메뉴 건너뛰기




Volumn 206, Issue 3, 2017, Pages 1549-1567

Inferring the joint demographic history of multiple populations: Beyond the diffusion approximation

Author keywords

Demographic inference; Diffusion approximation; Joint allele frequency spectrum; Moments equations

Indexed keywords

AFRICA; ARTICLE; DATA ANALYSIS SOFTWARE; DEMOGRAPHY; DIFFUSION; EVOLUTION; GENE FREQUENCY; GENETIC MODEL; GENOME ANALYSIS; HETEROZYGOSITY; HISTORY; HUMAN; HUMAN GENOME; MAXIMUM LIKELIHOOD METHOD; MIGRATION; MUTATION RATE; POPULATION GENETICS; PRIORITY JOURNAL; VALIDATION STUDY; BIOLOGICAL MODEL; BLACK PERSON; GENETICS; POPULATION;

EID: 85021873089     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.117.200493     Document Type: Article
Times cited : (145)

References (34)
  • 1
    • 84943171338 scopus 로고    scopus 로고
    • A global reference for human genetic variation
    • Genomes Project, 2015 A global reference for human genetic variation. Nature 526: 68-74.
    • (2015) Nature , vol.526 , pp. 68-74
  • 2
    • 0028446699 scopus 로고
    • On alternating segment Crank-Nicolson scheme
    • Baolin, Z., and L. Wenzhi, 1994 On alternating segment Crank-Nicolson scheme. Parallel Comput. 20: 897-902.
    • (1994) Parallel Comput , vol.20 , pp. 897-902
    • Baolin, Z.1    Wenzhi, L.2
  • 3
    • 84893828278 scopus 로고    scopus 로고
    • Distortion of genealogical properties when the sample is very large
    • Bhaskar, A., A. G. Clark, and Y. S. Song, 2014 Distortion of genealogical properties when the sample is very large. Proc. Natl. Acad. Sci. USA 111: 2385-2390.
    • (2014) Proc. Natl. Acad. Sci. USA , vol.111 , pp. 2385-2390
    • Bhaskar, A.1    Clark, A.G.2    Song, Y.S.3
  • 4
    • 84864697376 scopus 로고    scopus 로고
    • Inferring species trees directly from biallelic genetic markers: Bypassing gene trees in a full coalescent analysis
    • Bryant, D., R. Bouckaert, J. Felsenstein, N. A. Rosenberg, and A. RoyChoudhury, 2012 Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Mol. Biol. Evol. 29: 1917-1932.
    • (2012) Mol. Biol. Evol , vol.29 , pp. 1917-1932
    • Bryant, D.1    Bouckaert, R.2    Felsenstein, J.3    Rosenberg, N.A.4    Roychoudhury, A.5
  • 5
    • 84964659865 scopus 로고    scopus 로고
    • Computationally efficient composite likelihood statistics for demographic inference
    • Coffman, A. J., P. H. Hsieh, S. Gravel, and R. N. Gutenkunst, 2016 Computationally efficient composite likelihood statistics for demographic inference. Mol. Biol. Evol. 33: 591-593.
    • (2016) Mol. Biol. Evol , vol.33 , pp. 591-593
    • Coffman, A.J.1    Hsieh, P.H.2    Gravel, S.3    Gutenkunst, R.N.4
  • 6
    • 33646302342 scopus 로고
    • An Introduction to Population Genetics Theory
    • New York
    • Crow, J. F., and M. Kimura, 1970 An Introduction to Population Genetics Theory. Harper and Row, New York.
    • (1970) Harper and Row
    • Crow, J.F.1    Kimura, M.2
  • 7
    • 84946105401 scopus 로고    scopus 로고
    • PoMo: An allele frequency-based approach for species tree estimation
    • De Maio, N., D. Schrempf, and C. Kosiol, 2015 PoMo: an allele frequency-based approach for species tree estimation. Syst. Biol. 64: 1018-1031.
    • (2015) Syst. Biol , vol.64 , pp. 1018-1031
    • De Maio, N.1    Schrempf, D.2    Kosiol, C.3
  • 8
    • 0033274920 scopus 로고    scopus 로고
    • Genealogical processes for fleming-viot models with selection and recombination
    • Donnelly, P., and T. G. Kurtz, 1999 Genealogical processes for fleming-viot models with selection and recombination. Ann. Appl. Probab. 9: 1091-1148.
    • (1999) Ann. Appl. Probab , vol.9 , pp. 1091-1148
    • Donnelly, P.1    Kurtz, T.G.2
  • 9
    • 33750971421 scopus 로고    scopus 로고
    • Non-equilibrium theory of the allele frequency spectrum. Theor. Popul
    • Evans, S. N., Y. Shvets, and M. Slatkin, 2007 Non-equilibrium theory of the allele frequency spectrum. Theor. Popul. Biol. 71: 109-119.
    • (2007) Biol , vol.71 , pp. 109-119
    • Evans, S.N.1    Shvets, Y.2    Slatkin, M.3
  • 10
    • 72449161816 scopus 로고    scopus 로고
    • Mathematical population genetics
    • Springer, New York
    • Ewens, W. J., 2004 Mathematical population genetics, in Interdisciplinary Applied Mathematics, Vol. 27. Springer, New York.
    • (2004) Interdisciplinary Applied Mathematics , vol.27
    • Ewens, W.J.1
  • 11
    • 79954469204 scopus 로고    scopus 로고
    • Fastsimcoal: A continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios
    • Excoffier, L., and M. Foll, 2011 Fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios. Bioinformatics 27: 1332-1334.
    • (2011) Bioinformatics , vol.27 , pp. 1332-1334
    • Excoffier, L.1    Foll, M.2
  • 13
    • 0001122789 scopus 로고
    • The distribution of gene ratios for rare mutations
    • Fisher, R., 1930 The distribution of gene ratios for rare mutations. Proc. R. Soc. Edinb. 50: 205-220.
    • (1930) Proc. R. Soc. Edinb , vol.50 , pp. 205-220
    • Fisher, R.1
  • 14
    • 85022020967 scopus 로고    scopus 로고
    • National Heart, Lung, and Blood Institute (NHLBI) GO Exome Sequencing Project, 2014 Predicting discovery rates of genomic features
    • [corrigenda: Genetics 203: 997 (2016)]
    • Gravel, S. National Heart, Lung, and Blood Institute (NHLBI) GO Exome Sequencing Project, 2014 Predicting discovery rates of genomic features. Genetics 197: 601-610 [corrigenda: Genetics 203: 997 (2016)].
    • Genetics , vol.197 , pp. 601-610
    • Gravel, S.1
  • 16
    • 84892684329 scopus 로고    scopus 로고
    • Reconstructing Native American migrations from whole-genome and whole-exome data
    • Gravel, S., F. Zakharia, A. Moreno-Estrada, J. K. Byrnes, M. Muzzio et al., 2013 Reconstructing Native American migrations from whole-genome and whole-exome data. PLoS Genet. 9: e1004023.
    • (2013) Plos Genet , vol.9
    • Gravel, S.1    Zakharia, F.2    Moreno-Estrada, A.3    Byrnes, J.K.4    Muzzio, M.5
  • 17
    • 73449149044 scopus 로고    scopus 로고
    • Inferring the joint demographic history of multiple populations from multidimensional snp frequency data
    • Gutenkunst, R. N., R. D. Hernandez, S. H. Williamson, and C. D. Bustamante, 2009 Inferring the joint demographic history of multiple populations from multidimensional snp frequency data. PLoS Genet. 5: e1000695.
    • (2009) Plos Genet , vol.5
    • Gutenkunst, R.N.1    Hernandez, R.D.2    Williamson, S.H.3    Bustamante, C.D.4
  • 18
    • 85014905518 scopus 로고    scopus 로고
    • Slim 2: Flexible, interactive forward genetic simulations
    • Haller, B. C., and P. W. Messer, 2016 Slim 2: flexible, interactive forward genetic simulations. Mol. Biol. Evol. 34: 230-240.
    • (2016) Mol. Biol. Evol , vol.34 , pp. 230-240
    • Haller, B.C.1    Messer, P.W.2
  • 19
    • 85013082995 scopus 로고    scopus 로고
    • Efficient computation of the joint sample frequency spectra for multiple populations
    • Kamm, J. A., J. Terhorst, and Y. S. Song, 2017 Efficient computation of the joint sample frequency spectra for multiple populations. J. Comput. Graph. Stat. 26: 182-194.
    • (2017) J. Comput. Graph. Stat , vol.26 , pp. 182-194
    • Kamm, J.A.1    Terhorst, J.2    Song, Y.S.3
  • 20
    • 84975828278 scopus 로고    scopus 로고
    • Efficient coalescent simulation and genealogical analysis for large sample sizes. PLoS Comput
    • Kelleher, J., A. M. Etheridge, and G. McVean, 2016 Efficient coalescent simulation and genealogical analysis for large sample sizes. PLoS Comput. Biol. 12: e1004842.
    • (2016) Biol , vol.12
    • Kelleher, J.1    Etheridge, A.M.2    McVean, G.3
  • 21
    • 0000660047 scopus 로고
    • Diffusion models in population genetics
    • Kimura, M., 1964 Diffusion models in population genetics. J. Appl. Probab. 1: 177-232.
    • (1964) J. Appl. Probab , vol.1 , pp. 177-232
    • Kimura, M.1
  • 22
    • 0014494672 scopus 로고
    • The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations
    • Kimura, M., 1969 The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. Genetics 61: 893.
    • (1969) Genetics , vol.61 , pp. 893
    • Kimura, M.1
  • 23
    • 84866863890 scopus 로고    scopus 로고
    • Demographic inference using spectral methods on SNP data, with an analysis of the human out-ofafrica expansion
    • Lukić, S., and J. Hey, 2012 Demographic inference using spectral methods on SNP data, with an analysis of the human out-ofafrica expansion. Genetics 192: 619-639.
    • (2012) Genetics , vol.192 , pp. 619-639
    • Lukić, S.1    Hey, J.2
  • 24
    • 79955476379 scopus 로고    scopus 로고
    • Non-equilibrium allele frequency spectra via spectral methods
    • Lukić, S., J. Hey, and K. Chen, 2011 Non-equilibrium allele frequency spectra via spectral methods. Theor. Popul. Biol. 79: 203-219.
    • (2011) Theor. Popul. Biol , vol.79 , pp. 203-219
    • Lukić, S.1    Hey, J.2    Chen, K.3
  • 27
    • 84884467851 scopus 로고    scopus 로고
    • Recent human adaptation: Genomic approaches, interpretation and insights
    • Scheinfeldt, L. B., and S. A. Tishkoff, 2013 Recent human adaptation: genomic approaches, interpretation and insights. Nat. Rev. Genet. 14: 692-702.
    • (2013) Nat. Rev. Genet , vol.14 , pp. 692-702
    • Scheinfeldt, L.B.1    Tishkoff, S.A.2
  • 28
    • 84905572361 scopus 로고    scopus 로고
    • Inferring human population size and separation history from multiple genome sequences
    • Schiffels, S., and R. Durbin, 2014 Inferring human population size and separation history from multiple genome sequences. Nat. Genet. 46: 919-925.
    • (2014) Nat. Genet , vol.46 , pp. 919-925
    • Schiffels, S.1    Durbin, R.2
  • 29
    • 84903517143 scopus 로고    scopus 로고
    • A reference genome for common bean and genome-wide analysis of dual domestications
    • Schmutz, J., P. E. McClean, S. Mamidi, G. A. Wu, S. B. Cannon et al., 2014 A reference genome for common bean and genome-wide analysis of dual domestications. Nat. Genet. 46: 707-713.
    • (2014) Nat. Genet , vol.46 , pp. 707-713
    • Schmutz, J.1    McClean, P.E.2    Mamidi, S.3    Wu, G.A.4    Cannon, S.B.5
  • 30
    • 84966638530 scopus 로고    scopus 로고
    • The site frequency spectrum for general coalescents
    • Spence, J. P., J. A. Kamm, and Y. S. Song, 2016 The site frequency spectrum for general coalescents. Genetics 202: 1549-1561.
    • (2016) Genetics , vol.202 , pp. 1549-1561
    • Spence, J.P.1    Kamm, J.A.2    Song, Y.S.3
  • 31
    • 84943182461 scopus 로고    scopus 로고
    • An integrated map of structural variation in 2,504 human genomes
    • Sudmant, P. H., T. Rausch, E. J. Gardner, R. E. Handsaker, A. Abyzov et al., 2015 An integrated map of structural variation in 2,504 human genomes. Nature 526: 75-81.
    • (2015) Nature , vol.526 , pp. 75-81
    • Sudmant, P.H.1    Rausch, T.2    Gardner, E.J.3    Handsaker, R.E.4    Abyzov, A.5
  • 32
    • 0033910668 scopus 로고    scopus 로고
    • New estimates of intergenerational time intervals for the calculation of age and origins of mutations
    • Tremblay, M., and H. Vézina, 2000 New estimates of intergenerational time intervals for the calculation of age and origins of mutations. Am. J. Hum. Genet. 66: 651-658.
    • (2000) Am. J. Hum. Genet , vol.66 , pp. 651-658
    • Tremblay, M.1    Vézina, H.2
  • 33
    • 0001771498 scopus 로고
    • Evolution in mendelian populations
    • Wright, S., 1931 Evolution in mendelian populations. Genetics 16: 97-159.
    • (1931) Genetics , vol.16 , pp. 97-159
    • Wright, S.1
  • 34
    • 84931416490 scopus 로고    scopus 로고
    • Transition densities and sample frequency spectra of diffusion processes with selection and variable population size
    • Živković, D., M. Steinrücken, Y. S. Song, and W. Stephan, 2015 Transition densities and sample frequency spectra of diffusion processes with selection and variable population size. Genetics 200: 601-617
    • (2015) Genetics , vol.200 , pp. 601-617
    • Živković, D.1    Steinrücken, M.2    Song, Y.S.3    Stephan, W.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.