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

Abstract

Background & Aims: Molecular dating methods have been applied widely in recent years and provide an indispensable and detailed evolutionary timescale for macroevolutionary researches, particularly for studies on the evolutionary history of biodiversity patterns. Bayesian methods and Markov chain Monte Carlo methods can accommodate multi-dimensional and various type of data and parameter settings, which have helped the node-dating methods implemented in softwares such as BEAST, PAML-MCMCTree to become the most widely used molecular dating methods. One of the advantages of Bayesian frameworks is that they can employ complex models to consider a variety of uncertainty factors to make more accurate estimations of evolutionary divergence times. Progress: We review the principles and main types of Bayesian molecular dating methods and use Bayesian node-dating methods as an example to discuss potential errors in molecular clock models, selection and placement of fossil calibrating points, frequency of sampling, and setting a prior distribution for node calibrations based on fossils. We further describe advantages associated with different Bayesian time tree reconstruction software packages, the discussing principle of node age, and the comparison method of time tree under different models. We also provide suggestions for overcoming the challenges of overestimation and underestimation bias of node ages. Integration of the

The genetic equidistance and maximum genetic diversity hypothesis: Smoke and mirrors?

“…With the introduction of Bayesian method and Markov Chain Monte Carlo, algorithm of molecular clock was evolving fast [40][41][42][43] . The substitution model assumes substitution rates of different bases, frequency, heterogeneity, ratio of unchanged sites and so on 40 . The phenomenon that distinct rates among regions and clades, named "heterogeneity", could be coped by the applications of various models 34 .…”

“…However, the means of settlement had also already existed. With the introduction of Bayesian method and Markov Chain Monte Carlo, algorithm of molecular clock was evolving fast [40][41][42][43] . The substitution model assumes substitution rates of different bases, frequency, heterogeneity, ratio of unchanged sites and so on 40 .…”

“…Substitution rates of different bases at one site also differ so there exists various substitution models such as F81 44 , GTR 45 and JC69 46 . As for difference among sites, phylogeneticists utilized random variable like Gamma distribution to simulate it 40 . To sum up, advocators of the MGD hypothesis failed to provide a persuasive reason to deny the molecular clock hypothesis.…”