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Using non-homogeneous models of nucleotide substitution to identify host shift events: application to the origin of the 1918 'Spanish' influenza pandemic virus.
(2009-10)
Nonhomogeneous Markov models of nucleotide substitution have received scant attention. Here we explore the possibility of using nonhomogeneous models to identify host shift nodes along phylogenetic trees of pathogens ...
Estimating the distribution of selection coefficients from phylogenetic data using sitewise mutation-selection models.
(2012-03)
Estimation of the distribution of selection coefficients of mutations is a long-standing issue in molecular evolution. In addition to population-based methods, the distribution can be estimated from DNA sequence data by ...
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 ...
Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case.
(2018-07-01)
Primates have long been a test case for the development of phylogenetic methods for divergence time estimation. Despite a large number of studies, however, the timing of origination of crown Primates relative to the ...
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 ...
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 ...
Demographic History of the Human Commensal Drosophila melanogaster.
(2019-03-01)
The cohabitation of Drosophila melanogaster with humans is nearly ubiquitous. Though it has been well established that this fly species originated in sub-Saharan Africa, and only recently has spread globally, many details ...