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Bayesian mixed models and divergence time estimation of Chinese cavefishes (Cyprinidae : Sinocyclocheilus)
Li ZhiQiang1,2; Guo BaoCheng1,2; Li JunBing1,2; He ShunPing1; Chen Yiyu1; He, SP, Chinese Acad Sci, Inst Hydrobiol, Wuhan 430072, Peoples R China
2008-08-01
Source PublicationCHINESE SCIENCE BULLETIN
ISSN1001-6538
Volume53Issue:15Pages:2342-2352
AbstractThe genus Sinocyclocheilus is distributed in Yun-Gui Plateau and its surrounding region only, within more than 10 cave species showing different degrees of degeneration of eyes and pigmentation with wonderful adaptations. To present, published morphological and molecular phylogenetic hypotheses of Sinocyclocheilus from prior works are very different and the relationships within the genus are still far from clear. We obtained the sequences of cytochrome b (cyt b) and NADH dehydrogenase subunit 4 (ND4) of 34 species within Sinocyclocheilus, which represent the most dense taxon sampling to date. We performed Bayesian mixed models analyses with this data set. Under this phylogenetic framework, we estimated the divergence times of recovered clades using different methods under relaxed molecular clock. Our phyloegentic results supported the monophyly of Sinocyclocheilus and showed that this genus could be subdivided into 6 major clades. In addition, an earlier finding demonstrating the polyphyletic of cave species and the most basal position of S. jii was corroborated. Relaxed divergence-time estimation suggested that Sinocyclocheilus originated at the late Miocene, about 11 million years ago (Ma), which is older than what have been assumed.; The genus Sinocyclocheilus is distributed in Yun-Gui Plateau and its surrounding region only, within more than 10 cave species showing different degrees of degeneration of eyes and pigmentation with wonderful adaptations. To present, published morphological and molecular phylogenetic hypotheses of Sinocyclocheilus from prior works are very different and the relationships within the genus are still far from clear. We obtained the sequences of cytochrome b (cyt b) and NADH dehydrogenase subunit 4 (ND4) of 34 species within Sinocyclocheilus, which represent the most dense taxon sampling to date. We performed Bayesian mixed models analyses with this data set. Under this phylogenetic framework, we estimated the divergence times of recovered clades using different methods under relaxed molecular clock. Our phyloegentic results supported the monophyly of Sinocyclocheilus and showed that this genus could be subdivided into 6 major clades. In addition, an earlier finding demonstrating the polyphyletic of cave species and the most basal position of S. jii was corroborated. Relaxed divergence-time estimation suggested that Sinocyclocheilus originated at the late Miocene, about 11 million years ago (Ma), which is older than what have been assumed.
SubtypeArticle
KeywordSinocyclocheilus Phylogeny Relaxed Molecular Clock
Department[Li ZhiQiang; Guo BaoCheng; Li JunBing; He ShunPing; Chen Yiyu] Chinese Acad Sci, Inst Hydrobiol, Wuhan 430072, Peoples R China; [Li ZhiQiang; Guo BaoCheng; Li JunBing] Chinese Acad Sci, Grad Univ, Beijing 100049, Peoples R China
Subject AreaMultidisciplinary Sciences
DOI10.1007/s11434-008-0297-2
WOS HeadingsScience & Technology
Indexed BySCI
Language英语
WOS Research AreaScience & Technology - Other Topics
WOS SubjectMultidisciplinary Sciences
WOS IDWOS:000258384800009
WOS KeywordPHYLOGENETIC-RELATIONSHIPS ; MOLECULAR EVOLUTION ; SEQUENCE ALIGNMENT ; BLIND CAVEFISH ; ABSOLUTE RATES ; LIKELIHOOD ; CYPRINIFORMES ; TELEOSTEI ; INFERENCE ; LIZARDS
Citation statistics
Cited Times:7[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/152342/8044
Collection期刊论文
Corresponding AuthorHe, SP, Chinese Acad Sci, Inst Hydrobiol, Wuhan 430072, Peoples R China
Affiliation1.Chinese Acad Sci, Inst Hydrobiol, Wuhan 430072, Peoples R China
2.Chinese Acad Sci, Grad Univ, Beijing 100049, Peoples R China
Recommended Citation
GB/T 7714
Li ZhiQiang,Guo BaoCheng,Li JunBing,et al. Bayesian mixed models and divergence time estimation of Chinese cavefishes (Cyprinidae : Sinocyclocheilus)[J]. CHINESE SCIENCE BULLETIN,2008,53(15):2342-2352.
APA Li ZhiQiang,Guo BaoCheng,Li JunBing,He ShunPing,Chen Yiyu,&He, SP, Chinese Acad Sci, Inst Hydrobiol, Wuhan 430072, Peoples R China.(2008).Bayesian mixed models and divergence time estimation of Chinese cavefishes (Cyprinidae : Sinocyclocheilus).CHINESE SCIENCE BULLETIN,53(15),2342-2352.
MLA Li ZhiQiang,et al."Bayesian mixed models and divergence time estimation of Chinese cavefishes (Cyprinidae : Sinocyclocheilus)".CHINESE SCIENCE BULLETIN 53.15(2008):2342-2352.
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