Population genetics of polymorphism and divergence for diploid selection models with arbitrary dominance

Genetics

Volumn 168, Issue 1, 2004, Pages 463-475

  Williamson, Scott ^a   Fledel Alon, Adi ^a   Bustamante, Carlos D ^a  

^a Department of Obstetrics Gynecology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SUBSTITUTION; ARTICLE; CONTROLLED STUDY; DIPLOIDY; DNA POLYMORPHISM; DNA SEQUENCE; DOMINANT INHERITANCE; GENE FREQUENCY; GENE MUTATION; GENETIC MODEL; GENETIC SELECTION; GENETIC VARIABILITY; NONHUMAN; POISSON DISTRIBUTION; POPULATION GENETICS; PRIORITY JOURNAL; RECESSIVE INHERITANCE; SIMULATION; STATISTICAL DISTRIBUTION; THEORY;

COMPUTER SIMULATION; EVOLUTION, MOLECULAR; GENETICS, POPULATION; INHERITANCE PATTERNS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MUTATION; POLYMORPHISM, GENETIC; SELECTION (GENETICS);

EID: 5144231907     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: 10.1534/genetics.103.024745     Document Type: Article

References (50)

1. AKASHI, H., 1999 Inferring the fitness effects of DNA mutations from polymorphism and divergence data: statistical power to detect directional selection under stationarity and free recombination. Genetics 151: 221-238.
2. BUSTAMANTE, C. D., J. WAKELEY, S. A. SAWYER and D. L. HARTL, 2001 Directional selection and the site-frequency spectrum. Genetics 159: 1779-1788.
3. BUSTAMANTE, C. D., R. NIELSEN, S. A. SAWYER, K. M. OLSEN, M. D. PURUGGANAN et al., 2002 The cost of inbreeding: fixation of deleterious genes in Arabidopsis. Nature 416: 531-534.
4. BUSTAMANTE, C. D., R. NIELSEN and D. L. HARTL, 2003 Maximum likelihood and Bayesian methods for estimating the distribution of selective effects among classes of mutations using DNA polymorphism data. Theor. Popul. Biol. 63: 91-103.
5. CHARLESWORTH, B., and K. A. HUGHES, 2000 The maintenance of genetic variation in life-history traits, pp. 369-392 in Evolutionary Genetics: From Molecules to Morphology, edited by R. S. SINGH and C. B. KRIMBAS. Cambridge University Press, Cambridge, UK.
6. CHERRY, J. L., 2003 Selection in a subdivided population with dominance or local frequency dependence. Genetics 163: 1511-1518.
7. CHERRY, J. L., 2004 Selection, subdivision and extinction and recolonization. Genetics 166: 1105-1114.
8. CROW, J. F., 1993 Mutation, mean fitness, and genetic load, pp. 3-42 in Oxford Surveys in Evolutionary Biology, Vol. 9, edited by D. J. FUTUYMA and J. ANTONOVICS. Oxford University Press, Oxford.
9. CROW, J. F., and M. J. SIMMONS, 1983 The mutation load in Drosophila, pp. 1-35 in The Genetics and Biology of Drosophila, Vol. 3c, edited by M. ASHBURNER, H. L. CARSON and J. N. THOMPSON. Academic Press, New York.
10. DENNISTON, C., and J. F. CROW, 1990 Alternative fitness models with the same allele frequency dynamics. Genetics 125: 201-205.
11. EWENS, W. J., 1974 A note on the sampling theory for infinite alleles and infinite sites models. Theor. Popul. Biol. 6: 143-148.
12. FISHER, R. A., 1922 On the dominance ratio. Proc. R. Soc. Edinb. 50: 205-220.
13. FISHER, R. A., 1930 The Genetical Theory of Natural Selection. Clarendon Press, Oxford.
14. FU, Y.-X., and W.-H. LI, 1993 Statistical tests of neutrality of mutations. Genetics 133: 693-709.
15. GOLDING, G. B., 1997 The effect of purifying selection on genealogies, pp. 271-285 in Progress in Population Genetics and Human Evolution (IMA Volumes in Mathematics and Its Applications, Vol. 87), edited by P. DONNELLY and S. TAVARE. Springer, New York.
16. GRIFFITHS, R. C., 2003 The frequency spectrum of a mutation, and its age, in a general diffusion model. Theor. Popul. Biol. 64: 241-251.
17. HALDANE, J. B. S., 1922 Sex ratio and unisexual sterility in animal hybrids. J. Genet. 12: 101-109.
18. HALDANE, J. B. S., 1926 A mathematical theory of natural and artificial selection. Part III. Proc. Camb. Philos. Soc. 23: 363-372.
19. HARTL, D. L., E. N. MORIYAMA and S. A. SAWYER, 1994 Selection intensity for codon bias. Genetics 138: 227-234.
20. HUDSON, R. R., 2001 Two-locus sampling distributions and their application. Genetics 159: 1805-1817.
21. KACSER, H., and J. A. BURNS, 1981 The molecular basis of dominance. Genetics 97: 639-666.
22. KELLY, J. K., 2003 Deleterious mutations and the genetic variance of male fitness components in Mimulus guttatus. Genetics 164: 1071-1085.
23. KENDALL, M. G., and A. STUART, 1973 The Advanced Theory of Statistics, Vol. 2: Inference and Relationship. Charles Griffin & Co., London.
24. KIMURA, M., 1964 Diffusion models in population genetics. J. Appl. Prob. 1: 177-232.
25. KIMURA, M., 1968 Evolutionary rate at the molecular level. Nature 217: 624-626.
26. KIMURA, M., 1971 Theoretical foundation of population genetics at the molecular level. Theor. Popul. Biol. 2: 174-208.
27. LEWONTIN, R. C., 1974 The Genetic Basis of Evolutionary Change. Columbia University Press, New York.
28. LYNCH, M., and B. WALSH, 1998 Genetics and Analysis of Quantitative Traits. Sinauer Associates, Sunderland, MA.
29. MCDONALD, J. H., and M. KREITMAN, 1991 Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.
30. MULLER, H. J., 1942 Isolating mechanisms, evolution, and temperature. Biol. Symp. 6: 71-125.
31. NIELSEN, R., 2001 Statistical tests of selective neutrality in the age of genomics. Heredity 86: 641-647.
32. OHTA, T., 1992 The nearly neutral theory of molecular evolution. Annu. Rev. Ecol. Syst. 23: 263-286.
33. ORR, H. A., 1997 Haldane's rule. Annu. Rev. Ecol. Syst. 28: 195-218.
34. PRESGRAVES, D. C., and H. A. ORR, 1998 Haldane's rule in species lacking a hemizygous X. Science 282: 952-954.
35. PRESS, W. H., B. P. FLANNERY, S. A. TEUKOLSKY and W. T. VATTERLING, 1988 Numerical Recipes in C. Cambridge University Press, Cambridge, UK.
36. ROZE, D., and F. ROUSSET, 2003 Selection and drift in subdivided populations: a straightforward method for deriving diffusion approximations and applications involving dominance, selfing and local extinctions. Genetics 165: 2153-2166.
37. SAWYER, S. A., and D. L. HARTL, 1992 Population genetics of polymorphism and divergence. Genetics 132: 1161-1176.
38. SIMMONS, M. J., and J. F. CROW, 1977 Mutations affecting fitness in Drosophila populations. Annu. Rev. Genet. 11: 49-78.
39. TAJIMA, F., 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
40. TAKAHATA, N., and M. NEI, 1990 Allelic genealogy under overdominant and frequency-dependent selection and polymorphism of major histocompatibility complex loci. Genetics 124: 967-978.
41. TURELLI, M., and D. J. BEGUN, 1997 Haldane's rule and X-chromosome size in Drosophila. Genetics 147: 1799-1815.
42. TURELLI, M., and H. A. ORR, 1995 The dominance theory of Haldane's rule. Genetics 140: 389-402.
43. WAKELEY, J., 2003 Polymorphism and divergence for island-model species. Genetics 163: 411-420.
44. WATTERSON, G. A., 1975 On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7: 256-276.
45. WEINREICH, D. M., and D. M. RAND, 2000 Contrasting patterns of nonneutral evolution in proteins encoded in nuclear and mitochondrial genomes. Genetics 156: 385-399.
46. WHITLOCK, M. C., 2003 Fixation probability and time in subdivided populations. Genetics 164: 767-779.
47. WILLIS, J. H., 1999 Inbreeding load, average dominance, and the mutation rate for mildly deleterious alleles in Mimulus guttatus. Genetics 153: 1885-1898.
48. WRIGHT, S., 1931 Evolution in Mendelian populations. Genetics 16: 97-159.
49. WRIGHT, S., 1938 The distribution of gene frequencies under irreversible mutation. Proc. Natl. Acad. Sci. USA 24: 253-259.
50. WRIGHT, S., and T. DOBZHANSKY, 1948 Genetics of natural populations. XII. Experimental reproduction of some of the changes caused by natural selection in certain populations of Drosophila pseudoobscura. Genetics 31: 125-156.