Monte Carlo integration over stepping stone models for spatial genetic inference using approximate Bayesian computation

Molecular Ecology Resources

Volumn 10, Issue 5, 2010, Pages 873-885

  Baird, Stuart J E ^a,b   Santos, Filipe ^a,b  

^a CENTRO DE INVESTIGAÇÃO EM BIODIVERSIDADE E RECURSOS GENÉTICOS   (Portugal)

^b CENTRE DE BIOLOGIE ET DE GESTION DES POPULATIONS   (France)

Author keywords

Approximate Bayesian computation; Geometric probability; Monte Carlo integration; Nearest neighbour stepping stone models

Indexed keywords

EID: 77955735891     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/j.1755-0998.2010.02865.x     Document Type: Article

References (31)

1. Barton NH, Wilson IJ. Genealogies and geography. New Uses for New Phylogenies 1996, 23-56. Harvey PH, Leigh Brown AJMaynard Smith JNee S. eds, Oxford University Press, Oxford
2. Barton NH, Depaulis F, Etheridge AM. Neutral evolution in spatially continuous populations. Theoretical population biology 2002, 61:31-48.
3. Beaumont MA, Zhang WY, Balding DJ. Approximate Bayesian computation in population genetics. Genetics 2002, 162:2025-2035.
4. Buffon G. "Essai d'arithmétique morale" Histoire naturelle, générale er particulière 1777, Suplementary Volume 4. pp 46-123. Imprimerie Royale, Paris
5. Christiansen FB. The deviation from linkage equilibrium with multiple loci varying in a stepping-stone cline. Journal of Genetics 1987, 40:45-67.
6. Corander J, Sirén J, Arjas E. Bayesian spatial modeling of genetic population structure. Computational Statistics 2008, 23:111-129.
7. Cox JT, Durrett R. The stepping stone model: new formulas expose old myths. Annals of Applied Probability 2002, 12:1348-1377.
8. Currat M, Excoffier L. Modern humans did not admix with Neanderthals during their range expansion into Europe. Plos Biology 2004, 2:2264-2274.
9. Epperson BK. Geographical Genetics 2003, Princeton University Press, Princeton
10. François O, Ancelet S, Guillot G. Bayesian clustering using hidden Markov random fields. Genetics 2006, 174:805-816.
11. Guillot G, Mortier F, Estoup A. Geneland: a computer package for landscape genetics. Molecular Ecology Notes 2005, 5:712-716.
12. Guillot G, Leblois R, Coulon A, Frantz AC. Statistical methods in spatial genetics. Molecular Ecology 2009, 18:4734-4756.
13. Kimura M. Stepping Stone Model of Population. Annual Report National Institute of Genetics, Japan 1953, 3:62-63.
14. Kimura M, Weiss GH. The stepping stone model of population structure and the decrease of genetic correlation with distance. Genetics 1964, 49:561-576.
15. Knowles LL. Why does a method that fails continue to be used? Evolution 2008, 62:2713-2717.
16. Leblois R, Estoup A, Rousset F. Influence of mutational and sampling factors on the estimation of demographic parameters in a 'continuous' population under isolation by distance. Molecular Biology and Evolution 2003, 20:491-502.
17. Leblois R, Estoup A, Rousset F. Influence of spatial and temporal heterogeneities on the estimation of demographic parameters in a continuous population using individual microsatellite data. Genetics 2004, 166:1081-1092.
18. Malécot G. Les processus stochastiques en genetique de population 1949, 1-16. Publications de l'Institut de Statistique de Paris I, Volume 3
19. Malécot G. Quelques schemas probabilistes sur la variabilite des populations. Annales Universitatis Lyon Science 1950, 13:37-60.
20. Maruyama T. Analysis of population structure I One dimensional stepping stone models of finite length. Annals of Human Genetics 1970, 34:201-219.
21. Maruyama T. Analysis of population structure II Two dimensional stepping stone models of finite length and other geographically structured populations. Annals of Human Genetics 1971, 35:179-196.
22. Pritchard JK, Seielstad MT, Perez-Lezaun A, Feldman MW. Population growth of human Y chromosomes: a study of Y chromosome microsatellites. Molecular Biology and Evolution 1999, 16:1791-1798.
23. Rousset F. Genetic Structure and Selection in Subdivided Populations 2004, Princeton University Press, Princeton
24. Sawyer S. Results for the stepping stone model for migration in population genetics. Annals of Probability 1976, 4:699-728.
25. Geometric Probability 1978, Solomon, Society for Industrial and Applied Mathematics, Philadelphia
26. Tavare S, Balding DJ, Griffiths RC, Donnelly P. Inferring coalescence times from DNA sequence data. Genetics 1997, 145:505-518.
27. Wilkins JF. A seperation-of-timescales approach to the coalescent in a continuous population. Genetics 2004, 168:2227-2244.
28. Wilkins JF, Wakeley J. The coalescent in a continuous, finite, linear population. Genetics 2002, 161:873-888.
29. Wood GR, Robertson JM. Buffon got it straight. Statistics and Probability Letters 1998, 37:415-421.
30. Wright S. Isolation by distance. Genetics 1943, 28:114-138.
31. Yang ZH, Stephens D, Dawson KJ. Inferences from DNA data: population histories, evolutionary processes and forensic match probabilities - Discussion. Journal of the Royal Statistical Society A 2003, 166:188-201.