Journal Article

Measuring Microsatellite Conservation in Mammalian Evolution with a Phylogenetic Birth–Death Model

Sterling M. Sawaya, Dustin Lennon, Emmanuel Buschiazzo, Neil Gemmell and Vladimir N. Minin

in Genome Biology and Evolution

Published on behalf of Society for Molecular Biology and Evolution

Volume 4, issue 6, pages 636-647
Published in print January 2012 |
Published online May 2012 | e-ISSN: 1759-6653 | DOI:

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Microsatellites make up ∼3% of the human genome, and there is increasing evidence that some microsatellites can have important functions and can be conserved by selection. To investigate this conservation, we performed a genome-wide analysis of human microsatellites and measured their conservation using a binary character birth--death model on a mammalian phylogeny. Using a maximum likelihood method to estimate birth and death rates for different types of microsatellites, we show that the rates at which microsatellites are gained and lost in mammals depend on their sequence composition, length, and position in the genome. Additionally, we use a mixture model to account for unequal death rates among microsatellites across the human genome. We use this model to assign a probability-based conservation score to each microsatellite. We found that microsatellites near the transcription start sites of genes are often highly conserved, and that distance from a microsatellite to the nearest transcription start site is a good predictor of the microsatellite conservation score. An analysis of gene ontology terms for genes that contain microsatellites near their transcription start site reveals that regulatory genes involved in growth and development are highly enriched with conserved microsatellites.

Keywords: tandem repeats; simple sequence repeats; comparative genomics; promoters; Genomic Regions Enrichment of Annotations Tool

Journal Article.  7652 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology ; Evolutionary Biology ; Genetics and Genomics

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