메뉴 건너뛰기




Volumn 115, Issue 531, 2020, Pages 1472-1487

Efficiently Inferring the Demographic History of Many Populations With Allele Count Data

Author keywords

Coalescent theory; Demographic inference; Frequency spectrum; Population genetics

Indexed keywords


EID: 85090103452     PISSN: 01621459     EISSN: 1537274X     Source Type: Journal    
DOI: 10.1080/01621459.2019.1635482     Document Type: Article
Times cited : (85)

References (65)
  • 1
    • 85044968577 scopus 로고    scopus 로고
    • “On the Decidability of Population Size Histories From Finite Allele Frequency Spectra,”
    • Baharian, S., and Gravel, S., (2018), “On the Decidability of Population Size Histories From Finite Allele Frequency Spectra,” Theoretical Population Biology, 120, 42–51. DOI:10.1016/j.tpb.2017.12.008.
    • (2018) Theoretical Population Biology , vol.120 , pp. 42-51
    • Baharian, S.1    Gravel, S.2
  • 3
    • 84908206474 scopus 로고    scopus 로고
    • “Descartes’ Rule of Signs and the Identifiability of Population Demographic Models From Genomic Variation Data,”
    • Bhaskar, A., and Song, Y. S., (2014), “Descartes’ Rule of Signs and the Identifiability of Population Demographic Models From Genomic Variation Data,” Annals of Statistics, 42, 2469–2493. DOI:10.1214/14-AOS1264.
    • (2014) Annals of Statistics , vol.42 , pp. 2469-2493
    • Bhaskar, A.1    Song, Y.S.2
  • 4
    • 84922377375 scopus 로고    scopus 로고
    • “Efficient Inference of Population Size Histories and Locus-Specific Mutation Rates From Large-Sample Genomic Variation Data,”
    • Bhaskar, A., Wang, Y. X. R., and Song, Y. S., (2015), “Efficient Inference of Population Size Histories and Locus-Specific Mutation Rates From Large-Sample Genomic Variation Data,” Genome Research, 25, 268–279. DOI:10.1101/gr.178756.114.
    • (2015) Genome Research , vol.25 , pp. 268-279
    • Bhaskar, A.1    Wang, Y.X.R.2    Song, Y.S.3
  • 6
    • 84864697376 scopus 로고    scopus 로고
    • “Inferring Species Trees Directly From Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis,”
    • Bryant, D., Bouckaert, R., Felsenstein, J., Rosenberg, N. A., and RoyChoudhury, A., (2012), “Inferring Species Trees Directly From Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis,” Molecular Biology and Evolution, 29, 1917–1932. DOI:10.1093/molbev/mss086.
    • (2012) Molecular Biology and Evolution , vol.29 , pp. 1917-1932
    • Bryant, D.1    Bouckaert, R.2    Felsenstein, J.3    Rosenberg, N.A.4    RoyChoudhury, A.5
  • 7
    • 84856553089 scopus 로고    scopus 로고
    • “The Joint Allele Frequency Spectrum of Multiple Populations: A Coalescent Theory Approach,”
    • Chen, H., (2012), “The Joint Allele Frequency Spectrum of Multiple Populations: A Coalescent Theory Approach,” Theoretical Population Biology, 81, 179–195. DOI:10.1016/j.tpb.2011.11.004.
    • (2012) Theoretical Population Biology , vol.81 , pp. 179-195
    • Chen, H.1
  • 11
    • 3142769862 scopus 로고    scopus 로고
    • “Importance Sampling on Coalescent Histories. II: Subdivided Population Models,”
    • De Iorio, M., and Griffiths, R. C., (2004), “Importance Sampling on Coalescent Histories. II: Subdivided Population Models,” Advances in Applied Probability, 36, 434–454. DOI:10.1239/aap/1086957580.
    • (2004) Advances in Applied Probability , vol.36 , pp. 434-454
    • De Iorio, M.1    Griffiths, R.C.2
  • 12
    • 84946105401 scopus 로고    scopus 로고
    • “PoMo: An Allele Frequency-Based Approach for Species Tree Estimation,”
    • De Maio, N., Schrempf, D., and Kosiol, C., (2015), “PoMo: An Allele Frequency-Based Approach for Species Tree Estimation,” Systematic Biology, 64, 1018–1031. DOI:10.1093/sysbio/syv048.
    • (2015) Systematic Biology , vol.64 , pp. 1018-1031
    • De Maio, N.1    Schrempf, D.2    Kosiol, C.3
  • 13
    • 0030522180 scopus 로고    scopus 로고
    • “A Countable Representation of the Fleming-Viot Measure-Valued Diffusion,”
    • Donnelly, P., and Kurtz, T., (1996), “A Countable Representation of the Fleming-Viot Measure-Valued Diffusion,” The Annals of Probability, 24, 698–742. DOI:10.1214/aop/1039639359.
    • (1996) The Annals of Probability , vol.24 , pp. 698-742
    • Donnelly, P.1    Kurtz, T.2
  • 14
    • 0033243134 scopus 로고    scopus 로고
    • “Particle Representations for Measure-Valued Population Models,”
    • Donnelly, P., and Kurtz, T. G., (1999), “Particle Representations for Measure-Valued Population Models,” The Annals of Probability, 27, 166–205. DOI:10.1214/aop/1022677258.
    • (1999) The Annals of Probability , vol.27 , pp. 166-205
    • Donnelly, P.1    Kurtz, T.G.2
  • 17
    • 84887312794 scopus 로고    scopus 로고
    • “Robust Demographic Inference From Genomic and SNP Data,”
    • Excoffier, L., Dupanloup, I., Huerta-Sánchez, E., Sousa, V. C., and Foll, M., (2013), “Robust Demographic Inference From Genomic and SNP Data,” PLoS Genetics, 9, e1003905. DOI:10.1371/journal.pgen.1003905.
    • (2013) PLoS Genetics , vol.9 , pp. e1003905
    • Excoffier, L.1    Dupanloup, I.2    Huerta-Sánchez, E.3    Sousa, V.C.4    Foll, M.5
  • 18
    • 79954469204 scopus 로고    scopus 로고
    • “Fastsimcoal: A Continuous-Time Coalescent Simulator of Genomic Diversity Under Arbitrarily Complex Evolutionary Scenarios,”
    • Excoffier, L., and Foll, M., (2011), “Fastsimcoal: A Continuous-Time Coalescent Simulator of Genomic Diversity Under Arbitrarily Complex Evolutionary Scenarios,” Bioinformatics, 27, 1332–1334. DOI:10.1093/bioinformatics/btr124.
    • (2011) Bioinformatics , vol.27 , pp. 1332-1334
    • Excoffier, L.1    Foll, M.2
  • 19
    • 0033911640 scopus 로고    scopus 로고
    • “Hitchhiking Under Positive Darwinian Selection,”
    • Fay, J. C., and Wu, C. I., (2000), “Hitchhiking Under Positive Darwinian Selection,” Genetics, 155, 1405–1413.
    • (2000) Genetics , vol.155 , pp. 1405-1413
    • Fay, J.C.1    Wu, C.I.2
  • 20
    • 0019797407 scopus 로고
    • “Evolutionary Trees From DNA Sequences: A Maximum Likelihood Approach,”
    • Felsenstein, J., (1981), “Evolutionary Trees From DNA Sequences: A Maximum Likelihood Approach,” Journal of Molecular Evolution, 17, 368–376. DOI:10.1007/BF01734359.
    • (1981) Journal of Molecular Evolution , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 25
    • 0001301442 scopus 로고    scopus 로고
    • “The Age of a Mutation in a General Coalescent Tree,”
    • Griffiths, R., and Tavaré, S., (1998), “The Age of a Mutation in a General Coalescent Tree,” Communications in Statistics. Stochastic Models, 14, 273–295. DOI:10.1080/15326349808807471.
    • (1998) Communications in Statistics. Stochastic Models , vol.14 , pp. 273-295
    • Griffiths, R.1    Tavaré, S.2
  • 26
    • 0000788827 scopus 로고    scopus 로고
    • “Computational Methods for the Coalescent,”
    • Donnelly P., Tavaré S., (eds), Berlin: Springer-Verlag, and, (,), eds
    • Griffiths, R. C., and S., Tavaré (1997), “Computational Methods for the Coalescent,” in Progress in Population Genetics and Human Evolution (Vol. 87), eds. P., Donnelly and S., Tavaré, Berlin: Springer-Verlag, pp. 165–182.
    • (1997) Progress in Population Genetics and Human Evolution , vol.87 , pp. 165-182
    • Griffiths, R.C.1    Tavaré, S.2
  • 27
    • 73449149044 scopus 로고    scopus 로고
    • “Inferring the Joint Demographic History of Multiple Populations From Multidimensional SNP Frequency Data,”
    • Gutenkunst, R. N., Hernandez, R. D., Williamson, S. H., and Bustamante, C. D., (2009), “Inferring the Joint Demographic History of Multiple Populations From Multidimensional SNP Frequency Data,” PLoS Genetics, 5, e1000695. DOI:10.1371/journal.pgen.1000695.
    • (2009) PLoS Genetics , vol.5 , pp. e1000695
    • Gutenkunst, R.N.1    Hernandez, R.D.2    Williamson, S.H.3    Bustamante, C.D.4
  • 29
    • 67349176068 scopus 로고    scopus 로고
    • “Genetics in Geographically Structured Populations: Defining, Estimating and Interpreting FST,”
    • Holsinger, K. E., and Weir, B. S., (2009), “Genetics in Geographically Structured Populations: Defining, Estimating and Interpreting FST,” Nature Reviews Genetics, 10, 639–650. DOI:10.1038/nrg2611.
    • (2009) Nature Reviews Genetics , vol.10 , pp. 639-650
    • Holsinger, K.E.1    Weir, B.S.2
  • 30
    • 84901364718 scopus 로고    scopus 로고
    • “General Triallelic Frequency Spectrum Under Demographic Models With Variable Population Size,”
    • Jenkins, P. A., Mueller, J. W., and Song, Y. S., (2014), “General Triallelic Frequency Spectrum Under Demographic Models With Variable Population Size,” Genetics, 196, 295–311. DOI:10.1534/genetics.113.158584.
    • (2014) Genetics , vol.196 , pp. 295-311
    • Jenkins, P.A.1    Mueller, J.W.2    Song, Y.S.3
  • 31
    • 85021873089 scopus 로고    scopus 로고
    • “Inferring the Joint Demographic History of Multiple Populations: Beyond the Diffusion Approximation,”
    • Jouganous, J., Long, W., Ragsdale, A. P., and Gravel, S., (2017), “Inferring the Joint Demographic History of Multiple Populations: Beyond the Diffusion Approximation,” Genetics, 206, 1549–1567. DOI:10.1534/genetics.117.200493.
    • (2017) Genetics , vol.206 , pp. 1549-1567
    • Jouganous, J.1    Long, W.2    Ragsdale, A.P.3    Gravel, S.4
  • 32
    • 85013082995 scopus 로고    scopus 로고
    • “Efficient Computation of the Joint Sample Frequency Spectra for Multiple Populations,”
    • Kamm, J. A., Terhorst, J., and Song, Y. S., (2017), “Efficient Computation of the Joint Sample Frequency Spectra for Multiple Populations,” Journal of Computational and Graphical Statistics, 26, 182–194. DOI:10.1080/10618600.2016.1159212.
    • (2017) Journal of Computational and Graphical Statistics , vol.26 , pp. 182-194
    • Kamm, J.A.1    Terhorst, J.2    Song, Y.S.3
  • 33
    • 84975828278 scopus 로고    scopus 로고
    • “Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes,”
    • Kelleher, J., Etheridge, A. M., and McVean, G., (2016), “Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes,” PLoS Computational Biology, 12, e1004842. DOI:10.1371/journal.pcbi.1004842.
    • (2016) PLoS Computational Biology , vol.12 , pp. e1004842
    • Kelleher, J.1    Etheridge, A.M.2    McVean, G.3
  • 34
    • 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, 893–903.
    • (1969) Genetics , vol.61 , pp. 893-903
    • Kimura, M.1
  • 37
    • 0001006209 scopus 로고
    • “Local Computations With Probabilities on Graphical Structures and Their Application to Expert Systems,”
    • Lauritzen, S. L., and Spiegelhalter, D. J., (1988), “Local Computations With Probabilities on Graphical Structures and Their Application to Expert Systems,” Journal of the Royal Statistical Society, Series B, 50, 157–224. DOI:10.1111/j.2517-6161.1988.tb01721.x.
    • (1988) Journal of the Royal Statistical Society, Series B , vol.50 , pp. 157-224
    • Lauritzen, S.L.1    Spiegelhalter, D.J.2
  • 40
    • 84866863890 scopus 로고    scopus 로고
    • “Demographic Inference Using Spectral Methods on SNP Data, With an Analysis of the Human Out-of-Africa Expansion,”
    • Lukić, S., and Hey, J., (2012), “Demographic Inference Using Spectral Methods on SNP Data, With an Analysis of the Human Out-of-Africa Expansion,” Genetics, 192, 619–639. DOI:10.1534/genetics.112.141846.
    • (2012) Genetics , vol.192 , pp. 619-639
    • Lukić, S.1    Hey, J.2
  • 45
    • 41149157336 scopus 로고    scopus 로고
    • “Can One Learn History From the Allelic Spectrum?,”
    • Myers, S., Fefferman, C., and Patterson, N., (2008), “Can One Learn History From the Allelic Spectrum?,” Theoretical Population Biology, 73, 342–348. DOI:10.1016/j.tpb.2008.01.001.
    • (2008) Theoretical Population Biology , vol.73 , pp. 342-348
    • Myers, S.1    Fefferman, C.2    Patterson, N.3
  • 47
    • 0033965571 scopus 로고    scopus 로고
    • “Estimation of Population Parameters and Recombination Rates From Single Nucleotide Polymorphisms,”
    • Nielsen, R., (2000), “Estimation of Population Parameters and Recombination Rates From Single Nucleotide Polymorphisms,” Genetics, 154, 931–942.
    • (2000) Genetics , vol.154 , pp. 931-942
    • Nielsen, R.1
  • 48
    • 0025654424 scopus 로고
    • “The Coalescent and the Genealogical Process in Geographically Structured Population,”
    • Notohara, M., (1990), “The Coalescent and the Genealogical Process in Geographically Structured Population,” Journal of Mathematical Biology, 29, 59–75. DOI:10.1007/BF00173909.
    • (1990) Journal of Mathematical Biology , vol.29 , pp. 59-75
    • Notohara, M.1
  • 53
    • 0023375195 scopus 로고
    • “The Neighbor-Joining Method: A New Method for Reconstructing Phylogenetic Trees,”
    • Saitou, N., and Nei, M., (1987), “The Neighbor-Joining Method: A New Method for Reconstructing Phylogenetic Trees,” Molecular Biology and Evolution, 4, 406–425. DOI:10.1093/oxfordjournals.molbev.a040454.
    • (1987) Molecular Biology and Evolution , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 54
    • 0026460082 scopus 로고
    • “Population Genetics of Polymorphism and Divergence,”
    • Sawyer, S. A., and Hartl, D. L., (1992), “Population Genetics of Polymorphism and Divergence,” Genetics, 132, 1161–1176.
    • (1992) Genetics , vol.132 , pp. 1161-1176
    • Sawyer, S.A.1    Hartl, D.L.2
  • 55
    • 84984636568 scopus 로고    scopus 로고
    • “The Mutation Rate in Human Evolution and Demographic Inference,”
    • Scally, A., (2016), “The Mutation Rate in Human Evolution and Demographic Inference,” Current Opinion in Genetics & Development, 41, 36–43. DOI:10.1016/j.gde.2016.07.008.
    • (2016) Current Opinion in Genetics & Development , vol.41 , pp. 36-43
    • Scally, A.1
  • 56
    • 27544497650 scopus 로고    scopus 로고
    • “Calibrating a Coalescent Simulation of Human Genome Sequence Variation,”
    • Schaffner, S. F., Foo, C., Gabriel, S., Reich, D., Daly, W. J., and Altshuler, D., (2005), “Calibrating a Coalescent Simulation of Human Genome Sequence Variation,” Genome Research, 15, 1576–1583. DOI:10.1101/gr.3709305.
    • (2005) Genome Research , vol.15 , pp. 1576-1583
    • Schaffner, S.F.1    Foo, C.2    Gabriel, S.3    Reich, D.4    Daly, W.J.5    Altshuler, D.6
  • 58
    • 0024313579 scopus 로고
    • “Statistical Method for Testing the Neutral Mutation Hypothesis by DNA Polymorphism,”
    • Tajima, F., (1989), “Statistical Method for Testing the Neutral Mutation Hypothesis by DNA Polymorphism,” Genetics, 123, 585–595.
    • (1989) Genetics , vol.123 , pp. 585-595
    • Tajima, F.1
  • 59
    • 0024262745 scopus 로고
    • “The Coalescent in Two Partially Isolated Diffusion Populations,”
    • Takahata, N., (1988), “The Coalescent in Two Partially Isolated Diffusion Populations,” Genetics Research, 52, 213–222. DOI:10.1017/S0016672300027683.
    • (1988) Genetics Research , vol.52 , pp. 213-222
    • Takahata, N.1
  • 60
    • 85007071697 scopus 로고    scopus 로고
    • “Robust and Scalable Inference of Population History From Hundreds of Unphased Whole Genomes,”
    • Terhorst, J., Kamm, J. A., and Song, Y. S., (2017), “Robust and Scalable Inference of Population History From Hundreds of Unphased Whole Genomes,” Nature Genetics, 49, 303–309. DOI:10.1038/ng.3748.
    • (2017) Nature Genetics , vol.49 , pp. 303-309
    • Terhorst, J.1    Kamm, J.A.2    Song, Y.S.3
  • 61
    • 84934917155 scopus 로고    scopus 로고
    • “Fundamental Limits on the Accuracy of Demographic Inference Based on the Sample Frequency Spectrum,”
    • Terhorst, J., and Song, Y. S., (2015), “Fundamental Limits on the Accuracy of Demographic Inference Based on the Sample Frequency Spectrum,” Proceedings of the National Academy of Sciences of the United States of America, 112, 7677–7682. DOI:10.1073/pnas.1503717112.
    • (2015) Proceedings of the National Academy of Sciences of the United States of America , vol.112 , pp. 7677-7682
    • Terhorst, J.1    Song, Y.S.2
  • 62
    • 0031018637 scopus 로고    scopus 로고
    • “Estimating Ancestral Population Parameters,”
    • Wakeley, J., and Hey, J., (1997), “Estimating Ancestral Population Parameters,” Genetics, 145, 847–855.
    • (1997) Genetics , vol.145 , pp. 847-855
    • Wakeley, J.1    Hey, J.2
  • 63
    • 0016491430 scopus 로고
    • “On the Number of Segregating Sites in Genetical Models Without Recombination,”
    • Watterson, G., (1975), “On the Number of Segregating Sites in Genetical Models Without Recombination,” Theoretical Population Biology, 7, 256–276. DOI:10.1016/0040-5809(75)90020-9.
    • (1975) Theoretical Population Biology , vol.7 , pp. 256-276
    • Watterson, G.1
  • 64
    • 77951177432 scopus 로고    scopus 로고
    • “ABCtoolbox: A Versatile Toolkit for Approximate Bayesian Computations,”
    • Wegmann, D., Leuenberger, C., Neuenschwander, S., and Excoffier, L., (2010), “ABCtoolbox: A Versatile Toolkit for Approximate Bayesian Computations,” BMC Bioinformatics, 11, 116. DOI:10.1186/1471-2105-11-116.
    • (2010) BMC Bioinformatics , vol.11 , pp. 116
    • Wegmann, D.1    Leuenberger, C.2    Neuenschwander, S.3    Excoffier, L.4
  • 65
    • 33751342650 scopus 로고    scopus 로고
    • “Statistical Tests for Detecting Positive Selection by Utilizing High-Frequency Variants,”
    • Zeng, K., Fu, Y.-X., Shi, S., and Wu, C.-I., (2006), “Statistical Tests for Detecting Positive Selection by Utilizing High-Frequency Variants,” Genetics, 174, 1431–1439. DOI:10.1534/genetics.106.061432.
    • (2006) Genetics , vol.174 , pp. 1431-1439
    • Zeng, K.1    Fu, Y.-X.2    Shi, S.3    Wu, C.-I.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.