Likelihood-based inference in isolation-by-distance models using the spatial distribution of low-frequency alleles

Evolution

Volumn 63, Issue 11, 2009, Pages 2914-2925

  Novembre, John ^a,b   Slatkin, Montgomery ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Dispersal; Importance sampling; Intraallelic genealogy; Isolation by distance; Likelihood; Low frequency alleles

Indexed keywords

ALLELE; DATA SET; DICOTYLEDON; DISPERSAL; GENEALOGY; MUTATION; NUMERICAL MODEL; POPULATION DENSITY; POPULATION GENETICS; SAMPLING; SPATIAL DISTRIBUTION;

ARABIDOPSIS; ARTICLE; GENE FREQUENCY; GENETICS; PLANT GENE; STATISTICAL MODEL; THEORETICAL MODEL;

ARABIDOPSIS; GENE FREQUENCY; GENES, PLANT; LIKELIHOOD FUNCTIONS; MODELS, THEORETICAL;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 70350236880     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/j.1558-5646.2009.00775.x     Document Type: Article

References (33)

1. Barton, N. H., and F. Depaulis. 2002. Neutral evolution in spatially continuous populations. Theor Popul Biol 61 : 31 48.
2. Beerli, P., and J. Felsenstein. 2001. Maximum likelihood estimation of a migration matrix and effective population sizes in subpopulations by using a coalescent approach. Proc. Natl. Acad. Sci. USA 98 : 4563 4568.
3. Clark, J. S. 1998. Why trees migrate so fast: confronting theory with dispersal biology and the paleorecord. Am. Nat. 152 : 204 224.
4. Excoffier, L., P. E. Smouse, and J. M. Quattro. 1992. Analysis of molecular variance inferred from metric distances among dna haplotypes - application to human mitochondrial-DNA restriction data. Genetics 131 : 479 491.
5. Fearnhead, P. 2007. On the choice of genetic distance in spatial-genetic studies. Genetics 177 : 427 434.
6. Felsenstein, J. 1973. Maximum-likelihood estimation of evolutionary trees from continuous characters. Am. J. Hum. Genet. 25 : 471 492.
7. Felsenstein, J. 1975. A pain in the torus: some difficulties with models of isolation by distance. Am. Nat. 109 : 359 368.
8. Felsenstein, J. 1981. Evolutionary trees from gene frequencies and quantitative characters: finding maximum likelihood estimates. Evolution 35 : 1229 1242.
9. Hey, J., and R. Nielsen. 2007. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc. Natl. Acad. Sci. USA 104 : 2785 2790.
10. Iorio, M. D., R. C. Griffiths, R. Leblois, and F. Rousset. 2005. Stepwise mutation likelihood computation by sequential importance sampling in subdivided population models. Theor. Popul. Biol. 68 : 41 53.
11. Leblois, R., A. Estoup, and F. Rousset. 2003. Influence of mutational and sampling factors on the estimation of demographic parameters in a "continuous" population under isolation by distance. Mol. Biol. Evol. 20 : 491 502.
12. Leblois, R., F. Rousset, and A. Estoup. 2004. Influence of spatial and temporal heterogeneities on the estimation of demographic parameters in a continuous population using individual microsatellite data. Genetics 166 : 1081 1092.
13. Liu, J. S. 2002. Monte Carlo strategies in scientific computing. Springer, New York.
14. Meligkotsidou, L., and P. Fearnhead. 2007. Postprocessing of genealogical trees. Genetics 177 : 347 358.
15. Neigel, J. E., R. M. Ball, and J. C. Avise. 1991. Estimation of single generation migration distances from geographic-variation in animal mitochondrial-DNA. Evolution 45 : 423 432.
16. Nielsen, R., and J. Wakeley. 2001. Distinguishing migration from isolation: A Markov chain Monte Carlo approach. Genetics 158 : 885 896.
17. Nordborg, M., T. T. Hu, Y. Ishino, J. Jhaveri, C. Toomajian, et al. 2005. The pattern of polymorphism in arabidopsis thaliana. PLoS Biol 3 : e196.
18. Rannala, B., and J. A. Hartigan. 1995. Identity by descent in island-mainland populations. Genetics 139 : 429 437.
19. Rousset, F. 1997. Genetic differentiation and estimation of gene flow from f-statistics under isolation by distance. Genetics 145 : 1219 1228.
20. Rousset, F. 2000. Genetic differentiation between individuals. J. Evol. Biol. 13 : 58 62.
21. Rousset, F. 2004. Genetic structure and selection in subdivided populations (MPB-40) (Monographs in Population Biology). Princeton Univ. Press, Princeton, NJ.
22. Rousset, F., and R. Leblois. 2007. Likelihood and approximate likelihood analyses of genetic structure in a linear habitat: performance and robustness to model misspecification. Mol. Biol. Evol. 24 : 2730 2745.
23. Slatkin, M. 1987. Gene flow and the geographic structure of natural populations. Science 236 : 787 792.
24. Slatkin, M. 2002. A vectorized method of importance sampling with applications to models of mutation and migration. Theor. Popul. Biol. 62 : 339 348.
25. Slatkin, M. 2003. The Age of Alleles in Modern Developments in Theoretical Population Genetics: The Legacy of Gustave Malecot' edited by Slatkin, M. and Veuille, M.) Oxford Univ. Press, Oxford, pp. 233 260.
26. Slatkin, M., and W. P. Maddison. 1989. A cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics 123 : 603 613. (Pubitemid 19274683)
27. Slatkin, M., and B. Rannala. 1997. Estimating the age of alleles by use of intraallelic variability. Am. J. Hum. Genet. 60 : 447 458.
28. Stephens, M., and P. Donnelly. 2000. Inference in molecular population genetics. J. R. Stat. Soc. B 62 : 605 635.
29. Tufto, J., S. Engen, and K. Hindar. 1996. Inferring patterns of migration from gene frequencies under equilibrium conditions. Genetics 144 : 1911 1921.
30. Wilkins, J. F. 2004. A separation-of-timescales approach to the coalescent in a continuous population. Genetics 168 : 2227 2244.
31. Wilkins, J. F., and J. Wakeley. 2002. The coalescent in a continuous, finite, linear population. Genetics 161 : 873 888.
32. Wiuf, C. 2000. On the genealogy of a sample of neutral rare alleles. Theor. Popul. Biol. 58 : 61 75.
33. Wright, S. 1943. Isolation by distance. Genetics 28 : 114 138.