Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics

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

Volumn 104, Issue 8, 2007, Pages 2785-2790

  Hey, Jody ^a   Nielsen, Rasmus ^b  

^a RUTGERS UNIVERSITY   (United States)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Divergence; Population structure; Speciation

Indexed keywords

ARTICLE; CHIMPANZEE; MONTE CARLO METHOD; NONHUMAN; POPULATION GENETICS; POPULATION MODEL; POPULATION STRUCTURE; PRIORITY JOURNAL; PROBABILITY; SPECIES DIFFERENTIATION;

ANIMALS; BAYES THEOREM; GENEALOGY AND HERALDRY; GENETICS, POPULATION; MARKOV CHAINS; MODELS, GENETIC; MONTE CARLO METHOD; PAN TROGLODYTES;

PAN;

EID: 33847253975     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0611164104     Document Type: Article

References (37)

1. Felsenstein J (1988) Annu Rev Genet 22:521-565.
2. Griffiths RC (1989) J Math Biol 27:667-680.
3. Stephens M (2001) in Handbook of Statistical Genetics, eds Balding DJ, Bishop M, Cannings C (Wiley, West Sussex, UK).
4. Kuhner MK, Yamato J, Felsenstein J (1995) Genetics 140:1421-1430.
5. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E (1953) J Chem Phys 21:1087-1091.
6. Hastings WK (1970) Biometrika 57:97-109.
7. Kuhner MK, Yamato J, Felsenstein J (1998) Genetics 149:429-434.
8. Beerli P, Felsenstein J (1999) Genetics 152:763-773.
9. Kuhner MK, Yamato J, Felsenstein J (2000) Genetics 156:1393-1401.
10. Beerli P, Felsenstein J (2001) Proc Natl Acad Sci USA 98:4563-4568.
11. Thompson EA, Guo SW (1991) IMA J Math App Med Biol 8:149-169.
12. Wilson IJ, Balding DJ (1998) Genetics 150:499-510.
13. Beaumont MA (1999) Genetics 153:2013-2029.
14. Nielsen R (2000) Genetics 154:931-942.
15. Yang Z, Rannala B (1997) Mol Biol Evol 14:717-724.
16. Larget B, Simon DL (1999) Mol Biol Evol 16:750-759.
17. Mau B, Newton MA, Larget B (1999) Biometrics 55:1-12.
18. Stephens M (1999) Bulletin of the 52nd Session of the International Statistics Institute Book 1:273-276.
19. Geyer CJ, Thompson EA (1992) J R Stat Soc B 54:567-699.
20. Griffiths RC, Tavaré, S (1994) Theor Popul Biol 46:131-159.
21. Griffiths RC, Tavaré, S (1994) Stat Sci 9:307-319.
22. Stephens M, Donnelly P (2000) J R Stat Soc B 62:605-655.
23. Nielsen R, Wakeley J (2001) Genetics 158:885-896.
24. Hey J, Won Y-J, Sivasundar A, Nielsen R, Markert JA (2004) Mol Ecol 13:909-919.
25. Hey J, Nielsen R (2004) Genetics 167:747-760.
26. Palsbøll PJ, Berube M, Aguilar A, Notarbartolo-Di-Sciara G, Nielsen R (2004) Evol Int J Org Evol 58:670-675.
27. Hey J (2005) PLoS Biol 3:0965-0975.
28. Scott DW (1992) Multivariate Density Estimation: Theory, Practice, and Visualization (Wiley, New York).
29. Felsenstein J, Kuhner MK, Yamato J, Beerli P (1999) in Statistics in Genetics and Molecular Biology, ed Seillier-Moiseiwitsch F (Inst Math Stat and Am Math Soc, Hayward, CA), Vol 33, pp 163-185.
30. Kingman JFC (1982) Stochastic Processes App 13:235-248.
31. Felsenstein J (1992) Genet Res (Cambridge, UK) 60:209-220.
32. Maruyama T (1970) Theor Popul Biol 1:273-306.
33. Wright S (1931) Genetics 16:97-159.
34. Rannala B, Yang Z (2003) Genetics 164:1645-1656.
35. Press WH (1992) Numerical Recipes in C: The Art of Scientific Computing (Cambridge Univ Press, Cambridge, UK).
36. Won YJ, Hey J (2005) Mol Biol Evol 22:297-307.
37. Chernoff H (1954) Ann Math Stat 25:573-578.