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Approximate Bayesian computation in population genetics.
A key advantage of the method is that the nuisance parameters are automatically integrated out in the simulation step, so that the large numbers of nuisance parameters that arise in population genetics problems can be handled without difficulty.
Evaluating loci for use in the genetic analysis of population structure
It is suggested that genetic variation at a discrepant locus, Identified under these conditions, is likely to have been influenced by natural selection, either acting on the locus itself or at a closely linked locus.
Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation
Key methods used in DIY ABC, a computer program for inference based on approximate Bayesian computation (ABC), in which scenarios can be customized by the user to fit many complex situations involving any number of populations and samples, are described.
Detecting population expansion and decline using microsatellites.
- M. Beaumont
- 1 December 1999
A demographic model where a population varies in size either linearly or exponentially, and a method is presented whereby the posterior probability distribution of the genealogical and demographic parameters can be estimated using Markov chain Monte Carlo simulations.
Identifying adaptive genetic divergence among populations from genome scans
A hierarchical‐Bayesian method is developed, implemented via Markov chain Monte Carlo (MCMC), and its performance is assessed in distinguishing the loci simulated under selection from the neutral loci, finding that both methods can identify loci subject to adaptive selection when the selection coefficient is at least five times the migration rate.
COMPUTER PROGRAMS: onesamp: a program to estimate effective population size using approximate Bayesian computation
A web‐based program, onesamp, is developed that uses approximate Bayesian computation to estimate effective population size from a sample of microsatellite genotypes and provides an estimate ofeffective population size, along with 95% credible limits.
Adaptive approximate Bayesian computation
Sequential techniques can enhance the efficiency of the approximate Bayesian computation algorithm, as in Sisson et al.'s (2007) partial rejection control version, which compares favourably with two other versions of the approximation algorithm.
TESTING FOR GENETIC EVIDENCE OF POPULATION EXPANSION AND CONTRACTION: AN EMPIRICAL ANALYSIS OF MICROSATELLITE DNA VARIATION USING A HIERARCHICAL BAYESIAN MODEL
- J. F. Storz, M. Beaumont
- Environmental ScienceEvolution; international journal of organic…
- 1 January 2002
Alternative hypotheses about historical patterns of demographic expansion and contraction in Cynopterus sphinx and C. brachyotis are tested using a hierarchical Bayesian model based on Markov chain Monte Carlo simulations to estimate the posterior distribution of genealogical and demographic parameters.
Estimation of population growth or decline in genetically monitored populations.
- M. Beaumont
- 1 July 2003
A new general method is introduced that samples independent genealogical histories using importance sampling (IS) and then samples other parameters with Markov chain Monte Carlo (MCMC) and it is concluded that these have an approximately equivalent effect.
Approximate Bayesian Computation in Evolution and Ecology
- M. Beaumont
- 2 November 2010
Although the method arose in population genetics, ABC is increasingly used in other fields, including epidemiology, systems biology, ecology, and agent-based modeling, and many of these applications are briefly described.