Phylogenomics of Fargesia and Yushania reveals a history of reticulate evolution

doi:10.1111/jse.12719

KIB OpenIR

	Phylogenomics of Fargesia and Yushania reveals a history of reticulate evolution
	Ye,Xia-Ying ; Ma,Peng-Fei ; Guo,Cen ; Li,De-Zhu
	2021
发表期刊	JOURNAL OF SYSTEMATICS AND EVOLUTION
ISSN	1674-4918
卷号	59 期号:6 页码:1183-1197
摘要	Reticulate evolution is a common and important driving force in angiosperm evolution. In this study, we analyzed the phylogenetic signals of genomic regions with different inheritance patterns to understand the evolutionary process of organisms using species-rich Himalaya-Hengduan taxa of bamboos (Fargesia Franchet and Yushania Keng). We constructed phylogenetic trees using different sampling strategies and reconstruction methods based on genome skimming and double digest restriction-site-associated DNA sequencing data. We assessed the congruence of topologies generated from different datasets and employed several approaches to reveal the causes of phylogenetic incongruence, including the detection of hybridization and introgression using PhyloNetworks and the D-statistic test (ABBA-BABA test). We found that, in the plastome-based phylogeny, Fargesia bamboos can be clustered into three groups and Yushania was nested within one of them, which contradicts the nuclear-double digest restriction-site-associated DNA sequencing-based phylogeny. Moreover, the genetic variation of chloroplast DNA is significantly correlated with geographical distribution. The strong signal of incomplete lineage sorting, hybridization, introgression, and cytoplasmic gene flow found among genera and species suggests that reticulate evolution is the main cause for the phylogenetic incongruence between nuclear and chloroplast datasets. Our results add evidence that genomes with different inheritance patterns can reveal distinct evolutionary histories of species and suggest that reticulate evolution is prevalent in rapidly diversifying groups.
关键词	plastome ddRAD Fargesia phylogenetic incongruence reticulate evolution Yushania CONFLICTING GENE TREES BAMBOOS POACEAE ARUNDINARIEAE POACEAE PHYLOGENETIC-RELATIONSHIPS MORPHOLOGICAL EVOLUTION BALANCING SELECTION THAMNOCALAMUS GROUP ALLIES GRAMINEAE RADSEQ DATA GBSSI GENE
DOI	10.1111/jse.12719
WOS记录号	WOS:000637830100001
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/73542
专题	中国科学院昆明植物研究所
作者单位	1.[Ye, Xia-Ying 2.Ma, Peng-Fei 3.Guo, Cen 4.Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, Kunming 650201, Yunnan, Peoples R China 5.Zhaotong Univ, Agron & Life Sci Dept, Zhaotong 657000, Yunnan, Peoples R China
推荐引用方式 GB/T 7714	Ye,Xia-Ying,Ma,Peng-Fei,Guo,Cen,et al. Phylogenomics of Fargesia and Yushania reveals a history of reticulate evolution[J]. JOURNAL OF SYSTEMATICS AND EVOLUTION,2021,59(6):1183-1197.
APA	Ye,Xia-Ying,Ma,Peng-Fei,Guo,Cen,&Li,De-Zhu.(2021).Phylogenomics of Fargesia and Yushania reveals a history of reticulate evolution.JOURNAL OF SYSTEMATICS AND EVOLUTION,59(6),1183-1197.
MLA	Ye,Xia-Ying,et al."Phylogenomics of Fargesia and Yushania reveals a history of reticulate evolution".JOURNAL OF SYSTEMATICS AND EVOLUTION 59.6(2021):1183-1197.