Basal Jawed Vertebrate Phylogenomics Using Transcriptomic Data from Solexa Sequencing
文献类型：期刊论文
| 作者 | Chen, Ming1,2; Zou, Ming1,2; Yang, Lei3; He, Shunping1 |
| 刊名 | PLOS ONE
 |
| 出版日期 | 2012-04-27 |
| 卷号 | 7期号:4页码:e36256 |
| 关键词 | BAYESIAN PHYLOGENETIC INFERENCE MITOCHONDRIAL-DNA CARTILAGINOUS FISHES MAXIMUM-LIKELIHOOD DIVERGENCE TIMES EST SEQUENCES MIXED MODELS MONTE-CARLO ALIGNMENTS EVOLUTION |
| ISSN号 | 1932-6203 |
| 通讯作者 | Chen, M (reprint author), Chinese Acad Sci, Key Lab Aquat Biodivers & Conservat, Inst Hydrobiol, Wuhan, Peoples R China. |
| 中文摘要 | The traditionally accepted relationships among basal jawed vertebrates have been challenged by some molecular phylogenetic analyses based on mitochondrial sequences. Those studies split extant gnathostomes into two monophyletic groups: tetrapods and piscine branch, including Chondrichthyes, Actinopterygii and sarcopterygian fishes. Lungfish and bichir are found in a basal position on the piscine branch. Based on transcriptomes of an armored bichir (Polypterus delhezi) and an African lungfish (Protopterus sp.) we generated, expressed sequences and whole genome sequences available from public databases, we obtained 111 genes to reconstruct the phylogenetic tree of basal jawed vertebrates and estimated their times of divergence. Our phylogenomic study supports the traditional relationship. We found that gnathostomes are divided into Chondrichthyes and the Osteichthyes, both with 100% support values (posterior probabilities and bootstrap values). Chimaeras were found to have a basal position among cartilaginous fishes with a 100% support value. Osteichthyes were divided into Actinopterygii and Sarcopterygii with 100% support value. Lungfish and tetrapods form a monophyletic group with 100% posterior probability. Bichir and two teleost species form a monophyletic group with 100% support value. The previous tree, based on mitochondrial data, was significantly rejected by an approximately unbiased test (AU test, p=0). The time of divergence between lungfish and tetrapods was estimated to be 391.8 Ma and the divergence of bichir from pufferfish and medaka was estimated to be 330.6 Ma. These estimates closely match the fossil record. In conclusion, our phylogenomic study successfully resolved the relationship of basal jawed vertebrates based on transtriptomes, EST and whole genome sequences. |
| 英文摘要 | The traditionally accepted relationships among basal jawed vertebrates have been challenged by some molecular phylogenetic analyses based on mitochondrial sequences. Those studies split extant gnathostomes into two monophyletic groups: tetrapods and piscine branch, including Chondrichthyes, Actinopterygii and sarcopterygian fishes. Lungfish and bichir are found in a basal position on the piscine branch. Based on transcriptomes of an armored bichir (Polypterus delhezi) and an African lungfish (Protopterus sp.) we generated, expressed sequences and whole genome sequences available from public databases, we obtained 111 genes to reconstruct the phylogenetic tree of basal jawed vertebrates and estimated their times of divergence. Our phylogenomic study supports the traditional relationship. We found that gnathostomes are divided into Chondrichthyes and the Osteichthyes, both with 100% support values (posterior probabilities and bootstrap values). Chimaeras were found to have a basal position among cartilaginous fishes with a 100% support value. Osteichthyes were divided into Actinopterygii and Sarcopterygii with 100% support value. Lungfish and tetrapods form a monophyletic group with 100% posterior probability. Bichir and two teleost species form a monophyletic group with 100% support value. The previous tree, based on mitochondrial data, was significantly rejected by an approximately unbiased test (AU test, p=0). The time of divergence between lungfish and tetrapods was estimated to be 391.8 Ma and the divergence of bichir from pufferfish and medaka was estimated to be 330.6 Ma. These estimates closely match the fossil record. In conclusion, our phylogenomic study successfully resolved the relationship of basal jawed vertebrates based on transtriptomes, EST and whole genome sequences. |
| WOS标题词 | Science & Technology |
| 类目[WOS] | Multidisciplinary Sciences |
| 研究领域[WOS] | Science & Technology - Other Topics |
| 关键词[WOS] | BAYESIAN PHYLOGENETIC INFERENCE ; MITOCHONDRIAL-DNA ; CARTILAGINOUS FISHES ; MAXIMUM-LIKELIHOOD ; DIVERGENCE TIMES ; EST SEQUENCES ; MIXED MODELS ; MONTE-CARLO ; ALIGNMENTS ; EVOLUTION |
| 收录类别 | SCI |
| 资助信息 | National Natural Science Foundation of China (NSFC)[30530120]; National Science Foundation USA (NSF)[EF-0431326] |
| 语种 | 英语 |
| WOS记录号 | WOS:000305336000173 |
| 公开日期 | 2012-09-25 |
| 源URL | [http://ir.ihb.ac.cn/handle/342005/16797]  |
| 专题 | 水生生物研究所_水生生物多样性与资源保护研究中心_期刊论文 |
| 作者单位 | 1.Chinese Acad Sci, Key Lab Aquat Biodivers & Conservat, Inst Hydrobiol, Wuhan, Peoples R China 2.Chinese Acad Sci, Grad Univ, Beijing, Peoples R China 3.St Louis Univ, Lab Integrated Biodivers Conservat & Genom, Dept Biol, St Louis, MO 63103 USA |
| 推荐引用方式 GB/T 7714 | Chen, Ming,Zou, Ming,Yang, Lei,et al. Basal Jawed Vertebrate Phylogenomics Using Transcriptomic Data from Solexa Sequencing[J]. PLOS ONE,2012,7(4):e36256. |
| APA | Chen, Ming,Zou, Ming,Yang, Lei,&He, Shunping.(2012).Basal Jawed Vertebrate Phylogenomics Using Transcriptomic Data from Solexa Sequencing.PLOS ONE,7(4),e36256. |
| MLA | Chen, Ming,et al."Basal Jawed Vertebrate Phylogenomics Using Transcriptomic Data from Solexa Sequencing".PLOS ONE 7.4(2012):e36256. |
入库方式： OAI收割
来源：水生生物研究所
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