Variation patterns of the mitochondrial 16S rRNA gene with secondary structure constraints and their application to phylogeny of cyprinine fishes (Teleostei : Cypriniformes)
文献类型：期刊论文
| 作者 | Li, Junbing1,2; Wang, Xuzhen1; Kong, Xianghui3; Zhao, Kai4; He, Shunping1; Mayden, Richard L.5 |
| 刊名 | MOLECULAR PHYLOGENETICS AND EVOLUTION
 |
| 出版日期 | 2008-05-01 |
| 卷号 | 47期号:2页码:472-487 |
| 关键词 | mitochondrial 16S rRNA gene secondary structure constraints phylogeny Cyprininae |
| ISSN号 | 1055-7903 |
| 通讯作者 | He, SP, Chinese Acad Sci, Inst Hydrobiol, Lab Fish Phylogenet & Biogeog, Wuhan 430072, Hubei, Peoples R China |
| 中文摘要 | 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. |
| 英文摘要 | 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. |
| WOS标题词 | Science & Technology ; Life Sciences & Biomedicine |
| 学科主题 | Biochemistry & Molecular Biology; Evolutionary Biology; Genetics & Heredity |
| 类目[WOS] | Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity |
| 研究领域[WOS] | Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity |
| 关键词[WOS] | CYTOCHROME-B SEQUENCES ; MOLECULAR PHYLOGENY ; EUROPEAN CYPRINIDS ; DNA-SEQUENCES ; NUCLEOTIDE SUBSTITUTION ; CONTROL REGION ; EVOLUTION ; BIOGEOGRAPHY ; INFERENCE ; RATES |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000256110100003 |
| 公开日期 | 2010-10-13 |
| 源URL | [http://ir.ihb.ac.cn/handle/152342/8112]  |
| 专题 | 水生生物研究所_中科院水生所知识产出（2009年前）_期刊论文 |
| 作者单位 | 1.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 |
| 推荐引用方式 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,&Mayden, Richard L..(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. |
入库方式： OAI收割
来源：水生生物研究所
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