Complexity of the simplest species tree problem
文献类型：期刊论文
| 作者 | Zhu, Tianqi1,2 ; Yang, Ziheng1,3
|
| 刊名 | MOLECULAR BIOLOGY AND EVOLUTION
 |
| 出版日期 | 2021-09-01 |
| 卷号 | 38期号:9页码:3993-4009 |
| 关键词 | concatenation efficiency molecular clock MSC multispecies coalescent species tree |
| ISSN号 | 0737-4038 |
| DOI | 10.1093/molbev/msab009 |
| 英文摘要 | The multispecies coalescent model provides a natural framework for species tree estimation accounting for gene-tree conflicts. Although a number of species tree methods under the multispecies coalescent have been suggested and evaluated using simulation, their statistical properties remain poorly understood. Here, we use mathematical analysis aided by computer simulation to examine the identifiability, consistency, and efficiency of different species tree methods in the case of three species and three sequences under the molecular clock. We consider four major species-tree methods including concatenation, two-step, independent-sites maximum likelihood, and maximum likelihood. We develop approximations that predict that the probit transform of the species tree estimation error decreases linearly with the square root of the number of loci. Even in this simplest case, major differences exist among the methods. Full-likelihood methods are considerably more efficient than summary methods such as concatenation and two-step. They also provide estimates of important parameters such as species divergence times and ancestral population sizes,whereas these parameters are not identifiable by summary methods. Our results highlight the need to improve the statistical efficiency of summary methods and the computational efficiency of full likelihood methods of species tree estimation. |
| 资助项目 | Biotechnology and Biological Sciences Research Council[BB/P006493/1] ; BBSRC equipment grant[BB/R01356X/1] ; Natural Science Foundation[32070685] ; Natural Science Foundation[31671370] ; Youth Innovation Promotion Association of Chinese Academy of Sciences[201901] |
| WOS研究方向 | Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity |
| 语种 | 英语 |
| WOS记录号 | WOS:000693664800036 |
| 出版者 | OXFORD UNIV PRESS |
| 源URL | [http://ir.amss.ac.cn/handle/2S8OKBNM/59242]  |
| 专题 | 应用数学研究所 |
| 通讯作者 | Yang, Ziheng |
| 作者单位 | 1.Chinese Acad Sci, Acad Math & Syst Sci, Natl Ctr Math & Interdisciplinary Sci, Inst Appl Math, Beijing 100190, Peoples R China 2.Chinese Acad Sci, Acad Math & Syst Sci, Key Lab Random Complex Struct & Data Sci, Beijing 100190, Peoples R China 3.UCL, Dept Genet, Gower St, London WC1E 6BT, England |
| 推荐引用方式 GB/T 7714 | Zhu, Tianqi,Yang, Ziheng. Complexity of the simplest species tree problem[J]. MOLECULAR BIOLOGY AND EVOLUTION,2021,38(9):3993-4009. |
| APA | Zhu, Tianqi,&Yang, Ziheng.(2021).Complexity of the simplest species tree problem.MOLECULAR BIOLOGY AND EVOLUTION,38(9),3993-4009. |
| MLA | Zhu, Tianqi,et al."Complexity of the simplest species tree problem".MOLECULAR BIOLOGY AND EVOLUTION 38.9(2021):3993-4009. |
入库方式： OAI收割
来源：数学与系统科学研究院
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