Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach
A maximum likelihood estimator based on the coalescent for unequal migration rates and different subpopulation sizes is developed and used to estimate gene flow in the Nile valley by using mtDNA data from three human populations.
Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach.
A new method for the estimation of migration rates and effective population sizes is described, which uses a maximum-likelihood framework based on coalescence theory and is as good as or better than those from an optimized FST-based measure.
Comparison of Bayesian and maximum-likelihood inference of population genetic parameters
- P. Beerli
- Computer ScienceBioinform.
- 1 February 2006
Using simulated datasets, the Bayesian method generally fares better than the ML approach in accuracy and coverage, although for some values the two approaches are equal in performance.
The Strength of Phenotypic Selection in Natural Populations
Comparisons of estimated linear selection gradients and differentials suggest that indirect components of phenotypic selection were usually modest relative to direct components, and no evidence that stabilizing selection is stronger or more common than disruptive selection in nature.
Unified Framework to Evaluate Panmixia and Migration Direction Among Multiple Sampling Locations
The approximation of marginal likelihood using thermodynamic integration in MIGRATE allows the evaluation of complex population genetic models, not only of whether sampling locations belong to a single panmictic population, but also of competing complex structured population models.
How to use MIGRATE or why are Markov chain Monte Carlo programs difficult to use
- P. Beerli
- 1 May 2009
Computer-intensive programs that can estimate parameters using genetic data under various coalescent models have been developed; for example, programs that estimate gene flow and the goal of these applications is to calculate the probability of the parameters of the chosen model given the data.
BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics
BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference, is presented, which provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms.
Estimating Divergence Times from Molecular Data on Phylogenetic and Population Genetic Timescales
A review of recent advances in estimating divergence times from molecular data, emphasizing the continuum between processes at the phylogenetic and population genetic scales, and the importance of model testing during the process of divergence time estimation.
PERSPECTIVE: GENE DIVERGENCE, POPULATION DIVERGENCE, AND THE VARIANCE IN COALESCENCE TIME IN PHYLOGEOGRAPHIC STUDIES
It is shown that phylogeographic studies in vertebrates suggest that divergence of alleles in ancestral species can comprise from less than 10% to over 50% of the total divergence between sister species, suggesting that the problem of ancestral polymorphism in dating population divergence can be substantial.
Effect of unsampled populations on the estimation of population sizes and migration rates between sampled populations
- P. Beerli
- EconomicsMolecular Ecology
- 1 April 2004
Estimates of the scaled migration rate M are fairly robust as long as migration rates from the unknown populations are not huge, and when the migration rates are estimated as the number of immigrants Nm then a ghost population improves the estimates because of its effect on population size estimation.