Multiple Polyploidization Events across Asteraceae with Two Nested Events in the Early History Revealed by Nuclear Phylogenomics.
Biodiversity results from multiple evolutionary mechanisms, including genetic variation and natural selection. Whole-genome duplications (WGDs), or polyploidizations, provide opportunities for large-scale genetic modifications. Many evolutionarily successful lineages, including angiosperms and vertebrates, are ancient polyploids, suggesting that WGDs are a driving force in evolution. However, this hypothesis is challenged by the observed lower speciation and higher extinction rates of recently formed polyploids than diploids. Asteraceae includes about 10% of angiosperm species, is thus undoubtedly one of the most successful lineages and paleopolyploidization was suggested early in this family using a small number of datasets. Here, we used genes from 64 new transcriptome datasets and others to reconstruct a robust Asteraceae phylogeny, covering 73 species from 18 tribes in six subfamilies. We estimated their divergence times and further identified multiple potential ancient WGDs within several tribes and shared by the Heliantheae alliance, core Asteraceae (Asteroideae-Mutisioideae), and also with the sister family Calyceraceae. For two of the WGD events, there were subsequent great increases in biodiversity; the older one proceeded the divergence of at least 10 subfamilies within 10 My, with great variation in morphology and physiology, whereas the other was followed by extremely high species richness in the Heliantheae alliance clade. Our results provide different evidence for several WGDs in Asteraceae and reveal distinct association among WGD events, dramatic changes in environment and species radiations, providing a possible scenario for polyploids to overcome the disadvantages of WGDs and to evolve into lineages with high biodiversity.
State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China.
Chien-Hsun
CH
Huang
State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China.
Caifei
C
Zhang
State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China.
Mian
M
Liu
Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, State College, PA.
Yi
Y
Hu
State Key Laboratory of Evolutionary and Systematic Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China.
Tiangang
T
Gao
State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China hongma@fudan.edu.cn qij@fudan.edu.cn.
Ji
J
Qi
State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China hongma@fudan.edu.cn qij@fudan.edu.cn.
Hong
H
Ma
D019659:Asteraceae / Q000235:genetics*; D044822:Biodiversity; D005075:Biological Evolution; D030561:Databases, Nucleic Acid; D019143:Evolution, Molecular; D020440:Gene Duplication; D014644:Genetic Variation; D018745:Genome, Plant; D008957:Models, Genetic; D010802:Phylogeny; D011123:Polyploidy; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods; D059467:Transcriptome
Asteraceae; divergence time estimation; orthologous nuclear gene; phylogeny; transcriptome; whole-genome duplication