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Phylogenomic conflict analyses in the apple genus Malus *** widespread hybridization and allopolyploidy driving diversification,with insights into the complex biogeographic history in the Northern Hemisphere

引用

Journal of Integrative Plant Biology 2022年第5期64卷 1020-1043页

作者： Bin-Bin Liu Chen Ren Myounghai Kwak Richard GJHodel 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 Botanythe Chinese Academy of SciencesBeijing 100093China Department of Botany National Museum of Natural HistorySmithsonian InstitutionPO Box 37012Washington 20013–7012DCUSA Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical GardenThe Chinese Academy of SciencesGuangzhou 510650China Guangdong Provincial Key Laboratory of Applied Botany South China Botanical GardenThe Chinese Academy of SciencesGuangzhou 510650China National Institute of Biological Resources Incheon 22689South Korea School of Ecology and Nature Conservation Beijing Forestry UniversityBeijing 100083China Department of Plant and Microbial Biology North Carolina State UniversityRaleigh 27965NCUSA State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development Ministry of Education Key Laboratory of Biodiversity and Ecological EngineeringInstitute of Plant BiologyCenter of Evolutionary BiologySchool of Life SciencesFudan UniversityShanghai 200433China Department of Biology Huck Institutes of the Life SciencesPennsylvania State University510D Mueller LaboratoryUniversity ParkPennsylvania 16802USA College of Life Sciences Liaocheng UniversityLiaocheng 252059China

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

关键词： deep genome skimming genomic discordance historical biogeography massive extinction reticulate evolution single-copy nuclear genes

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