Resolving the systematic positions of enigmatic taxa: Manipulating the chloroplast genome data of Saxifragales
文献类型：期刊论文
| 作者 | Dong, Wenpan2; Xu, Chao1; Wu, Ping1; Cheng, Tao; Yu, Jing; Zhou, Shiliang1; Hong, De-Yuan |
| 刊名 | MOLECULAR PHYLOGENETICS AND EVOLUTION
 |
| 出版日期 | 2018 |
| 卷号 | 126页码:321-330 |
| 关键词 | Analytical methodology Paeoniaceae Phylogenomics Saxifragales Systematics error |
| ISSN号 | 1055-7903 |
| DOI | 10.1016/j.ympev.2018.04.033 |
| 文献子类 | Article |
| 英文摘要 | Accurately resolving the phylogeny of enigmatic taxa is always a challenge in phylogenetic inference. Such uncertainties could be due to systematic errors or model violations. Here, we provide an example demonstrating how these factors affect the positioning of Paeoniaceae within Saxifragales based on chloroplast genome data. We newly assembled 14 chloroplast genomes from Saxifragales, and by combining these genomes with those of 63 other angiosperms, three datasets were assembled to test different hypotheses proposed by recent studies. These datasets were subjected to maximum parsimony, maximum likelihood and Bayesian analyses with site-homogeneous/heterogeneous models, different data partitioning strategies, and the inclusion/exclusion of weak phylogenetic signals. Three datasets exhibited remarkable heterogeneity among sites and among taxa of Saxifragales. Phylogenetic analyses under homogeneous models or maximum parsimony showed a closer relationship of Paeoniaceae with herbaceous families in the order. Data partitioning strategies did not change the general tree topology. However, PhyloBayes analysis under the CAT + GTR model resulted in a relationship closer to woody families. We conclude that although genomic data significantly increase the phylogenetic resolution of enigmatic taxa with high support, the phylogenetic results inferred from such data might be analysis or signal dependent. The analytical pipeline outlined here combines phylogenomic inference methods with evaluation of lineage-specific rates of substitution, model selection, and assessment of systematic error. These methods would be applicable to resolve similar difficult questions in the tree of life. |
| 学科主题 | Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity |
| 出版地 | SAN DIEGO |
| 电子版国际标准刊号 | 1095-9513 |
| WOS关键词 | EARLY LAND PLANTS ; PHYLOGENETIC-RELATIONSHIPS ; HETEROGENEOUS MODELS ; OUTGROUP SELECTION ; SCALE DATA ; PHYLOGENOMICS ; ANGIOSPERMS ; EVOLUTION ; PERFORMANCE ; ANCIENT |
| 语种 | 英语 |
| WOS记录号 | WOS:000437663900029 |
| 出版者 | ACADEMIC PRESS INC ELSEVIER SCIENCE |
| 资助机构 | NSFCNational Natural Science Foundation of China (NSFC) [30930010, 31270239] |
| 源URL | [http://ir.ibcas.ac.cn/handle/2S10CLM1/20566]  |
| 专题 | 植物研究所_系统与进化植物学研究中心_系统与进化植物学研究中心_学位论文 |
| 作者单位 | 1.Peking Univ, Acad Adv Interdisciplinary Studies, Peking Tsinghua Ctr Life Sci, Beijing 100871, Peoples R China 2.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, 20 Nanxincun, Beijing 100093, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China |
| 推荐引用方式 GB/T 7714 | Dong, Wenpan,Xu, Chao,Wu, Ping,et al. Resolving the systematic positions of enigmatic taxa: Manipulating the chloroplast genome data of Saxifragales[J]. MOLECULAR PHYLOGENETICS AND EVOLUTION,2018,126:321-330. |
| APA | Dong, Wenpan.,Xu, Chao.,Wu, Ping.,Cheng, Tao.,Yu, Jing.,...&Hong, De-Yuan.(2018).Resolving the systematic positions of enigmatic taxa: Manipulating the chloroplast genome data of Saxifragales.MOLECULAR PHYLOGENETICS AND EVOLUTION,126,321-330. |
| MLA | Dong, Wenpan,et al."Resolving the systematic positions of enigmatic taxa: Manipulating the chloroplast genome data of Saxifragales".MOLECULAR PHYLOGENETICS AND EVOLUTION 126(2018):321-330. |
入库方式： OAI收割
来源：植物研究所
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