Accuracy of coalescent likelihood estimates: Do we need more sites, more sequences, or more loci?

Molecular Biology and Evolution

Volumn 23, Issue 3, 2006, Pages 691-700

  Felsenstein, Joseph ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Coalescent; Maximum likelihood; Population size; Sampling design

Indexed keywords

ACCURACY; ARTICLE; CLINICAL ARTICLE; CONTROLLED STUDY; COST; GENE LOCUS; GENE SEQUENCE; GENETIC VARIABILITY; HUMAN; NONHUMAN; POPULATION BIOLOGY; SAMPLE SIZE;

GENETICS, POPULATION; HUMANS; LIKELIHOOD FUNCTIONS; MATHEMATICS; MODELS, GENETIC; PHYLOGENY; VARIATION (GENETICS);

EID: 33244495782     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msj079     Document Type: Article

References (24)

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 152:763-773.
3. _. 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.
4. Edwards, A. W. F. 1970. Estimation of the branch points of a branching diffusion process. J. R. Stat. Soc. B 32:155-174.
5. Felsenstein, J. 1988. Phytogenies from molecular sequences: inference and reliability. Annu. Rev. Genet. 22:521-565.
6. _. 1992a. Estimating effective population size from samples of sequences: inefficiency of pairwise and segregating sites as compared to phylogenetic estimates. Genet. Res. 59:139-147.
7. _. 1992b. Estimating effective population size from samples of sequences: a bootstrap Monte Carlo approach. Genet. Res. 60:209-220.
8. Fu, Y.-X. 1994. A phylogenetic estimator of effective population size or mutation rate. Genetics 136:685-692.
9. Fu, Y.-X., and W.-H. Li. 1993. Statistical tests of neutrality of mutations. Genetics 133:693-709.
10. Griffiths, R. C. 1989. Genealogical tree probabilities in the infinitely-many-site model. J. Math. Biol. 27:667-680.
11. Griffiths, R. C., and P. Marjoram. 1996. Ancestral inferences from samples of DNA sequences with recombination. J. Comput. Biol. 3:479-502.
12. Griffiths, R. C., and S. Tavaré. 1994a. Sampling theory for neutral alleles in a varying environment. Philos. Trans. R. Soc. Lond. Ser. B Biol. Sci. 344:403-410.
13. _. 1994b. Ancestral inference in population genetics. Stat. Sci. 9:307-319.
14. Kingman, J. F. C. 1982a. The coalescent. Stoch. Proc. Appl. 13:235-248.
15. _. 1982b. On the genealogy of large populations. J. Appl. Prob. 19A:27-43.
16. _. 1982c. Exchangeability and the evolution of large populations. Pp. 97-112 in G. Koch and F. Spizzichino, eds. Exchangeability in probability and statistics. Proceedings of the International Conference on Exchangeability in Probability and Statistics, Rome, 6th-9th April, 1981, in honour of Professor Bruno de Finetti. North-Holland/Elsevier, Amsterdam.
17. Kuhner, M. K., J. Yamato, and J. Felsenstein. 1995. Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling. Genetics 140: 1421-1430.
18. _. 1997. Applications of Metropolis-Hastings genealogy sampling. Pp. 183-192 in P. Donnelly and S. Tavare, eds. Progress in population genetics and human evolution. IMA volumes in mathematics and its applications, Vol. 87. Springer Verlag, Berlin, Germany.
19. _. 1998. Maximum likelihood estimation of population growth rates based on the coalescent. Genetics 149: 429-434.
20. _. 2000. Maximum likelihood estimation of recombination rates from population data. Genetics 156:1393-1401.
21. Pluzhnikov, A., and P. Donnelly. 1996. Optimal sequencing strategies for surveying molecular genetic diversity. Genetics 144:1247-1262.
22. Tajima, F. 1983. Evolutionary relationships of DNA sequences in finite populations. Genetics 105:437-460.
23. Watterson, G. A. 1975. On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7:256-276.
24. Wilson, I. R., G. Weale, and D. G. Balding. 2003. Inferences from DNA data: population histories, evolutionary processes, and forensic match probabilities. J. R. Stat. Soc. Ser. A 166:155-188.