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

doi:10.19615/j.cnki.2096-9899.210516

Vertebrata Palasiatica ›› 2021, Vol. 59 ›› Issue (4): 333-341.DOI: 10.19615/j.cnki.2096-9899.210516

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

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

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)

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Abstract

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

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

CLC Number:

Q91-3

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

张驰. 2021, 59(4): 333-341, 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.

Figures/Tables 3

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)

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}

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)

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

贝叶斯支端定年法推断分异时间和演化速率

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