Parallel ddRAD and Genome Skimming Analyses Reveal a Radiative and Reticulate Evolutionary History of the Temperate Bamboos

doi:10.1093/sysbio/syaa076

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	Parallel ddRAD and Genome Skimming Analyses Reveal a Radiative and Reticulate Evolutionary History of the Temperate Bamboos
	Guo,Cen ; Ma,Peng-Fei ; Yang,Guo-Qian ; Ye,Xia-Ying ; Guo,Ying ; Liu,Jing-Xia ; Liu,Yun-Long ; Eaton,Deren A. R.; Guo,Zhen-Hua; Li,De-Zhu
	2021
发表期刊	SYSTEMATIC BIOLOGY
ISSN	1063-5157
卷号	70 期号:4 页码:756-773
摘要	Rapid evolutionary radiations are among the most challenging phylogenetic problems, wherein different types of data (e.g., morphology and molecular) or genetic markers (e.g., nuclear and organelle) often yield inconsistent results. The tribe Arundinarieae, that is, the temperate bamboos, is a Glade of tetraploid originated 22 Ma and subsequently radiated in East Asia. Previous studies of Arundinarieae have found conflicting relationships and/or low support. Here, we obtain nuclear markers from ddRAD data for 213 Arundinarieae taxa and parallel sampling of chloroplast genomes from genome skimming for 147 taxa. We first assess the feasibility of using ddRAD-seq data for phylogenetic estimates of paleopolyploid and rapidly radiated lineages, optimize clustering thresholds, and analysis workflow for orthology identification. Reference-based ddRAD data assembly approaches perform well and yield strongly supported relationships that are generally concordant with morphology-based taxonomy. We recover five major lineages, two of which are notable (the pachymorph and leptomorph lineages), in that they correspond with distinct rhizome morphologies. By contrast, the phylogeny from chloroplast genomes differed significantly. Based on multiple lines of evidence, the ddRAD tree is favored as the best species tree estimation for temperate bamboos. Using a time-calibrated ddRAD tree, we find that Arundinarieae diversified rapidly around the mid-Miocene corresponding with intensification of the East Asian monsoon and the evolution of key innovations including the leptomorph rhizomes. Our results provide a highly resolved phylogeny of Arundinarieae, shed new light on the radiation and reticulate evolutionary history of this tribe, and provide an empirical example for the study of recalcitrant plant radiations.
关键词	Arundinarieae ddRAD paleopolyploid genome skimming rapid diversification incongruence ARUNDINARIEAE POACEAE BAMBUSOIDEAE SOUTH CHINA SEA WOODY BAMBOOS PHYLOGENOMIC ANALYSES ADAPTIVE RADIATION ECOLOGICAL OPPORTUNITY PLANT DIVERSIFICATION ASIAN MONSOON RADSEQ DATA GENE TREES
DOI	10.1093/sysbio/syaa076
WOS记录号	WOS:000671573900009
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/73658
专题	中国科学院昆明植物研究所
作者单位	1.[Guo, Cen 2.Ma, Peng-Fei 3.Yang, Guo-Qian 4.Ye, Xia-Ying 5.Guo, Ying 6.Liu, Jing-Xia 7.Liu, Yun-Long 8.Guo, Zhen-Hua 9.Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, Kunming 650201, Yunnan, Peoples R China 10.Univ Chinese Acad Sci, Kunming Coll Life Sci, Kunming 650201, Yunnan, Peoples R China 11.[Eaton, Deren A. R.] Columbia Univ, Dept Ecol Evolut & Environm Biol, New York, NY 10027 USA
推荐引用方式 GB/T 7714	Guo,Cen,Ma,Peng-Fei,Yang,Guo-Qian,et al. Parallel ddRAD and Genome Skimming Analyses Reveal a Radiative and Reticulate Evolutionary History of the Temperate Bamboos[J]. SYSTEMATIC BIOLOGY,2021,70(4):756-773.
APA	Guo,Cen.,Ma,Peng-Fei.,Yang,Guo-Qian.,Ye,Xia-Ying.,Guo,Ying.,...&Li,De-Zhu.(2021).Parallel ddRAD and Genome Skimming Analyses Reveal a Radiative and Reticulate Evolutionary History of the Temperate Bamboos.SYSTEMATIC BIOLOGY,70(4),756-773.
MLA	Guo,Cen,et al."Parallel ddRAD and Genome Skimming Analyses Reveal a Radiative and Reticulate Evolutionary History of the Temperate Bamboos".SYSTEMATIC BIOLOGY 70.4(2021):756-773.