| 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
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| 2016-12-01 | |
| 发表期刊 | MOLECULAR PHYLOGENETICS AND EVOLUTION
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| 卷号 | 105期号:1页码:166-176 |
| 摘要 | The 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. |
| 关键词 | Coalescence Rosids Phylogenomics Nuclear Genes Gene Tree Species Tree |
| DOI | 10.1016/j.ympev.2016.06.007 |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000384964700014 |
| 引用统计 | |
| 文献类型 | 期刊论文 |
| 条目标识符 | http://ir.kib.ac.cn/handle/151853/33537 |
| 专题 | 中国西南野生生物种质资源库 |
| 作者单位 | 1.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 |
| 推荐引用方式 GB/T 7714 | 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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