Biodiv Sci


Principles, error sources and optimization suggestions of prevailing molecular dating methods

Yangkang Chen1, Yi Wang1, Jialiang Li1, Wentao Wang1, Duanyu Feng2, Kangshan Mao1*   

  1. 1 Key Laboratory for Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610065

    2 College of Mathematics, Sichuan University, Chengdu, 610065

  • Received:2020-07-08 Revised:2020-08-15 Online:2020-10-10 Published:2020-10-10
  • Contact: Kangshan Mao

Abstract: In recent years, molecular dating methods have been widely applied, which provides an indispensable and detailed evolutionary timescale for macrobiological research, especially for studies on the evolutionary history of biodiversity and its distribution pattern. Bayesian methods and Markov chain Monte Carlo methods can accommodate multi-dimensional and multi-type data and parameter settings, which have helped the node-dating method implemented in BEAST, PAML-MCMCTree and other software to become the most widely used type of molecular clock methods. One of the advantages of Bayesian framework is that it can use complex models to consider all kinds of uncertainty factors, so as to make relatively accurate estimation of evolutionary divergence time. This synthesis introduces the principle and main types of Bayesian molecular clock methods, and takes Bayesian node-dating method as an example to discuss the potential errors in molecular clock models, selection and placement of fossil calibrating points, and the prior distribution of node calibrations based on fossils, etc. Finally, important issues that should be paid attention to when using Bayesian node-dating of molecular dating methods to reconstruct evolutionary timescale was summarized, and reasonable suggestions for common occasions that can lead to potential overestimation and underestimation bias of the node ages were provided, aiming at improvements of the reliability of Bayesian node-dating methods.

Key words: molecular clock, molecular dating, Bayesian node-dating, phylogeny, evolutionary timescale, divergence age.