메뉴 건너뛰기




Volumn 194, Issue 3, 2013, Pages 721-736

Asymptotic distributions of coalescence times and ancestral lineage numbers for populations with temporally varying size

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; COALESCENCE TIME; GENE FREQUENCY; GENEALOGY; HUMAN; POPULATION; POPULATION DISTRIBUTION; POPULATION SIZE; PRIORITY JOURNAL; TIME;

EID: 84879764213     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.113.151522     Document Type: Article
Times cited : (20)

References (47)
  • 1
    • 84975742565 scopus 로고    scopus 로고
    • A map of human genome variation from population scale sequencing
    • Altshuler, D., E. Lander, L. Ambrogio, T. Bloom, K. Cibulskis et al., 2010 A map of human genome variation from population scale sequencing. Nature 467: 1061-1073.
    • (2010) Nature , vol.467 , pp. 1061-1073
    • Altshuler, D.1    Lander, E.2    Ambrogio, L.3    Bloom, T.4    Cibulskis, K.5
  • 2
    • 34047237616 scopus 로고    scopus 로고
    • Estimation of the number of individuals founding colonized populations
    • Anderson, E., and M. Slatkin, 2007 Estimation of the number of individuals founding colonized populations. Evolution 61: 972-983.
    • (2007) Evolution , vol.61 , pp. 972-983
    • Anderson, E.1    Slatkin, M.2
  • 4
    • 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. Theor. Popul. Biol. 81: 179-195.
    • (2012) Theor. Popul. Biol , vol.81 , pp. 179-195
    • Chen, H.1
  • 5
    • 84874020219 scopus 로고    scopus 로고
    • Intercoalescence time distribtution of incomplete genealogies in temporally varying populations, and applications in population genetic inference
    • Chen, H., 2013 Intercoalescence time distribtution of incomplete genealogies in temporally varying populations, and applications in population genetic inference. Ann. Hum. Genet. 77: 158-173.
    • (2013) Ann. Hum. Genet , vol.77 , pp. 158-173
    • Chen, H.1
  • 6
    • 35048822012 scopus 로고    scopus 로고
    • The joint allele-frequency spectrum in closely related species
    • Chen, H., R. E. Green, S. Pääbo, and M. Slatkin, 2007 The joint allele-frequency spectrum in closely related species. Genetics 177: 387-398.
    • (2007) Genetics , vol.177 , pp. 387-398
    • Chen, H.1    Green, R.E.2    Pääbo, S.3    Slatkin, M.4
  • 7
    • 78650037203 scopus 로고    scopus 로고
    • Deep resequencing reveals excess rare recent var-iants consistent with explosive population growth
    • Coventry, A., L. M. Bull-Otterson, X. Liu, A. G. Clark, T. J. Maxwell et al., 2010 Deep resequencing reveals excess rare recent var-iants consistent with explosive population growth. Nat. Com-mun. 1: 131.
    • (2010) Nat. Com-mun , vol.1 , pp. 131
    • Coventry, A.1    Bull-Otterson, L.M.2    Liu, X.3    Clark, A.G.4    Maxwell, T.J.5
  • 8
    • 37349067917 scopus 로고    scopus 로고
    • Founding events in species in-vasions: Genetic variation, adaptive evolution, and the role of multiple introductions
    • Dlugosch, K., and I. Parker, 2007 Founding events in species in-vasions: genetic variation, adaptive evolution, and the role of multiple introductions. Mol. Ecol. 17: 431-449.
    • (2007) Mol. Ecol , vol.17 , pp. 431-449
    • Dlugosch, K.1    Parker, I.2
  • 9
    • 84976027932 scopus 로고
    • The transient behaviour of the moran model in population genetics
    • Donnelly, P., 1984 The transient behaviour of the moran model in population genetics. Math. Proc. Camb. Philos. Soc. 95: 349-358.
    • (1984) Math. Proc. Camb. Philos. Soc , vol.95 , pp. 349-358
    • Donnelly, P.1
  • 10
    • 0029559462 scopus 로고
    • Coalescents and genealogical structure under neutrality
    • Donnelly, P., and S. Tavaré, 1995 Coalescents and genealogical structure under neutrality. Annu. Rev. Genet. 29: 401-421.
    • (1995) Annu. Rev. Genet , vol.29 , pp. 401-421
    • Donnelly, P.1    Tavaré, S.2
  • 11
    • 33750971421 scopus 로고    scopus 로고
    • Non-equilibrium theory of the allele frequency spectrum
    • Evans, S., Y. Shvets, and M. Slatkin, 2007 Non-equilibrium theory of the allele frequency spectrum. Theor. Popul. Biol. 71: 109-119.
    • (2007) Theor. Popul. Biol , vol.71 , pp. 109-119
    • Evans, S.1    Shvets, Y.2    Slatkin, M.3
  • 12
    • 0015310384 scopus 로고
    • The sampling theory of selectively neutral al-leles
    • Ewens, W., 1972 The sampling theory of selectively neutral al-leles. Theor. Popul. Biol. 3: 87-112.
    • (1972) Theor. Popul. Biol , vol.3 , pp. 87-112
    • Ewens, W.1
  • 14
    • 0001947091 scopus 로고    scopus 로고
    • Likelihoods on coalescents: A Monte Carlo sampling approach to inferring pa-rameters from population samples of molecular data
    • Felsenstein, J., M. Kuhner, J. Yamato, and P. Beerli, 1999 Likelihoods on coalescents: a Monte Carlo sampling approach to inferring pa-rameters from population samples of molecular data. Lect. Notes Monogr. Ser., 163-185.
    • (1999) Lect. Notes Monogr. Ser , pp. 163-185
    • Felsenstein, J.1    Kuhner, M.2    Yamato, J.3    Beerli, P.4
  • 15
    • 0029391126 scopus 로고
    • Statistical properties of segregating sites
    • Fu, Y. X., 1995 Statistical properties of segregating sites. Theor. Popul. Biol. 48: 172-197.
    • (1995) Theor. Popul. Biol , vol.48 , pp. 172-197
    • Fu, Y.X.1
  • 16
    • 0018980316 scopus 로고
    • Lines of descent in the diffusion approxima-tion of neutral Wright-Fisher models. Theor. Popul
    • Griffiths, R. C., 1980 Lines of descent in the diffusion approxima-tion of neutral Wright-Fisher models. Theor. Popul. Biol. 17: 37-50.
    • (1980) Biol , vol.17 , pp. 37-50
    • Griffiths, R.C.1
  • 17
    • 0021711355 scopus 로고
    • Asymptotic line-of-descent distributions
    • Griffiths, R. C., 1984 Asymptotic line-of-descent distributions. J. Math. Biol. 21: 67-75.
    • (1984) J. Math. Biol , vol.21 , pp. 67-75
    • Griffiths, R.C.1
  • 18
    • 33745955125 scopus 로고    scopus 로고
    • Coalescent lineage distributions
    • Griffiths, R. C., 2006 Coalescent lineage distributions. Adv. Appl. Probab. 38: 405-429.
    • (2006) Adv. Appl. Probab , vol.38 , pp. 405-429
    • Griffiths, R.C.1
  • 19
    • 0028782096 scopus 로고
    • Sampling theory for neutral alleles in a varying enviroment
    • Griffiths, R. C., and S. Tavaré, 1994a Sampling theory for neutral alleles in a varying enviroment. Philos. Trans. R. Soc. Lond. B 344: 403-410.
    • (1994) Philos. Trans. R. Soc. Lond. B , vol.344 , pp. 403-410
    • Griffiths, R.C.1    Tavaré, S.2
  • 20
    • 34548452457 scopus 로고
    • Simulating probability dis-tributions in the coalescent
    • Griffiths, R. C., and S. Tavaré, 1994b Simulating probability dis-tributions in the coalescent. Theor. Popul. Biol. 46: 131-159.
    • (1994) Theor. Popul. Biol , vol.46 , pp. 131-159
    • Griffiths, R.C.1    Tavaré, S.2
  • 21
    • 0001301442 scopus 로고    scopus 로고
    • The age of a mutation in a general coalescent tree
    • Griffiths, R. C., and S. Tavaré, 1998 The age of a mutation in a general coalescent tree. Stoch. Models 14: 273-295.
    • (1998) Stoch. Models , vol.14 , pp. 273-295
    • Griffiths, R.C.1    Tavaré, S.2
  • 22
    • 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
  • 23
    • 84858784460 scopus 로고    scopus 로고
    • Var-iation and Evolution: A Primer in Coalescent Theory. Oxford University Press, New York
    • Hein, J., M. Schierup, and C. Wiuf, 2005 Gene Genealogies, Var-iation and Evolution: A Primer in Coalescent Theory. Oxford University Press, New York.
    • (2005) Gene Genealogies
    • Hein, J.1    Schierup, M.2    Wiuf, C.3
  • 24
    • 0001935493 scopus 로고
    • Gene genealogies and the coalescent pro-cess
    • Hudson, R. R., 1990 Gene genealogies and the coalescent pro-cess. Oxford Surv. Evol. Biol. 7: 44.
    • (1990) Oxford Surv. Evol. Biol , vol.7 , pp. 44
    • Hudson, R.R.1
  • 25
    • 0036184745 scopus 로고    scopus 로고
    • Generating samples under a Wright-Fisher neutral model of genetic variation
    • Hudson, R. R., 2002 Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
    • (2002) Bioinformatics , vol.18 , pp. 337-338
    • Hudson, R.R.1
  • 26
    • 0001017871 scopus 로고
    • Solution of a process of random genetic drift with a continuous model
    • Kimura, M., 1955 Solution of a process of random genetic drift with a continuous model. Proc. Natl. Acad. Sci. USA 41: 144-150.
    • (1955) Proc. Natl. Acad. Sci. USA , vol.41 , pp. 144-150
    • Kimura, M.1
  • 27
    • 33845412091 scopus 로고
    • The coalescent. Stochastic Process
    • Kingman, J., 1982a The coalescent. Stochastic Process. Appl. 13: 235-248.
    • (1982) Appl , vol.13 , pp. 235-248
    • Kingman, J.1
  • 28
    • 0002743467 scopus 로고
    • Exchangeability and the Evolution of Large Populations
    • edited by G. Koch and F. Spizzichino. North-Holland, Amsterdam
    • Kingman, J., 1982b Exchangeability and the Evolution of Large Populations, pp. 97-112 in Exchangeability in Probability and Statistics, edited by G. Koch and F. Spizzichino. North-Holland, Amsterdam.
    • (1982) Exchangeability In Probability and Statistics , pp. 97-112
    • Kingman, J.1
  • 29
    • 79955476379 scopus 로고    scopus 로고
    • Non-equilibrium allele fre-quency spectra via spectral methods
    • Lukić, S., J. Hey, and K. Chen, 2011 Non-equilibrium allele fre-quency 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
  • 30
    • 39649117755 scopus 로고    scopus 로고
    • The impact of next-generation sequencing technology on genetics
    • Mardis, E. R., 2008 The impact of next-generation sequencing technology on genetics. Trends Genet. 24: 133-140.
    • (2008) Trends Genet , vol.24 , pp. 133-140
    • Mardis, E.R.1
  • 31
    • 1642282195 scopus 로고    scopus 로고
    • The allele frequency spectrum in genome-wide human variation data reveals signals of differeential demographic history in three large world populations
    • Marth, G. T., E. Czabarka, J. Murvai, and S. T. Sherry, 2004 The allele frequency spectrum in genome-wide human variation data reveals signals of differeential demographic history in three large world populations. Genetics 2004: 351-372.
    • (2004) Genetics , vol.2004 , pp. 351-372
    • Marth, G.T.1    Czabarka, E.2    Murvai, J.3    Sherry, S.T.4
  • 32
    • 79955371587 scopus 로고    scopus 로고
    • Recovering population parameters from a single gene genealogy: An unbiased estimator of the growth rate
    • Maruvka, Y., N. Shnerb, Y. Bar-Yam, and J. Wakeley, 2011 Recovering population parameters from a single gene genealogy: an unbiased estimator of the growth rate. Mol. Biol. Evol. 28: 1617-1631.
    • (2011) Mol. Biol. Evol , vol.28 , pp. 1617-1631
    • Maruvka, Y.1    Shnerb, N.2    Bar-Yam, Y.3    Wakeley, J.4
  • 33
    • 0000913208 scopus 로고    scopus 로고
    • Coalescent theory
    • edited by D. J. Balding, M. Bishop, and C. Cannings. Wiley, Chichester, UK
    • Nordborg, M., 2001 Coalescent theory, pp. 179-212 in Handbook of Statistical Genetics, edited by D. J. Balding, M. Bishop, and C. Cannings. Wiley, Chichester, UK.
    • (2001) Handbook of Statistical Genetics , pp. 179-212
    • Nordborg, M.1
  • 34
    • 0141566652 scopus 로고    scopus 로고
    • New explicit expressions for relative frequencies of single-nucleotide polymorphisms with application to statistical inference on population growth
    • Polanski, A., and M. Kimmel, 2003 New explicit expressions for relative frequencies of single-nucleotide polymorphisms with application to statistical inference on population growth. Genet-ics 165: 427-436.
    • (2003) Genet-ics , vol.165 , pp. 427-436
    • Polanski, A.1    Kimmel, M.2
  • 35
    • 0037289895 scopus 로고    scopus 로고
    • A note on dis-tributions of times to coalescence, under time-dependent pop-ulation size
    • Polanski, A., A. Bobrowski, and M. Kimmel, 2003 A note on dis-tributions of times to coalescence, under time-dependent pop-ulation size. Theor. Popul. Biol. 63: 33-40.
    • (2003) Theor. Popul. Biol , vol.63 , pp. 33-40
    • Polanski, A.1    Bobrowski, A.2    Kimmel, M.3
  • 36
    • 0037385394 scopus 로고    scopus 로고
    • Geographic distribution of disease mutations in the Ashkenazi Jewish popula-tion supports genetic drift over selection
    • Risch, N., H. Tang, H. Katzenstein, and J. Ekstein, 2003 Geographic distribution of disease mutations in the Ashkenazi Jewish popula-tion supports genetic drift over selection. Am. J. Hum. Genet. 72: 812-822.
    • (2003) Am. J. Hum. Genet , vol.72 , pp. 812-822
    • Risch, N.1    Tang, H.2    Katzenstein, H.3    Ekstein, J.4
  • 37
    • 0026460082 scopus 로고
    • Population genetics of poly-morphism and divergence
    • Sawyer, S. A., and D. L. Hartl, 1992 Population genetics of poly-morphism and divergence. Genetics 132: 1161-1176.
    • (1992) Genetics , vol.132 , pp. 1161-1176
    • Sawyer, S.A.1    Hartl, D.L.2
  • 38
    • 84863235001 scopus 로고    scopus 로고
    • A simple method for find-ing explicit analytic transition densities of diffusion processes with general diploid selection
    • Song, Y. S., and M. Steinrücken, 2012 A simple method for find-ing explicit analytic transition densities of diffusion processes with general diploid selection. Genetics 190: 1117-1129.
    • (2012) Genetics , vol.190 , pp. 1117-1129
    • Song, Y.S.1    Steinrücken, M.2
  • 39
    • 0024313579 scopus 로고
    • Statistical methods for testing the neutral muta-tions hypothesis by DNA polymorphism
    • Tajima, F., 1989 Statistical methods for testing the neutral muta-tions hypothesis by DNA polymorphism. Genetics 123: 585-595.
    • (1989) Genetics , vol.123 , pp. 585-595
    • Tajima, F.1
  • 40
    • 0022390691 scopus 로고
    • Gene genealogy and variance of interpopulational nucleotide differences
    • Takahata, N., and M. Nei, 1985 Gene genealogy and variance of interpopulational nucleotide differences. Genetics 110: 325-344.
    • (1985) Genetics , vol.110 , pp. 325-344
    • Takahata, N.1    Nei, M.2
  • 41
    • 0021514720 scopus 로고
    • Line-of-descent and genealogical processes, and their applications in population genetics models
    • Tavaré, S., 1984 Line-of-descent and genealogical processes, and their applications in population genetics models. Theor. Popul. Biol. 26: 119-164.
    • (1984) Theor. Popul. Biol , vol.26 , pp. 119-164
    • Tavaré, S.1
  • 42
  • 43
    • 0016491430 scopus 로고
    • On the number of segregating sites in genet-ical models without recombination
    • Watterson, G., 1975 On the number of segregating sites in genet-ical models without recombination. Theor. Popul. Biol. 7: 256-276.
    • (1975) Theor. Popul. Biol , vol.7 , pp. 256-276
    • Watterson, G.1
  • 44
    • 0001769846 scopus 로고
    • Lines of descent and the coalescent
    • Watterson, G., 1984 Lines of descent and the coalescent. Theor. Popul. Biol. 26: 77-92.
    • (1984) Theor. Popul. Biol , vol.26 , pp. 77-92
    • Watterson, G.1
  • 45
    • 20344380699 scopus 로고    scopus 로고
    • Simultaneous inference of selection and popula-tion growth from patterns of variation in the human genome
    • Williamson, S. H., R. Hernandez, A. Fledel-Alon, L. Zhu, R. Nielsen et al., 2005 Simultaneous inference of selection and popula-tion growth from patterns of variation in the human genome. Proc. Natl. Acad. Sci. USA 102: 7882-7887.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 7882-7887
    • Williamson, S.H.1    Hernandez, R.2    Fledel-Alon, A.3    Zhu, L.4    Nielsen, R.5
  • 46
    • 0036671454 scopus 로고    scopus 로고
    • The matrix coalescent and an application to human single-nucleotide polymorphisms
    • Wooding, S., and A. Rogers, 2002 The matrix coalescent and an application to human single-nucleotide polymorphisms. Genet-ics 161: 1641-1650.
    • (2002) Genet-ics , vol.161 , pp. 1641-1650
    • Wooding, S.1    Rogers, A.2
  • 47
    • 79955475534 scopus 로고    scopus 로고
    • Analytical results on the neu-tral non-equilibrium allele frequency spectrum based on diffu-sion theory
    • Živković, D., and W. Stephan, 2011 Analytical results on the neu-tral non-equilibrium allele frequency spectrum based on diffu-sion theory. Theor. Popul. Biol. 79: 184-191.
    • (2011) Theor. Popul. Biol , vol.79 , pp. 184-191
    • Živković, D.1    Stephan, W.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.