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Front. Physiol. | doi: 10.3389/fphys.2018.01833

A phylogenomic framework and divergence history of Cephalochordata amphioxus

 Jun-Yuan Chen1*,  Qi-Lin Zhang2, 3, Guan-Ling Zhang3, Zhi-Xiang Dong3, Hong-Wei Li3, Jun Guo3, Feng Wang3, Xian-Yu Deng3 and Lian-Bing Lin3
  • 1Nanjing Institute of Geology and Paleontology (CAS), China
  • 2Nanjing University, China
  • 3Kunming University of Science and Technology, China

Amphioxus, Cephalochordates, is the living proxy of vertebrate ancestor and is widely used as evolutionary biology models of chordates. Their phylogeny, divergence history, and speciation characteristics, however, remains poorly understood, and phylogenomic studies to explore these problems are missing completely. Here, we newly determined the transcriptome of Branchiostoma japonicum. Combined with mass sequences of all other 18 species, a 19-way phylogeny was constructed via multiple methods, which consistently supports a phylogeny of ((B. belcheri + B. japonicum) + (B. lanceolatum + B. floridae) + A. lucayanum) among amphioxus. Congruent phylogenetic signals were found in single mitochondrial genes, 12S RNA, and complete mitochondrial genomes according to previous reports, indicating that 12S RNA may have potential as molecular markers in the phylogenetic analysis of amphioxus. Molecular dating analysis indicated a radiation of the cephalochordates during the Cretaceous (~104-61 million years ago), supporting an association between the diversification and speciation of the cephalochordates with continental drift and associated changes of the 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, indicating that pathogens and changes of energy requirements are an important driving force for amphioxus speciation. This study represents the first large-scale phylogenomic analysis including most major amphioxus genera based on phylogenomic data, providing a new perspective on both phylogeny and divergence speciation of cephalochordates.

Keywords: Cephalochordata, Amphioxus (lancelet), phylogenomics, Divergence history, speciation process, Protein domains, evolutionary genomics

Received: 08 Sep 2018; Accepted: 06 Dec 2018.

Edited by:

Ruriko Yoshida, University of Kentucky, United States

Reviewed by:

Grady Weyenberg, University of Hawaii at Hilo, United States
Neil Moore, University of Kentucky, United States
Joseph Rusinko, Hobart and William Smith Colleges, United States  

Copyright: © 2018 Chen, Zhang, Zhang, Dong, Li, Guo, Wang, Deng and Lin. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Prof. Jun-Yuan Chen, Nanjing Institute of Geology and Paleontology (CAS), Nanjing, China, chenjy@nju.edu.cn