Dating phylogenies with sequentially sampled tips.
Tanja Stadler,Ziheng Yang +1 more
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TLDR
Preliminary time estimates for old nodes to be sensitive to the priors on times and rates are found and it is suggested that multifurcating consensus trees should be avoided in dating analysis.Abstract:
We develop a Bayesian Markov chain Monte Carlo (MCMC) algorithm for estimating divergence times using sequentially sampled molecular sequences. This type of data is commonly collected during viral epidemics and is sometimes available from different species in ancient DNA studies. We derive the distribution of ages of nodes in the tree under a birth-death-sequential-sampling (BDSS) model and use it as the prior for divergence times in the dating analysis. We implement the prior in the MCMCtree program in the PAML package for divergence dating. The BDSS prior is very flexible and, with different parameters, can generate trees of very different shapes, suitable for examining the sensitivity of posterior time estimates. We apply the method to a data set of SIV/HIV-2 genes in comparison with a likelihood-based dating method, and to a data set of influenza H1 genes from different hosts in comparison with the Bayesian program BEAST. We examined the impact of tree topology on time estimates and suggest that multifurcating consensus trees should be avoided in dating analysis. We found posterior time estimates for old nodes to be sensitive to the priors on times and rates and suggest that previous Bayesian dating studies may have produced overconfident estimates.read more
Citations
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The fossilized birth–death process for coherent calibration of divergence-time estimates
TL;DR: The fossilized birth–death process is introduced—a fossil calibration method that unifies extinct and extant species with a single macroevolutionary model, eliminating the need for ad hoc calibration priors and yielding more accurate node age estimates while providing a coherent measure of statistical uncertainty.
Journal ArticleDOI
Molecular-clock methods for estimating evolutionary rates and timescales.
Simon Y. W. Ho,Sebastián Duchêne +1 more
TL;DR: The different forms of evolutionary rate heterogeneity are described and explained how they can be accommodated in molecular‐clock analyses, and an outline of the various clock methods and models that are available is provided.
Journal ArticleDOI
Bayesian molecular clock dating of species divergences in the genomics era
TL;DR: The molecular clock hypothesis has become a powerful tool in evolutionary biology, making it possible to use molecular sequences to estimate the geological ages of species divergence events and to estimate a timescale for life on Earth.
Journal ArticleDOI
Morphological Phylogenetics in the Genomic Age
TL;DR: This work states that morphology remains a powerful independent source of evidence for testing molecular clades, and - through fossil phenotypes - the primary means for time-scaling phylogenies, and approaches for analysing phenotypic traits and fossils together with genomic data need to be refined.
Journal ArticleDOI
A genetic method for dating ancient genomes provides a direct estimate of human generation interval in the last 45,000 years
Priya Moorjani,Priya Moorjani,Sriram Sankararaman,Qiaomei Fu,Molly Przeworski,Nick Patterson,David Reich,David Reich +7 more
TL;DR: The idea is that an ancient genome has evolved less than the genomes of present-day individuals and thus has experienced fewer recombination events since the common ancestor, and the mean generation interval in humans over this period has been 26–30 y.
References
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A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.
Stéphane Guindon,Olivier Gascuel +1 more
TL;DR: This work has used extensive and realistic computer simulations to show that the topological accuracy of this new method is at least as high as that of the existing maximum-likelihood programs and much higher than the performance of distance-based and parsimony approaches.
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TL;DR: BEAST is a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree that provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions.
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TL;DR: PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML), which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses.
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Koichiro Tamura,Masatoshi Nei +1 more
TL;DR: In this paper, a new mathematical method for estimating the number of transitional and transversional substitutions per site, as well as the total number of nucleotide substitutions was proposed, taking into account excess transitions, unequal nucleotide frequencies, and variation of substitution rate among different sites.