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The impact of the rate prior on Bayesian estimation of divergence times with multiple Loci.
(2014-07)
Bayesian methods provide a powerful way to estimate species divergence times by combining information from molecular sequences with information from the fossil record. With the explosive increase of genomic data, divergence ...
RelTime Rates Collapse to a Strict Clock When Estimating the Timeline of Animal Diversification.
(2017-05-01)
Establishing an accurate timescale for the history of life is crucial to understand evolutionary processes. For this purpose, relaxed molecular clock models implemented in a Bayesian MCMC framework are generally used. ...
Identifying changes in selective constraints: host shifts in influenza.
(2009-11)
The natural reservoir of Influenza A is waterfowl. Normally, waterfowl viruses are not adapted to infect and spread in the human population. Sometimes, through reassortment or through whole host shift events, genetic ...
Comparison of different strategies for using fossil calibrations to generate the time prior in Bayesian molecular clock dating.
(2017-09)
Fossil calibrations are the utmost source of information for resolving the distances between molecular sequences into estimates of absolute times and absolute rates in molecular clock dating analysis. The quality of ...
Geogenetic patterns in mouse lemurs (genus Microcebus) reveal the ghosts of Madagascar's forests past.
(2016-07-19)
Phylogeographic analysis can be described as the study of the geological and climatological processes that have produced contemporary geographic distributions of populations and species. Here, we attempt to understand how ...
Characterization of the uncertainty of divergence time estimation under relaxed molecular clock models using multiple loci.
(2015-03)
Genetic sequence data provide information about the distances between species or branch lengths in a phylogeny, but not about the absolute divergence times or the evolutionary rates directly. Bayesian methods for dating ...
Finding Direction in the Search for Selection.
(2017-01)
Tests for positive selection have mostly been developed to look for diversifying selection where change away from the current amino acid is often favorable. However, in many cases we are interested in directional selection ...
Bayesian Molecular Clock Dating Using Genome-Scale Datasets.
(2019)
Bayesian methods for molecular clock dating of species divergences have been greatly developed during the past decade. Advantages of the methods include the use of relaxed-clock models to describe evolutionary rate variation ...
Dating Microbial Evolution with MCMCtree.
(2022)
This protocol explains how to use the program MCMCtree to estimate divergence times in microbial phylogenies. The main advantage of MCMCtree is the implementation of an approximation to the molecular data likelihood that ...