A Simulation-Based Evaluation of Tip-Dating Under the Fossilized Birth-Death Process

doi:10.1093/sysbio/syz038

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	A Simulation-Based Evaluation of Tip-Dating Under the Fossilized Birth-Death Process
	Luo, Arong 2,4; Duchene, David A.2; Zhang, Chi 5,6; Zhu, Chao-Dong 1,3,4; Ho, Simon Y. W.2
刊名	SYSTEMATIC BIOLOGY
	2020-03-01
卷号	69 期号:2 页码:325-344
关键词	Bayesian phylogenetics evolutionary simulation fossilized birth-death process molecular clock tip-dating total-evidence dating
ISSN号	1063-5157
DOI	10.1093/sysbio/syz038
通讯作者	Luo, Arong(luoar@ioz.ac.cn)
英文摘要	Bayesian molecular dating is widely used to study evolutionary timescales. This procedure usually involves phylogenetic analysis of nucleotide sequence data, with fossil-based calibrations applied as age constraints on internal nodes of the tree. An alternative approach is tip-dating, which explicitly includes fossil data in the analysis. This can be done, for example, through the joint analysis of molecular data from present-day taxa and morphological data from both extant and fossil taxa. In the context of tip-dating, an important development has been the fossilized birth-death process, which allows non-contemporaneous tips and sampled ancestors while providing a model of lineage diversification for the prior on the tree topology and internal node times. However, tip-dating with fossils faces a number of considerable challenges, especially, those associated with fossil sampling and evolutionary models for morphological characters. We conducted a simulation study to evaluate the performance of tip-dating using the fossilized birth-death model. We simulated fossil occurrences and the evolution of nucleotide sequences and morphological characters under a wide range of conditions. Our analyses of these data show that the number and the maximum age of fossil occurrences have a greater influence than the degree of among-lineage rate variation or the number of morphological characters on estimates of node times and the tree topology. Tip-dating with the fossilized birth-death model generally performs well in recovering the relationships among extant taxa but has difficulties in correctly placing fossil taxa in the tree and identifying the number of sampled ancestors. The method yields accurate estimates of the ages of the root and crown group, although the precision of these estimates varies with the probability of fossil occurrence. The exclusion of morphological characters results in a slight overestimation of node times, whereas the exclusion of nucleotide sequences has a negative impact on inference of the tree topology. Our results provide an overview of the performance of tip-dating using the fossilized birth-death model, which will inform further development of the method and its application to key questions in evolutionary biology.
资助项目	Strategic Priority Research Program of the Chinese Academy of Sciences[XDB31000000] ; Youth Innovation Promotion Association of the Chinese Academy of Sciences[2017118] ; Chinese Academy of Sciences ; Australian Research Council[DP160104173] ; Australian Research Council[FT160100167] ; 100 Young Talents Program of the Chinese Academy of Sciences ; National Science Fund for Distinguished Young Scholars[31625024]
WOS关键词	PHYLOGENETIC ESTIMATION ; DNA-SEQUENCES ; TIME ; EVOLUTION ; TREE ; RADIATION ; DIVERSIFICATION ; UNCERTAINTY ; CALIBRATION ; DISPERSAL
WOS研究方向	Evolutionary Biology
语种	英语
出版者	OXFORD UNIV PRESS
WOS记录号	WOS:000522858100009
资助机构	Strategic Priority Research Program of the Chinese Academy of Sciences ; Youth Innovation Promotion Association of the Chinese Academy of Sciences ; Chinese Academy of Sciences ; Australian Research Council ; 100 Young Talents Program of the Chinese Academy of Sciences ; National Science Fund for Distinguished Young Scholars
内容类型	期刊论文
源URL	[http://119.78.100.205/handle/311034/17273]
专题	古脊椎动物与古人类研究所_图书馆1
通讯作者	Luo, Arong
作者单位	1.Chinese Acad Sci, Inst Zool, State Key Lab Integrated Pest Management, Beijing 100101, Peoples R China 2.Univ Sydney, Sch Life & Environm Sci, Sydney, NSW 2006, Australia 3.Univ Chinese Acad Sci, Coll Life Sci, Beijing 100049, Peoples R China 4.Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China 5.Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, Beijing 100044, Peoples R China 6.Chinese Acad Sci, Ctr Excellence Life & Paleoenvironm, Beijing 100044, Peoples R China
推荐引用方式 GB/T 7714	Luo, Arong,Duchene, David A.,Zhang, Chi,et al. A Simulation-Based Evaluation of Tip-Dating Under the Fossilized Birth-Death Process[J]. SYSTEMATIC BIOLOGY,2020,69(2):325-344.
APA	Luo, Arong,Duchene, David A.,Zhang, Chi,Zhu, Chao-Dong,&Ho, Simon Y. W..(2020).A Simulation-Based Evaluation of Tip-Dating Under the Fossilized Birth-Death Process.SYSTEMATIC BIOLOGY,69(2),325-344.
MLA	Luo, Arong,et al."A Simulation-Based Evaluation of Tip-Dating Under the Fossilized Birth-Death Process".SYSTEMATIC BIOLOGY 69.2(2020):325-344.