Microsatellite Mutation Models: Insights From a Comparison of Humans and Chimpanzees

Using genomic data from homologous microsatellite loci of pure AC repeats in humans and chimpanzees, several models of microsatellite evolution are tested and compared using likelihood-ratio tests and the Akaike information criterion. A proportional-rate, linear-biased, one-phase model emerges as th...

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Published inGenetics (Austin) Vol. 168; no. 1; pp. 383 - 395
Main Authors Sainudiin, Raazesh, Durrett, Richard T, Aquadro, Charles F, Nielsen, Rasmus
Format Journal Article
LanguageEnglish
Published United States Genetics Soc America 01.09.2004
Genetics Society of America
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Summary:Using genomic data from homologous microsatellite loci of pure AC repeats in humans and chimpanzees, several models of microsatellite evolution are tested and compared using likelihood-ratio tests and the Akaike information criterion. A proportional-rate, linear-biased, one-phase model emerges as the best model. A focal length toward which the mutational and/or substitutional process is linearly biased is a crucial feature of microsatellite evolution. We find that two-phase models do not lead to a significantly better fit than their one-phase counterparts. The performance of models based on the fit of their stationary distributions to the empirical distribution of microsatellite lengths in the human genome is consistent with that based on the human-chimp comparison. Microsatellites interrupted by even a single point mutation exhibit a twofold decrease in their mutation rate when compared to pure AC repeats. In general, models that allow chimps to have a larger per-repeat unit slippage rate and/or a shorter focal length compared to humans give a better fit to the human-chimp data as well as the human genomic data.
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Communicating editor: M. Feldman
Corresponding author: Department of Statistical Science, 301 Malott Hall, Cornell University, Ithaca, NY 14853. E-mail: rs228@cornell.edu
ISSN:0016-6731
1943-2631
DOI:10.1534/genetics.103.022665