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Volumn 201, Issue 3, 2015, Pages 1157-1169

Inferring bottlenecks from genome-wide samples of short sequence blocks

Author keywords

Demographic inference; Generating function; Maximum likelihood; Population bottleneck; Sus cebifrons

Indexed keywords

ARTICLE; BOTTLENECK POPULATION; DEMOGRAPHY; GENE MUTATION; GENE SEQUENCE; GENEALOGY; GENOME; NONHUMAN; PHILIPPINES; PIG; PRIORITY JOURNAL; SUS CEBIFRONS; ANIMAL; BIOLOGICAL MODEL; ISLAND (GEOLOGICAL); MUTATION; NUCLEOTIDE SEQUENCE; PEDIGREE; POPULATION DYNAMICS;

EID: 84946913278     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.115.179861     Document Type: Article
Times cited : (25)

References (52)
  • 1
    • 77956397064 scopus 로고    scopus 로고
    • A new model for extinction and recolonisation in two dimensions: Quantifying phylogeography
    • Barton, N. H., J. Kelleher, and A. M. Etheridge, 2010 A new model for extinction and recolonisation in two dimensions: quantifying phylogeography. Evolution 64(9): 2701-2715.
    • (2010) Evolution , vol.64 , Issue.9 , pp. 2701-2715
    • Barton, N.H.1    Kelleher, J.2    Etheridge, A.M.3
  • 2
    • 84908206474 scopus 로고    scopus 로고
    • Descartes rule of signs and the identifiability of population demographic models from genomic variation data
    • Bhaskar, A., and Y. S. Song, 2014 Descartes rule of signs and the identifiability of population demographic models from genomic variation data. Ann. Stat. 42(6): 2469-2493.
    • (2014) Ann. Stat , vol.42 , Issue.6 , pp. 2469-2493
    • Bhaskar, A.1    Song, Y.S.2
  • 3
    • 84937029830 scopus 로고    scopus 로고
    • Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations
    • (in press)
    • Bosse, M., H. J. Megens, O. Madsen, R. P. Crooijmans, O. A. Ryder et al., 2015 Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations. Genome Res. (in press).
    • (2015) Genome Res
    • Bosse, M.1    Megens, H.J.2    Madsen, O.3    Crooijmans, R.P.4    Ryder, O.A.5
  • 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(2): 179-195.
    • (2012) Theor. Popul. Biol , vol.81 , Issue.2 , pp. 179-195
    • Chen, H.1
  • 5
    • 78951476873 scopus 로고    scopus 로고
    • The confounding effects of population structure, genetic diversity and the sampling scheme on the detection and quantification of population size changes
    • Chikhi, L., V. C. Sousa, P. Luisi, B. Goossens, and M. A. Beaumont, 2010 The confounding effects of population structure, genetic diversity and the sampling scheme on the detection and quantification of population size changes. Genetics 186: 983-995.
    • (2010) Genetics , vol.186 , pp. 983-995
    • Chikhi, L.1    Sousa, V.C.2    Luisi, P.3    Goossens, B.4    Beaumont, M.A.5
  • 6
    • 84866077853 scopus 로고    scopus 로고
    • Patterns of neutral diversity under general models of selective sweeps
    • Coop, G., and P. L. Ralph, 2012 Patterns of neutral diversity under general models of selective sweeps. Genetics 192: 205-224.
    • (2012) Genetics , vol.192 , pp. 205-224
    • Coop, G.1    Ralph, P.L.2
  • 7
    • 79959435199 scopus 로고    scopus 로고
    • Genome-wide genetic marker discovery and genotyping using next-generation sequencing
    • Davey, J. W., P. A. Hohenlohe, P. D. Etter, J. Q. Boone, J. M. Catchen et al., 2011 Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat. Rev. Genet. 12(7): 499-510.
    • (2011) Nat. Rev. Genet , vol.12 , Issue.7 , pp. 499-510
    • Davey, J.W.1    Hohenlohe, P.A.2    Etter, P.D.3    Boone, J.Q.4    Catchen, J.M.5
  • 8
    • 0004128472 scopus 로고
    • Cambridge University Press, Cambridge, UK
    • Edwards, A. W. F., 1972 Likelihood. Cambridge University Press, Cambridge, UK.
    • (1972) Likelihood
    • Edwards, A.W.F.1
  • 10
    • 0002339122 scopus 로고
    • The number of evolutionary trees
    • Felsenstein, J., 1978 The number of evolutionary trees. Mol. Phylogenet. Evol. 27(1): 27-33.
    • (1978) Mol. Phylogenet. Evol , vol.27 , Issue.1 , pp. 27-33
    • Felsenstein, J.1
  • 12
    • 84884581710 scopus 로고    scopus 로고
    • Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus
    • Frantz, L., J. Schraiber, O. Madsen, H. J. Megens, M. Bosse et al., 2013 Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus. Genome Biol. 14(9): R107.
    • (2013) Genome Biol , vol.14 , Issue.9
    • Frantz, L.1    Schraiber, J.2    Madsen, O.3    Megens, H.J.4    Bosse, M.5
  • 13
    • 84928321268 scopus 로고    scopus 로고
    • Testing models of speciation from genome sequences: Divergence and asymmetric admixture in island South-East Asian Sus species during the plio-pleistocene climatic fluctuations
    • Frantz, L. A. F., O. Madsen, H. J. Megens, M. A. M. Groenen, and K. Lohse, 2014 Testing models of speciation from genome sequences: divergence and asymmetric admixture in island South-East Asian Sus species during the plio-pleistocene climatic fluctuations. Mol. Ecol. 23(22): 5566-5574.
    • (2014) Mol. Ecol , vol.23 , Issue.22 , pp. 5566-5574
    • Frantz, L.A.F.1    Madsen, O.2    Megens, H.J.3    Groenen, M.A.M.4    Lohse, K.5
  • 14
    • 0027453041 scopus 로고
    • Statistical tests of neutrality of mutations
    • Fu, Y. X., and W. H. Li, 1993 Statistical tests of neutrality of mutations. Genetics 133: 693-709.
    • (1993) Genetics , vol.133 , pp. 693-709
    • Fu, Y.X.1    Li, W.H.2
  • 15
    • 0034086970 scopus 로고    scopus 로고
    • Detecting bottlenecks and selective sweeps from DNA sequence polymorphism
    • Galtier, N., F. Depaulis, and N. H. Barton, 2000 Detecting bottlenecks and selective sweeps from DNA sequence polymorphism. Genetics 155: 981-987.
    • (2000) Genetics , vol.155 , pp. 981-987
    • Galtier, N.1    Depaulis, F.2    Barton, N.H.3
  • 16
    • 84878716362 scopus 로고    scopus 로고
    • Inferring population size changes with sequence and SNP data: Lessons from human bottlenecks
    • Gattepaille, L. M., M. Jakobsson, and M. G. Blum, 2013 Inferring population size changes with sequence and SNP data: lessons from human bottlenecks. Heredity 110(5): 409-419.
    • (2013) Heredity , vol.110 , Issue.5 , pp. 409-419
    • Gattepaille, L.M.1    Jakobsson, M.2    Blum, M.G.3
  • 17
    • 0001301442 scopus 로고    scopus 로고
    • The age of a mutation in the general coalescent tree
    • Griffiths, R., and S. Tavaré, 1998 The age of a mutation in the general coalescent tree. Stoch. Models 14(1-2): 273-295.
    • (1998) Stoch. Models , vol.14 , Issue.1-2 , pp. 273-295
    • Griffiths, R.1    Tavaré, S.2
  • 18
    • 84869003221 scopus 로고    scopus 로고
    • Analyses of pig genomes provide insight into porcine demography and evolution
    • Groenen, M. A. M., A. L. Archibald, and H. Uenishi, C. K. Tuggle, Y. Takeuchiet al., 2012 Analyses of pig genomes provide insight into porcine demography and evolution. Nature 491(7424): 393-398.
    • (2012) Nature , vol.491 , Issue.7424 , pp. 393-398
    • Groenen, M.A.M.1    Archibald, A.L.2    Uenishi, H.3    Tuggle, C.K.4    Takeuchi, Y.5
  • 19
    • 80053386624 scopus 로고    scopus 로고
    • Bayesian inference of ancient human demography from individual genome sequences
    • Gronau, I., M. Hubisz, B. Gulko, C. Danko, and A. Siepel, 2011 Bayesian inference of ancient human demography from individual genome sequences. Nat. Genet. 43(10): 1031-1035.
    • (2011) Nat. Genet , vol.43 , Issue.10 , pp. 1031-1035
    • Gronau, I.1    Hubisz, M.2    Gulko, B.3    Danko, C.4    Siepel, A.5
  • 20
    • 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(10): e1000695.
    • (2009) PLoS Genet , vol.5 , Issue.10
    • Gutenkunst, R.N.1    Hernandez, R.D.2    Williamson, S.H.3    Bustamante, C.D.4
  • 21
    • 22344444998 scopus 로고    scopus 로고
    • Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations
    • Haddrill, P. R., K. R. Thornton, B. Charlesworth, and P. Andolfatto, 2005 Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations. Genome Res. 15(6): 790-799.
    • (2005) Genome Res , vol.15 , Issue.6 , pp. 790-799
    • Haddrill, P.R.1    Thornton, K.R.2    Charlesworth, B.3    Andolfatto, P.4
  • 22
    • 84879671007 scopus 로고    scopus 로고
    • Inferring demographic history from a spectrum of shared haplotype lengths
    • Harris, K., and R. Nielsen, 2013 Inferring demographic history from a spectrum of shared haplotype lengths. PLoS Genet. 9(6): e1003521.
    • (2013) PLoS Genet , vol.9 , Issue.6
    • Harris, K.1    Nielsen, R.2
  • 23
    • 84891529646 scopus 로고    scopus 로고
    • Likelihood-based inference of population history from low-coverage de novo genome assemblies
    • Hearn, J., G. N. Stone, L. Bunnefeld, J. A. Nicholls, N. H. Barton et al., 2014 Likelihood-based inference of population history from low-coverage de novo genome assemblies. Mol. Ecol. 23(1): 198-211.
    • (2014) Mol. Ecol , vol.23 , Issue.1 , pp. 198-211
    • Hearn, J.1    Stone, G.N.2    Bunnefeld, L.3    Nicholls, J.A.4    Barton, N.H.5
  • 24
    • 3142714474 scopus 로고    scopus 로고
    • Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis
    • Hey, J., and R. Nielsen, 2004 Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167: 747-760.
    • (2004) Genetics , vol.167 , pp. 747-760
    • Hey, J.1    Nielsen, R.2
  • 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
    • 84911437070 scopus 로고    scopus 로고
    • Maximum-likelihood inference of population size contractions from microsatellite data
    • Leblois, R., P. Pudlo, J. Néron, F. Bertaux, C. Reddy Beeravolu et al., 2014 Maximum-likelihood inference of population size contractions from microsatellite data. Mol. Biol. Evol. 31(10): 2805-2823.
    • (2014) Mol. Biol. Evol , vol.31 , Issue.10 , pp. 2805-2823
    • Leblois, R.1    Pudlo, P.2    Néron, J.3    Bertaux, F.4    Reddy Beeravolu, C.5
  • 27
    • 79960914105 scopus 로고    scopus 로고
    • Inference of human population history from individual whole-genome sequences
    • Li, H., and R. Durbin, 2011 Inference of human population history from individual whole-genome sequences. Nature 475(7357): 493-496.
    • (2011) Nature , vol.475 , Issue.7357 , pp. 493-496
    • Li, H.1    Durbin, R.2
  • 28
    • 68549104404 scopus 로고    scopus 로고
    • 1000 Genome Project Data Processing Subgroup et al., 2009 The sequence alignment/map format and samtools
    • Li, H., B. Handsaker, A. Wysoker, and T. Fennell; 1000 Genome Project Data Processing Subgroup et al., 2009 The sequence alignment/map format and samtools. Bioinformatics 25(16): 2078-2079.
    • Bioinformatics , vol.25 , Issue.16 , pp. 2078-2079
    • Li, H.1    Handsaker, B.2    Wysoker, A.3    Fennell, T.4
  • 29
    • 84901303939 scopus 로고    scopus 로고
    • Neanderthal admixture in Eurasia confirmed by maximum-likelihood analysis of three genomes
    • Lohse, K., and L. A. F. Frantz, 2014 Neanderthal admixture in Eurasia confirmed by maximum-likelihood analysis of three genomes. Genetics 196: 1241-1251.
    • (2014) Genetics , vol.196 , pp. 1241-1251
    • Lohse, K.1    Frantz, L.A.F.2
  • 30
    • 81255210687 scopus 로고    scopus 로고
    • A general method for calculating likelihoods under the coalescent process
    • Lohse, K., R. J. Harrison, and N. H. Barton, 2011 A general method for calculating likelihoods under the coalescent process. Genetics 58: 977-987.
    • (2011) Genetics , vol.58 , pp. 977-987
    • Lohse, K.1    Harrison, R.J.2    Barton, N.H.3
  • 32
    • 20044366577 scopus 로고    scopus 로고
    • New phylogenetic perspectives among species of southeast asian wild pig (Sus sp.) based on mtDNA sequences and morphometric data
    • Lucchini, V., E. Meijaard, C. H. Diong, C. P. Groves, and E. Randi, 2005 New phylogenetic perspectives among species of southeast asian wild pig (Sus sp.) based on mtDNA sequences and morphometric data. J. Zool. 266(1): 25-35.
    • (2005) J. Zool , vol.266 , Issue.1 , pp. 25-35
    • Lucchini, V.1    Meijaard, E.2    Diong, C.H.3    Groves, C.P.4    Randi, E.5
  • 33
    • 1642282195 scopus 로고    scopus 로고
    • The allele frequency spectrum in genome-wide human variation data reveals signals of differential 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 differential demographic history in three large world populations. Genetics 166: 351-372.
    • (2004) Genetics , vol.166 , pp. 351-372
    • Marth, G.T.1    Czabarka, E.2    Murvai, J.3    Sherry, S.T.4
  • 36
    • 84899534182 scopus 로고    scopus 로고
    • Killer whale nuclear genome and mtDNA reveal widespread population bottleneck during the last glacial maximum
    • Moura, A. E., C. Janse van Rensburg, M. Pilot, A. Tehrani, and P. B. Best et al., 2014 Killer whale nuclear genome and mtDNA reveal widespread population bottleneck during the last glacial maximum. Mol. Biol. Evol. 31(5): 1121-1131.
    • (2014) Mol. Biol. Evol , vol.31 , Issue.5 , pp. 1121-1131
    • Moura, A.E.1    Janse van Rensburg, C.2    Pilot, M.3    Tehrani, A.4    Best, P.B.5
  • 37
    • 61649119281 scopus 로고    scopus 로고
    • Statistical inferences in phylogeography
    • Nielsen, R., and M. A. Beaumont, 2009 Statistical inferences in phylogeography. Mol. Ecol. 18(6): 1034-1047.
    • (2009) Mol. Ecol , vol.18 , Issue.6 , pp. 1034-1047
    • Nielsen, R.1    Beaumont, M.A.2
  • 38
    • 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(4): 1237-1240.
    • (1998) Am. J. Hum. Genet , vol.63 , Issue.4 , pp. 1237-1240
    • Nordborg, M.1
  • 39
    • 84879835308 scopus 로고    scopus 로고
    • Evolutionary dynamics of copy number variation in pig genomes in the context of adaptation and domestication
    • Paudel, Y., O. Madsen, H. J. Megens, L. Frantz, M. Bosse et al., 2013 Evolutionary dynamics of copy number variation in pig genomes in the context of adaptation and domestication. BMC Genomics 14(1): 449.
    • (2013) BMC Genomics , vol.14 , Issue.1 , pp. 449
    • Paudel, Y.1    Madsen, O.2    Megens, H.J.3    Frantz, L.4    Bosse, M.5
  • 40
    • 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. Genetics 165: 427-436.
    • (2003) Genetics , vol.165 , pp. 427-436
    • Polanski, A.1    Kimmel, M.2
  • 41
    • 0001915002 scopus 로고
    • Information and the accuracy attainable in the estimation of statistical parameters
    • Rao, C. R., 1945 Information and the accuracy attainable in the estimation of statistical parameters. Bull. Calcutta Math. Soc. 37: 81-89.
    • (1945) Bull. Calcutta Math. Soc , vol.37 , pp. 81-89
    • Rao, C.R.1
  • 42
    • 84863561074 scopus 로고    scopus 로고
    • Resequencing data provide no evidence for a human bottleneck in Africa during the penultimate glacial period
    • Sjödin, P. E., A. Sjöstrand, M. Jakobsson, and M. G. Blum, 2012 Resequencing data provide no evidence for a human bottleneck in Africa during the penultimate glacial period. Mol. Biol. Evol. 29(7): 1851-1860.
    • (2012) Mol. Biol. Evol , vol.29 , Issue.7 , pp. 1851-1860
    • Sjödin, P.E.1    Sjöstrand, A.2    Jakobsson, M.3    Blum, M.G.4
  • 43
    • 67849119548 scopus 로고    scopus 로고
    • The impact of sampling schemes on the site frequency spectrum in nonequilibrium subdivided populations
    • Städler, T., B. Haubold, C. Merino, W. Stephan, and P. Pfaffelhuber, 2009 The impact of sampling schemes on the site frequency spectrum in nonequilibrium subdivided populations. Genetics 182: 205-216.
    • (2009) Genetics , vol.182 , pp. 205-216
    • Städler, T.1    Haubold, B.2    Merino, C.3    Stephan, W.4    Pfaffelhuber, P.5
  • 44
    • 0021066244 scopus 로고
    • Evolutionary relationships of DNA sequences in finite populations
    • Tajima, F., 1983 Evolutionary relationships of DNA sequences in finite populations. Genetics 105: 437-460.
    • (1983) Genetics , vol.105 , pp. 437-460
    • Tajima, F.1
  • 45
    • 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
  • 46
    • 84934917155 scopus 로고    scopus 로고
    • Fundamental limits on the accuracy of demographic inference based on the sample frequency spectrum
    • Terhorst, J., and Y. S. Song, 2015 Fundamental limits on the accuracy of demographic inference based on the sample frequency spectrum. Proc. Natl. Acad. Sci. USA 112(25): 7677-7682.
    • (2015) Proc. Natl. Acad. Sci. USA , vol.112 , Issue.25 , pp. 7677-7682
    • Terhorst, J.1    Song, Y.S.2
  • 47
    • 84868704770 scopus 로고    scopus 로고
    • A high density recombination map of the pig reveals a correlation between sex-specific recombination and gc content
    • Tortereau, F., B. Servin, L. Frantz, H. J. Megens, D. Milan et al., 2012 A high density recombination map of the pig reveals a correlation between sex-specific recombination and gc content. BMC Genomics 13(1): 586.
    • (2012) BMC Genomics , vol.13 , Issue.1 , pp. 586
    • Tortereau, F.1    Servin, B.2    Frantz, L.3    Megens, H.J.4    Milan, D.5
  • 48
    • 29444451610 scopus 로고    scopus 로고
    • Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes
    • Voight, B. F., A. M. Adams, L. A. Frisse, Y. Qian, R. R. Hudson et al., 2005 Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes. Proc. Natl. Acad. Sci. USA 102(51): 18508-18513.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , Issue.51 , pp. 18508-18513
    • Voight, B.F.1    Adams, A.M.2    Frisse, L.A.3    Qian, Y.4    Hudson, R.R.5
  • 49
    • 0032047371 scopus 로고    scopus 로고
    • Segregating sites in Wright's island model
    • Wakeley, J., 1998 Segregating sites in Wright's island model. Theor. Popul. Biol. 53(2): 166-174.
    • (1998) Theor. Popul. Biol , vol.53 , Issue.2 , pp. 166-174
    • Wakeley, J.1
  • 50
    • 0032736182 scopus 로고    scopus 로고
    • Nonequilibrium migration in human history
    • Wakeley, J., 1999 Nonequilibrium migration in human history. Genetics 153: 1863-1871.
    • (1999) Genetics , vol.153 , pp. 1863-1871
    • Wakeley, J.1
  • 51
    • 0037277564 scopus 로고    scopus 로고
    • Estimating ancestral population sizes and divergence times
    • Wall, J. D., 2003 Estimating ancestral population sizes and divergence times. Genetics 163: 395-404.
    • (2003) Genetics , vol.163 , pp. 395-404
    • Wall, J.D.1
  • 52
    • 0036961518 scopus 로고    scopus 로고
    • Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci
    • Yang, Z., 2002 Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci. Genetics 162: 1811-1823.
    • (2002) Genetics , vol.162 , pp. 1811-1823
    • Yang, Z.1


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