The distribution of coalescence times and distances between microsatellite alleles with changing effective population size

Theoretical Population Biology

Volumn 77, Issue 3, 2010, Pages 152-163

  Chevalet, Claude ^a   Nikolic, Natacha ^a  

^a CEMAGREF   (France)

Author keywords

Coalescence times; Demography; Fourier transform; Genetic diversity; Laplace transform; Microsatellite; Population effective size

Indexed keywords

MICROSATELLITE DNA;

ALLELE; BIODIVERSITY; COALESCENCE; COMMON ANCESTRY; DEMOGRAPHY; FOURIER TRANSFORM; GENETIC MARKER; LAPLACE TRANSFORM; POPULATION SIZE;

ALLELE; ARTICLE; BIOLOGICAL MODEL; GENETICS; MUTATION;

ALLELES; MICROSATELLITE REPEATS; MODELS, GENETIC; MUTATION;

EID: 77949586838     PISSN: 00405809     EISSN: 10960325     Source Type: Journal    
DOI: 10.1016/j.tpb.2010.01.001     Document Type: Article

References (38)

1. Abramowitz, M., Stegun, I., 1965. Handbook of mathematical functions. Electronic release (http://www.math.sfu.ca/cbm/aands/toc.htm).
2. Bobrowski A., and Kimmel M. Asymptotic behavior of joint distributions of characteristics of a pair of randomly chosen individuals in discrete-time Fisher-Wright models with mutations and drift. Theor. Popul. Biol. 66 (2004) 355-367
3. Bowcock A.M., Ruiz-Linares A., Tomfohrde J., Minch E., Kidd J.R., and Cavalli-Sforza L.L. High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368 (1994) 455-457
4. Caballero A. Developments in the prediction of effective population size. Heredity 73 (1994) 657-679
5. Charlesworth B., Charlesworth D., and Barton N.H. The effects of genetic and geographic structure on neutral variation. Annu. Rev. Ecol. Syst. 34 (2003) 99-125
6. Chevalet C., Gillois M., and Nassar R. Identity coefficients in finite populations : Evolution of identity coefficients in a random mating dioecious population. Genetics 86 (1977) 697-713
7. Drummond A.J., Rambaut A., Shapiro B., and Pybus O.G. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol. Biol. Evol. 22 (2005) 1185-1192
8. Ewens W.J. On the concept of effective population size. Theor. Popul. Biol. 21 (1982) 373-378
9. Feller W. An Introduction to Probability Theory and its Applications, Volume II. second edition (1971), John Wiley & Sons, New York
10. Felsenstein J. Inbreeding and variance effective numbers in populations with overlapping generations. Genetics 68 (1971) 581-597
11. Gillois, M., 1964. La relation d'identité en génétique. Thèse, Université de Paris, 294p.
12. Gillois M. Relation d'identité en génétique. Ann. Inst. Henri Poincaré B 2 (1965) 1-94
13. Goldstein D.B., Ruiz-Linares A., Cavalli-Sforza L.L., and Feldman M.W. An evaluation of genetic distances for use with microsatellite loci. Genetics 139 (1995) 463-471
14. Gregorius H.R. On the concept of effective number. Theor. Popul. Biol. 40 (1991) 269-283
15. Kimmel M., and Chakraborty R. Measures of variation at DNA repeat loci under a general stepwise mutation model. Theor. Popul. Biol. 50 (1996) 345-367
16. Kimmel M., Chakraborty R., Stiverst D.N., and Deka R. Dynamics of repeat polymorphisms under a forward-backward mutation model: Within- and between-population variability at microsatellite loci. Genetics 143 (1996) 549-555
17. Kimmel M., Chakraborty R., King J.P., Bamshad M., Watkins W.S., and Jorde L.B. Signature of population expansion in microsatellite repeat data. Genetics 148 (1998) 1921-1930
18. Kimura M., and Weiss G.H. The stepping stone model of population structure and the decrease of genetic correlation with distance. Genetics 49 (1964) 561-576
19. King J.P., Kimmel M., and Chakraborty R. A power analysis of microsatellite-based statistics for inferring past population growth. Mol. Biol. Evol. 17 (2000) 1859-1868
20. Malécot G. Un traitement stochastique des problèmes linéaires (mutations, linkage, migration) en génétique de population. Ann. Univ. Lyon, Sci. A 14 (1951) 79-117
21. Malécot G. Heterozygosity and relationship in regularly subdivided populations. Theor. Popul. Biol. 8 (1975) 212-241
22. Malécot G. Evolution, parentés, migrations. In: Chevalet C., and Micali A. (Eds). Modèles Mathématiques en Biologie. Lecture Notes in Biomathematics vol. 41 (1981) 95-119
23. Notohara M., and Umeda T. The coalescence time of sampled genes in the structured coalescent model. Theor. Popul. Biol. 70 (2006) 289-299
24. Ohta T., and Kimura M. A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population. Genet. Res., Camb. 22 (1973) 201-204
25. Polanski A., Bobrowski A., and Kimmel M. A note on distributions of times to coalescence, under time-dependent population size. Theor. Popul. Biol. 63 (2002) 33-40
26. Pritchard J.K., and Feldman M.W. Statistics for microsatellite variation based on coalescence. Theor. Popul. Biol. 50 (1996) 325-344
27. Pybus O.G., Rambaut A., and Harvey P.H. An integrated framework for the inference of viral population history from reconstructed genealogies. Genetics 155 (2000) 1429-1437
28. Reich D.E., Feldman M.W., and Goldstein D.B. Statistical properties of two tests that use multilocus data sets to detect population expansions. Mol. Biol. Evol. 16 (1999) 453-466
29. Reich D.E., and Goldstein D.B. Genetic evidence for a Paleolithic human population expansion in Africa. Proc. Natl. Acad. Sci. USA 95 (1998) 8119-8123
30. Shriver M.D., Jin L., Boerwinkle E., Deka R., Ferrell R.E., and Chakraborty R. A novel measure of genetic distance for highly polymorphic tandem repeat loci. Mol. Biol. Evol. 12 (1995) 914-920
31. Shriver M.D., Jin L., Ferrell R.E., and Deka R. Microsatellite data support an early population expansion in Africa. Genome Res. 7 (1997) 586-591
32. Sun J.X., Mullikin J.C., Patterson N., and Reich D.E. Rosatellites are molecular clocks that support accurate inferences about history. Mol. Biol. Evol. 26 (2009) 1017-1027
33. Wang J.L. Estimation of effective population sizes from data on genetic markers. Phil. Trans. R. Soc. Lond. B Biol. Sci. 360 (2005) 1395-1409
34. Waples R.S. Genetic estimates of contemporary effective population size: to what time periods do the estimates apply. Mol. Ecol. 2005 14 (2005) 3335-3352
35. Watkins J.C. Likelihood-based estimation of microsatellite mutation rates. Theor. Popul. Biol. 71 (2006) 147-159
36. Wehrhahn C.F. The evolution of selectively similar electrophoretically detectable alleles in finite natural populations. Genetics 80 (1975) 375-394
37. Whitlock M.C., and Barton N.H. The effective size of a subdivided population. Genetics 146 (1997) 427-441
38. Whittaker J.C., Harbord R.M., Boxall N., Mackay I., Dawson R.M., G, and Sibly. Likelihood-Based Estimation of Microsatellite Mutation Rates. Genetics 164 (2003) 781-787