Importance sampling on coalescent histories. II: Subdivided population models

Advances in Applied Probability

Volumn 36, Issue 2, 2004, Pages 434-454

  De Iorio, Maria ^a   Griffiths, Robert C ^b  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Coalescent process; Diffusion process; Importance sampling; Migration; Subdivided population

Indexed keywords

ALGORITHMS; COALESCENCE; DIFFUSION; GENES; MARKOV PROCESSES; MATHEMATICAL MODELS; MUTAGENESIS; SAMPLING;

COALESCENT HISTORIES; IMPORTANCE SAMPLING; POPULATION GENE FREQUENCIES; SUBDIVIDED POPULATION;

PROBABILITY DISTRIBUTIONS;

EID: 3142769862     PISSN: 00018678     EISSN: None     Source Type: Journal    
DOI: 10.1239/aap/1086957580     Document Type: Article

References (18)

1. Bahlo, M. and Griffiths, R. C. (2000). Inference from gene trees in a subdivided population. Theoret. Pop. Biol. 57, 79-95.
2. Bahlo, M. and Griffiths, R. C. (2001). Coalescence time for two genes from a subdivided population. J. Math. Biol. 43, 397-410.
3. Beerli, P. and Felsenstein, J. (1999). Maximum likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics 152, 763-773.
4. Carbone, I. and Kohn, M. (2001). A microbial population-species interface: nested cladistic and coalescent inference with multilocus data. Molecular Ecology 10, 947-964.
5. De Iorio, M. and Griffiths, R. C. (2004). Importance sampling on coalescent histories. I. Adv. Appl. Prob. 36, 417-433.
6. De Iorio, M., Griffiths, R. C., Leblois, R. and Rousset, F. (2004). Stepwise mutation likelihood computation by sequential importance sampling in subdivided population models. Tech. Rep., Oxford University.
7. Ewens, W. J. (1972). The sampling theory of selectively neutral alleles. Theoret. Pop. Biol. 3, 87-112.
8. Fearnhead, P. and Donnelly, P. (2001). Estimating recombination rates from population genetics data. Genetics 159, 1299-1318.
9. Griffiths, R. C. and Tavaré, S. (1994a). Ancestral inference in population genetics. Statist. Sci. 9, 307-319.
10. Griffiths, R. C. and Tavaré, S. (1994b). Sampling theory for neutral alleles in a varying environment. Proc. R. Soc. London B 344, 403-410.
11. Griffiths, R. C. and Tavaré, S. (1994c). Simulating probability distributions in the coalescent. Theoret. Pop. Biol. 46, 131-159.
12. Griffiths, R. C. and Tavaré, S. (1996). Markov chain inference methods in population genetics. Math. Comput. Modelling 23, 141-158.
13. Griffiths, R. C. and Tavaré, S. (1997). Computational methods for the coalescent. In Progress in Population Genetics and Human Evolution (IMA Vols Math. Appl. 87), eds P. Donnelly and S. Tavaré, Springer, Berlin, pp. 165-182.
14. Griffiths, R. C. and Tavaré, S. (1999). The ages of mutations in gene trees. Ann. Appl. Prob. 9, 567-590.
15. Herbots, H. M. (1997). The structured coalescent. In Progress in Population Genetics and Human Evolution (IMA Vols Math. Appl. 87), eds P. Donnelly and S. Tavaré, Springer, Berlin, pp. 231-255.
16. Nath, M. and Griffiths, R. C. (1996). Estimation in an island model using simulation. Theoret. Pop. Biol. 3, 227-253.
17. Notohara, M. (1990). The coalescent and the genealogical process in geographically structured populations. J. Math. Biol. 29, 59-75.
18. Stephens, M. and Donnelly, P. (2000). Inference in molecular population genetics. J. R. Statist. Soc. B 62, 605-655.