MBE Advance Access originally published online on August 29, 2003
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Mol. Biol. Evol. 20(12):2123-2131. 2003
DOI: 10.1093/molbev/msg228
© 2003 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038
The Relationship Between Microsatellite Slippage Mutation Rate and the Number of Repeat Units
,
* Department of Mathematics
Program in Molecular and Computational Biology, Department of Biological Sciences, University of Southern California
E-mail: fsun{at}hto.usc.edu.
Microsatellite markers are widely used for genetic studies, but the relationship between microsatellite slippage mutation rate and the number of repeat units remains unclear. In this study, microsatellite distributions in the human genome are collected from public sequence databases. We observe that there is a threshold size for slippage mutations. We consider a model of microsatellite mutation consisting of point mutations and single stepwise slippage mutations. From two sets of equations based on two stochastic processes and equilibrium assumptions, we estimate microsatellite slippage mutation rates without assuming any relationship between microsatellite slippage mutation rate and the number of repeat units. We use the least squares method with constraints to estimate expansion and contraction mutation rates. The estimated slippage mutation rate increases exponentially as the number of repeat units increases. When slippage mutations happen, expansion occurs more frequently for short microsatellites and contraction occurs more frequently for long microsatellites. Our results agree with the length-dependent mutation pattern observed from experimental data, and they explain the scarcity of long microsatellites.
Key Words: microsatellites Markov processes branching processes
![]()
CiteULike
Connotea
Del.icio.us What's this?
This article has been cited by other articles:
![]() |
V. Lumb, M. K. Das, N. Singh, V. Dev, Wajihullah, and Y. D. Sharma Characteristics of Genetic Hitchhiking around Dihydrofolate Reductase Gene Associated with Pyrimethamine Resistance in Plasmodium falciparum Isolates from India Antimicrob. Agents Chemother., December 1, 2009; 53(12): 5173 - 5180. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. G. Gibbons and A. Rokas Comparative and Functional Characterization of Intragenic Tandem Repeats in 10 Aspergillus Genomes Mol. Biol. Evol., March 1, 2009; 26(3): 591 - 602. [Abstract] [Full Text] [PDF] |
||||
![]() |
E. Loire, F. Praz, D. Higuet, P. Netter, and G. Achaz Hypermutability of Genes in Homo sapiens Due to the Hosting of Long Mono-SSR Mol. Biol. Evol., January 1, 2009; 26(1): 111 - 121. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. L. Seyfert, M. E. A. Cristescu, L. Frisse, S. Schaack, W. K. Thomas, and M. Lynch The Rate and Spectrum of Microsatellite Mutation in Caenorhabditis elegans and Daphnia pulex Genetics, April 1, 2008; 178(4): 2113 - 2121. [Abstract] [Full Text] [PDF] |
||||
![]() |
Y. D. Kelkar, S. Tyekucheva, F. Chiaromonte, and K. D. Makova The genome-wide determinants of human and chimpanzee microsatellite evolution Genome Res., January 1, 2008; 18(1): 30 - 38. [Abstract] [Full Text] [PDF] |
||||
![]() |
G. T. Skalski Joint Estimation of Migration Rate and Effective Population Size Using the Island Model Genetics, October 1, 2007; 177(2): 1043 - 1057. [Abstract] [Full Text] [PDF] |
||||
![]() |
J.-H. Lee, S. Waffenschmidt, L. Small, and U. Goodenough Between-Species Analysis of Short-Repeat Modules in Cell Wall and Sex-Related Hydroxyproline-Rich Glycoproteins of Chlamydomonas Plant Physiology, August 1, 2007; 144(4): 1813 - 1826. [Abstract] [Full Text] [PDF] |
||||
![]() |
O. Paun and E. Horandl Evolution of Hypervariable Microsatellites in Apomictic Polyploid Lineages of Ranunculus carpaticola: Directional Bias at Dinucleotide Loci Genetics, September 1, 2006; 174(1): 387 - 398. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. Gressel and A. A. Levy Agriculture: The selector of improbable mutations PNAS, August 15, 2006; 103(33): 12215 - 12216. [Full Text] [PDF] |
||||
![]() |
M. Imwong, D. Sudimack, S. Pukrittayakamee, L. Osorio, J. M. Carlton, N. P. J. Day, N. J. White, and T. J. C. Anderson Microsatellite Variation, Repeat Array Length, and Population History of Plasmodium vivax Mol. Biol. Evol., May 1, 2006; 23(5): 1016 - 1018. [Full Text] [PDF] |
||||
![]() |
E. A Archie, C. J Moss, and S. C Alberts The ties that bind: genetic relatedness predicts the fission and fusion of social groups in wild African elephants Proc R Soc B, March 7, 2006; 273(1586): 513 - 522. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. C. Noller, M. C. McEllistrem, K. A. Shutt, and L. H. Harrison Locus-Specific Mutational Events in a Multilocus Variable-Number Tandem Repeat Analysis of Escherichia coli O157:H7 J. Clin. Microbiol., February 1, 2006; 44(2): 374 - 377. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. Jongwutiwes, C. Putaporntip, T. Iwasaki, M. U. Ferreira, H. Kanbara, and A. L. Hughes Mitochondrial Genome Sequences Support Ancient Population Expansion in Plasmodium vivax Mol. Biol. Evol., August 1, 2005; 22(8): 1733 - 1739. [Abstract] [Full Text] [PDF] |
||||
![]() |
Z. Tu, S. Li, and C. Mao The Changing Tails of a Novel Short Interspersed Element in Aedes aegypti: Genomic Evidence for Slippage Retrotransposition and the Relationship Between 3' Tandem Repeats and the poly(dA) Tail Genetics, December 1, 2004; 168(4): 2037 - 2047. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. R. Dettman and J. W. Taylor Mutation and Evolution of Microsatellite Loci in Neurospora Genetics, November 1, 2004; 168(3): 1231 - 1248. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. S. Taylor, C. P. Ponting, and R. R. Copley Occurrence and Consequences of Coding Sequence Insertions and Deletions in Mammalian Genomes Genome Res., April 1, 2004; 14(4): 555 - 566. [Abstract] [Full Text] [PDF] |
||||







