MrBayes分子钟定年之程序

doi:10.19615/j.cnki.1000-3118.190408

古脊椎动物学报 ›› 2019, Vol. 57 ›› Issue (3): 241-252.DOI: 10.19615/j.cnki.1000-3118.190408

• • 上一篇

MrBayes分子钟定年之程序

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:2019-01-14 出版日期:2019-07-20 发布日期:2019-07-20
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)(XDB26000000)

Molecular clock dating using MrBayes

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:2019-01-14 Published:2019-07-20 Online:2019-07-20

摘要/Abstract

摘要：

介绍了利用MrBayes进行分子钟定年的研究概况和程序。利用一个整合分子序列和形态特征的膜翅目昆虫的数据,展示了两种现代方法：全证据定年和节点定年,并对这两种方法的相似点和不同之处进行比较和讨论。此外,还用无分子钟的方法对同一数据进行分析,并与分子钟定年法进行比较。

关键词: 贝叶斯系统发育推断, 分子钟定年, 马尔可夫链蒙特卡罗, MrBayes

Abstract:

This paper provides an overview and a protocol of molecular clock dating using MrBayes. Two modern approaches, total-evidence dating and node dating, are demonstrated using a truncated dataset of Hymenoptera with molecular sequences and morphological characters. The similarity and difference of the two methods are compared and discussed. Besides, a non-clock analysis is performed on the same dataset to compare with the molecular clock dating analyses.

Key words: Bayesian phylogenetic inference, molecular clock dating, MCMC, MrBayes

中图分类号:

Q91-3

张驰. MrBayes分子钟定年之程序. 古脊椎动物学报, 2019, 57(3): 241-252.

ZHANG Chi. Molecular clock dating using MrBayes. Vertebrata Palasiatica, 2019, 57(3): 241-252.

图/表 5

Fig. 1 Probability density functions of lognormal, gamma, and normal distributions, all with mean 0.001and standard deviation 0.0007

Fig. 2 The fossilized birth-death (FBD) process and diversified sampling of extant taxa Exactly one representative taxa per clade descending from time xcut is sampled (blue dots). The fossils are sampled with a constant rate between tmrca and xcut (red dots)

Fig. 3 Probability density functions of offset lognormal, offset gamma, offset exponential,and truncated normal distributions, all with mean 390 and minimum 300

Fig. 4 Majority-rule consensus trees of extant taxa from total-evidence dating (A) and node dating (B), under the diversified sampling and IGR models The node heights are in units of million years and the error bars indicate the 95% HPD intervalsThe numbers at the internal nodes are the posterior probabilities of the corresponding clades

Fig. 5 Majority-rule consensus tree of extant taxa from a non-clock analysis under the gamma-Dirichlet priorThe branch lengths are measured by expected substitutions per siteThe numbers at the internal nodes are the posterior probabilities of the corresponding clades

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MrBayes分子钟定年之程序

Molecular clock dating using MrBayes

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