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Multiple Polyploidization Events across Asteraceae with Two Nested Events in the Early History Revealed by Nuclear Phylogenomics.
Mol Biol Evol. 2016 11; 33(11):2820-2835.MB

Abstract

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.

Authors+Show Affiliations

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.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.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.Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, State College, PA.State Key Laboratory of Evolutionary and Systematic Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China.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.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.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

27604225

Citation

Huang, Chien-Hsun, et al. "Multiple Polyploidization Events Across Asteraceae With Two Nested Events in the Early History Revealed By Nuclear Phylogenomics." Molecular Biology and Evolution, vol. 33, no. 11, 2016, pp. 2820-2835.
Huang CH, Zhang C, Liu M, et al. Multiple Polyploidization Events across Asteraceae with Two Nested Events in the Early History Revealed by Nuclear Phylogenomics. Mol Biol Evol. 2016;33(11):2820-2835.
Huang, C. H., Zhang, C., Liu, M., Hu, Y., Gao, T., Qi, J., & Ma, H. (2016). Multiple Polyploidization Events across Asteraceae with Two Nested Events in the Early History Revealed by Nuclear Phylogenomics. Molecular Biology and Evolution, 33(11), 2820-2835.
Huang CH, et al. Multiple Polyploidization Events Across Asteraceae With Two Nested Events in the Early History Revealed By Nuclear Phylogenomics. Mol Biol Evol. 2016;33(11):2820-2835. PubMed PMID: 27604225.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Multiple Polyploidization Events across Asteraceae with Two Nested Events in the Early History Revealed by Nuclear Phylogenomics. AU - Huang,Chien-Hsun, AU - Zhang,Caifei, AU - Liu,Mian, AU - Hu,Yi, AU - Gao,Tiangang, AU - Qi,Ji, AU - Ma,Hong, Y1 - 2016/09/07/ PY - 2016/9/9/pubmed PY - 2017/6/22/medline PY - 2016/9/9/entrez KW - Asteraceae KW - divergence time estimation KW - orthologous nuclear gene KW - phylogeny KW - transcriptome KW - whole-genome duplication SP - 2820 EP - 2835 JF - Molecular biology and evolution JO - Mol. Biol. Evol. VL - 33 IS - 11 N2 - 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. SN - 1537-1719 UR - https://www.unboundmedicine.com/medline/citation/27604225/Multiple_Polyploidization_Events_across_Asteraceae_with_Two_Nested_Events_in_the_Early_History_Revealed_by_Nuclear_Phylogenomics_ L2 - https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msw157 DB - PRIME DP - Unbound Medicine ER -