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题名: Basal Jawed Vertebrate Phylogenomics Using Transcriptomic Data from Solexa Sequencing
作者: Chen, Ming1, 2; Zou, Ming1, 2; Yang, Lei3; He, Shunping1
通讯作者: Chen, M (reprint author), Chinese Acad Sci, Key Lab Aquat Biodivers & Conservat, Inst Hydrobiol, Wuhan, Peoples R China.
关键词: BAYESIAN PHYLOGENETIC INFERENCE ; MITOCHONDRIAL-DNA ; CARTILAGINOUS FISHES ; MAXIMUM-LIKELIHOOD ; DIVERGENCE TIMES ; EST SEQUENCES ; MIXED MODELS ; MONTE-CARLO ; ALIGNMENTS ; EVOLUTION
刊名: PLOS ONE
发表日期: 2012-04-27
DOI: 10.1371/journal.pone.0036256
卷: 7, 期:4, 页:e36256
收录类别: SCI
文章类型: Article
部门归属: [Chen, Ming; Zou, Ming; He, Shunping] Chinese Acad Sci, Key Lab Aquat Biodivers & Conservat, Inst Hydrobiol, Wuhan, Peoples R China; [Chen, Ming; Zou, Ming] Chinese Acad Sci, Grad Univ, Beijing, Peoples R China; [Yang, Lei] St Louis Univ, Lab Integrated Biodivers Conservat & Genom, Dept Biol, St Louis, MO 63103 USA
WOS标题词: Science & Technology
资助者: National Natural Science Foundation of China (NSFC)[30530120]; National Science Foundation USA (NSF)[EF-0431326]
类目[WOS]: Multidisciplinary Sciences
研究领域[WOS]: Science & Technology - Other Topics
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.
关键词[WOS]: BAYESIAN PHYLOGENETIC INFERENCE ; MITOCHONDRIAL-DNA ; CARTILAGINOUS FISHES ; MAXIMUM-LIKELIHOOD ; DIVERGENCE TIMES ; EST SEQUENCES ; MIXED MODELS ; MONTE-CARLO ; ALIGNMENTS ; EVOLUTION
语种: 英语
WOS记录号: WOS:000305336000173
ISSN号: 1932-6203
Citation statistics:
内容类型: 期刊论文
URI标识: http://ir.ihb.ac.cn/handle/342005/16797
Appears in Collections:水生生物多样性与资源保护研究中心_期刊论文

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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

Recommended Citation:
Chen, Ming; Zou, Ming; Yang, Lei; He, Shunping.Basal Jawed Vertebrate Phylogenomics Using Transcriptomic Data from Solexa Sequencing,PLOS ONE,2012,7(4):e36256
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