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A Phylogenomic Framework and Divergence History of Cephalochordata Amphioxus
Zhang, Qi-Lin1,2; Zhang, Guan-Ling1; Yuan, Ming-Long3; Dong, Zhi-Xiang1; Li, Hong-Wei1; Guo, Jun1; Wang, Feng1; Deng, Xian-Yu1; Chen, Jun-Yuan (陈均远)2,4; Lin, Lian-Bing1
2018-12-18
Source PublicationFRONTIERS IN PHYSIOLOGY
ISSN1664-042X
Volume9Pages:13
Abstract

Amphioxus, or cephalochordates, are often used as the living invertebrate proxy of vertebrate ancestors and are widely used as evolutionary biology models of chordates. However, their phylogeny, divergence history, and speciation characteristics remain poorly understood, and phylogenomic studies to explore these problems lacking entirely from the literature. Here, we determined a new transcriptome of Branchiostoma japonicum. Combined with mass sequences of all other 18 species, a 19-way phylogeny was constructed via multiple methods (ML, BI, PhyloBayes, and ASTRAL), consistently supporting a phylogeny of [(B. belched + B. japonicum) + (B. lanceolatum + B. floridae) + Asymmetron lucayanum] in amphioxus. Congruent phylogenetic signals were found across mitochondrial genes, 12S RNA, and complete mitochondrial genomes according to previous reports, indicating that 12S RNA may have potential as a molecular marker for phylogenetic analysis in amphioxus. Molecular dating analysis indicated a radiation of the cephalochordates during the Cretaceous (similar to 104-61 million years ago), supporting an association between the diversification and speciation of cephalochordates with continental drift and associated changes in their respective habitats during this time. The identified functional enrichment analysis for species-specific domains indicated that their function mainly involves immune response, apoptosis, and lipid metabolism and utilization, signaling that pathogens and changes of energy requirements are an important driving force for amphioxus speciation. This study represents the first large-scale phylogenomic analysis of most major amphioxus genera based on phylogenomic data, providing a new perspective on both phylogeny and divergence speciation of cephalochordates.

KeywordCephalochordata Amphioxus Phylogenomics Divergence History Speciation Process Protein Domains Evolutionary Genomics
DOI10.3389/fphys.2018.01833
Language英语
WOS KeywordAsymmetron-lucayanum ; Molecular Evolution ; Absolute Rates ; Genome ; Model ; Times ; Transcriptome ; Annotation ; Sequences ; Orthologs
Funding ProjectNational Natural Science Foundation of China[31760042] ; National Natural Science Foundation of China[41272008] ; program B for Outstanding Ph.D. candidate of Nanjing University[201702B075]
WOS Research AreaPhysiology
WOS SubjectPhysiology
WOS IDWOS:000453704400001
Funding OrganizationNational Natural Science Foundation of China ; program B for Outstanding Ph.D. candidate of Nanjing University
PublisherFRONTIERS MEDIA SA
Citation statistics
Document Type期刊论文
Identifierhttp://ir.nigpas.ac.cn/handle/332004/16183
Collection中国科学院南京地质古生物研究所
其他
Corresponding AuthorChen, Jun-Yuan (陈均远); Lin, Lian-Bing
Affiliation1.Kunming Univ Sci & Technol, Fac Life Sci & Technol, Kunming, Yunnan, Peoples R China
2.Nanjing Univ, Sch Life Sci, Evodevo Inst, Nanjing, Jiangsu, Peoples R China
3.Lanzhou Univ, Coll Pastoral Agr Sci & Technol, State Key Lab Grassland Agroecosyst, Lanzhou, Gansu, Peoples R China
4.Chinese Acad Sci, Nanjing Inst Geol & Palaeontol, State Key Lab Palaeobiol & Stratig LPS, Nanjing, Jiangsu, Peoples R China
Corresponding Author AffilicationNanjing Institute of Geology and Palaeonotology,CAS
Recommended Citation
GB/T 7714
Zhang, Qi-Lin,Zhang, Guan-Ling,Yuan, Ming-Long,et al. A Phylogenomic Framework and Divergence History of Cephalochordata Amphioxus[J]. FRONTIERS IN PHYSIOLOGY,2018,9:13.
APA Zhang, Qi-Lin.,Zhang, Guan-Ling.,Yuan, Ming-Long.,Dong, Zhi-Xiang.,Li, Hong-Wei.,...&Lin, Lian-Bing.(2018).A Phylogenomic Framework and Divergence History of Cephalochordata Amphioxus.FRONTIERS IN PHYSIOLOGY,9,13.
MLA Zhang, Qi-Lin,et al."A Phylogenomic Framework and Divergence History of Cephalochordata Amphioxus".FRONTIERS IN PHYSIOLOGY 9(2018):13.
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