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A particularly interesting result from the Kumar and Hedges paper is that, for a large number of studies compiled, dating results using Generation 2 and Generation 3 methods are highly consistent (the regression coefficient is nearly 1).This is despite the disparate philosophies and statistical implementations that underlie them. Advances in time estimation methods for molecular data.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.In Bayesian relaxed-clock (BRC) approaches, there are various types of priors, including priors on calibration points, branch-lengths, clock models, and branching processes.Priors on calibration points have been well studied [].

This approach requires the use of priors on the branching process, yet little is known about their impact on divergence time estimates.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. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.In the future, it will be interesting to see if a similar consistency can be found between the latter and Generation 4 methods. Ultrametricity: All descendants of any node are equidistant from that node For extant species, branches, in units of time, are ultrametric. Generation 4: Utilize all the data and estimate relative clock rates but without the need to model rate variation or speciation/extinction. " data-medium-file=" data-large-file=" class="aligncenter size-full wp-image-7871" src=" alt="2015-02_clock" width="241" height="136" /the temporal distinction between Generations 3 and 4 as asserted by these authors is somewhat tenuous; instead, these may be better thought of as alternative modern dating philosophies, with different advantages depending on the dataset in question.Make no mistake, the Generation 3 framework has some well-known caveats.These models effectively place a prior on how phylogenetic trees grow.Probability distributions over models of diversification were employed in some of the earliest attempts to use likelihood techniques to reconstruct genealogies [].


  1. Divergence time estimation, molecular dating methods, rate heterogeneity, review. INTRODUCTION. The use of DNA sequences to estimate the timing of.

  2. Mar 7, 2016. Molecular dating is a key tool in deciphering the history of life. In a recent Molecular Biology and Evolution paper, Sudhir Kumar and Blair.

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