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Volumn 181, Issue 4, 2009, Pages 1507-1519

Approximate Bayesian computation without summary statistics: The case of admixture

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; BAYES THEOREM; GENE FREQUENCY; HYBRID; METHODOLOGY; PARENT; POPULATION; PRIORITY JOURNAL; SIMULATION; STATISTICS; TECHNIQUE; BIOLOGICAL MODEL; COMPUTER SIMULATION; CROSS BREEDING; EVALUATION; GENETIC DRIFT; GENETICS; HUMAN; JAMAICA; POPULATION GENETICS; RACE; STATISTICAL MODEL; UNITED STATES;

EID: 67650327255     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.108.098129     Document Type: Article
Times cited : (59)

References (53)
  • 1
    • 70349934981 scopus 로고    scopus 로고
    • Adaptivity for approximate Bayesian computation algorithms: A population Monte Carlo approach
    • in press
    • BEAUMONT, M., J. CORNUET, J. MARIN and C. ROBERT, 2009 Adaptivity for approximate Bayesian computation algorithms: a population Monte Carlo approach. Biometrika (in press).
    • (2009) Biometrika
    • Beaumont, M.1    Cornuet, J.2    Marin, J.3    Robert, C.4
  • 2
    • 0032713236 scopus 로고    scopus 로고
    • Detecting population expansion and decline using microsatellites
    • BEAUMONT, M. A., 1999 Detecting population expansion and decline using microsatellites. Genetics 153: 2013-2029.
    • (1999) Genetics , vol.153 , pp. 2013-2029
    • Beaumont, M.A.1
  • 3
    • 0043210659 scopus 로고    scopus 로고
    • Estimation of population growth or decline in genetically monitored populations
    • BEAUMONT, M. A., 2003 Estimation of population growth or decline in genetically monitored populations. Genetics 164: 1139-1160.
    • (2003) Genetics , vol.164 , pp. 1139-1160
    • Beaumont, M.A.1
  • 4
    • 1842532350 scopus 로고    scopus 로고
    • The Bayesian revolution in genetics
    • BEAUMONT, M. A., and B. RANNALA, 2004 The Bayesian revolution in genetics. Nat. Rev. Genet. 5: 251-261.
    • (2004) Nat. Rev. Genet. , vol.5 , pp. 251-261
    • Beaumont, M.A.1    Rannala, B.2
  • 5
    • 0036964474 scopus 로고    scopus 로고
    • Approximate Bayesian computation in population genetics
    • BEAUMONT, M. A., W. ZHANG and D. J. BALDING, 2002 Approximate Bayesian computation in population genetics. Genetics 162: 2025-2035.
    • (2002) Genetics , vol.162 , pp. 2025-2035
    • Beaumont, M.A.1    Zhang, W.2    Balding, D.J.3
  • 6
    • 34948847222 scopus 로고    scopus 로고
    • A new approach to estimate parameters of speciation models with application to apes
    • BECQUET, C., and M. PRZEWORSKI, 2007 A new approach to estimate parameters of speciation models with application to apes. Genome Res. 17: 1505-1519.
    • (2007) Genome Res. , vol.17 , pp. 1505-1519
    • Becquet, C.1    Przeworski, M.2
  • 7
    • 0035836728 scopus 로고    scopus 로고
    • Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach
    • BEERLI, P., and J. FELSENSTEIN, 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.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 4563-4568
    • Beerli, P.1    Felsenstein, J.2
  • 9
    • 38849101650 scopus 로고    scopus 로고
    • Origin and number of founders in an introduced insular primate: Estimation from nuclear genetic data
    • BONHOMME, M., A. BLANCHER, S. CUARTERO, L. CHIKHI and B. CROUAU-ROY, 2008 Origin and number of founders in an introduced insular primate: estimation from nuclear genetic data. Mol. Ecol. 17: 1009-1019.
    • (2008) Mol. Ecol. , vol.17 , pp. 1009-1019
    • Bonhomme, M.1    Blancher, A.2    Cuartero, S.3    Chikhi, L.4    Crouau-Roy, B.5
  • 10
    • 0034918729 scopus 로고    scopus 로고
    • Estimation of admixture proportions: A likelihood-based approach using Markov Chain Monte Carlo
    • CHIKHI, L., M. W. BRUFORD and M. A. BEAUMONT, 2001 Estimation of admixture proportions: a likelihood-based approach using Markov chain Monte Carlo. Genetics 158: 1347-1362. (Pubitemid 32667117)
    • (2001) Genetics , vol.158 , Issue.3 , pp. 1347-1362
    • Chikhi, L.1    Bruford, M.W.2    Beaumont, M.A.3
  • 11
    • 1642308566 scopus 로고    scopus 로고
    • Estimating admixture proportions with microsatellites: Comparison of methods based on simulated data
    • CHOISY, M., P. FRANCK and J.-M. CORNUET, 2004 Estimating admixture proportions with microsatellites: comparison of methods based on simulated data. Mol. Ecol. 13: 955-968.
    • (2004) Mol. Ecol. , vol.13 , pp. 955-968
    • Choisy, M.1    Franck, P.2    Cornuet, J.-M.3
  • 12
    • 33751088530 scopus 로고    scopus 로고
    • A note on the accuracy of PAC-likelihood inference with microsatellite data
    • CORNUET, J. M., and M. A. BEAUMONT, 2007 A note on the accuracy of PAC-likelihood inference with microsatellite data. Theor. Popul. Biol. 71: 12-19.
    • (2007) Theor. Popul. Biol. , vol.71 , pp. 12-19
    • Cornuet, J.M.1    Beaumont, M.A.2
  • 13
    • 40849086684 scopus 로고    scopus 로고
    • Testing for archaic hominin admixture on the X chromosome: Model likelihoods for the modern human rrm2p4 region from summaries of genealogical topology under the structured coalescent
    • COX, M. P., F. L. MENDEZ, T. M. KARAFET, M. M. PILKINGTON, S. B. KINGAN et al., 2008 Testing for archaic hominin admixture on the X chromosome: model likelihoods for the modern human rrm2p4 region from summaries of genealogical topology under the structured coalescent. Genetics 178: 427-437.
    • (2008) Genetics , vol.178 , pp. 427-437
    • Cox, M.P.1    Mendez, F.L.2    Karafet, T.M.3    Pilkington, M.M.4    Kingan, S.B.5
  • 14
    • 5344241252 scopus 로고    scopus 로고
    • Genetic analysis of complex demographic scenarios: Spatially expanding populations of the cane toad, Bufo marinus
    • ESTOUP, A., M. BEAUMONT, F. SENNEDOT, C. MORITZ AND J.-M. CORNUET, 2004 Genetic analysis of complex demographic scenarios: spatially expanding populations of the cane toad, Bufo marinus. Evol. Int. J. Org. Evol. 58: 2021-2036.
    • (2004) Evol. Int. J. Org. Evol. , vol.58 , pp. 2021-2036
    • Estoup, A.1    Beaumont, M.2    Sennedot, F.3    Moritz, C.4    Cornuet, J.-M.5
  • 16
    • 17444424890 scopus 로고    scopus 로고
    • Bayesian analysis of an admixture model with mutations and arbitrarily linked markers
    • EXCOFFIER, L., A. ESTOUP and J.-M. CORNUET, 2005 Bayesian analysis of an admixture model with mutations and arbitrarily linked markers. Genetics 169: 1727-1738.
    • (2005) Genetics , vol.169 , pp. 1727-1738
    • Excoffier, L.1    Estoup, A.2    Cornuet, J.-M.3
  • 18
    • 35348983887 scopus 로고    scopus 로고
    • A second generation human haplotype map of over 3.1 million SNPs
    • FRAZER, K., D. BALLINGER, D. COX, D. HINDS, L. STUVE et al., 2007 A second generation human haplotype map of over 3.1 million SNPs. Nature 449: 851.
    • (2007) Nature , vol.449 , pp. 851
    • Frazer, K.1    Ballinger, D.2    Cox, D.3    Hinds, D.4    Stuve, L.5
  • 19
    • 0031038941 scopus 로고    scopus 로고
    • Estimating the age of the common ancestor of a sample of DNA sequences
    • FU, Y. X., and W. H. LI, 1997 Estimating the age of the common ancestor of a sample of DNA sequences. Mol. Biol. Evol. 14: 195-199.
    • (1997) Mol. Biol. Evol. , vol.14 , pp. 195-199
    • Fu, Y.X.1    Li, W.H.2
  • 21
    • 19644371954 scopus 로고    scopus 로고
    • Molecular analysis reveals tighter social regulation of immigration in patrilocal populations than in matrilocal populations
    • HAMILTON, G., M. STONEKING and L. EXCOFFIER, 2005 Molecular analysis reveals tighter social regulation of immigration in patrilocal populations than in matrilocal populations. Proc. Natl. Acad. Sci. USA 102: 7476-7480.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 7476-7480
    • Hamilton, G.1    Stoneking, M.2    Excoffier, L.3
  • 22
    • 0037803577 scopus 로고    scopus 로고
    • The study of structured populations - New hope for a difficult and divided science
    • HEY, J., and C. A. MACHADO, 2003 The study of structured populations - new hope for a difficult and divided science. Nat. Rev. Genet. 4: 535-543.
    • (2003) Nat. Rev. Genet. , vol.4 , pp. 535-543
    • Hey, J.1    Machado, C.A.2
  • 23
    • 3142714474 scopus 로고    scopus 로고
    • Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis
    • HEY, J., and R. NIELSEN, 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.
    • (2004) Genetics , vol.167 , pp. 747-760
    • Hey, J.1    Nielsen, R.2
  • 24
    • 0035692320 scopus 로고    scopus 로고
    • Two-locus sampling distributions and their application
    • HUDSON, R. R., 2001 Two-locus sampling distributions and their application. Genetics 159: 1805-1817. (Pubitemid 34087616)
    • (2001) Genetics , vol.159 , Issue.4 , pp. 1805-1817
    • Hudson, R.R.1
  • 25
    • 51449104123 scopus 로고    scopus 로고
    • Approximately sufficient statistics and Bayesian computation
    • JOYCE, P., and P. MARJORAM, 2008 Approximately sufficient statistics and Bayesian computation. Stat. Appl. Genet. Mol. Biol. 7: 26.
    • (2008) Stat. Appl. Genet. Mol. Biol. , vol.7 , pp. 26
    • Joyce, P.1    Marjoram, P.2
  • 26
    • 0346906674 scopus 로고    scopus 로고
    • LEA (likelihood-based estimation of admixture): A program to simultaneously estimate admixture and the time since admixture
    • LANGELLA, O., L. CHIKHI and M. BEAUMONT, 2001 LEA (likelihood-based estimation of admixture): a program to simultaneously estimate admixture and the time since admixture. Mol. Ecol. Notes 1: 357-358.
    • (2001) Mol. Ecol. Notes , vol.1 , pp. 357-358
    • Langella, O.1    Chikhi, L.2    Beaumont, M.3
  • 27
    • 0347361674 scopus 로고    scopus 로고
    • Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data
    • LI, N., and M. STEPHENS, 2003 Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics 165: 2213-2233.
    • (2003) Genetics , vol.165 , pp. 2213-2233
    • Li, N.1    Stephens, M.2
  • 30
    • 0000762002 scopus 로고
    • Definition and estimation of fixation indices
    • NEI, M., 1986 Definition and estimation of fixation indices. Evol. Int. J. Org. Evol. 40: 643-645.
    • (1986) Evol. Int. J. Org. Evol. , vol.40 , pp. 643-645
    • Nei, M.1
  • 32
    • 38349185030 scopus 로고    scopus 로고
    • Colonization history of the Swiss Rhine Basin by the bullhead (Cottus gobio): Inference under a Bayesian spatially explicit framework
    • NEUENSCHWANDER, S., C. R. LARGIADÈR, N. RAY, M. CURRAT, P. VONLANTHEN et al., 2008 Colonization history of the Swiss Rhine Basin by the bullhead (Cottus gobio): inference under a Bayesian spatially explicit framework. Mol. Ecol. 17: 757-772.
    • (2008) Mol. Ecol. , vol.17 , pp. 757-772
    • Neuenschwander, S.1    Largiadèr, C.R.2    Ray, N.3    Currat, M.4    Vonlanthen, P.5
  • 35
    • 0032472024 scopus 로고    scopus 로고
    • Estimating African American admixture proportions by use of population-specific alleles
    • PARRA, E. J., A. MARCINI, J. AKEY, J. MARTINSON, M. A. BATZER et al., 1998 Estimating African American admixture proportions by use of population-specific alleles. Am. J. Hum. Genet. 63: 1839-1851.
    • (1998) Am. J. Hum. Genet. , vol.63 , pp. 1839-1851
    • Parra, E.J.1    Marcini, A.2    Akey, J.3    Martinson, J.4    Batzer, M.A.5
  • 36
    • 34447650844 scopus 로고    scopus 로고
    • Introduction history of Drosophila subobscura in the New World: A microsatellite-based survey using ABC methods
    • PASCUAL, M., M. P. CHAPUIS, F. MESTRES, J. BALANYÀ, R. B. HUEY et al., 2007 Introduction history of Drosophila subobscura in the New World: a microsatellite-based survey using ABC methods. Mol. Ecol. 16: 3069-3083.
    • (2007) Mol. Ecol. , vol.16 , pp. 3069-3083
    • Pascual, M.1    Chapuis, M.P.2    Mestres, F.3    Balanyà, J.4    Huey, R.B.5
  • 38
    • 0032735986 scopus 로고    scopus 로고
    • Population growth of human Y chromosomes: A study of Y chromosome microsatellites
    • PRITCHARD, J. K., M. T. SEIELSTAD, A. PEREZ-LEZAUN and M. W. FELDMAN, 1999 Population growth of human Y chromosomes: a study of Y chromosome microsatellites. Mol. Biol. Evol. 16: 1791-1798.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 1791-1798
    • Pritchard, J.K.1    Seielstad, M.T.2    Perez-Lezaun, A.3    Feldman, M.W.4
  • 39
    • 5344244656 scopus 로고    scopus 로고
    • R DEVELOPMENT CORE TEAM, R Foundation for Statistical Computing, Vienna
    • R DEVELOPMENT CORE TEAM, 2008 R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna.
    • (2008) R: A Language and Environment for Statistical Computing
  • 40
    • 36549055538 scopus 로고    scopus 로고
    • A multilocus perspective on colonization accompanied by selection and gene flow
    • ROSENBLUM, E. B., M. J. HICKERSON and C. MORITZ, 2007 A multilocus perspective on colonization accompanied by selection and gene flow. Evol. Int. J. Org. Evol. 61: 2971-2985.
    • (2007) Evol. Int. J. Org. Evol. , vol.61 , pp. 2971-2985
    • Rosenblum, E.B.1    Hickerson, M.J.2    Moritz, C.3
  • 41
    • 34250779026 scopus 로고    scopus 로고
    • Fast and accurate estimation of the population-scaled mutation rate, theta, from microsatellite genotype data
    • ROYCHOUDHURY, A., and M. STEPHENS, 2007 Fast and accurate estimation of the population-scaled mutation rate, theta, from microsatellite genotype data. Genetics 176: 1363-1366.
    • (2007) Genetics , vol.176 , pp. 1363-1366
    • Roychoudhury, A.1    Stephens, M.2
  • 43
    • 0034354410 scopus 로고    scopus 로고
    • Dealing with label switching in mixture models
    • STEPHENS, M., 2000 Dealing with label switching in mixture models. J. R. Stat. Soc. Ser. B (Methodol.) 62: 795-809.
    • (2000) J. R. Stat. Soc. Ser. B (Methodol.) , vol.62 , pp. 795-809
    • Stephens, M.1
  • 44
    • 0034354581 scopus 로고    scopus 로고
    • Inference in molecular population genetics
    • STEPHENS, M., and P. DONNELLY, 2000 Inference in molecular population genetics. J. R. Stat. Soc. B 62: 605-635.
    • (2000) J. R. Stat. Soc. B , vol.62 , pp. 605-635
    • Stephens, M.1    Donnelly, P.2
  • 45
    • 0036856317 scopus 로고    scopus 로고
    • Genetic evidence for long-term population decline in a savannah-dwelling primate: Inferences from a hierarchical Bayesian model
    • STORZ, J. F., M. A. BEAUMONT and S. C. ALBERTS, 2002 Genetic evidence for long-term population decline in a savannah-dwelling primate: inferences from a hierarchical Bayesian model. Mol. Biol. Evol. 19: 1981-1990.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 1981-1990
    • Storz, J.F.1    Beaumont, M.A.2    Alberts, S.C.3
  • 46
    • 3142749747 scopus 로고    scopus 로고
    • Comparative evaluation of a new effective population size estimator based on approximate Bayesian computation
    • TALLMON, D. A., G. LUIKART and M. A. BEAUMONT, 2004 Comparative evaluation of a new effective population size estimator based on approximate Bayesian computation. Genetics 167: 977-988.
    • (2004) Genetics , vol.167 , pp. 977-988
    • Tallmon, D.A.1    Luikart, G.2    Beaumont, M.A.3
  • 47
    • 0031014291 scopus 로고    scopus 로고
    • Inferring coalescence times from DNA sequence data
    • TAVARÉ, S., D. J. BALDING, R. C. GRIFFITHS and P. DONNELLY, 1997 Inferring coalescence times from DNA sequence data. Genetics 145: 505-518. (Pubitemid 27068401)
    • (1997) Genetics , vol.145 , Issue.2 , pp. 505-518
    • Tavare, S.1    Balding, D.J.2    Griffiths, R.C.3    Donnelly, P.4
  • 48
    • 0015746472 scopus 로고
    • The Icelandic admixture problem
    • THOMPSON, E. A., 1973 The Icelandic admixture problem. Ann. Hum. Genet. 37: 69-80.
    • (1973) Ann. Hum. Genet. , vol.37 , pp. 69-80
    • Thompson, E.A.1
  • 49
    • 33644763127 scopus 로고    scopus 로고
    • Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster
    • THORNTON, K., and P. ANDOLFATTO, 2006 Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster. Genetics 172: 1607-1619.
    • (2006) Genetics , vol.172 , pp. 1607-1619
    • Thornton, K.1    Andolfatto, P.2
  • 50
    • 0038124411 scopus 로고    scopus 로고
    • Maximum-likelihood estimation of admixture proportions from genetic data
    • WANG, J., 2003 Maximum-likelihood estimation of admixture proportions from genetic data. Genetics 164: 747-765. (Pubitemid 36773510)
    • (2003) Genetics , vol.164 , Issue.2 , pp. 747-765
    • Wang, J.1
  • 51
    • 33746435844 scopus 로고    scopus 로고
    • A coalescent-based estimator of admixture from DNA sequences
    • WANG, J., 2006 A coalescent-based estimator of admixture from DNA sequences. Genetics 173: 1679-1692.
    • (2006) Genetics , vol.173 , pp. 1679-1692
    • Wang, J.1
  • 52
    • 0031827528 scopus 로고    scopus 로고
    • Inference of population history using a likelihood approach
    • WEISS, G., and A. VON HAESELER, 1998 Inference of population history using a likelihood approach. Genetics 149: 1539-1546. (Pubitemid 28334543)
    • (1998) Genetics , vol.149 , Issue.3 , pp. 1539-1546
    • Weiss, G.1    Von Haeseler, A.2
  • 53
    • 0031669749 scopus 로고    scopus 로고
    • Genealogical inference from microsatellite data
    • WILSON, I. J., and D. J. BALDING, 1998 Genealogical inference from microsatellite data. Genetics 150: 499-510.
    • (1998) Genetics , vol.150 , pp. 499-510
    • Wilson, I.J.1    Balding, D.J.2


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