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66
S: PhyloBayes 3. A Bayesian software package for phylogenetic reconstruction and molecular dating
 Bioinformatics
"... Motivation: A variety of probabilistic models describing the evolution of DNA or protein sequences have been proposed for phylogenetic reconstruction or for molecular dating. However, there still lacks a common implementation allowing one to freely combine these independent features, so as to test t ..."
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Cited by 187 (8 self)
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Motivation: A variety of probabilistic models describing the evolution of DNA or protein sequences have been proposed for phylogenetic reconstruction or for molecular dating. However, there still lacks a common implementation allowing one to freely combine these independent features, so as to test their ability to jointly improve phylogenetic and dating accuracy. Results: We propose a software package, PhyloBayes 3, which can be used for conducting Bayesian phylogenetic reconstruction and molecular dating analyses, using a large variety of amino acid replacement and nucleotide substitution models, including empirical mixtures or nonparametric models, as well as alternative clock relaxation processes. Availability: PhyloBayes is freely available from our web site
Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Systematic Biology 58
, 2009
"... The estimation of phylogenetic divergence times from sequence data is an important component of many molecular evolutionary studies. There is now a general appreciation that the procedure of divergence dating is considerably more complex than that initially described in the 1960s by Zuckerkandl an ..."
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Cited by 90 (6 self)
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The estimation of phylogenetic divergence times from sequence data is an important component of many molecular evolutionary studies. There is now a general appreciation that the procedure of divergence dating is considerably more complex than that initially described in the 1960s by Zuckerkandl and Pauling (1962, 1965). In particular, there has been much critical attention toward the assumption of a global molecular clock, resulting in the development of increasingly sophisticated techniques for inferring divergence times from sequence data. In response to the documentation of widespread departures from clocklike behavior, a variety of local and relaxedclock methods have been proposed and implemented. Localclock methods permit different molecular clocks in different parts of the phy
Improving marginal likelihood estimation for Bayesian phylogenetic model selection. Syst Biol
, 2011
"... Abstract.—The marginal likelihood is commonly used for comparing different evolutionary models in Bayesian phylogenetics and is the central quantity used in computing Bayes Factors for comparing model fit. A popular method for estimating marginal likelihoods, the harmonic mean (HM) method, can be e ..."
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Cited by 40 (1 self)
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Abstract.—The marginal likelihood is commonly used for comparing different evolutionary models in Bayesian phylogenetics and is the central quantity used in computing Bayes Factors for comparing model fit. A popular method for estimating marginal likelihoods, the harmonic mean (HM) method, can be easily computed from the output of a Markov chain Monte Carlo analysis but often greatly overestimates the marginal likelihood. The thermodynamic integration (TI) method is much more accurate than the HM method but requires more computation. In this paper, we introduce a new method, steppingstone sampling (SS), which uses importance sampling to estimate each ratio in a series (the “stepping stones”) bridging the posterior and prior distributions. We compare the performance of the SS approach to the TI and HM methods in simulation and using real data. We conclude that the greatly increased accuracy of the SS and TI methods argues for their use instead of the HM method, despite the extra computation needed. [Bayes factor; harmonic mean; phylogenetics, marginal likelihood;
The Impact of the Representation of Fossil Calibrations on Bayesian Estimation of Species Divergence Times
, 2009
"... Abstract.—Bayesian inference provides a powerful framework for integrating different sources of information (in particular, molecules and fossils) to derive estimates of species divergence times. Indeed, it is currently the only framework that can adequately account for uncertainties in fossil calib ..."
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Cited by 39 (13 self)
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Abstract.—Bayesian inference provides a powerful framework for integrating different sources of information (in particular, molecules and fossils) to derive estimates of species divergence times. Indeed, it is currently the only framework that can adequately account for uncertainties in fossil calibrations. We use 2 Bayesian Markov chain Monte Carlo programs, MULTIDIVTIME and MCMCTREE, to analyze 3 empirical data sets to estimate divergence times in amphibians, actinopterygians, and felids. We evaluate the impact of various factors, including the priors on rates and times, fossil calibrations, substitution model, the violation of the molecular clock and the ratedrift model, and the exact and approximate likelihood calculation. Assuming the molecular clock caused seriously biased time estimates when the clock is violated, but 2 different ratedrift models produced similar estimates. The prior on times, which incorporates fossilcalibration information, had the greatest impact on posterior time estimation. In particular, the strategies used by the 2 programs to incorporate minimum and maximumage bounds led to very different time priors and were responsible for large differences in posterior time estimates in a previous study. The results highlight the critical importance of fossil calibrations to molecular dating and the need for probabilistic modeling of fossil depositions, preservations, and sampling to provide statistical summaries of information
A phylogenetic model for investigating correlated evolution of substitution rates and continuous phenotypic characters
"... The comparative approach is routinely used to test for possible correlations between phenotypic or lifehistory traits. To correct for phylogenetic inertia, the method of independent contrasts assumes that continuous characters evolve along the phylogeny according to a multivariate Brownian process. ..."
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Cited by 24 (3 self)
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The comparative approach is routinely used to test for possible correlations between phenotypic or lifehistory traits. To correct for phylogenetic inertia, the method of independent contrasts assumes that continuous characters evolve along the phylogeny according to a multivariate Brownian process. Brownian diffusion processes have also been used to describe time variations of the parameters of the substitution process, such as the rate of substitution or the ratio of synonymous to nonsynonymous substitutions. Here, we develop a probabilistic framework for testing the coupling between continuous characters and parameters of the molecular substitution process. Rates of substitution and continuous characters are jointly modeled as a multivariate Brownian diffusion process of unknown covariance matrix. The covariancematrix, the divergence times and the phylogenetic variationsof substitution rates and continuous characters are all jointly estimated in a BayesianMonte Carlo framework, imposing on the covariance matrix a prior conjugate to the Brownian process so as to achieve a greater computational efficiency. The coupling between rates and phenotypes is assessed by measuring the posterior probability of positive or negative covariances, whereas divergence dates and phenotypic variations are marginally reconstructed in the context of the joint analysis. As an illustration, we apply the model to a set of 410 mammalian cytochrome b sequences. We observe a negative correlation between the rate of substitution and mass and longevity, which was previously observed. We also find a positive correlation between ω = dN/dS and mass and longevity, which we interpret as an indirect effect of variations of effective population size, thus in partial agreement with the nearly neutral theory. The method can easily be extended to any parameter of the substitution process and to any continuous phenotypic or environmental character.
Performance of RelaxedClock Methods in Estimating Evolutionary Divergence Times and Their Credibility Intervals
"... The rapid expansion of sequence data and the development of statistical approaches that embrace varying evolutionary rates among lineages have encouraged many more investigators to use DNA and protein data to time species divergences. Here, we report results from a systematic evaluation, by means of ..."
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Cited by 16 (4 self)
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The rapid expansion of sequence data and the development of statistical approaches that embrace varying evolutionary rates among lineages have encouraged many more investigators to use DNA and protein data to time species divergences. Here, we report results from a systematic evaluation, by means of computer simulation, of the performance of two frequently used relaxedclock methods for estimating these times and their credibility intervals (CrIs). These relaxedclock methods allow rates to vary in a phylogeny randomly over lineages (e.g., BEAST software) and in autocorrelated fashion (e.g., MultiDivTime software). We applied these methods for analyzing sequence data sets simulated using naturally derived parameters (evolutionary rates, sequence lengths, and base substitution patterns) and assuming that clock calibrations are known without error. We find that the estimated times are, on average, close to the true times as long as the assumed model of lineage rate changes matches the actual model. The 95 % CrIs also contain the true time for 95 % of the simulated data sets. However, the use of incorrect lineage rate model reduces this frequency to 83%, indicating that the relaxedclock methods are not robust to the violation of underlying lineage rate model. Because these rate models are rarely known a priori and are difficult to detect empirically, we suggest building composite CrIs using CrIs produced from MultiDivTime and BEAST analysis. These composite CrIs are found to contain the true time for 97 % data sets. Our analyses also verify the usefulness of the common practice of interpreting the congruence of times inferred from different methods as a reflection of the accuracy of time estimates. Overall, our results show that simple strategies can be used to enhance our ability to estimate times and their CrIs when using the relaxedclock methods.
Integration of bayesian molecular clock methods and fossilbased soft bounds reveals early cenozoic origin of African lacertid lizards,”
 BMC Evolutionary Biology,
, 2009
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Building trees of algae: some advances in phylogenetic and evolutionary analysis
 Eur. J. Phycol
, 2008
"... Molecular phylogenetics has become a prominent aspect of algal systematics. The field of phylogenetic reconstruction is fastevolving and novel techniques take time to penetrate taxonomic research. We highlight a selection of advances in phylogenetic inference and evolutionary analysis methods that ..."
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Cited by 7 (3 self)
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Molecular phylogenetics has become a prominent aspect of algal systematics. The field of phylogenetic reconstruction is fastevolving and novel techniques take time to penetrate taxonomic research. We highlight a selection of advances in phylogenetic inference and evolutionary analysis methods that could, in our opinion, benefit algal systematic studies. The focus of the paper is on modelbased techniques. Following a brief introduction to maximum likelihood and Bayesian phylogenetic inference methods, we address model selection and partitioning strategies, and illustrate some issues concerning systematic error (phylogenetic bias), data saturation and tree rooting. We discuss the importance of experimental design (taxon and character sampling) and explore methods to test the reliability of phylogenetic results. Finally, we address methods for estimating ancestral states of discrete and continuous characters and techniques for dating phylogenetic trees. For each of these topics, we provide a brief circumscription, refer to the more specialized literature, and list a selection of software to carry out the analyses.
A Hierarchical Bayesian Model for Calibrating Estimates of Species Divergence Times
 SYST. BIOL
, 2012
"... In Bayesian divergence time estimation methods, incorporating calibrating information from the fossil record is commonly done by assigning prior densities to ancestral nodes in the tree. Calibration prior densities are typically parametric distributions offset by minimum age estimates provided by t ..."
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Cited by 6 (4 self)
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In Bayesian divergence time estimation methods, incorporating calibrating information from the fossil record is commonly done by assigning prior densities to ancestral nodes in the tree. Calibration prior densities are typically parametric distributions offset by minimum age estimates provided by the fossil record. Specification of the parameters of calibration densities requires the user to quantify his or her prior knowledge of the age of the ancestral node relative to the age of its calibrating fossil. The values of these parameters can, potentially, result in biased estimates of node ages if they lead to overly informative prior distributions. Accordingly, determining parameter values that lead to adequate prior densities is not straightforward. In this study, I present a hierarchical Bayesian model for calibrating divergence time analyses with multiple fossil age constraints. This approach applies a Dirichlet process prior as a hyperprior on the parameters of calibration prior densities. Specifically, this model assumes that the rate parameters of exponential prior distributions on calibrated nodes are distributed according to a Dirichlet process, whereby the rate parameters are clustered into distinct parameter categories. Both simulated and biological data are analyzed to evaluate the performance of the Dirichlet process hyperprior. Compared with fixed exponential prior densities, the hierarchical Bayesian approach results in more accurate and precise estimates of internal node ages. When this hyperprior is applied using Markov chain Monte Carlo methods, the ages of calibrated nodes are sampled from mixtures of exponential distributions and uncertainty in the values of calibration density parameters is taken into account.