Recombination and the properties of Tajima's D in the context of approximate-likelihood calculation

Genetics

Volumn 171, Issue 4, 2005, Pages 2143-2148

  Thornton, Kevin ^a  

^a Department of Obstetrics Gynecology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BAYES THEOREM; GENE LINKAGE DISEQUILIBRIUM; GENE MUTATION; GENETIC POLYMORPHISM; GENETIC RECOMBINATION; LINKAGE ANALYSIS; MATHEMATICAL ANALYSIS; MATHEMATICAL GENETICS; MATHEMATICAL MODEL; MUTATION RATE; NONHUMAN; PRIORITY JOURNAL; PROBABILITY; SINGLE NUCLEOTIDE POLYMORPHISM;

BIAS (EPIDEMIOLOGY); COMPUTER SIMULATION; DEMOGRAPHY; GENETICS, POPULATION; LIKELIHOOD FUNCTIONS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; RECOMBINATION, GENETIC;

EID: 27544474343     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.105.043786     Document Type: Article

References (20)

1. AKEY, J. M., M. A. EBERLE, M. J. RIEDER, C. S. CARLSON, M. D. SHRIVER et al., 2004 Population history and natural selection shape patterns of genetic variation in 132 genes. PloS Biol. 2(10):1591-1599.
2. BEAUMONT, M. A., W. ZHANG and D. J. BALDING, 2002 Approximate Bayesian computation in population genetics. Genetics 162:2025-2035.
3. BRAVERMAN, J. M., R. R. HUDSON, N. L. KAPLAN, C. H. LANGLEY AND W. STEPHAN, 1995 The hitchhiking effect on the site frequency-spectrum of DNA polymorphisms. Genetics 140: 783-796.
4. FU, Y. X., and W. H. LI, 1993 Statistical tests of neutrality of mutations. Genetics 133: 693-709.
5. GELMAN, A., J. B. CARLIN, H. S. STERN and D. B. RUBIN, 2003 Bayesian Data Analysis, Ed. 2. Chapman & Hall/CRC Press, London/New York/Cleveland/Boca Raton, FL.
6. GLINKA, S., L. OMETTO, S. MOUSSET, W. STEPHAN and D. D. LORENZO, 2003 Demography and natural selection have shaped genetic variation in Drosophila melanogaster: a multilocus approach. Genetics 165: 1269-1278.
7. HADDRILL, P., K. THORNTON, B. CHARLESWORTH and P. ANDOLFATTO, 2005 Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations. Genome Res. 15: 790-799.
8. HUDSON, R. R., 1983 Properties of a neutral allele model with intragenic recombination. Theor. Popul. Biol. 23: 183-201.
9. HUDSON, R. R., 2002 Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
10. MARJORAM, P., J. MOLITOR, V. PLAGNOL and S. TAVARE, 2003 Markov chain Monte Carlo without likelihoods. Proc. Natl. Acad. Sci. USA 100: 15324-15328.
11. PRITCHARD, J. K., M. T. SEIELSTAD, A. PEREZ-LEZAUN and M. W. FELDMAN, 1999 Population growth of human Y chromosomes: a study of Y chromosome microsatellites. Mol. Biol. Evol. 16: 1791-1798.
12. PRZEWORSKI, M., 2003 Estimating the time since the fixation of a beneficial allele. Genetics 164: 1667-1676.
13. STAJICH, J. E., and M. W. HAHN, 2005 Disentangling the effects of demography and selection in human history. Mol. Biol. Evol. 22: 63-73.
14. TAJIMA, F., 1983 Evolutionary relationship of DNA sequences in finite populations. Genetics 105: 437-460.
15. TAJIMA, F., 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
16. TENAILLON, M. I., J. U'REN, O. TENAILLON and B. S. GAUT, 2004 Selection versus demography: a multilocus investigation of the domestication process in maize. Mol. Biol. Evol. 21(7): 1214-1225.
17. THORNTON, K., 2003 libsequence: a C++ class library for evolutionary genetic analysis. Bioinformatics 19: 2325-2327.
18. WALL, J. D., 1999 Recombination and the power of statistical tests of neutrality. Genet. Res. 74: 65-79.
19. WALL, J. D., 2000 A comparison of estimators of the population recombination rate. Mol. Biol. Evol. 17: 156-163.
20. WATTERSON, G. A., 1975 Number of segregating sites in genetic models without recombination. Theor. Popul. Biol. 7: 256-276.