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Volumn 197, Issue 4, 2014, Pages 1329-1341

How population growth affects linkage disequilibrium

Author keywords

Admixture; Linkage disequilibrium; Population growth; Selection

Indexed keywords

NUCLEOTIDE;

EID: 84905653382     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.114.166454     Document Type: Article
Times cited : (38)

References (49)
  • 1
    • 0034892915 scopus 로고    scopus 로고
    • Lower-than-expected linkage disequilibrium between tightly linked markers in humans suggests a role for gene conversion
    • Ardlie, K., S. Liu-Cordero, M. Eberle, M. Daly, J. Barrett et al., 2001 Lower-than-expected linkage disequilibrium between tightly linked markers in humans suggests a role for gene conversion. Am. J. Hum. Genet. 69: 582-589.
    • (2001) Am. J. Hum. Genet. , vol.69 , pp. 582-589
    • Ardlie, K.1    Liu-Cordero, S.2    Eberle, M.3    Daly, M.4    Barrett, J.5
  • 2
    • 61449135985 scopus 로고    scopus 로고
    • Fast and flexible simulation of DNA sequence data
    • Chen, G. K., P. Marjoram, and J. D. Wall, 2009 Fast and flexible simulation of DNA sequence data. Genome Res. 19: 136-142.
    • (2009) Genome Res. , vol.19 , pp. 136-142
    • Chen, G.K.1    Marjoram, P.2    Wall, J.D.3
  • 5
    • 0002629270 scopus 로고
    • Maximum likelihood from incomplete data via the EM algorithm
    • Dempster, A. P., N. M. Laird, and D. B. Rubin, 1977 Maximum likelihood from incomplete data via the EM algorithm. J. R. Stat. Soc. B 39: 1-38.
    • (1977) J. R. Stat. Soc. B , vol.39 , pp. 1-38
    • Dempster, A.P.1    Laird, N.M.2    Rubin, D.B.3
  • 7
    • 0034835229 scopus 로고    scopus 로고
    • Gene conversion and different population histories may explain the contrast between polymorphism and linkage disequilibrium levels
    • Frisse, L., R. Hudson, A. Bartoszewicz, J. Wall, J. Donfack et al., 2001 Gene conversion and different population histories may explain the contrast between polymorphism and linkage disequilibrium levels. Am. J. Hum. Genet. 69: 831-843.
    • (2001) Am. J. Hum. Genet. , vol.69 , pp. 831-843
    • Frisse, L.1    Hudson, R.2    Bartoszewicz, A.3    Wall, J.4    Donfack, J.5
  • 8
    • 0029391126 scopus 로고
    • Statistical properties of segregating sites
    • Fu, Y., 1995 Statistical properties of segregating sites. Theor. Popul. Biol. 48: 172-197.
    • (1995) Theor. Popul. Biol. , vol.48 , pp. 172-197
    • Fu, Y.1
  • 9
    • 84857190907 scopus 로고    scopus 로고
    • Implementing the Nelder-Mead simplex algorithm with adaptive parameters
    • Gao, F., and L. Han, 2012 Implementing the Nelder-Mead simplex algorithm with adaptive parameters. Comput. Optim. Appl. 51: 259-277.
    • (2012) Comput. Optim. Appl. , vol.51 , pp. 259-277
    • Gao, F.1    Han, L.2
  • 10
    • 0001301442 scopus 로고    scopus 로고
    • The age of a mutation in a general coalescent tree
    • Griffiths, R., 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.1    Tavaré, S.2
  • 12
    • 35348983887 scopus 로고    scopus 로고
    • A second generation human haplotype map of over 3.1 million SNPs
    • HapMap
    • HapMap, 2007 A second generation human haplotype map of over 3.1 million SNPs. Nature 449: 851-862.
    • (2007) Nature , vol.449 , pp. 851-862
  • 13
    • 0242500969 scopus 로고    scopus 로고
    • Novel multilocus measure of linkage disequilibrium to estimate past effective population size
    • Hayes, B., P. Visscher, H. McPartlan, and M. Goddard, 2003 Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Res. 13: 635-643.
    • (2003) Genome Res. , vol.13 , pp. 635-643
    • Hayes, B.1    Visscher, P.2    McPartlan, H.3    Goddard, M.4
  • 14
    • 0016565853 scopus 로고
    • Linkage disequilibrium among multiple neutral alleles produced by mutation in finite population
    • Hill, W. G., 1975 Linkage disequilibrium among multiple neutral alleles produced by mutation in finite population. Theor. Popul. Biol. 8: 117-126.
    • (1975) Theor. Popul. Biol. , vol.8 , pp. 117-126
    • Hill, W.G.1
  • 15
    • 0019771734 scopus 로고
    • Estimation of effective population size from data on linkage disequilibrium
    • Hill, W. G., 1981 Estimation of effective population size from data on linkage disequilibrium. Genet. Res. 38: 209-216.
    • (1981) Genet. Res. , vol.38 , pp. 209-216
    • Hill, W.G.1
  • 16
    • 33646226097 scopus 로고
    • Linkage disequilibrium in finite populations
    • Hill, W. G., and A. Robertson, 1968 Linkage disequilibrium in finite populations. Theor. Appl. Genet. 38: 226-231.
    • (1968) Theor. Appl. Genet. , vol.38 , pp. 226-231
    • Hill, W.G.1    Robertson, A.2
  • 17
    • 0021909851 scopus 로고
    • The sampling distribution of linkage disequilibrium under an infinite allele model without selection
    • Hudson, R. R., 1985 The sampling distribution of linkage disequilibrium under an infinite allele model without selection. Genetics 109: 611-631.
    • (1985) Genetics , vol.109 , pp. 611-631
    • Hudson, R.R.1
  • 19
    • 0026639787 scopus 로고
    • Expected behavior of conditional linkage disequilibrium
    • Kaplan, N., and B. Weir, 1992 Expected behavior of conditional linkage disequilibrium. Am. J. Hum. Genet. 51: 333.
    • (1992) Am. J. Hum. Genet. , vol.51 , pp. 333
    • Kaplan, N.1    Weir, B.2
  • 20
    • 0014494672 scopus 로고
    • The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutation
    • Kimura, M., 1969 The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutation. Genetics 61: 893-903.
    • (1969) Genetics , vol.61 , pp. 893-903
    • Kimura, M.1
  • 21
    • 0033039497 scopus 로고    scopus 로고
    • Prospects for whole-genome linkage disequilibrium mapping of common disease genes
    • Kruglyak, L., 1999 Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat. Genet. 22: 139-144.
    • (1999) Nat. Genet. , vol.22 , pp. 139-144
    • Kruglyak, L.1
  • 22
    • 0002907949 scopus 로고
    • The interaction of selection and linkage. I. General considerations; heterotic models
    • Lewontin, R. C., 1964 The interaction of selection and linkage. I. General considerations; heterotic models. Genetics 49: 49-67.
    • (1964) Genetics , vol.49 , pp. 49-67
    • Lewontin, R.C.1
  • 23
    • 0014127475 scopus 로고
    • An estimate of average heterozygosity in man
    • Lewontin, R. C., 1967 An estimate of average heterozygosity in man. Am. J. Hum. Genet. 19: 681-685.
    • (1967) Am. J. Hum. Genet. , vol.19 , pp. 681-685
    • Lewontin, R.C.1
  • 24
    • 0001180494 scopus 로고
    • Moving blocks jacknife and bootstrap capture weak dependence
    • in, edited by R. LePage, and L. Billard. John Wiley & Sons, New York
    • Lieu, R. Y., and K. Singh, 1992 Moving blocks jacknife and bootstrap capture weak dependence, pp. 225-248 in Exploring the "Limits" of the Bootstrap, edited by R. LePage, and L. Billard. John Wiley & Sons, New York.
    • (1992) Exploring the "Limits" of the Bootstrap , pp. 225-248
    • Lieu, R.Y.1    Singh, K.2
  • 25
    • 0015669794 scopus 로고
    • Linkage disequilibrium in two-locus, finite, random mating models without selection or mutation
    • Littler, R., 1973 Linkage disequilibrium in two-locus, finite, random mating models without selection or mutation. Theor. Popul. Biol. 4: 259-275.
    • (1973) Theor. Popul. Biol. , vol.4 , pp. 259-275
    • Littler, R.1
  • 26
    • 26444452499 scopus 로고
    • Stochastic integrals and their application to population genetics
    • in, Protein Polymorphism, and the Neutral Theory, edited by M. Kimura. Springer-Verlag, Berlin
    • Maruyama, T., 1982 Stochastic integrals and their application to population genetics, pp. 151-166 in Molecular Evolution, Protein Polymorphism, and the Neutral Theory, edited by M. Kimura. Springer-Verlag, Berlin.
    • (1982) Molecular Evolution , pp. 151-166
    • Maruyama, T.1
  • 27
    • 79957956814 scopus 로고    scopus 로고
    • Human population dispersal "out of Africa" estimated from linkage disequilibrium and allele frequencies of SNPs
    • McEvoy, B., J. Powell, M. Goddard, and P. Visscher, 2011 Human population dispersal "out of Africa" estimated from linkage disequilibrium and allele frequencies of SNPs. Genome Res. 21: 821-829.
    • (2011) Genome Res. , vol.21 , pp. 821-829
    • McEvoy, B.1    Powell, J.2    Goddard, M.3    Visscher, P.4
  • 28
    • 0036811711 scopus 로고    scopus 로고
    • A genealogical interpretation of linkage disequilibrium
    • McVean, G., 2002 A genealogical interpretation of linkage disequilibrium. Genetics 162: 987-991.
    • (2002) Genetics , vol.162 , pp. 987-991
    • McVean, G.1
  • 29
    • 84889320525 scopus 로고    scopus 로고
    • Linkage disequilibrium, recombination and selection
    • in, Ed. 3, edited by D. Balding, M. Bishop, and C. Cannings. John Wiley and Sons, Chichester, UK
    • McVean, G., 2007 Linkage disequilibrium, recombination and selection, pp. 909-944 in Handbook of Statistical Genetics, Ed. 3, edited by D. Balding, M. Bishop, and C. Cannings. John Wiley and Sons, Chichester, UK.
    • (2007) Handbook of Statistical Genetics , pp. 909-944
    • McVean, G.1
  • 30
    • 0014569408 scopus 로고
    • Linkage disequilibrium at steady state determined by random genetic drift and recurrent mutation
    • Ohta, T., and M. Kimura, 1969 Linkage disequilibrium at steady state determined by random genetic drift and recurrent mutation. Genetics 63: 229.
    • (1969) Genetics , vol.63 , pp. 229
    • Ohta, T.1    Kimura, M.2
  • 31
    • 0015100342 scopus 로고
    • Linkage disequilibrium between two segregating nucleotide sites under the steady flux of mutations in a finite population
    • Ohta, T., and M. Kimura, 1971 Linkage disequilibrium between two segregating nucleotide sites under the steady flux of mutations in a finite population. Genetics 68: 571-580.
    • (1971) Genetics , vol.68 , pp. 571-580
    • Ohta, T.1    Kimura, M.2
  • 32
    • 84975795680 scopus 로고
    • Genomes Project Consortium, 2012 An integrated map of genetic variation from 1,092 human genomes
    • 1000 Genomes Project Consortium, 2012 An integrated map of genetic variation from 1,092 human genomes. Nature 491: 56-65.
    • (1000) Nature , vol.491 , pp. 56-65
  • 34
    • 0034977045 scopus 로고    scopus 로고
    • Linkage disequilibrium in humans: Models and data
    • Pritchard, J., and M. Przeworski, 2001 Linkage disequilibrium in humans: models and data. Am. J. Hum. Genet. 69: 1-14.
    • (2001) Am. J. Hum. Genet. , vol.69 , pp. 1-14
    • Pritchard, J.1    Przeworski, M.2
  • 35
    • 70349316959 scopus 로고    scopus 로고
    • Linkage disequilibrium between loci of unknown phase
    • Rogers, A. R., and C. Huff, 2009 Linkage disequilibrium between loci of unknown phase. Genetics 182: 839-844.
    • (2009) Genetics , vol.182 , pp. 839-844
    • Rogers, A.R.1    Huff, C.2
  • 36
    • 0029983205 scopus 로고    scopus 로고
    • Ascertainment bias in estimates of average heterozygosity
    • Rogers, A. R., and L. B. Jorde, 1996 Ascertainment bias in estimates of average heterozygosity. Am. J. Hum. Genet. 58: 1033-1041.
    • (1996) Am. J. Hum. Genet. , vol.58 , pp. 1033-1041
    • Rogers, A.R.1    Jorde, L.B.2
  • 38
    • 0034940158 scopus 로고    scopus 로고
    • The value of isolated populations
    • Shifman, S., and A. Darvasi, 2001 The value of isolated populations. Nat. Genet. 28: 309-310.
    • (2001) Nat. Genet. , vol.28 , pp. 309-310
    • Shifman, S.1    Darvasi, A.2
  • 39
    • 43749105558 scopus 로고    scopus 로고
    • Linkage disequilibrium-understanding the evolutionary past and mapping the medical future
    • Slatkin, M., 2008 Linkage disequilibrium-understanding the evolutionary past and mapping the medical future. Nat. Rev. Genet. 9: 477-485.
    • (2008) Nat. Rev. Genet. , vol.9 , pp. 477-485
    • Slatkin, M.1
  • 40
    • 33750997276 scopus 로고    scopus 로고
    • Analytic computation of the expectation of the linkage disequilibrium coefficient r2
    • Song, Y., and J. Song, 2007 Analytic computation of the expectation of the linkage disequilibrium coefficient r2. Theor. Popul. Biol. 71: 49-60.
    • (2007) Theor. Popul. Biol. , vol.71 , pp. 49-60
    • Song, Y.1    Song, J.2
  • 41
    • 0017852492 scopus 로고
    • The effect of intragenic recombination on the number of alleles in a finite population
    • Strobeck, C., and K. Morgan, 1978 The effect of intragenic recombination on the number of alleles in a finite population. Genetics 88: 829-844.
    • (1978) Genetics , vol.88 , pp. 829-844
    • Strobeck, C.1    Morgan, K.2
  • 42
    • 0015070635 scopus 로고
    • Linkage disequilibrium and homozygosity of chromosome segments in finite populations
    • Sved, J. A., 1971 Linkage disequilibrium and homozygosity of chromosome segments in finite populations. Theor. Popul. Biol. 2: 125-141.
    • (1971) Theor. Popul. Biol. , vol.2 , pp. 125-141
    • Sved, J.A.1
  • 43
    • 70349263972 scopus 로고    scopus 로고
    • Correlation measures for linkage disequilibrium within and between populations
    • Sved, J. A., 2009 Correlation measures for linkage disequilibrium within and between populations. Genet. Res. 91: 183-192.
    • (2009) Genet. Res. , vol.91 , pp. 183-192
    • Sved, J.A.1
  • 44
    • 0015598170 scopus 로고
    • Correlation and probability methods for one and two loci
    • Sved, J. A., and M. W. Feldman, 1973 Correlation and probability methods for one and two loci. Theor. Popul. Biol. 4: 129-132.
    • (1973) Theor. Popul. Biol. , vol.4 , pp. 129-132
    • Sved, J.A.1    Feldman, M.W.2
  • 45
    • 38849164368 scopus 로고    scopus 로고
    • Apparent mutational hotspots and long distance linkage disequilibrium resulting from a bottleneck
    • Tenaillon, M., F. Austerlitz, and O. Tenaillon, 2008 Apparent mutational hotspots and long distance linkage disequilibrium resulting from a bottleneck. J. Evol. Biol. 21: 541-550.
    • (2008) J. Evol. Biol. , vol.21 , pp. 541-550
    • Tenaillon, M.1    Austerlitz, F.2    Tenaillon, O.3
  • 46
    • 34147165220 scopus 로고    scopus 로고
    • Recent human effective population size estimated from linkage disequilibrium
    • Tenesa, A., P. Navarro, B. Hayes, D. Duffy, G. Clarke et al., 2007 Recent human effective population size estimated from linkage disequilibrium. Genome Res. 17: 520-526.
    • (2007) Genome Res. , vol.17 , pp. 520-526
    • Tenesa, A.1    Navarro, P.2    Hayes, B.3    Duffy, D.4    Clarke, G.5
  • 47
    • 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
  • 48
    • 0016247512 scopus 로고
    • Behavior of pairs of loci in finite monoecious populations
    • Weir, B., and C. Cockerham, 1974 Behavior of pairs of loci in finite monoecious populations. Theor. Popul. Biol. 6: 323-354.
    • (1974) Theor. Popul. Biol. , vol.6 , pp. 323-354
    • Weir, B.1    Cockerham, C.2


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