Plastid phylogenomic analyses of Fagales reveal signatures of conflict and ancient chloroplast capture

doi:10.1016/j.ympev.2021.107232

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	Plastid phylogenomic analyses of Fagales reveal signatures of conflict and ancient chloroplast capture
	Yang,Ying-Ying ; Qu,Xiao-Jian ; Zhang,Rong ; Stull,Gregory W.; Yi,Ting-Shuang
	2021
发表期刊	MOLECULAR PHYLOGENETICS AND EVOLUTION
ISSN	1055-7903
卷号	163 页码:107232
摘要	Plastid phylogenomic analyses have shed light on many recalcitrant relationships across the angiosperm Tree of Life and continue to play an important role in plant phylogenetics alongside nuclear data sets given the utility of plastomes for revealing ancient and recent introgression. Here we conduct a plastid phylogenomic study of Fagales, aimed at exploring contentious relationships (e.g., the placement of Myricaceae and some intergeneric relationships in Betulaceae, Juglandaceae, and Fagaceae) and dissecting conflicting phylogenetic signals across the plastome. Combining 102 newly sequenced samples with publically available plastomes, we analyzed a dataset including 256 species and 32 of the 34 total genera of Fagales, representing the largest plastome-based study of the order to date. We find strong support for a sister relationship between Myricaceae and Juglandaceae, as well as strongly supported conflicting signal for alternative generic relationships in Betulaceae and Juglandaceae. These conflicts highlight the sensitivity of plastid phylogenomic analyses to genic composition, perhaps due to the prevalence of uninformative loci and heterogeneity in signal across different regions of the plastome. Phylogenetic relationships were geographically structured in subfamily Quercoideae, with Quercus being nonmonophyletic and its sections forming clades with co-distributed Old World or New World genera of Quercoideae. Compared against studies based on nuclear genes, these results suggest extensive introgression and chloroplast capture in the early diversification of Quercus and Quercoideae. This study provides a critical plastome perspective on Fagales phylogeny, setting the stage for future studies employing more extensive data from the nuclear genome.
关键词	Betulaceae Juglandaceae Myricaceae Quercus Phylogenetics Chloroplast capture RESTRICTION SITE VARIATION INTERSPECIFIC GENE FLOW DNA-SEQUENCES EVOLUTIONARY HISTORY MOLECULAR PHYLOGENY CLADISTIC-ANALYSIS SEED PLANTS NUCLEAR BETULACEAE DIVERSIFICATION
DOI	10.1016/j.ympev.2021.107232
WOS记录号	WOS:000687260600008
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/73310
专题	中国科学院昆明植物研究所
作者单位	1.[Yang, Ying-Ying 2.Zhang, Rong 3.Stull, Gregory W. 4.Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, Kunming 650201, Yunnan, Peoples R China 5.Univ Chinese Acad Sci, Kunming Coll Life Sci, Kunming 650201, Yunnan, Peoples R China 6.Chinese Acad Sci, Kunming Inst Bot, CAS Key Lab Plant Divers & Biogeog East Asia, Kunming 650201, Yunnan, Peoples R China 7.Shandong Normal Univ, Coll Life Sci, Shandong Prov Key Lab Plant Stress Res, Jinan 250014, Shandong, Peoples R China
推荐引用方式 GB/T 7714	Yang,Ying-Ying,Qu,Xiao-Jian,Zhang,Rong,et al. Plastid phylogenomic analyses of Fagales reveal signatures of conflict and ancient chloroplast capture[J]. MOLECULAR PHYLOGENETICS AND EVOLUTION,2021,163:107232.
APA	Yang,Ying-Ying,Qu,Xiao-Jian,Zhang,Rong,Stull,Gregory W.,&Yi,Ting-Shuang.(2021).Plastid phylogenomic analyses of Fagales reveal signatures of conflict and ancient chloroplast capture.MOLECULAR PHYLOGENETICS AND EVOLUTION,163,107232.
MLA	Yang,Ying-Ying,et al."Plastid phylogenomic analyses of Fagales reveal signatures of conflict and ancient chloroplast capture".MOLECULAR PHYLOGENETICS AND EVOLUTION 163(2021):107232.

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