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Phylogenomic analyses of large-scale nuclear genes provide new insights into the evolutionary relationships within the rosids
Zhao, Lei1,2; Li, Xia1; Zhang, Ning3; Zhang, Shu-Dong1; Yi, Ting-Shuang1; Ma, Hong4; Guo, Zhen-Hua1; Li, De-Zhu1
2016-12-01
Source PublicationMOLECULAR PHYLOGENETICS AND EVOLUTION
Volume105Issue:1Pages:166-176
AbstractThe Rosids is one of the largest groups of flowering plants, with 140 families and 70,000 species. Previous phylogenetic studies of the rosids have primarily utilized organelle genes that likely differ in evolutionary histories from nuclear genes. To better understand the evolutionary history of rosids, it is necessary to investigate their phylogenetic relationships using nuclear genes. Here, we employed large-scale phylogenomic datasets composed of nuclear genes, including 891 clusters of putative orthologous genes. Combined with comprehensive taxon sampling covering 63 species representing 14 out of the 17 orders, we reconstructed the rosids phylogeny with coalescence and concatenation methods, yielding similar tree topologies from all datasets. However, these topologies did not agree on the placement of Zygophyllales. Through comprehensive analyses, we found that missing data and gene tree heterogeneity were potential factors that may mislead concatenation methods, in particular, large amounts of missing data under high gene tree heterogeneity. Our results provided new insights into the deep phylogenetic relationships of the rosids, and demonstrated that coalescence methods may effectively resolve the phylogenetic relationships of the rosids with missing data under high gene tree heterogeneity. (C) 2016 Elsevier Inc. All rights reserved.
KeywordCoalescence Rosids Phylogenomics Nuclear Genes Gene Tree Species Tree
DOI10.1016/j.ympev.2016.06.007
Indexed BySCI
Language英语
WOS Research AreaBiochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
WOS SubjectBiochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
WOS IDWOS:000384964700014
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Cited Times:6[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.kib.ac.cn/handle/151853/33537
Collection中国西南野生生物种质资源库
Affiliation1.Chinese Acad Sci, Kunming Inst Bot, Plant Germplasm & Genom Ctr, Germplasm Bank Wild Species, Kunming 650201, Yunnan, Peoples R China
2.Univ Chinese Acad Sci, Kunming Coll Life Sci, Kunming 650201, Yunnan, Peoples R China
3.Smithsonian Inst, Natl Museum Nat Hist, Dept Bot, MRC 166, Washington, DC 20013 USA
4.Fudan Univ, Minist Educ, Key Lab Biodivers Sci & Ecol Engn,Sch Life Sci, Inst Plant Biol,Inst Biodivers Sci,Ctr Evolutiona, Shanghai 200032, Peoples R China
Recommended Citation
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Zhao, Lei,Li, Xia,Zhang, Ning,et al. Phylogenomic analyses of large-scale nuclear genes provide new insights into the evolutionary relationships within the rosids[J]. MOLECULAR PHYLOGENETICS AND EVOLUTION,2016,105(1):166-176.
APA Zhao, Lei.,Li, Xia.,Zhang, Ning.,Zhang, Shu-Dong.,Yi, Ting-Shuang.,...&Li, De-Zhu.(2016).Phylogenomic analyses of large-scale nuclear genes provide new insights into the evolutionary relationships within the rosids.MOLECULAR PHYLOGENETICS AND EVOLUTION,105(1),166-176.
MLA Zhao, Lei,et al."Phylogenomic analyses of large-scale nuclear genes provide new insights into the evolutionary relationships within the rosids".MOLECULAR PHYLOGENETICS AND EVOLUTION 105.1(2016):166-176.
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