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Bayesian inference of recent migration rates using multilocus genotypes.
A new Bayesian method that uses individual multilocus genotypes to estimate rates of recent immigration (over the last several generations) among populations is presented and allows genotype frequencies to deviate from Hardy-Weinberg equilibrium proportions within populations.
Detecting immigration by using multilocus genotypes.
The test has power to detect immigrant ancestors, for these data, up to two generations in the past even though the overall differentiation of allele frequencies among populations is low.
Bayesian species delimitation using multilocus sequence data
A Bayesian modeling approach is used to generate the posterior probabilities of species assignments taking account of uncertainties due to unknown gene trees and the ancestral coalescent process and the method is illustrated by analyzing sequence data from rotifers, fence lizards, and human populations.
Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference
The results of the method are found to be insensitive to changes in the rate parameter of the branching process, and the best trees estimated by the new method are the same as those from the maximum likelihood analysis of separate topologies, but the posterior probabilities are quite different from the bootstrap proportions.
Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method.
An improved Bayesian method is presented for estimating phylogenetic trees using DNA sequence data, and the posterior probabilities of phylogenies are used to estimate the maximum posterior probability (MAP) tree, which has a probability of approximately 95%.
Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci.
A Bayes method for simultaneous estimation of the species divergence times and current and ancestral population sizes is developed and applied to published noncoding DNA sequences from the human and the great apes.
Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models.
This simulation study shows that Bayesian posterior probabilities have the meaning that is typically ascribed to them, and suggests that the Bayesian method be implemented with the most complex models of those currently available, to reduce the chance that the method will concentrate too much probability on too few trees.
Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds.
A Bayesian Markov chain Monte Carlo algorithm for estimating species divergence times that uses heterogeneous data from multiple gene loci and accommodates multiple fossil calibration nodes is implemented, and soft bounds are used so that the probability that the true divergence time is outside the bounds is small but nonzero.
Unguided Species Delimitation Using DNA Sequence Data from Multiple Loci
Simulation results indicate that the power of the method to delimit species increases with an increase of the divergence times in the species tree, and with an increased number of gene loci, and of the impact of the prior on population size parameters (θ) on Bayesian species delimitation.
Phylogenetic methods come of age: testing hypotheses in an evolutionary context.
The use of molecular phylogenies to examine evolutionary questions has become commonplace with the automation of DNA sequencing and the availability of efficient computer programs to perform…