메뉴 건너뛰기




Volumn 176, Issue 3, 2007, Pages 1741-1757

Estimating the number of ancestral lineages using a maximum-likelihood method based on rejection sampling

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; COMPUTER SIMULATION; CONTROLLED STUDY; DEMOGRAPHY; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC MODEL; HUMAN; MAXIMUM LIKELIHOOD METHOD; MUTATIONAL ANALYSIS; PLESIOMORPHY; POLYMORPHIC LOCUS; POPULATION GENETICS; PRIORITY JOURNAL; SAMPLING;

EID: 34547116476     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.106.066233     Document Type: Article
Times cited : (9)

References (53)
  • 2
    • 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
  • 3
    • 33845603795 scopus 로고
    • A note on sampling from combinations of distributions
    • BIGNAMI, A., and A. DE MATTEIS, 1971 A note on sampling from combinations of distributions. IMA J. Appl. Math. 8: 80-81.
    • (1971) IMA J. Appl. Math , vol.8 , pp. 80-81
    • BIGNAMI, A.1    DE MATTEIS, A.2
  • 4
    • 0002468908 scopus 로고
    • Essai sur l'évolution du nombre des hommes
    • BIRABEN, J.-N., 1979 Essai sur l'évolution du nombre des hommes. Population 1: 13-25.
    • (1979) Population , vol.1 , pp. 13-25
    • BIRABEN, J.-N.1
  • 5
    • 19544368505 scopus 로고    scopus 로고
    • On statistical tests of phylogenetic tree imbalance: The Sackin and other indices revisited
    • BLUM, M. G. B., and O. FRANCXOIS, 2005 On statistical tests of phylogenetic tree imbalance: the Sackin and other indices revisited. Math. Biosci. 195: 141-153.
    • (2005) Math. Biosci , vol.195 , pp. 141-153
    • BLUM, M.G.B.1    FRANCXOIS, O.2
  • 6
    • 0036305733 scopus 로고    scopus 로고
    • MOUSE (Mitochondrial and Other Useful SEquences) a compilation of population genetic markers
    • BURCKHARDT, F., 2002 MOUSE (Mitochondrial and Other Useful SEquences) a compilation of population genetic markers. Bioinformatics 18: 890-891.
    • (2002) Bioinformatics , vol.18 , pp. 890-891
    • BURCKHARDT, F.1
  • 7
    • 0023163377 scopus 로고
    • Mitochondrial DNA and human evolution
    • CANN, R. L., M. STONEKING and A. C. WILSON, 1987 Mitochondrial DNA and human evolution. Nature 325: 31-36.
    • (1987) Nature , vol.325 , pp. 31-36
    • CANN, R.L.1    STONEKING, M.2    WILSON, A.C.3
  • 8
    • 0034657861 scopus 로고    scopus 로고
    • Bootstrap confidence intervals: When, which, what? A practical guide for medical statisticians
    • CARPENTER, J., and J. BITHELL, 2000 Bootstrap confidence intervals: When, which, what? A practical guide for medical statisticians. Stat. Med. 19: 1141-1164.
    • (2000) Stat. Med , vol.19 , pp. 1141-1164
    • CARPENTER, J.1    BITHELL, J.2
  • 10
    • 14044258418 scopus 로고    scopus 로고
    • Modern humans did not admix with Neanderthals during their range expansion into Europe
    • CURRAT, M., and L. EXCOFFIER, 2004 Modern humans did not admix with Neanderthals during their range expansion into Europe. PLoS Biol. 2: 2264-2274.
    • (2004) PLoS Biol , vol.2 , pp. 2264-2274
    • CURRAT, M.1    EXCOFFIER, L.2
  • 12
    • 0027945629 scopus 로고
    • Estimating effective population size or mutation rate using the frequencies of mutations of various classes in a sample of DNA sequences
    • FU, Y.-X., 1994 Estimating effective population size or mutation rate using the frequencies of mutations of various classes in a sample of DNA sequences. Genetics 138: 1375-1386.
    • (1994) Genetics , vol.138 , pp. 1375-1386
    • FU, Y.-X.1
  • 13
    • 0032146015 scopus 로고    scopus 로고
    • Probability of a segregating pattern in a sample of DNA sequences
    • FU, Y.-X., 1998 Probability of a segregating pattern in a sample of DNA sequences. Theor. Popul. Biol. 54: 1-10.
    • (1998) Theor. Popul. Biol , vol.54 , pp. 1-10
    • FU, Y.-X.1
  • 14
    • 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
  • 15
    • 33747457749 scopus 로고    scopus 로고
    • Reconstructing human origins in the genomic era
    • GARRIGAN, D., and M. F. HAMMER, 2006 Reconstructing human origins in the genomic era. Nat. Rev. Genet. 7: 669-680.
    • (2006) Nat. Rev. Genet , vol.7 , pp. 669-680
    • GARRIGAN, D.1    HAMMER, M.F.2
  • 16
    • 33751077282 scopus 로고    scopus 로고
    • Analysis of one million base pairs of Neanderthal DNA
    • GREEN, R. E., J. KRAUSE, S. E. PTAK, A. W. BRIGGS, M. T. RONAN et al., 2006 Analysis of one million base pairs of Neanderthal DNA. Nature 444: 330-336.
    • (2006) Nature , vol.444 , pp. 330-336
    • GREEN, R.E.1    KRAUSE, J.2    PTAK, S.E.3    BRIGGS, A.W.4    RONAN, M.T.5
  • 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
    • 34548452457 scopus 로고
    • Sampling probability distributions in the coalescent
    • GRIFFITHS, R. C., and S. TAVARÉ, 1994a Sampling probability distributions 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
  • 19
    • 0028782096 scopus 로고
    • Sampling theory for neutral alleles in a varying environment
    • GRIFFITHS, R. C., and S. TAVARÉ, 1994b Sampling theory for neutral alleles in a varying environment. 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
    • 0022376704 scopus 로고
    • Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
    • HASEGAWA, M., H. KISHINO and T. YANO, 1985 Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22: 160-174.
    • (1985) J. Mol. Evol , vol.22 , pp. 160-174
    • HASEGAWA, M.1    KISHINO, H.2    YANO, T.3
  • 21
    • 33646890870 scopus 로고    scopus 로고
    • A unique recent origin of the allotetraploid species Arabidopsis suecica: Evidence from nuclear DNA markers
    • JAKOBSSON, M., J. HAGENBLAD, S. TAVARÉ, T. SÄLL, C. HALLDÉN et al., 2006 A unique recent origin of the allotetraploid species Arabidopsis suecica: evidence from nuclear DNA markers. Mol. Biol. Evol. 23: 1217-1231.
    • (2006) Mol. Biol. Evol , vol.23 , pp. 1217-1231
    • JAKOBSSON, M.1    HAGENBLAD, J.2    TAVARÉ, S.3    SÄLL, T.4    HALLDÉN, C.5
  • 22
    • 0031992675 scopus 로고    scopus 로고
    • Mitochondrial mutation rate revisited: Hot spots and polymorphism
    • JAZIN, E., H. SOODYALL, P. JALONEN, E. LINDHOLM, M. STONEKING et al., 1998 Mitochondrial mutation rate revisited: hot spots and polymorphism. Nat. Genet. 18: 109-110.
    • (1998) Nat. Genet , vol.18 , pp. 109-110
    • JAZIN, E.1    SOODYALL, H.2    JALONEN, P.3    LINDHOLM, E.4    STONEKING, M.5
  • 23
    • 0033218629 scopus 로고    scopus 로고
    • No BLUE among phylogenetic estimators
    • JOYCE, P., 1999 No BLUE among phylogenetic estimators. J. Math. Biol. 39: 421-438.
    • (1999) J. Math. Biol , vol.39 , pp. 421-438
    • JOYCE, P.1
  • 24
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • edited by H. N. Munro. Academic Press, New York
    • JUKES, T. H., and C. R. CANTOR, 1969 Evolution of protein molecules, pp. 21-132 in Mammalian Protein Metabolism, edited by H. N. Munro. Academic Press, New York.
    • (1969) Mammalian Protein Metabolism , pp. 21-132
    • JUKES, T.H.1    CANTOR, C.R.2
  • 25
    • 0029912371 scopus 로고    scopus 로고
    • Mitochondrial DNA analysis of Mongolian populations and implications for the origin of New World founders
    • KOLMAN, C. J., N. SAMBUUGHIN and E. BERMINGHAM, 1996 Mitochondrial DNA analysis of Mongolian populations and implications for the origin of New World founders. Genetics 142: 1321-1334.
    • (1996) Genetics , vol.142 , pp. 1321-1334
    • KOLMAN, C.J.1    SAMBUUGHIN, N.2    BERMINGHAM, E.3
  • 26
  • 27
    • 0029027992 scopus 로고
    • Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling
    • KUHNER, M. K., J. YAMATO and J. FELSENSTEIN, 1995 Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling. Genetics 140: 1421-1430.
    • (1995) Genetics , vol.140 , pp. 1421-1430
    • KUHNER, M.K.1    YAMATO, J.2    FELSENSTEIN, J.3
  • 28
    • 0032779612 scopus 로고    scopus 로고
    • Pattern of nucleotide substitution and rate heterogeneity in the hypervariable regions I and II of human mtDNA
    • MEYER, S., G. WEISS and A. VON HAESELER, 1999 Pattern of nucleotide substitution and rate heterogeneity in the hypervariable regions I and II of human mtDNA. Genetics 152: 1103-1110.
    • (1999) Genetics , vol.152 , pp. 1103-1110
    • MEYER, S.1    WEISS, G.2    VON HAESELER, A.3
  • 29
    • 33751073995 scopus 로고    scopus 로고
    • Sequencing and analysis of Neanderthal genomic DNA
    • NOONAN, J. P., G. COOP, S. KUDARAVALLI, D. SMITH, J. KRAUSE et al., 2006 Sequencing and analysis of Neanderthal genomic DNA. Science 314: 1113-1118.
    • (2006) Science , vol.314 , pp. 1113-1118
    • NOONAN, J.P.1    COOP, G.2    KUDARAVALLI, S.3    SMITH, D.4    KRAUSE, J.5
  • 30
    • 0032231870 scopus 로고    scopus 로고
    • On the probability of Neanderthal ancestry
    • NORDBORG, M., 1998 On the probability of Neanderthal ancestry. Am. J. Hum. Genet. 63: 1237-1240.
    • (1998) Am. J. Hum. Genet , vol.63 , pp. 1237-1240
    • NORDBORG, M.1
  • 31
  • 32
    • 0030898192 scopus 로고    scopus 로고
    • A high observed substitution rate in the human mitochondrial DNA control region
    • PARSONS, T. J., D. S. MUNIEC, K. SULLIVAN, N. WOODYATT, R. ALLISTON-GREINER et al., 1997 A high observed substitution rate in the human mitochondrial DNA control region. Nat. Genet. 15: 363-368.
    • (1997) Nat. Genet , vol.15 , pp. 363-368
    • PARSONS, T.J.1    MUNIEC, D.S.2    SULLIVAN, K.3    WOODYATT, N.4    ALLISTON-GREINER, R.5
  • 33
    • 33746585377 scopus 로고    scopus 로고
    • Possible ancestral structure in human populations
    • PLAGNOL, V., and J. D. WALL, 2006 Possible ancestral structure in human populations. PLoS Genet. 2: e105.
    • (2006) PLoS Genet , vol.2
    • PLAGNOL, V.1    WALL, J.D.2
  • 34
    • 0032735986 scopus 로고    scopus 로고
    • Population growth of human Y chromosomes: A study of Y chromosome microsatellites
    • PRITCHARD, J. K., M. T. SEIELSTAD, A. PÉREZ-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    PÉREZ-LEZAUN, A.3    FELDMAN, M.W.4
  • 35
    • 0030928378 scopus 로고    scopus 로고
    • Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
    • RAMBAUT, A., and N. C. GRASSLY, 1997 Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13: 235-238.
    • (1997) Comput. Appl. Biosci , vol.13 , pp. 235-238
    • RAMBAUT, A.1    GRASSLY, N.C.2
  • 36
    • 33745459792 scopus 로고    scopus 로고
    • The mean and variance of the numbers of r-pronged nodes and r-caterpillars in Yule-generated genealogical trees
    • ROSENBERG, N. A., 2006 The mean and variance of the numbers of r-pronged nodes and r-caterpillars in Yule-generated genealogical trees. Ann. Comb. 10: 129-146.
    • (2006) Ann. Comb , vol.10 , pp. 129-146
    • ROSENBERG, N.A.1
  • 37
    • 9144223062 scopus 로고    scopus 로고
    • The peopling of the new world: Perspectives from molecular anthropology
    • SCHURR, T. G., 2004 The peopling of the new world: perspectives from molecular anthropology. Annu. Rev. Anthropol. 33: 551-583.
    • (2004) Annu. Rev. Anthropol , vol.33 , pp. 551-583
    • SCHURR, T.G.1
  • 38
    • 19344377078 scopus 로고    scopus 로고
    • No evidence of Neanderthal mtDNA contribution to early modern humans
    • SERRE, D., A. LANGANEY, M. CHECH, M. TESCHLER-NICOLA, M. PAUNOVIC et al., 2004 No evidence of Neanderthal mtDNA contribution to early modern humans. PLoS Biol. 2: 313-317.
    • (2004) PLoS Biol , vol.2 , pp. 313-317
    • SERRE, D.1    LANGANEY, A.2    CHECH, M.3    TESCHLER-NICOLA, M.4    PAUNOVIC, M.5
  • 39
    • 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
  • 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
    • 0035144108 scopus 로고    scopus 로고
    • Testing multiregionality of modern human origins
    • TAKAHATA, N., S.-H. LEE and Y. SATTA, 2001 Testing multiregionality of modern human origins. Mol. Biol. Evol. 18: 172-183.
    • (2001) Mol. Biol. Evol , vol.18 , pp. 172-183
    • TAKAHATA, N.1    LEE, S.-H.2    SATTA, Y.3
  • 42
    • 0027157960 scopus 로고
    • Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees
    • TAMURA, K., and M. NEI, 1993 Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10: 512-526.
    • (1993) Mol. Biol. Evol , vol.10 , pp. 512-526
    • TAMURA, K.1    NEI, M.2
  • 43
    • 0036262985 scopus 로고    scopus 로고
    • Frequentist estimation of coalescence times from nucleotide sequence data using a tree-based partition
    • TANG, H., D. O. SIEGMUND, P. SHEN, P. J. OEFNER and M. W. FELDMAN, 2002 Frequentist estimation of coalescence times from nucleotide sequence data using a tree-based partition. Genetics 161: 447-459.
    • (2002) Genetics , vol.161 , pp. 447-459
    • TANG, H.1    SIEGMUND, D.O.2    SHEN, P.3    OEFNER, P.J.4    FELDMAN, M.W.5
  • 44
    • 0021514720 scopus 로고
    • Line-of-descent and genealogical processes, andtheir applications in population genetics models
    • TAVARÉ, S., 1984 Line-of-descent and genealogical processes, andtheir applications in population genetics models. Theor. Popul. Biol. 26: 119-164.
    • (1984) Theor. Popul. Biol , vol.26 , pp. 119-164
    • TAVARÉ, S.1
  • 45
    • 34547110169 scopus 로고    scopus 로고
    • TAVARÉ, S., 2004 Ancestral inference in population genetics, pp. 1-188 in Lectures on Probability Theory and Statistics. Ecole d'Eté de Probabilités de Saint-Flour XXXI-2001, 1837, edited by J. Picard. Springer-Verlag, Berlin.
    • TAVARÉ, S., 2004 Ancestral inference in population genetics, pp. 1-188 in Lectures on Probability Theory and Statistics. Ecole d'Eté de Probabilités de Saint-Flour XXXI-2001, Vol. 1837, edited by J. Picard. Springer-Verlag, Berlin.
  • 46
  • 48
    • 0242524432 scopus 로고    scopus 로고
    • Patterns of human genetic diversity: Implications for human evolutionary history and disease
    • TISHKOFF, S. A., and B. C. VERRELLI, 2003 Patterns of human genetic diversity: implications for human evolutionary history and disease. Annu. Rev. Genomics Hum. Genet. 4: 293-340.
    • (2003) Annu. Rev. Genomics Hum. Genet , vol.4 , pp. 293-340
    • TISHKOFF, S.A.1    VERRELLI, B.C.2
  • 49
    • 0026046333 scopus 로고
    • African populations and the evolution of human mitochondrial DNA
    • VIGILANT, L., M. STONEKING, H. HARPENDING, K. HAWKES and A. C. WILSON, 1991 African populations and the evolution of human mitochondrial DNA. Science 253: 1503-1507.
    • (1991) Science , vol.253 , pp. 1503-1507
    • VIGILANT, L.1    STONEKING, M.2    HARPENDING, H.3    HAWKES, K.4    WILSON, A.C.5
  • 50
    • 0016491430 scopus 로고
    • On the number of segregating sites in genetical models without recombination
    • WATTERSON, G. A., 1975 On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7: 256-276.
    • (1975) Theor. Popul. Biol , vol.7 , pp. 256-276
    • WATTERSON, G.A.1
  • 51
    • 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.
    • (1998) Genetics , vol.149 , pp. 1539-1546
    • WEISS, G.1    VON HAESELER, A.2
  • 52
    • 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
  • 53
    • 0031876602 scopus 로고    scopus 로고
    • Correlation between the substitution rate and rate variation among sites in protein evolution
    • ZHANG, J., and X. GU, 1998 Correlation between the substitution rate and rate variation among sites in protein evolution. Genetics 149: 1615-1625.
    • (1998) Genetics , vol.149 , pp. 1615-1625
    • ZHANG, J.1    GU, X.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.