贝叶斯支端定年法推断分异时间和演化速率

doi:10.19615/j.cnki.2096-9899.210516

古脊椎动物学报 ›› 2021, Vol. 59 ›› Issue (4): 333-341.DOI: 10.19615/j.cnki.2096-9899.210516

• • 上一篇

贝叶斯支端定年法推断分异时间和演化速率

张驰¹^,²()

1 中国科学院古脊椎动物与古人类研究所,中国科学院脊椎动物演化与人类起源重点实验室北京 100044
2 中国科学院生物演化与环境卓越创新中心北京 100044

收稿日期:2021-01-18 出版日期:2021-09-20 发布日期:2021-10-18
通讯作者: zhangchi@ivpp.ac.cn
基金资助:
中国科学院率先行动百人计划青年俊才(C类)和中国科学院战略性先导科技专项(B类) (编号：)资助(XDB26000000)

Using Bayesian tip-dating method to estimate divergence times and evolutionary rates

ZHANG Chi¹^,²()

1 Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences Beijing 100044
2 CAS Center for Excellence in Life and Paleoenvironment Beijing 100044

Received:2021-01-18 Published:2021-09-20 Online:2021-10-18

1. 附件.pdf(93KB)

摘要/Abstract

摘要：

贝叶斯支端定年法是近些年开发的推断类群分异时间和演化速率的方法。它克服了传统分步计算的缺陷,但涉及的统计学知识也更多。本文从贝叶斯统计计算的角度分层剖析了支端定年法的原理和计算过程,按照分异时间的先验分布、演化速率的先验分布、特征状态变化的模型和马氏链蒙特卡罗算法几个部分,叙述并讨论了定年计算中的主要模型和算法。旨在一定程度上为古生物学家分析实际数据提供参考。

关键词: 贝叶斯支端定年法, 石化生灭过程, 宽松钟, Mk模型, MrBayes

Abstract:

Bayesian tip dating is a recently developed method to estimate divergence times and evolutionary rates. It overcomes several drawbacks in traditional stepwise approach. However, it also requires more knowledge about statistics. This paper hierarchically explains the theory and computation in the Bayesian tip-dating approach, and divides the whole process into prior for the divergence times, prior for the evolutionary rates, model for the character changes and Markov chain Monte Carlo algorithm, which are key components in this method. The aim is to provide a general guidance for paleontologists in empirical data analyses.

Key words: Bayesian tip dating, fossilized birth-death process, relaxed clock, Mk model, MrBayes

中图分类号:

Q91-3

张驰. 贝叶斯支端定年法推断分异时间和演化速率. 古脊椎动物学报, 2021, 59(4): 333-341.

ZHANG Chi. Using Bayesian tip-dating method to estimate divergence times and evolutionary rates. Vertebrata Palasiatica, 2021, 59(4): 333-341.

图/表 3

图1 石化生灭过程可能得到的时间树 A. 生灭过程对应的完整树; B. 只保留和样本相关的分支得到的样本树,包含两个现生类群(红点)和两个化石(蓝点)

Fig. 1 Example timetree generated from the fossilized birth-death process A. compete tree by keeping all branches; B. sampled tree by only keeping branches leading to two extant taxa (red dots) and two fossils (blue dots)

图2 用于各个概率分布公式中参数的示例树上化石F1和F2的特征状态为0,现生类群S1和S2的特征状态为1,内部节点的特征状态用x0, x1, x2表示化石的年代分别为t3 = 100 Ma, t5 = 50 Ma, 树根的时间为t1, 其他分异时间为t2和t4记t = {t1, t2, t3, t4, t5}。各个枝上的特征演化速率为r = {r1, r2, r3, r4, r5}

Fig. 2 Example parameters and symbols used in the probability distributions The character states for fossils F1 and F2 are 0, for extant taxa S1 and S2 are 1, for internal nodes are x0, x1, x2. The ages of fossils F1 and F2 are t3 = 100 Ma and t5 = 50 Ma The root age is t1 and the remaining divergence times are t2 and t4. Denote t = {t1, t2, t3, t4, t5}. The evolutionary rates on the branches are r = {r1, r2, r3, r4, r5}

图3 马氏链蒙特卡罗算法在一维情形的示例参数θ的后验分布π(θ)为估计的目标(曲线)

Fig. 3 Illustration of the MCMC algorithm for one dimensional parameter The posterior distribution π(θ) of parameter θ is the target distribution to be estimated (curve)

参考文献 23

[1]	Barido-Sottani J, Vaughan T G, Stadler T, 2020. A Multi-Type Birth-Death model for Bayesian inference of lineage-specific birth and death rates. Syst Biol, 69:973-986 DOI PMID
[2]	Brusatte S L, Benton M J, Ruta M et al., 2008. Superiority, competition, and opportunism in the evolutionary radiation of dinosaurs. Science, 321:1485-1488 DOI PMID
[3]	Drummond A, Ho S, Phillips M et al., 2006. Relaxed phylogenetics and dating with confidence. Plos Biol, 4:e88 DOI URL
[4]	Gavryushkina A, Zhang C, 2020. Total-Evidence Dating and the Fossilized Birth-Death Model. In: Ho S Y W ed. The Molecular Evolutionary Clock. Switzerland: Springer Nature. 175-193
[5]	Gavryushkina A, Welch D, Stadler T et al., 2014. Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration. Plos Comput Biol, 10:e1003919 DOI URL
[6]	Hastings W K, 1970. Monte Carlo sampling methods using Markov chains and their applications. Biometrika, 57:97-109 DOI URL
[7]	Kishino H, Thorne J L, Bruno W J, 2001. Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol Biol Evol, 18:352-361 PMID
[8]	Klopfstein S, Ryer R, Coiro M et al., 2019. Mismatch of the morphology model is mostly unproblematic in total-evidence dating: insights from an extensive simulation study. bioRxiv, 679084
[9]	Lakner C, van der Mark P, Huelsenbeck, et al., 2008. Efficiency of Markov chain Monte Carlo tree proposals in Bayesian phylogenetics. Syst Biol, 57:86-103 DOI URL
[10]	Laurin M, 2004. The evolution of body size, Cope’s rule and the origin of amniotes. Syst Biol, 53:594-622 DOI URL
[11]	Lee M S Y, 2016. Multiple morphological clocks and total-evidence tip-dating in mammals. Biol Lett, 12:20160033 DOI URL
[12]	Lepage T, Bryant D, Philippe H et al., 2007. A general comparison of relaxed molecular clock models. Mol Biol Evol, 24:2669-2680 DOI URL
[13]	Lewis P O, 2001. A likelihood approach to estimating phylogeny from discrete morphological character data. Syst Biol, 50:913-925 PMID
[14]	Metropolis N, Rosenbluth A W, Rosenbluth M N et al., 1953. Equation of state calculations by fast computing machines. J Chem Phys, 21:1087-1092 DOI URL
[15]	O’Reilly J E, Donoghue P C J, 2016. Tips and nodes are complementary not competing approaches to the calibration of molecular clocks. Biol Lett, 12:20150975
[16]	Ronquist F, Klopfstein S, Vilhelmsen L et al., 2012. A total-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera. Syst Biol, 61:973-999 DOI PMID
[17]	Stadler T, 2010. Sampling-through-time in birth-death trees. J Theor Biol, 267:396-404 DOI PMID
[18]	Thorne J L, Kishino H, 2002. Divergence time and evolutionary rate estimation with multilocus data. Syst Biol, 51:689-702 DOI URL
[19]	Wang M, Lloyd G T, 2016. Rates of morphological evolution are heterogeneous in Early Cretaceous birds. Proc Royal Soc B Biol Sci, 283:20160214
[20]	Yang Z, Rannala B, 2006. Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Mol Biol Evol, 23:212-226 DOI URL
[21]	Zhang C, Wang M, 2019. Bayesian tip dating reveals heterogeneous morphological clocks in Mesozoic birds. Roy Soc Open Sci, 6:182062 DOI PMID
[22]	Zhang C, Stadler T, Klopfstein S et al., 2016. Total-evidence dating under the fossilized birth-death process. Syst Biol, 65:228-249 DOI PMID
[23]	Zhang C, Huelsenbeck J P, Ronquist F, 2020. Using parsimony-guided tree proposals to accelerate convergence in Bayesian phylogenetic inference. Syst Biol, 69:1016-1032 DOI PMID

贝叶斯支端定年法推断分异时间和演化速率

Using Bayesian tip-dating method to estimate divergence times and evolutionary rates

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