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| 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 | |
| Liu, Bin-Bin; Ren, Chen2,3; Kwak, Myounghai4; Hodel, Richard G. J.; Xu, Chao; He, Jian5; Zhou, Wen-Bin; Huang, Chien-Hsun; Ma, Hong9; Qian, Guan-Ze; Hong, De-Yuan; Wen, Jun1 | |
| 2022 | |
| 发表期刊 | JOURNAL OF INTEGRATIVE PLANT BIOLOGY
 |
| ISSN | 1672-9072 |
| 卷号 | 64期号:5页码:1020-1043 |
| 摘要 | 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 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 events. The nuclear phylogeny recovered the monophyly of Malus s.l. (including Docynia); however, the genus was supported to be biphyletic in the plastid phylogeny. An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance. Our conflict analysis demonstrated that ILS, hybridization, and allopolyploidy could explain the widespread nuclear gene tree discordance. One deep hybridization event (Malus doumeri) and one recent event (Malus coronaria) were detected in Malus s.l. Furthermore, our historical 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 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 |
| 学科领域 | Biochemistry & Molecular Biology ; Plant Sciences |
| DOI | 10.1111/jipb.13246 |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS关键词 | CHLOROPLAST CAPTURE ; MOLECULAR PHYLOGENY ; LAND BRIDGES ; MALOIDEAE ; EVOLUTION ; DISJUNCT ; ROSACEAE ; PACKAGE ; CLIMATE ; TIME |
| WOS研究方向 | Science Citation Index Expanded (SCI-EXPANDED) |
| WOS记录号 | WOS:000795723300001 |
| 出版者 | WILEY |
| 文献子类 | Article |
| 出版地 | HOBOKEN |
| EISSN | 1744-7909 |
| 资助机构 | National Natural Science Foundation of China [32000163, 31620103902] |
| 作者邮箱 | hongdy@ibcas.ac.cn ; wenj@si.edu |
| 引用统计 | |
| 文献类型 | 期刊论文 |
| 条目标识符 | http://ir.ibcas.ac.cn/handle/2S10CLM1/28467 |
| 专题 | 系统与进化植物学国家重点实验室 |
| 作者单位 | 1.Chinese Acad Sci, State Key Lab Systemat & Evolutionary Bot, Inst Bot, Beijing 100093, Peoples R China 2.Smithsonian Inst, Natl Museum Nat Hist, Dept Bot, POB 37012, Washington, DC 20013 USA 3.Chinese Acad Sci, Key Lab Plant Resources Conservat & Sustainable U, South China Bot Garden, Guangzhou 510650, Peoples R China 4.Chinese Acad Sci, South China Bot Garden, Guangdong Prov Key Lab Appl Bot, Guangzhou 510650, Peoples R China 5.Natl Inst Biol Resources, Incheon 22689, South Korea 6.Beijing Forestry Univ, Sch Ecol & Nat Conservat, Beijing 100083, Peoples R China 7.North Carolina State Univ, Dept Plant & Microbial Biol, Raleigh, NC 27965 USA 8.Fudan Univ, State Key Lab Genet Engn, Minist Educ,Ctr Evolutionary Biol,Sch Life Sci, Key Lab Biodivers & Ecol Engn,Inst Plant Biol, Shanghai 200433, Peoples R China 9.Fudan Univ, Sch Life Sci,Collaborat Innovat Ctr Genet & Dev, Ctr Evolutionary Biol,Minist Educ, Key Lab Biodivers & Ecol Engn,Inst Plant Biol, Shanghai 200433, Peoples R China 10.Penn State Univ, Huck Inst Life Sci, Dept Biol, 510D Mueller Lab, University Pk, PA 16802 USA 11.Liaocheng Univ, Coll Life Sci, Liaocheng 252059, Shandong, Peoples R China |
| 推荐引用方式 GB/T 7714 | Liu, Bin-Bin,Ren, Chen,Kwak, Myounghai,et al. 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]. JOURNAL OF INTEGRATIVE PLANT BIOLOGY,2022,64(5):1020-1043. |
| APA | Liu, Bin-Bin.,Ren, Chen.,Kwak, Myounghai.,Hodel, Richard G. J..,Xu, Chao.,...&Wen, Jun.(2022).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.JOURNAL OF INTEGRATIVE PLANT BIOLOGY,64(5),1020-1043. |
| MLA | Liu, Bin-Bin,et al."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".JOURNAL OF INTEGRATIVE PLANT BIOLOGY 64.5(2022):1020-1043. |
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| Phylogenomic_conflic（3053KB） | 期刊论文 | 出版稿 | 开放获取 | CC BY-NC-SA | 浏览 请求全文 | |
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