DNA Dinucleotide Evolution in Humans: Fitting Theory to Facts

Overview

Journal Genetics

Publisher Oxford University Press

Specialty Genetics

Date 2001 Oct 19

PMID 11606548

Citations 8

Authors

A Renwick

L Davison

H Spratt

J P King

M Kimmel

Affiliations

Soon will be listed here.

Abstract

We examine length distributions of approximately 6000 human dinucleotide microsatellite loci, representing chromosomes 1-22, from the GDB database. Under the stepwise mutation model, results from theory and simulation are compared with the empirical data. In both constant and expanding population scenarios, a simple single-step model with parameters chosen to account for the observed variance of microsatellite lengths produces results inconsistent with the observed heterozygosity and the dispersion of length skewness. Complicating the model by allowing a variable mutation rate accounts for the homozygosity, and introducing a small probability of a large mutation step accounts for the dispersion in skewnesses. We discuss these results in light of the long-term evolution of microsatellites.

Citing Articles

Large numbers of vertebrates began rapid population decline in the late 19th century.

Li H, Xiang-Yu J, Dai G, Gu Z, Ming C, Yang Z Proc Natl Acad Sci U S A. 2016; 113(49):14079-14084.

PMID: 27872315 PMC: 5150392. DOI: 10.1073/pnas.1616804113.

Analysis of BAC-end sequences in common bean (Phaseolus vulgaris L.) towards the development and characterization of long motifs SSRs.

Muller B, Sakamoto T, de Menezes I, Prado G, Martins W, Brondani C Plant Mol Biol. 2014; 86(4-5):455-70.

PMID: 25164100 DOI: 10.1007/s11103-014-0240-7.

Mutational dynamics of microsatellites.

Bhargava A, Fuentes F Mol Biotechnol. 2009; 44(3):250-66.

PMID: 20012711 DOI: 10.1007/s12033-009-9230-4.

The rate and spectrum of microsatellite mutation in Caenorhabditis elegans and Daphnia pulex.

Seyfert A, Cristescu M, Frisse L, Schaack S, Thomas W, Lynch M Genetics. 2008; 178(4):2113-21.

PMID: 18430937 PMC: 2323801. DOI: 10.1534/genetics.107.081927.

Mutation rate variation at human dinucleotide microsatellites.

Xu H, Chakraborty R, Fu Y Genetics. 2005; 170(1):305-12.

PMID: 15716501 PMC: 1449715. DOI: 10.1534/genetics.104.036855.

References

Zhu Y, Queller D, Strassmann J . A phylogenetic perspective on sequence evolution in microsatellite loci. J Mol Evol. 2000; 50(4):324-38. DOI: 10.1007/s002399910036. View

King J, Kimmel M, Chakraborty R . A power analysis of microsatellite-based statistics for inferring past population growth. Mol Biol Evol. 2000; 17(12):1859-68. DOI: 10.1093/oxfordjournals.molbev.a026287. View

Chakraborty R, Jin L . A unified approach to study hypervariable polymorphisms: statistical considerations of determining relatedness and population distances. EXS. 1993; 67:153-75. DOI: 10.1007/978-3-0348-8583-6_14. View

Weber J, Wong C . Mutation of human short tandem repeats. Hum Mol Genet. 1993; 2(8):1123-8. DOI: 10.1093/hmg/2.8.1123. View

Dib C, Faure S, Fizames C, Samson D, Drouot N, Vignal A . A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature. 1996; 380(6570):152-4. DOI: 10.1038/380152a0. View

Kimmel M, Chakraborty R . Measures of variation at DNA repeat loci under a general stepwise mutation model. Theor Popul Biol. 1996; 50(3):345-67. DOI: 10.1006/tpbi.1996.0035. View

Cooper G, Burroughs N, Rand D, Rubinsztein D, Amos W . Markov chain Monte Carlo analysis of human Y-chromosome microsatellites provides evidence of biased mutation. Proc Natl Acad Sci U S A. 1999; 96(21):11916-21. PMC: 18387. DOI: 10.1073/pnas.96.21.11916. View

Mountain J, Cavalli-Sforza L . Multilocus genotypes, a tree of individuals, and human evolutionary history. Am J Hum Genet. 1997; 61(3):705-18. PMC: 1715971. DOI: 10.1086/515510. View

Richards R, Sutherland G . Dynamic mutation: possible mechanisms and significance in human disease. Trends Biochem Sci. 1997; 22(11):432-6. DOI: 10.1016/s0968-0004(97)01108-0. View

10.

Di Rienzo A, Donnelly P, Toomajian C, Sisk B, Hill A, Petzl-Erler M . Heterogeneity of microsatellite mutations within and between loci, and implications for human demographic histories. Genetics. 1998; 148(3):1269-84. PMC: 1460025. DOI: 10.1093/genetics/148.3.1269. View

11.

Kimmel M, Chakraborty R, King J, Bamshad M, Watkins W, Jorde L . Signatures of population expansion in microsatellite repeat data. Genetics. 1998; 148(4):1921-30. PMC: 1460085. DOI: 10.1093/genetics/148.4.1921. View

12.

Reich D, Goldstein D . Genetic evidence for a Paleolithic human population expansion in Africa. Proc Natl Acad Sci U S A. 1998; 95(14):8119-23. PMC: 20939. DOI: 10.1073/pnas.95.14.8119. View

13.

Deka R, Guangyun S, Smelser D, Zhong Y, Kimmel M, Chakraborty R . Rate and directionality of mutations and effects of allele size constraints at anonymous, gene-associated, and disease-causing trinucleotide loci. Mol Biol Evol. 1999; 16(9):1166-77. DOI: 10.1093/oxfordjournals.molbev.a026207. View

14.

Chakraborty R, Kimmel M, Stivers D, Davison L, Deka R . Relative mutation rates at di-, tri-, and tetranucleotide microsatellite loci. Proc Natl Acad Sci U S A. 1997; 94(3):1041-6. PMC: 19636. DOI: 10.1073/pnas.94.3.1041. View