Simultaneous inference of selection and population growth from patterns of variation in the human genome

Proceedings of the National Academy of Sciences of the United States of America

Volumn 102, Issue 22, 2005, Pages 7882-7887

  Williamson, Scott H ^a   Hernandez, Ryan ^a   Fledel Alon, Adi ^a   Zhu, Lan ^a   Nielsen, Rasmus ^a,b   Bustamante, Carlos D ^a  

^a Plant Breeding and Genetics Section in the School of Integrative Plant Science   (United States)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SUBSTITUTION; ARTICLE; DEMOGRAPHY; DNA POLYMORPHISM; DNA SEQUENCE; GENE MUTATION; GENETIC VARIABILITY; HUMAN; HUMAN GENOME; MODEL; NATURAL SELECTION; POPULATION GROWTH; POPULATION SIZE; PREDICTION; PRIORITY JOURNAL;

COMPUTATIONAL BIOLOGY; GENES; GENOME, HUMAN; GENOMICS; HUMANS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MUTATION; POLYMORPHISM, GENETIC; POPULATION GROWTH; SELECTION (GENETICS);

EID: 20344380699     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0502300102     Document Type: Article

References (45)

1. Wright, S. (1938) Proc. Natl. Acad. Sci. USA 24, 253-259.
2. Sawyer, S. A. & Hartl, D. L. (1992) Genetics 132, 1161-1176.
3. Kaplan, N. L., Darden, T. & Hudson, R. R. (1988) Genetics 120, 819-829.
4. Williamson, S., Fledel-Alon, A. & Bustamante, C. D. (2004) Genetics 168, 463-475.
5. Slatkin, M. & Hudson, R. R. (1991) Genetics 129, 555-562.
6. Griffiths, R. C. & Tavare, S. (1994) Philos. Trans. R. Soc. London Ser. B 344, 403-410.
7. Hudson, R. R. (1990) Oxf. Surv. Evol. Biol. 1, 1-14.
8. Nielsen, R. (2001) Heredity 86, 641-647.
9. McDonald, J. H. & Kretman, M. (1991) Nature 351, 652-654.
10. Rand, D. M. & Kann, L. M. (1996) Mol. Biol. Evol. 13, 735-748.
11. Bustamante, C. D., Nielsen, R., Sawyer, S. A., Olsen, K. M., Purugganan, M. D. & Hartl, D. L. (2002) Nature 416, 531-534.
12. Smith, N. G. C. & Eyre-Walker, A. (2002) Nature 415, 1022-1024.
13. Akashi, H. (1999) Genetics 151, 221-238.
14. Akashi, H. & Schaeffer, S. W. (1997) Genetics 146, 295-307.
15. Livingston, R. J., von Niederhausern, A., Jegga, A. G., Crawford, D. C., Carlson, C. S., Rieder, M. J. Gowrisankar, S., Aronow, B. J., Weiss, R. B. & Nickerson, D. A. (2004) Genome Res. 14, 1821-1831.
16. Miyata, T., Miyazawa, S. & Yasunaga, T. (1979) J. Mol. Evol. 12, 219-236.
17. Grantham, R. (1974) Science 185, 862-864.
18. Altshul, S. F. (1991) J. Mol. Biol. 219, 555-565.
19. Henikoff, S. & Henikoff, J. G. (1992) Proc. Natl. Acad. Sci. USA 89, 10915-10919.
20. Yampolsky, L. Y. & Stoltzfus, A. (2005) Genetics, in press.
21. Miyazawa, S. & Jernigan, R. L. (1993) Protein Eng. 6, 267-278.
22. Ramensky, V., Bork, P. & Sunyaev, S. (2002) Nucleic Acids Res. 30, 3894-3900.
23. Kimura, M. (1964) J. Appl. Prob. 1, 177-232.
24. Crow, J. F. & Kimura M. (1970) An Introduction to Population Genetics Theory (Harper and Row, New York).
25. Ewens, W. J. (1979) Mathematical Population Genetics (Springer, New York).
26. Kimura, M. (1955) Proc. Natl. Acad. Sci. USA 41, 144-150.
27. Hartl, D. L., Moriyama, E. N. & Sawyer, S. A. (1994) Genetics 138, 227-234.
28. Bustamante, C. D., Wakeley, J., Sawyer, S. A. & Hartl, D. L. (2001) Genetics 159, 1779-1788.
29. Kimura, M. (1955) Cold Spring Harbor Symp. Quant. Biol. 20, 33-53.
30. Press, W. H., Flannery, B. P., Teukolsky, S. A. & Vatterling, W. T. (1988) Numerical Recipes in C (Cambridge Univ. Press, Cambridge, U.K.), 2nd Ed.
31. Collins, F. S., Brooks, L. D. & Chakravarti, A. (1998) Genome Res. 8, 1229-1231.
32. Nielsen, R., Hubisz, M. J. & Clark, A. G. (2004) Genetics 168, 2373-2382.
33. Marth, G. T., Czabarka, E., Murvai, J. & Sherry, S. T. (2004) Genetics 166, 351-372.
34. Simmons, M. J. & Crow, J. F. (1977) Annu. Rev. Genet. 11, 49-78.
35. Hudson, R. R. (2002) Bioinformatics 18, 337-338.
36. Thornton, K. (2003) Bioinformatics 19, 2325-2327.
37. Ohta, T. (1973) Nature 246, 96-98.
38. Cargill, M., Altshuler, D., Ireland, J., Sklar, P., Ardlie, K., Patil, N., Shaw, N., Lane, C. R., Lim, E. P., Kalyanaraman, N., et al. (1999) Nat. Genet. 22, 231-238.
39. Sunyaev, S. R., Lathe, W. C., III, Ramensky, V. E. & Bork, P. (2000) Trends Genet. 16, 335-337.
40. Ptak, S. E. & Przeworski, M. (2002) Trends Genet. 18, 559-563.
41. Clark, A. G. (2003) Curr. Opin. Genet. Dev. 13, 1-7.
42. Pritchard, J. K. & Cox, N. J. (2002) Hum. Mol. Genet. 11, 2417-2423.
43. Chakravarti, A. (1999) Nat. Genet. 21, 56-60.
44. Reich, D. E. & Lander, E. S. (2001) Trends Genet. 17, 502-510.
45. Hill, W. G. & Robertson, A. (1966) Genet. Res. 8, 269-294.