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. 2000 Nov;156(3):1427–1436. doi: 10.1093/genetics/156.3.1427

The effects of rate variation on ancestral inference in the coalescent.

L Markovtsova 1, P Marjoram 1, S Tavaré 1
PMCID: PMC1461332  PMID: 11063714

Abstract

We describe a Markov chain Monte Carlo approach for assessing the role of site-to-site rate variation in the analysis of within-population samples of DNA sequences using the coalescent. Our framework is a Bayesian one. We discuss methods for assessing the goodness-of-fit of these models, as well as problems concerning the separate estimation of effective population size and mutation rate. Using a mitochondrial data set for illustration, we show that ancestral inference concerning coalescence times can be dramatically affected if rate variation is ignored.

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Selected References

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