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Basal Jawed Vertebrate Phylogenomics Using Transcriptomic Data from Solexa Sequencing
Chen, Ming1,2; Zou, Ming1,2; Yang, Lei3; He, Shunping1; Chen, M (reprint author), Chinese Acad Sci, Key Lab Aquat Biodivers & Conservat, Inst Hydrobiol, Wuhan, Peoples R China.
2012-04-27
Source PublicationPLOS ONE
ISSN1932-6203
Volume7Issue:4Pages:e36256
AbstractThe 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.; 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.
SubtypeArticle
KeywordBayesian Phylogenetic Inference Mitochondrial-dna Cartilaginous Fishes Maximum-likelihood Divergence Times Est Sequences Mixed Models Monte-carlo Alignments Evolution
Department[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
DOI10.1371/journal.pone.0036256
WOS HeadingsScience & Technology
Funding OrganizationNational Natural Science Foundation of China (NSFC)[30530120]; National Science Foundation USA (NSF)[EF-0431326] ; National Natural Science Foundation of China (NSFC)[30530120]; National Science Foundation USA (NSF)[EF-0431326] ; National Natural Science Foundation of China (NSFC)[30530120]; National Science Foundation USA (NSF)[EF-0431326] ; National Natural Science Foundation of China (NSFC)[30530120]; National Science Foundation USA (NSF)[EF-0431326]
Indexed BySCI
Language英语
WOS Research AreaScience & Technology - Other Topics
WOS SubjectMultidisciplinary Sciences
WOS IDWOS:000305336000173
WOS KeywordBAYESIAN PHYLOGENETIC INFERENCE ; MITOCHONDRIAL-DNA ; CARTILAGINOUS FISHES ; MAXIMUM-LIKELIHOOD ; DIVERGENCE TIMES ; EST SEQUENCES ; MIXED MODELS ; MONTE-CARLO ; ALIGNMENTS ; EVOLUTION
Funding OrganizationNational Natural Science Foundation of China (NSFC)[30530120]; National Science Foundation USA (NSF)[EF-0431326] ; National Natural Science Foundation of China (NSFC)[30530120]; National Science Foundation USA (NSF)[EF-0431326] ; National Natural Science Foundation of China (NSFC)[30530120]; National Science Foundation USA (NSF)[EF-0431326] ; National Natural Science Foundation of China (NSFC)[30530120]; National Science Foundation USA (NSF)[EF-0431326]
Citation statistics
Cited Times:20[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/16797
Collection水生生物多样性与资源保护研究中心_期刊论文
Corresponding AuthorChen, M (reprint author), Chinese Acad Sci, Key Lab Aquat Biodivers & Conservat, Inst Hydrobiol, Wuhan, Peoples R China.
Affiliation1.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
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,&Chen, M .(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.
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