Molecular timetrees using relaxed clocks and uncertain phylogenies

Frontiers in Bioinformatics

Bioinformatics

Sudip Sharma¹  Jose Barba-Montoya¹  Sudhir Kumar¹ 

[1] Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States;Department of Biology, Temple University, Philadelphia, PA, United States;

关键词: relaxed molecular clock;    phylogenetic uncertainty;    phylogenomics;    bootstrap;    timetree;   

DOI  :  10.3389/fbinf.2023.1225807

 received in 2023-05-19, accepted in 2023-07-21,  发布年份 2023

来源: Frontiers

【 摘 要 】

A common practice in molecular systematics is to infer phylogeny and then scale it to time by using a relaxed clock method and calibrations. This sequential analysis practice ignores the effect of phylogenetic uncertainty on divergence time estimates and their confidence/credibility intervals. An alternative is to infer phylogeny and times jointly to incorporate phylogenetic errors into molecular dating. We compared the performance of these two alternatives in reconstructing evolutionary timetrees using computer-simulated and empirical datasets. We found sequential and joint analyses to produce similar divergence times and phylogenetic relationships, except for some nodes in particular cases. The joint inference performed better when the phylogeny was not well resolved, situations in which the joint inference should be preferred. However, joint inference can be infeasible for large datasets because available Bayesian methods are computationally burdensome. We present an alternative approach for joint inference that combines the bag of little bootstraps, maximum likelihood, and RelTime approaches for simultaneously inferring evolutionary relationships, divergence times, and confidence intervals, incorporating phylogeny uncertainty. The new method alleviates the high computational burden imposed by Bayesian methods while achieving a similar result.

【 授权许可】

Unknown   
Copyright © 2023 Barba-Montoya, Sharma and Kumar.