Phylogenomic approaches untangle early divergences and complex diversifications of the olive plant family

doi:10.1186/s12915-022-01297-0

	Phylogenomic approaches untangle early divergences and complex diversifications of the olive plant family
	Dong, Wenpan ; Li, Enze ; Liu, Yanlei 1; Xu, Chao 1; Wang, Yushuang ; Liu, Kangjia ; Cui, Xingyong ; Sun, Jiahui 2; Suo, Zhili 1; Zhang, Zhixiang ; Wen, Jun 3; Zhou, Shiliang 1
	2022
发表期刊	BMC BIOLOGY
卷号	20 期号:1
摘要	Background Deep-branching phylogenetic relationships are often difficult to resolve because phylogenetic signals are obscured by the long history and complexity of evolutionary processes, such as ancient introgression/hybridization, polyploidization, and incomplete lineage sorting (ILS). Phylogenomics has been effective in providing information for resolving both deep- and shallow-scale relationships across all branches of the tree of life. The olive family (Oleaceae) is composed of 25 genera classified into five tribes with tribe Oleeae consisting of four subtribes. Previous phylogenetic analyses showed that ILS and/or hybridization led to phylogenetic incongruence in the family. It was essential to distinguish phylogenetic signal conflicts, and explore mechanisms for the uncertainties concerning relationships of the olive family, especially at the deep-branching nodes. Results We used the whole plastid genome and nuclear single nucleotide polymorphism (SNP) data to infer the phylogenetic relationships and to assess the variation and rates among the main clades of the olive family. We also used 2608 and 1865 orthologous nuclear genes to infer the deep-branching relationships among tribes of Oleaceae and subtribes of tribe Oleeae, respectively. Concatenated and coalescence trees based on the plastid genome, nuclear SNPs and multiple nuclear genes suggest events of ILS and/or ancient introgression during the diversification of Oleaceae. Additionally, there was extreme heterogeneity in the substitution rates across the tribes. Furthermore, our results supported that introgression/hybridization, rather than ILS, is the main factor for phylogenetic discordance among the five tribes of Oleaceae. The tribe Oleeae is supported to have originated via ancient hybridization and polyploidy, and its most likely parentages are the ancestral lineage of Jasmineae or its sister group, which is a ghost lineage, and Forsythieae. However, ILS and ancient introgression are mainly responsible for the phylogenetic discordance among the four subtribes of tribe Oleeae. Conclusions This study showcases that using multiple sequence datasets (plastid genomes, nuclear SNPs and thousands of nuclear genes) and diverse phylogenomic methods such as data partition, heterogeneous models, quantifying introgression via branch lengths (QuIBL) analysis, and species network analysis can facilitate untangling long and complex evolutionary processes of ancient introgression, paleopolyploidization, and ILS.
关键词	Ancient introgression Gene tree conflict Incomplete lineage sorting Oleaceae Phylogenomics Rate heterogeneity
学科领域	Biology
DOI	10.1186/s12915-022-01297-0
收录类别	SCI
语种	英语
WOS关键词	NUCLEAR RIBOSOMAL DNA ; GENE TREE DISCORDANCE ; MOLECULAR EVOLUTION ; SUBSTITUTION RATES ; LIFE-HISTORY ; GENOME ; SEQUENCE ; OLEACEAE ; SELECTION ; ALIGNMENT
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
WOS记录号	WOS:000787304100002
出版者	BMC
文献子类	Article
出版地	LONDON
EISSN	1741-7007
资助机构	CACMS Innovation Fund ; Science and Technology Basic Resources Investigation Program of China [2021FY100200]
作者邮箱	wpdong@bjfu.edu.cn ; sunjh_2010@sina.com ; wenj@si.edu
作品OA属性	Green Published, gold
引用统计	被引频次：26[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/28901
专题	系统与进化植物学国家重点实验室
作者单位	1.Beijing Forestry Univ, Sch Ecol & Nat Conservat, Lab Systemat Evolut & Biogeog Woody Plants, Beijing 100083, Peoples R China 2.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China 3.China Acad Chinese Med Sci, Natl Resource Ctr Chinese Mat Med, State Key Lab Breeding Base Daodi Herbs, Beijing 100700, Peoples R China 4.Smithsonian Inst, Natl Museum Nat Hist, Dept Bot, Washington, DC 20013 USA
推荐引用方式 GB/T 7714	Dong, Wenpan,Li, Enze,Liu, Yanlei,et al. Phylogenomic approaches untangle early divergences and complex diversifications of the olive plant family[J]. BMC BIOLOGY,2022,20(1).
APA	Dong, Wenpan.,Li, Enze.,Liu, Yanlei.,Xu, Chao.,Wang, Yushuang.,...&Zhou, Shiliang.(2022).Phylogenomic approaches untangle early divergences and complex diversifications of the olive plant family.BMC BIOLOGY,20(1).
MLA	Dong, Wenpan,et al."Phylogenomic approaches untangle early divergences and complex diversifications of the olive plant family".BMC BIOLOGY 20.1(2022).

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