Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In this study, 785 single-copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic rela-tionships and estimate the historical biogeography of the apple genus Malus sensu lato, an econo-mically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events. The nuclear phylogeny recovered the monophyly of Malus s.l. (including Docynia); however, the genus was supported to be biphyletic in the plastid phy-logeny. An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance. Our conflict analysis dem-onstrated that ILS, hybridization, and allopolyploidy could explain the widespread nuclear gene tree dis-cordance. One deep hybridization event (Malus doumeri) and one recent event (Malus coronaria) were detected in Malus s.l. Furthermore, our histor-ical biogeographic analysis integrating living and fossil data supported a widespread East Asian-western North American origin of Malus s.l. in the Eocene, followed by several extinction and dispersal events in the Northern Hemisphere. We also propose a general workflow for assessing phylogenomic dis-cordance and biogeographic analysis using deep genome skimming data sets.

Bin-Bin Liu;Chen Ren;Myounghai Kwak;Richard G.J.Hodel;Chao Xu;Jian He;Wen-Bin Zhou;Chien-Hsun Huang;Hong Ma;Guan-Ze Qian;De-Yuan Hong;Jun Wen

State Key Laboratory of Systematic and Evolutionary Botany,Institute of Botany,the Chinese Academy of Sciences,Beijing 100093,China;Department of Botany,National Museum of Natural History,Smithsonian Institution,PO Box 37012,Washington 20013–7012,DC,USA;Key Laboratory of Plant Resources Conservation and Sustainable Utilization,South China Botanical Garden,The Chinese Academy of Sciences,Guangzhou 510650,China;Guangdong Provincial Key Laboratory of Applied Botany,South China Botanical Garden,The Chinese Academy of Sciences,Guangzhou 510650,China;National Institute of Biological Resources,Incheon 22689,South Korea;School of Ecology and Nature Conservation,Beijing Forestry University,Beijing 100083,China;Department of Plant and Microbial Biology,North Carolina State University,Raleigh 27965,NC,USA;State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development,Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering,Institute of Plant Biology,Center of Evolutionary Biology,School of Life Sciences,Fudan University,Shanghai 200433,China;Department of Biology,Huck Institutes of the Life Sciences,Pennsylvania State University,510D Mueller Laboratory,University Park,Pennsylvania 16802,USA;College of Life Sciences,Liaocheng University,Liaocheng 252059,China

植物学报（英文版）

[1]Bin-Bin Liu;Chen Ren;Myounghai Kwak;Richard G.J.Hodel;Chao Xu;Jian He;Wen-Bin Zhou;Chien-Hsun Huang;Hong Ma;Guan-Ze Qian;De-Yuan Hong;Jun Wen-.Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere)[J].植物学报（英文版）,2022(05):1020-1043

allopolyploidy,mically,disjunctly,Docynia,biphyletic,logeny,cordance,doumeri,coronaria

Phylogenomic,analyses,apple,genus,Malus,reveal,widespread,hybridization,driving,diversification,insights,into,complex,biogeographic,history,Northern,Hemisphere,evidence,from,increasing,number,studies,has,demonstrated,that,different,data,sets,analytical,approaches,often,reconstruct,strongly,supported,conflicting,relationships,In,this,study,single,copy,genes,complete,plastomes,were,used,infer,phylogenetic,estimate,historical,biogeography,sensu,lato,econo,important,lineage,distributed,involved,known,suspected,events,phylogeny,recovered,monophyly,including,however,was,plastid,An,ancient,chloroplast,capture,Eocene,western,best,explains,cytonuclear,discordance,Our,analysis,ILS,could,tree,One,deep,one,recent,detected,Furthermore,our,integrating,living,fossil,East,Asian,American,origin,followed,by,several,extinction,dispersal,We,also,propose,general,workflow,assessing,phylogenomic,using,genome,skimming

0.517044