title: Measuring microsatellite conservation in mammalian evolution with a phylogenetic birth-death model.
abstract: 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.
authors.affiliation: Centre for Reproduction and Genomics, Department of Anatomy and Structural Biology, University of Otago, Dunedin, New Zealand.
authors.forename: Sterling M
authors.initials: SM
authors.lastname: Sawaya
authors.forename: Dustin
authors.initials: D
authors.lastname: Lennon
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Buschiazzo
authors.forename: Neil
authors.initials: N
authors.lastname: Gemmell
authors.forename: Vladimir N
authors.initials: VN
authors.lastname: Minin
mesh_terms: D000818:Animals; D001483:Base Sequence; D017124:Conserved Sequence; D019143:Evolution, Molecular; D018507:Gene Expression Regulation, Developmental; D006801:Humans; D008322:Mammals / Q000145:classification / Q000235:genetics* / Q000254:growth & development; D018895:Microsatellite Repeats; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny