A coalescent model of recombination hotspots

Genetics

Volumn 164, Issue 1, 2003, Pages 407-417

  Wiuf, Carsten ^a   Posada, David ^a  

^a Variagenics   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CALCULATION; CHROMOSOME; GENE LOCATION; GENETIC ANALYSIS; GENETIC MODEL; GENETIC RECOMBINATION; GENETIC VARIABILITY; GENOME; HUMAN; PRIORITY JOURNAL; SIMULATION;

COMPUTER SIMULATION; MODELS, GENETIC; RECOMBINATION, GENETIC;

EID: 0038530758     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (27)

1. DALY, M., J. D. RIOUX, S. F. SCAFFNER, T. J. HUDSON and E. S. LANDER, 2001 High-resolution haplotype structure in the human genome. Nat. Genet. 29: 229-232.
2. ETHIER, S., and R. C. GRIFFITHS, 1990 On the two-locus sampling distribution. J. Math. Biol. 29: 131-159.
3. FEARNHEAD, P., and P. DONNELLY, 2001 Estimating recombination rates from population genetic data. Genetics 159: 1299-1318.
4. FERNHEAD, P., and P. DONNELLY, 2002 Approximate likelihood methods for estimating local recombination rate. J. R. Stat. Soc. B 64: 657-680.
5. FISHER, R. A., M. F. LYON and A. R. G. OWEN, 1947 The sex chromosome in the house mouse. Heredity 1: 335-365.
6. GABRIEL, S. B., S. F. SCHAFFNER, H. NGUYEN, J. M. MOORE, J. ROY et al., 2002 The structure of haplotype blocks in the human genome. Science 296: 2225-2229.
7. GRIFFITHS, R. C., 1981 Neutral two-locus multiple alleles model with recombination. Theor. Popul. Biol. 19: 169-186.
8. GRIFFITHS, R. C., 1991 The two-locus ancestral graph, pp. 100-117 in Selected Proceedings of the Symposium on Applied Probability, Sheffield 1989 (IMS Lecture Notes - Monograph Series, Vol. 18), edited by. I. V. BASAWA and R. L. TAYLOR. Institute of Mathematical Statistics, Hayward, CA.
9. HUDSON, R. R., 1983 Properties of a neutral allele model with intragenic recombination. Theor. Popul. Biol. 23: 183-201.
10. HUDSON, R. R., 1990 Gene genealogies and the coalescent process, pp. 1-44 in Oxford Surveys in Evolutionary Biology, Vol. 7, edited by D. FUTUYMA and J. ANTONOVICS. Oxford University Press, New York.
11. HUDSON, R. R., and N. KAPLAN, 1985 Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics III: 147-164.
12. JEFFREYS, A.J., L. KAUPPI and R. NEUMANN, 2001 Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nat. Genet. 29: 217-222.
13. JOHNSON, G. C. L., L. ESPOSITO, B.J. BARATT, A. N. SMITH, J. HEWARD et al., 2001 Haplotype tagging for the identification of common disease genes. Nat. Genet. 29: 233-237.
14. KAPLAN, N., and R. R. HUDSON, 1985 The use of sample genealogies for studying a selectively neutral m-loci model with recombination. Theor. Popul. Biol. 28: 382-396.
15. KARLIN, S., and H. M. TAYLOR, 1975 A First Course in Stochastic Processes. Academic Press, New York.
16. KINGMAN, J. F. C., 1982 The coalescent. Stoch. Proc. Appl. 13: 235-248.
17. MCPEEK, M. S., and T. P. SPEED, 1995 Modeling interference in genetic recombination. Genetics 139: 1031-1044.
18. MYERS, S. R., and R. C. GRIFFITHS, 2003 Bounds on the minimum number of recombination events in a sample history. Genetics 163: 375-394.
19. NACHMAN, M. W., 2001 Single nucleotide polymorphisms and recombination rate in humans. Trends Genet. 17: 481-485.
20. ROSENBERG, N. A., and M. NORDBORG, 2002 Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nat. Rev. Genet. 3: 380-390.
21. SIMONSEN, K., and G. A. CHURCHILI, 1997 A Markov chain model of coalescence with recombination. Theor. Popul. Biol. 52: 43-59.
22. WALL, J. D., 2000 A comparison of estimators of the population recombination rate. Mol. Biol. Evol. 17: 156-163.
23. WATTERSON, G., 1975 On the number of segregating sites in genetic models without recombination. Theor. Popul. Biol. 7: 256-276.
24. WIUF, C., 2000 A coalescence approach to gene conversion. Theor. Popul. Biol. 57: 357-367.
25. WIUF, C., and J. HEIN, 2000 The coalescent with gene conversion. Genetics 155: 451-462.
26. YANG, Z., 1996 Among-site rate variation and its impact on phylogenetic analysis. Trends Ecol. Evol. 11: 367-372.
27. ZHANG, K., M. DENG, T. CHEN, M. S. WATERMAN and F. SUN, 2002 A dynamic programming algorithm for haplotype block partition. Proc. Natl. Acad. Sci. USA 99: 7335-7339.