Phylogenomic analysis of the hemp family(Cannabaceae)reveals deep cyto-nuclear discordance and provides new insights into generic relationships  

作　　者：Xiao-Gang Fu Shui-Yin Liu Robin van Velzen Gregory WStull Qin Tian Yun-Xia Li Ryan A.Folk Robert P.Guralnick Heather R.Kates Jian-Jun Jin Zhong-Hu Li Douglas E.Soltis Pamela S.Soltis Ting-Shuang Yi 

机构地区：[1]Key Laboratory of Resource Biology and Biotechnology in Western China,Ministry of Education,College of Life Sciences,Northwest University,Xi'an 710069,China [2]Germplasm Bank of Wild Species,Kunming Institute of Botany,Chinese Academy of Sciences,Kunming 650201,China [3]University of Chinese Academy of Sciences,Beijing 100049,China [4]Biosystematics Group,Wageningen University and Research Center,Wageningen 6708 PB,the Netherlands [5]Department of Biological Sciences,Mississippi State University,Starkville,MS 39762,USA [6]Florida Museum of Natural History,University of Florida,Gainesville,FL 32611,USA [7]Department of Ecology,Evolution,and Environmental Biology,Columbia University,New York,NY 10027,USA [8]Department of Biology,University of Florida,Gainesville,FL 32611,USA

出　　处：《Journal of Systematics and Evolution》2023年第5期806-826,共21页植物分类学报（英文版）

基　　金：supported by the National Natural Science Foundation of China,key international(regional)cooperative research project(No.31720103903);the Strategic Priority Research Program of Chinese Academy of Sciences(No.XDB310o000o);the Science and Technology Basic Resources Investigation Program of China(No.2019FY100900);the Large-scale Scientific Facilities of the Chinese Academy of Sciences(No.2017-LSF-GBOWS-02);the National Natural Science Foundation of China(No.31270274);the Yunling International High-end Experts Program of Yunnan Province,China(No.YNQR-GDWG-2017-002 and No.YNQR-GDWG-2018-012);the CAS President's International Fellowship Initiative(No.2020PBo009);the China Postdoctoral Science Foundation(CPSF)International Postdoctoral Exchange Program,and the CAS Special Research Assistant Project;supported in part by USA Department of Energy grant DE-SCo018247.We are grateful to the following institutes for providing specimens or silica-dried materials:Herbarium of Kunming Institute of Botany,Chinese Academy of Sciences;the Germplasm Bank of Wild Species in the Southwest China and Molecular Biology Experiment Center,Kunming Institute of Botany,Chinese Academy of Sciences;the herbarium of the California Academy of Sciences;the Harvard University Herbaria;University of Texas at Austin Herbarium;The Ohio State University Herbarium;National Herbarium of the Netherlands;and the herbaria of the Royal Botanic Gardens,Kew,the Missouri Botanical Garden,the New York Botanical Garden,the San Francisco Botanical Garden,and the California Botanical Garden.We are also grateful to Prof.Susanne S.Renner for providing Cannabaceae materials;to Jiajin Wu for help with sampling;to Prof.Huafeng Wang,Dr.Diego F.Morales-Briones,Dr.Nelson Zamora Villalobos,Dr.Rong Zhang,Dr.Hui Liu,Siyun Chen,Chenxuan Yang,Yingying Yang,and Henrique Borges Zamengo for their generous technical support and necessary assistance;and to the iFlora High Performance Computing Center of Germplasm Bank of Wild Species(iFlora HPC Center of GBOWS,KIB,CAS)for computing.

摘　　要：Cannabaceae are a relatively small family of angiosperms,but they include several species of huge economic and cultural significance:marijuana or hemp(Cannabis sativa)and hops(Humulus lupulus).Previous phylogenetic studies have clarified the most deep relationships in Cannabaceae,but relationships remain ambiguous among several major lineages.Here,we sampled 82 species representing all genera of Cannabaceae and utilized a new dataset of 90 nuclear genes and 82 chloroplast loci from Hyb-Seq to investigate the phylogenomics of Cannabaceae.Nuclear phylogenetic analyses revealed a robust and consistent backbone for Cannabaceae.We observed nuclear gene-tree conflict at several deep nodes in inferred species trees,also cyto-nuclear discordance concerning the relationship between Gironniera and Lozanella and the relationships among Trema s.l.(including Parasponia),Cannabis+Humulus,and Chaetachme+Pteroceltis.Coalescent simulations and network analyses suggest that observed deep cyto-nuclear discordances were most likely to stem from incomplete lineage sorting(ILS);nuclear gene-tree conflict might be caused by both ILS and gene flow between species.All genera of Cannabaceae were recovered as monophyletic,except for Celtis,which consisted of two distinct clades:Celtis I(including most Celtis species)and Celtis II(including Celtis gomphophylla and Celtis schippii).We suggest that Celtis II should be recognized as the independent genus Sparrea based on both molecular and morphological evidence.Our work provides the most comprehensive and reliable phylogeny to date for Cannabaceae,enabling further exploration of evolutionary patterns across this family and highlighting the necessity of comparing nuclear with chloroplast data to examine the evolutionary history of plant groups.

关 键 词：ancient hybridization CANNABACEAE CELTIS classification cyto-nuclear discordance incomplete lineage sorting PHYLOGENOMICS Sparrea 

分 类 号：Q94[生物学—植物学]