Comparison of Bayesian and maximum-likelihood inference of population genetic parameters

ArticleinBioinformatics 22(3):341-5 · March 2006with48 Reads
DOI: 10.1093/bioinformatics/bti803 · Source: PubMed
Abstract
Unlabelled: Comparison of the performance and accuracy of different inference methods, such as maximum likelihood (ML) and Bayesian inference, is difficult because the inference methods are implemented in different programs, often written by different authors. Both methods were implemented in the program MIGRATE, that estimates population genetic parameters, such as population sizes and migration rates, using coalescence theory. Both inference methods use the same Markov chain Monte Carlo algorithm and differ from each other in only two aspects: parameter proposal distribution and maximization of the likelihood function. 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. Motivation: The Markov chain Monte Carlo-based ML framework can fail on sparse data and can deliver non-conservative support intervals. A Bayesian framework with appropriate prior distribution is able to remedy some of these problems. Results: The program MIGRATE was extended to allow not only for ML(-) maximum likelihood estimation of population genetics parameters but also for using a Bayesian framework. Comparisons between the Bayesian approach and the ML approach are facilitated because both modes estimate the same parameters under the same population model and assumptions.
    • "This indicates that we can be confident in model choice but that parameter estimates for models including hybrids must be interpreted with caution (Fig. S1b). Convergence issues in models including hybrid individuals may be related to the fact that different runs provided a good fit of our data for contrasting combinations of estimates of effective population sizes and migration rates (see Beerli, 2006Beerli, , 2009). "
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    • "To determine the extent of genetic interchange between the populations of this study, current and historical migration rates and gene flow were assessed using Bayesian analyses in both the migrate-n v. 3.6.11 (Beerli, 2006Beerli, , 2009) and the IMa2 (Hey & Nielsen, 2007; Hey, 2010) programs, as independent estimates of similar parameters. Migrate-n was run through the CIPRES Science Gateway on the nuclear and mitochondrial sequence data separately for all populations together and running four MCMC simulations for 50 million genera- tions each with chain-swap and heating implemented (temperatures at 1, 1.5, 3, and 1 million , as per the default settings). "
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