Inferring population history with DIY ABC: A user-friendly approach to approximate Bayesian computation

Bioinformatics

Volumn 24, Issue 23, 2008, Pages 2713-2719

  Cornuet, Jean Marie ^a,b   Santos, Filipe ^b   Beaumont, Mark A ^c   Robert, Christian P ^d   Marin, Jean Michel ^e   Balding, David J ^a   Guillemaud, Thomas ^f   Estoup, Arnaud ^b  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

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

^c UNIVERSITY OF READING   (United Kingdom)

^d UNIVERSITÉ PARIS DAUPHINE   (France)

^e INRIA SACLAY   (France)

^f CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BAYES THEOREM; COMPUTER ANALYSIS; COMPUTER INTERFACE; COMPUTER SIMULATION; DATA ANALYSIS SOFTWARE; GENETIC ANALYSIS; MATHEMATICAL COMPUTING; POPULATION DIFFERENTIATION; POPULATION GENETICS; POPULATION SIZE; PRIORITY JOURNAL;

EID: 56649113038     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn514     Document Type: Article

References (35)

1. Beaumont,M.A. (1999) Detecting population expansion and decline using microsatellites. Genetics, 153, 2013-2029.
2. Beaumont,M.A. (2003) Estimation of population growth or decline in genetically monitored populations. Genetics, 164, 1139-1160.
3. Beaumont, M.A. (2008) Joint determination of topology, divergence time and immigration in population trees. In Matsumura,S., Forster,P. and Renfrew,C. (eds) Simulations, Genetics and Human Prehistory, (McDonald Institute Monographs), McDonald Institute for Archaeological Research, Cambridge, pp 134-154.
4. Beaumont,M.A. et al. (2002) Approximate Bayesian computation in Population Genetics. Genetics, 162, 2025-2035.
5. Bertorelle,G. and Excoffier,L. (1998) Inferring admixture proportion from molecular data. Mol. Biol. Evol., 15, 1298-1311.
6. Clegg,S.M. et al. (2002) Genetic consequences of sequential founder events by an island colonising bird. Proc. Natl Acad. Sci. 99, 8127-8132.
7. De Iorio,M. and Griffiths,R.C. (2004) Importance sampling on coalescence histories. ii: Subdivided population models. Adv. Appl. Probab., 36, 434-454.
8. Dib,C. et al. (1996) A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature, 380, 152-154
9. Estoup,A. et al. (2002) Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis. Mol. Ecol., 11, 1591-1604.
10. Estoup,A. and Clegg,S.M. (2003) Bayesian inferences on the recent island colonization history by the bird Zosterops lateralis lateralis. Mol. Ecol., 12, 657-674.
11. Estoup,A. et al. (2004) Genetic analysis of complex demographic scenarios: Spatially expanding populations of the cane toad, Bufo marinus. Evolution, 58, 2021-2036.
12. Franck,P. et al. (2000) Hybrid origins of honeybees from Italy ( Apis mellifera ligustica) and Sicily (A. m. sicula). Mol. Ecol. 9, 907-992.
13. Excoffier,L. et al. (2005) Bayesian analysis of an admixture model with mutations and arbitrarily linked markers. Genetics, 169 1727-1738.
14. Fagundes,N.J.R. et al. (2007). Statistical evaluation of alternative models of human evolution. Proc. Natl Acad. Sci., 104, 17614-17619.
15. Garza,J.C. and Williamson,E. (2001) Detection of reduction in population size using data from microsatellite DNA. Mol. Ecol., 10, 305-318.
16. Griffiths,R.C. and Tavaré,S. (1994) Simulating probability distributions in the coalescent. Theor. Popul. Biol., 46, 131-159.
17. Hamilton,G. et al. (2005) Molecular analysis reveals tighter social regulation of immigration in patrilocal populations than in matrilocal populations. Proc. Natl Acad. Sci. USA, 102, 7476-7480.
18. Hey,J. and Nielsen,R. (2004) Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics, 167, 747-760.
19. Hickerson,M.J. et al. (2007) msBayes: Pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian computation. BMC Bioinformatics, 8, 268-274.
20. Ihaka,R. and Gentleman,R. (1996) R: A language for data analysis and graphics. J. Comput. Graph. Stat., 5, 299-314.
21. Laval,G. and Excoffier,L. (2004) SIMCOAL 2.0: A program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history. Bioinformatics, 20, 2485-2487.
22. Marjoram,P. et al. (2003) Markov chain Monte Carlo without likelihood. Proc. Natl Acad. Sci., 100, 15324-15328.
23. Miller,N. et al. (2005) Multiple transatlantic introductions of the western corn rootworm. Science, 310, 992.
24. Nei,M. (1987). Molecular Evolutionary Genetics. Columbia University Press, New York, 512 pp.
25. Nordborg,M. (2007) Coalescent theory. In Handbook of Statistical Genetics Balding,D.J. et al. (eds) 3rd edn. Wiley & Sons, Chichester, UK, pp. 843-877.
26. O'Ryan,C. et al. (1998) Genetics of fragmented populations of African buffalo (Syncerus caffer) in South Africa. Anim. Conserv., 1, 85-94.
27. Pascual,M. et al. (2007) Introduction history of Drosophila subobscura in the New World: A microsatellite based survey using ABC methods. Mol. Ecol., 16, 3069-3083.
28. Pritchard,J. et al. (1999) Population growth of human Y chromosomes: A study of Y chromosome microsatellites. Mol. Biol. Evol., 16, 1791-1798.
29. Raymond M. and Rousset,F. (1995) Genepop (version 1.2), population genetics software for exact tests and ecumenicism. J. Hered., 86, 248-249.
30. Stephens,M. and Donnelly,P. (2000) Inference in molecular population genetics (with discussion). J. R. Stat. Soc. B, 62, 605-655.
31. Tavaré,S. et al. (1997) Inferring coalescence times from DNA sequences. Genetics, 145, 505-518.
32. Wang,J. (2003) Maximum-likelihood estimation of admixture proportions from genetic data. Genetics, 164, 747-765.
33. Weir,B.S. and Cockerham,C.C. (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358-1370.
34. Weis,G. and von Haeseler,A. (1998) Inference of population history using a likelihood approach. Genetics, 149, 1539-1546.
35. Wilson,I.J. et al. (2003) Inferences from DNA data: Population histories,evolutionary processes, and forensic match probabilities. J. R. Stat. Soc. A, 166, 155-187.