KIB OpenIR
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
Source PublicationSYSTEMATIC BIOLOGY
ISSN1063-5157
Volume70Issue:4Pages:756-773
AbstractRapid 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.
KeywordArundinarieae 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
DOI10.1093/sysbio/syaa076
WOS IDWOS:000671573900009
Citation statistics
Document Type期刊论文
Identifierhttp://ir.kib.ac.cn/handle/151853/73658
Collection中国科学院昆明植物研究所
Affiliation1.[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
Recommended Citation
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.
Files in This Item:
There are no files associated with this item.
Related Services
Recommend this item
Bookmark
Usage statistics
Export to Endnote
Google Scholar
Similar articles in Google Scholar
[Guo,Cen]'s Articles
[Ma,Peng-Fei]'s Articles
[Yang,Guo-Qian]'s Articles
Baidu academic
Similar articles in Baidu academic
[Guo,Cen]'s Articles
[Ma,Peng-Fei]'s Articles
[Yang,Guo-Qian]'s Articles
Bing Scholar
Similar articles in Bing Scholar
[Guo,Cen]'s Articles
[Ma,Peng-Fei]'s Articles
[Yang,Guo-Qian]'s Articles
Terms of Use
No data!
Social Bookmark/Share
All comments (0)
No comment.
 

Items in the repository are protected by copyright, with all rights reserved, unless otherwise indicated.