Using temporally spaced sequences to simultaneously estimate migration rates, mutation rate and population sizes in measurably evolving populations

Genetics

Volumn 168, Issue 4, 2004, Pages 2407-2420

  Ewing, Greg ^a   Nicholls, Geoff ^a   Rodrigo, Allen ^a,b  

^a UNIVERSITY OF AUCKLAND   (New Zealand)

^b UNIVERSITY OF AUCKLAND   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BAYES THEOREM; BEHAVIOR; BLOOD; DNA SEQUENCE; GENE MUTATION; GENE SEQUENCE; HUMAN; MIGRATION; MONTE CARLO METHOD; POPULATION GENETICS; POPULATION SIZE; PRIORITY JOURNAL; SPERM;

EVOLUTION; GENETICS, POPULATION; MUTATION;

EID: 11244269484     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: 10.1534/genetics.104.030411     Document Type: Article

References (31)

1. BAHLO, M., and R. C. GRIFFITHS, 2000 Inference from gene trees in a subdivided population. Theor. Popul. Biol. 57: 79-95.
2. BEERLI, P., and J. FELSENSTEIN, 1999 Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics 152: 765-773.
3. BEERLI, P., and J. FELSENSTEIN, 2001 Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proc. Natl. Acad. Sci. USA 98 (8): 4563-4568.
4. DRUMMOND, A., and A. RODRIGO, 2000 Reconstruction genealogies of serial samples under the assumption of a molecular clock using serial-sample UPGMA. Mol. Biol. Evol. 17 (12): 1807-1815.
5. DRUMMOND, A. J., G. K. NICHOLLS, A. G. RODRIGO and W. SOLOMON, 2002 Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161: 1307-1320.
6. DRUMMOND, A. J., G. K. NICHOLLS, A. G. RODRIGO and W. SOLOMON, 2003a Tools for Constructing Chronologies, pp. 151-174. Springer-Verlag, Berlin, Heidelberg, Germany/New York.
7. DRUMMOND, A. J., O. G. PYBUS, A. RAMBAUT, R. FORSBERG and A. G. RODRIGO, 2003b Measurably evolving populations. Trends Ecol. Evol. 8 (9): 481-488.
8. FELSENSTEIN, J., 1981 Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17: 368-376.
9. FISHER, R. A., 1930 The Genetical Theory of Natural Selection. Clarendon Press, Oxford.
10. GEYER, C. J., 1992 Practical Markov chain Monte Carlo. Stat. Sci. 7: 473-511.
11. GREEN, P. J., 1995 Reversible jump Markov chain Monte Carlo computation and bayesian model determination. Biometrika 82:711-732.
12. GREEN, P. J., 2003 Highly Structured Stochastic Systems (http://www.oup. co.uk/isbn/0-19-851055-1).
13. HASTINGS, W. K., 1970 Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57: 97-109.
14. HUDSON, R. R., 1990 Gene genealogies and the coalescent process, pp. 1-44 in Oxford Surveys in Evolutionary Biology, Vol. 7. Oxford University Press, Oxford.
15. KINGMAN, J., 1982a The coalescent. Stoch. Proc. Appl. 13: 235-248.
16. KINGMAN, J., 1982b On the genealogy of large populations. J. Appl. Probab. 19A: 27-43.
17. METROPOLIS, N., A. ROSENBLUTH, M. ROSENBLUTH, A. TELLER and E. TELLER, 1953 Equations of state calculations by fast computing machines. J. Chem. Phys. 21: 1087-1091.
18. NAGYLAKI, T., 1980 The strong-migration limit in geographically structured populations. J. Math. Biol. 2: 101-114.
19. NICKLE, D. C., M. A. JENSEN, D. SHRINER, S. J. BRODIE, L. M. FRENKEL et al., 2003 Volutionary indicators of human immunodeficiency virus type 1 reservoirs and compartments. J. Virol. 77: 5540-5546.
20. NIELSEN, R., and J. WAKELEY, 2001 Distinguishing migration from isolation: Markov chain Monte Carlo approach. Genetics 158: 885-896.
21. NOTOHARA, M., 1990 The coalescent and the genealogical process in geographically structured population. J. Math. Biol. 29: 59-75.
22. NOTOHARA, M., 1993 The strong-migration limit for the genealogical process in geographically structured populations. J. Math. Biol. 31: 115-122.
23. PERELSON, A. S., A. U. NEUMANN, M. MARKOWITZ, J. M. LEONARD and D. D. Ho, 1996 HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time. Science 271: 1582-1586.
24. Poss, M., A. G. RODRIGO, J. J. GOSINK, G. H. LEARN, D. DE VANGE PANTELEEF et al., 1998 Evolution of envelope sequences from the genital tract and peripheral blood of women infected with clade A human immunodeficiency virus type 1. J. Virol. 72 (10): 8240-8251.
25. RODRIGO, A. G., and J. FELSENSTEIN, 1999 The Evolution of HIV. Johns Hopkins University Press, Baltimore.
26. RODRIGUEZ, F., J. L. OLIVER, A. MARIN and J. R. MEDINA, 1990 The general stochastic model of nucleotide substitution. J. Theor Biol. 142: 485-501.
27. SHANKARAPPA, R., J. B. MARGOLICK, S. J. GANGE, A. G. RODRIGO, D. UPCHURCH et al., 1999 Consistant viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. J. Virol. 73: 10489-10502.
28. WANG, T. H., Y. K. DONALDSON, R. P. BRETTLE, J. E. BELL and P. SIMMONDS, 2001 Identification of shared populations of human immunodeficiency virus type 1 infecting microglia and tissue macrophages outside the central nervous system. J. Virol. 75 (23): 11686-11699.
29. WONG, J. K., C. CIGNACIO, F. TORRIAN, D. HAVLIR, N. J. FITCH et al., 1997 In vivo compartmentalization of human immunodeficiency virus: evidence from the examination of pol sequences from autopsy tissues. J. Virol. 71 (3): 2059-2071.
30. WRIGHT, S., 1931 Evolution in Mendelian populations. Genetics 16: 97-159.
31. ZHANG, L., L. ROWE, T. HE, C. CHUNG, J. YU et al., 2002 Compartmentalization of surface envelope glycoprotein of human immunodeficiency virus type 1 during acute and chronic infection. J. Virol. 76 (18): 9465-9473.