Genetics, Vol. 159, 839-852, October 2001, Copyright © 2001

Dynamics of Microsatellite Divergence Under Stepwise Mutation and Proportional Slippage/Point Mutation Models

Peter P. Calabresea, Richard T. Durrettb, and Charles F. Aquadroc
a Department of Applied Mathematics, Cornell University, Ithaca, New York 14853
b Department of Mathematics, Cornell University, Ithaca, New York 14853
c Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853

Corresponding author: Richard T. Durrett, Department of Mathematics, 523 Malott Hall, Cornell University, Ithaca, NY 14853., rtd1{at}cornell.edu (E-mail)

Communicating editor: S. TAVARÉ

Recently Kruglyak, Durrett, Schug, and Aquadro showed that microsatellite equilibrium distributions can result from a balance between polymerase slippage and point mutations. Here, we introduce an elaboration of their model that keeps track of all parts of a perfect repeat and a simplification that ignores point mutations. We develop a detailed mathematical theory for these models that exhibits properties of microsatellite distributions, such as positive skewness of allele lengths, that are consistent with data but are inconsistent with the predictions of the stepwise mutation model. We use our theoretical results to analyze the successes and failures of the genetic distances ({delta}µ)2 and DSW when used to date four divergences: African vs. non-African human populations, humans vs. chimpanzees, Drosophila melanogaster vs. D. simulans, and sheep vs. cattle. The influence of point mutations explains some of the problems with the last two examples, as does the fact that these genetic distances have large stochastic variance. However, we find that these two features are not enough to explain the problems of dating the human-chimpanzee split. One possible explanation of this phenomenon is that long microsatellites have a mutational bias that favors contractions over expansions.




This article has been cited by other articles:


Home page
 J HeredHome page
F. Lopez-Giraldez, J. Marmi, and X. Domingo-Roura
High Incidence of Nonslippage Mechanisms Generating Variability and Complexity in Eurasian Badger Microsatellites
J. Hered., September 1, 2007; 98(6): 620 - 628.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
R. Sainudiin, R. T. Durrett, C. F. Aquadro, and R. Nielsen
Microsatellite Mutation Models: Insights From a Comparison of Humans and Chimpanzees
Genetics, September 1, 2004; 168(1): 383 - 395.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
P. Almeida and C. Penha-Goncalves
Long Perfect Dinucleotide Repeats Are Typical of Vertebrates, Show Motif Preferences and Size Convergence
Mol. Biol. Evol., July 1, 2004; 21(7): 1226 - 1233.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
D. Dieringer and C. Schlotterer
Two Distinct Modes of Microsatellite Mutation Processes: Evidence From the Complete Genomic Sequences of Nine Species
Genome Res., October 1, 2003; 13(10): 2242 - 2251.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
C. L. Ross, K. A. Dyer, T. Erez, S. J. Miller, J. Jaenike, and T. A. Markow
Rapid Divergence of Microsatellite Abundance Among Species of Drosophila
Mol. Biol. Evol., July 1, 2003; 20(7): 1143 - 1157.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
P. Calabrese and R. Durrett
Dinucleotide Repeats in the Drosophila and Human Genomes Have Complex, Length-Dependent Mutation Processes
Mol. Biol. Evol., May 1, 2003; 20(5): 715 - 725.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
W. Amos, C. M. Hutter, M. D. Schug, and C. F. Aquadro
Directional Evolution of Size Coupled with Ascertainment Bias for Variation in Drosophila Microsatellites
Mol. Biol. Evol., April 1, 2003; 20(4): 660 - 662.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
R. M. Sibly, A. Meade, N. Boxall, M. J. Wilkinson, D. W. Corne, and J. C. Whittaker
The Structure of Interrupted Human AC Microsatellites
Mol. Biol. Evol., March 1, 2003; 20(3): 453 - 459.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
A. M. Roy-Engel, A.-H. Salem, O. O. Oyeniran, L. Deininger, D. J. Hedges, G. E. Kilroy, M. A. Batzer, and P. L. Deininger
Active Alu Element "A-Tails": Size Does Matter
Genome Res., September 1, 2002; 12(9): 1333 - 1344.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
M. T. Webster, N. G. C. Smith, and H. Ellegren
Microsatellite evolution inferred from human- chimpanzee genomic sequence alignments
PNAS, June 25, 2002; 99(13): 8748 - 8753.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Brohede, C. R. Primmer, A. Moller, and H. Ellegren
Heterogeneity in the rate and pattern of germline mutation at individual microsatellite loci
Nucleic Acids Res., May 1, 2002; 30(9): 1997 - 2003.
[Abstract] [Full Text] [PDF]