Bayesian coalescent inference of past population dynamics from molecular sequences

Molecular Biology and Evolution

Volumn 22, Issue 5, 2005, Pages 1185-1192

  Drummond, A J ^a   Rambaut, A ^a   Shapiro, B ^a   Pybus, O G ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Coalescent inference; Demographic model selection; Holocene; Markov chain Monte Carlo; Megafaunal extinctions; Skyline plot

Indexed keywords

MITOCHONDRIAL DNA;

ARTICLE; BAYES THEOREM; BUFFALO; DEMOGRAPHY; EVOLUTIONARY HOMOLOGY; HEPATITIS C VIRUS; MATHEMATICAL ANALYSIS; MOLECULAR GENETICS; MONTE CARLO METHOD; NONHUMAN; POPULATION DYNAMICS; PROBABILITY;

ALGORITHMS; ANIMALS; BAYES THEOREM; BISON; DNA, MITOCHONDRIAL; EGYPT; EVOLUTION, MOLECULAR; GENETICS, POPULATION; HEPACIVIRUS; HEPATITIS C; HUMANS; MARKOV CHAINS; MODELS, GENETIC; MONTE CARLO METHOD; POPULATION DENSITY; POPULATION DYNAMICS; TIME FACTORS;

EID: 17744381574     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msi103     Document Type: Article

References (36)

1. Akaike, H. 1974. A new look at the statistical model identification. IEEE Trans. Automat. Control AC-19:716-723.
2. Alroy, J. 1999. Putting North America's end-Pleistocene megafaunal extinction in context: large-scale analyses of spatial patterns, extinction rates, and size distributions. Pp. 105-143 in R. D. E. MacPhee, ed. Extinctions in near time: causes, contexts, and consequences. Kluwer Academic, New York.
3. Bahlo, M., and R. C. Griffiths. 2000. Inference from gene trees in a subdivided population. Theor. Popul. Biol. 57:79-95.
4. Beaumont, M. A. 1999. Detecting population expansion and decline using microsatellites. Genetics 153:2013-2029.
5. 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 98:4563-4568.
6. Donnelly, P., and S. Tavare. 1995. Coalescents and genealogical structure under neutrality. Annu. Rev. Genet. 29:401-421.
7. 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.
8. Drummond, A., O. G. Pybus, and A. Rambaut. 2003. Inference of viral evolutionary rates from molecular sequences. Adv. Parasitol. 54:331-358.
9. Drummond, A. J., O. G. Pybus, A. Rambaut, R. Forsberg, and A. G. Rodrigo. 2003. Measurably evolving populations. Trends Ecol. Evol. 18:481-488.
10. Fearnhead, P., and P. Donnelly. 2001. Estimating recombination rates from population genetic data. Genetics 159:1299-1318.
11. Felsenstein, J. 1992. Estimating effective population size from samples of sequences: inefficiency of pairwise and segregating sites as compared to phylogenetic estimates. Genet. Res. 59:139-147.
12. Flanagan, N. S., A. Tobler, A. Davison, O. G. Pybus, D. D. Kapan, S. Planas, M. Linares, D. Heckel, and W. O. McMillan. 2004. Historical demography of Mullerian mimicry in the Neotropical Heliconius butterflies. Proc. Natl. Acad. Sci. USA 101:9704-9709.
13. Frank, C., M. K. Mohamed, G. T. Strickland et al. (11 co-authors). 2000. The role of parenteral antischistosomal therapy in the spread of hepatitis C virus in Egypt. Lancet 355:887-891.
14. Fu, Y. X. 1994. A phylogenetic estimator of effective population size or mutation rate. Genetics 136:685-692.
15. Griffiths, R. C., and P. Marjoram. 1996. Ancestral inference from samples of DNA sequences with recombination. J. Comput. Biol. 3:479-502.
16. Griffiths, R. C., and S. Tavare. 1994. Sampling theory for neutral alleles in a varying environment. Philos. Trans. R. Soc. Lond. B Biol. Sci. 344:403-410.
17. Hasegawa, M., H. Kishino, and T. Yano. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174.
18. Jeffreys, H. 1946. An invariant form for the prior probability in estimation problems. Proc. R. Soc. A 186:453-461.
19. Joy, D. A., X. Feng, J. Mu et al. (12 co-authors). 2003. Early origin and recent expansion of Plasmodium falciparum. Science 300:318-321.
20. Kuhner, M. K., J. Yamato, and J. Felsenstein. 1998. Maximum likelihood estimation of population growth rates based on the coalescent. Genetics 149:429-434.
21. _. 2000. Maximum likelihood estimation of recombination rates from population data. Genetics 156:1393-1401.
22. Opgen-Rhein, R., L. Fahrmeir, and K. Strimmer. 2005. Inference of demographic history from genealogical trees using reversible jump Markov chain Monte Carlo. BMC Evol. Biol. 5:6.
23. Pybus, O. G., M. A. Charleston, S. Gupta, A. Rambaut, E. C. Holmes, and P. H. Harvey. 2001. The epidemic behavior of the hepatitis C virus. Science 292:2323-2325.
24. Pybus, O. G., A. J. Drummond, T. Nakano, B. H. Robertson, and A. Rambaut. 2003. The epidemiology and iatrogenic transmission of hepatitis C virus in Egypt: a Bayesian coalescent approach. Mol. Biol. Evol. 20:381-387.
25. Pybus, O. G., and A. Rambaut. 2002. GENIE: estimating demographic history from molecular phylogenies. Bioinformatics 18:1404-1405.
26. Pybus, O. G., A. Rambaut, and P. H. Harvey. 2000. An integrated framework for the inference of viral population history from reconstructed genealogies. Genetics 155:1429-1437.
27. Ray, S. C., R. R. Arthur, A. Carella, J. Bukh, and D. L. Thomas. 2000. Genetic epidemiology of hepatitis C virus throughout Egypt. J. Infect. Dis. 182:698-707.
28. Reich, D. E., and D. B. Goldstein. 1998. Genetic evidence for a Paleolithic human population expansion in Africa. Proc. Natl. Acad. Sci. USA 95:8119-8123.
29. Rodrigo, A. G., and J. Felsenstein. 1999. Coalescent approaches to HIV population genetics. Pp. 233-272 in K. Crandall, ed. Molecular evolution of HIV. Johns Hopkins University Press, Baltimore, Md.
30. Roman, J., and S. R. Palumbi. 2003. Whales before whaling in the North Atlantic. Science 301:508-510.
31. Shapiro, B., A. J. Drummond, A. Rambaut et al. (27 co-authors). 2004. Rise and fall of the Beringian steppe bison. Science 306:1561-1565.
32. Smith, D. B., S. Pathirana, F. Davidson, E. Lawlor, J. Power, P. L. Yap, and P. Simmonds. 1997. The origin of hepatitis C virus genotypes. J. Gen. Virol. 78(Pt 2):321-328.
33. Storz, J. F., M. A. Beaumont, and S. C. Alberts. 2002. Genetic evidence for long-term population decline in a Savannah-dwelling primate: inferences from a hierarchical Bayesian model. Mol. Biol. Evol. 19:1981-1990.
34. Strickland, G. T., H. Elhefni, T. Salman, I. Waked, M. Abdel-Hamid, N. N. Mikhail, G. Esmat, and A. Fix. 2002. Role of hepatitis C infection in chronic liver disease in Egypt. Am. J. Trop. Med. Hyg. 67:436-442.
35. Strimmer, K., and O. G. Pybus. 2001. Exploring the demographic history of DNA sequences using the generalized skyline plot. Mol. Biol. Evol. 18:2298-2305.
36. Yesner, D. R. 2001. Human dispersal into interior Alaska: antecedent conditions, mode of colonization, and adaptations. Quat. Sci. Rev. 20:315-327.