英语
WOS Research AreaBiochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
WOS SubjectBiochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
WOS IDWOS:000256110100003
WOS KeywordCYTOCHROME-B SEQUENCES ; MOLECULAR PHYLOGENY ; EUROPEAN CYPRINIDS ; DNA-SEQUENCES ; NUCLEOTIDE SUBSTITUTION ; CONTROL REGION ; EVOLUTION ; BIOGEOGRAPHY ; INFERENCE ; RATES
Citation statistics
Cited Times:40[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/152342/8112
Collection期刊论文
Corresponding AuthorHe, SP, Chinese Acad Sci, Inst Hydrobiol, Lab Fish Phylogenet & Biogeog, Wuhan 430072, Hubei, Peoples R China
Affiliation1.Chinese Acad Sci, Inst Hydrobiol, Lab Fish Phylogenet & Biogeog, Wuhan 430072, Hubei, Peoples R China
2.Chinese Acad Sci, Grad Sch, Beijing 100039, Peoples R China
3.Henan Normal Univ, Coll Life Sci, Xinxiang 453007, Peoples R China
4.Qinghai Univ, Agr & Anim Husb Coll, Xining 810003, Peoples R China
5.St Louis Univ, Dept Biol, St Louis, MO 63103 USA
Recommended Citation
GB/T 7714
Li, Junbing,Wang, Xuzhen,Kong, Xianghui,et al. Variation patterns of the mitochondrial 16S rRNA gene with secondary structure constraints and their application to phylogeny of cyprinine fishes (Teleostei : Cypriniformes)[J]. MOLECULAR PHYLOGENETICS AND EVOLUTION,2008,47(2):472-487.
APA Li, Junbing.,Wang, Xuzhen.,Kong, Xianghui.,Zhao, Kai.,He, Shunping.,...&He, SP, Chinese Acad Sci, Inst Hydrobiol, Lab Fish Phylogenet & Biogeog, Wuhan 430072, Hubei, Peoples R China.(2008).Variation patterns of the mitochondrial 16S rRNA gene with secondary structure constraints and their application to phylogeny of cyprinine fishes (Teleostei : Cypriniformes).MOLECULAR PHYLOGENETICS AND EVOLUTION,47(2),472-487.
MLA Li, Junbing,et al."Variation patterns of the mitochondrial 16S rRNA gene with secondary structure constraints and their application to phylogeny of cyprinine fishes (Teleostei : Cypriniformes)".MOLECULAR PHYLOGENETICS AND EVOLUTION 47.2(2008):472-487.
Files in This Item: Download All
File Name/Size DocType Version Access License
Variation patterns o(329KB) 开放获取--View Download
Related Services
Recommend this item
Bookmark
Usage statistics
Export to Endnote
Google Scholar
Similar articles in Google Scholar
[Li, Junbing]'s Articles
[Wang, Xuzhen]'s Articles
[Kong, Xianghui]'s Articles
Baidu academic
Similar articles in Baidu academic
[Li, Junbing]'s Articles
[Wang, Xuzhen]'s Articles
[Kong, Xianghui]'s Articles
Bing Scholar
Similar articles in Bing Scholar
[Li, Junbing]'s Articles
[Wang, Xuzhen]'s Articles
[Kong, Xianghui]'s Articles
Terms of Use
No data!
Social Bookmark/Share
File name: Variation patterns of the mitochondrial 16S rRNA gene with secondary structure constraints and their application to phylogeny of cyprinine fishes (Teleostei Cypriniformes).pdf
Format: Adobe PDF
This file does not support browsing at this time
All comments (0)
No comment.
 

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