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17 Feb

Molecular dating is a key tool in deciphering the history of life.

In a recent Molecular Biology and Evolution paper, Sudhir Kumar and Blair Hedges have reviewed the state of the subject, summarizing the philosophical and methodological history of this often-integrative endeavor. Generation 2: Don’t assume a strict molecular clock.

The two most commonly used BPPs are the Yule (also called ‘pure-birth’) process, which models tree formation with a constant rate of speciation and no extinction, and the birth-death process, which includes speciation as well as a constant rate of lineage extinction.

Birth-death priors have been used in Bayesian phylogenetics [], many phylogenetic analyses still use the Yule prior (probably because the BEAST manual recommend the use of the Yule prior, see p. Few studies have used both priors in Bayesian dating, and even fewer have compared the impact of prior choice, even though recent studies have started to do so (e.g.

Dating with the Yule prior suggested that extant cycad genera diversified in the Paleogene and with two diversification rate shifts.

Priors on calibration points have been well studied [].In particular, their binning of this history into 4 sequential “generations” provides a convenient way of thinking about the evolution of this science, which I paraphrase below. Utilize only those data that pass tests of clocklike behavior.Generation 3: Utilize all the data, and allow the molecular clock(s) to vary in rate across phylogeny according to some prior model.But, as Kumar and Hedges point out, Generation 4 methods have a number of advantages that will be useful for dealing with genomic data efficiently.Specifically, they scale well with large numbers of characters or taxa, and they are free of the need for specification of clock models.