Genealogical inference from microsatellite data

Ease and accuracy of typing, together with high levels of polymorphism and widespread distribution in the genome, make microsatellite (or short tandem repeat) loci an attractive potential source of information about both population histories and evolutionary processes. However, microsatellite data are difficult to interpret, in particular because of the frequency of back-mutations. Stochastic models for the underlying genetic processes can be specified, but in the past they have been too complicated for direct analysis. Recent developments in stochastic simulation methodology now allow direct inference about both historical events, such as genealogical coalescence times, and evolutionary parameters, such as mutation rates. A feature of the Markov chain Monte Carlo (MCMC) algorithm that we propose here is that the likelihood computations are simplified by treating the (unknown) ancestral allelic states as auxiliary parameters. We illustrate the algorithm by analyzing microsatellite samples simulated under the model. Our results suggest that a single microsatellite usually does not provide enough information for useful inferences, but that several completely linked microsatellites can be informative about some aspects of genealogical history and evolutionary processes. We also reanalyze data from a previously published human Y chromosome microsatellite study, finding evidence for an effective population size for human Y chromosomes in the low thousands and a recent time since their most recent common ancestor: the 95% interval runs from [approximately]15,000 to 130,000 years, with most likely values around 30,000 years.