Abstract
This paper presents a likelihood approach to population samples of microsatellite alleles. A Markov chain recursion method previously published by GRIFFITHS and TAVARE is applied to estimate the likelihood function under different models of microsatellite evolution. The method presented can be applied to estimate a fundamental population genetics parameter θ as well as parameters of the mutational model. The new likelihood estimator provides a better estimator of θ in terms of the mean square error than previous approaches. Furthermore, it is demonstrated how the method may easily be applied to test models of microsatellite evolution. In particular it is shown how to compare a one-step model of microsatellite evolution to a multi-step model by a likelihood ratio test.
Full Text
The Full Text of this article is available as a PDF (605.4 KB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Bowcock A. M., Ruiz-Linares A., Tomfohrde J., Minch E., Kidd J. R., Cavalli-Sforza L. L. High resolution of human evolutionary trees with polymorphic microsatellites. Nature. 1994 Mar 31;368(6470):455–457. doi: 10.1038/368455a0. [DOI] [PubMed] [Google Scholar]
- Craighead L., Paetkau D., Reynolds H. V., Vyse E. R., Strobeck C. Microsatellite analysis of paternity and reproduction in Arctic grizzly bears. J Hered. 1995 Jul-Aug;86(4):255–261. doi: 10.1093/oxfordjournals.jhered.a111578. [DOI] [PubMed] [Google Scholar]
- Deka R., Chakroborty R., Ferrell R. E. A population genetic study of six VNTR loci in three ethnically defined populations. Genomics. 1991 Sep;11(1):83–92. doi: 10.1016/0888-7543(91)90104-m. [DOI] [PubMed] [Google Scholar]
- Di Rienzo A., Peterson A. C., Garza J. C., Valdes A. M., Slatkin M., Freimer N. B. Mutational processes of simple-sequence repeat loci in human populations. Proc Natl Acad Sci U S A. 1994 Apr 12;91(8):3166–3170. doi: 10.1073/pnas.91.8.3166. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Goldstein D. B., Ruiz Linares A., Cavalli-Sforza L. L., Feldman M. W. An evaluation of genetic distances for use with microsatellite loci. Genetics. 1995 Jan;139(1):463–471. doi: 10.1093/genetics/139.1.463. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hudson R. R., Kaplan N. L. On the divergence of alleles in nested subsamples from finite populations. Genetics. 1986 Aug;113(4):1057–1076. doi: 10.1093/genetics/113.4.1057. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Moran P. A. Wandering distributions and the electrophoretic profile. Theor Popul Biol. 1975 Dec;8(3):318–330. doi: 10.1016/0040-5809(75)90049-0. [DOI] [PubMed] [Google Scholar]
- O'Brien P. Allele frequencies in a multidimensional Wright-Fisher model with general mutation. J Math Biol. 1982;15(2):227–237. doi: 10.1007/BF00275075. [DOI] [PubMed] [Google Scholar]
- Ohta T., Kimura M. A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population. Genet Res. 1973 Oct;22(2):201–204. doi: 10.1017/s0016672300012994. [DOI] [PubMed] [Google Scholar]
- Shriver M. D., Jin L., Chakraborty R., Boerwinkle E. VNTR allele frequency distributions under the stepwise mutation model: a computer simulation approach. Genetics. 1993 Jul;134(3):983–993. doi: 10.1093/genetics/134.3.983. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Todd J. A., Aitman T. J., Cornall R. J., Ghosh S., Hall J. R., Hearne C. M., Knight A. M., Love J. M., McAleer M. A., Prins J. B. Genetic analysis of autoimmune type 1 diabetes mellitus in mice. Nature. 1991 Jun 13;351(6327):542–547. doi: 10.1038/351542a0. [DOI] [PubMed] [Google Scholar]
- Wehrhahn C. F. The evolution of selectively similar electrophoretically detectable alleles in finite natural populations. Genetics. 1975 Jun;80(2):375–394. doi: 10.1093/genetics/80.2.375. [DOI] [PMC free article] [PubMed] [Google Scholar]