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Volumn 31, Issue 9, 2014, Pages 2516-2527

Investigating population history using temporal genetic differentiation

Author keywords

Ancient DNA; FST; Genetic differentiation; Population structure; Time serial sampling

Indexed keywords

ARTICLE; DIPLOIDY; EFFECTIVE POPULATION SIZE; GENE FREQUENCY; GENETIC ALGORITHM; GENETIC DRIFT; GENETIC VARIABILITY; GENOME; HABITAT; HISTORY; HUMAN; MIGRANT; MIGRATION; POPULATION; POPULATION AND POPULATION RELATED PHENOMENA; POPULATION REPLACEMENT; POPULATION STRUCTURE; TIME; ALGORITHM; ANIMAL; BIOLOGY; EPIDEMIOLOGY; GENETIC VARIATION; PHYLOGENY; POPULATION DYNAMICS; PROCEDURES;

EID: 84906766045     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msu192     Document Type: Article
Times cited : (44)

References (78)
  • 1
    • 17444424295 scopus 로고    scopus 로고
    • Serial SimCoal: A population genetics model for data from multiple populations and points in time
    • Anderson CNK, Ramakrishnan U, Chan YL, Hadly EA. 2005. Serial SimCoal: a population genetics model for data from multiple populations and points in time. Bioinformatics 21:1733-1734.
    • (2005) Bioinformatics , vol.21 , pp. 1733-1734
    • Anderson, C.N.K.1    Ramakrishnan, U.2    Chan, Y.L.3    Hadly, E.A.4
  • 2
    • 0034532485 scopus 로고    scopus 로고
    • Monte Carlo evaluation of the likelihood for N(e) from temporally spaced samples
    • Anderson EC, Williamson EG, Thompson EA. 2000. Monte Carlo evaluation of the likelihood for N(e) from temporally spaced samples. Genetics 156:2109-2118.
    • (2000) Genetics , vol.156 , pp. 2109-2118
    • Anderson, E.C.1    Williamson, E.G.2    Thompson, E.A.3
  • 3
    • 0043210659 scopus 로고    scopus 로고
    • Estimation of population growth or decline in genetically monitored populations
    • Beaumont MA. 2003. Estimation of population growth or decline in genetically monitored populations. Genetics 164:1139-1160.
    • (2003) Genetics , vol.164 , pp. 1139-1160
    • Beaumont, M.A.1
  • 4
    • 0036964474 scopus 로고    scopus 로고
    • Approximate Bayesian computation in population genetics
    • Beaumont MA, Zhang WY, Balding DJ. 2002. Approximate Bayesian computation in population genetics. Genetics 162:2025-2035.
    • (2002) Genetics , vol.162 , pp. 2025-2035
    • Beaumont, M.A.1    Zhang, W.Y.2    Balding, D.J.3
  • 5
    • 0036191720 scopus 로고    scopus 로고
    • Likelihoodbased estimation of the effective population size using temporal changes in allele frequencies: A genealogical approach
    • Berthier P, Beaumont MA, Cornuet J-M, Luikart G. 2002. Likelihoodbased estimation of the effective population size using temporal changes in allele frequencies: a genealogical approach. Genetics 160:741-751.
    • (2002) Genetics , vol.160 , pp. 741-751
    • Berthier, P.1    Beaumont, M.A.2    Cornuet, J.-M.3    Luikart, G.4
  • 9
    • 33646483919 scopus 로고    scopus 로고
    • Bayesian estimation of the timing and severity of a population bottleneck from ancient DNA
    • Chan YL, Anderson CNK, Hadly EA. 2006. Bayesian estimation of the timing and severity of a population bottleneck from ancient DNA. PLoS Genet. 2:451-460.
    • (2006) PLoS Genet. , vol.2 , pp. 451-460
    • Chan, Y.L.1    Anderson, C.N.K.2    Hadly, E.A.3
  • 10
    • 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, Sousa VC, Luisi P, Goossens B, Beaumont MA. 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
  • 11
    • 84855947176 scopus 로고    scopus 로고
    • Abc: An R package for approximate Bayesian computation (ABC)
    • Csillery K, Francois O, Blum MGB. 2012. abc: an R package for approximate Bayesian computation (ABC). Methods Ecol Evol. 25: 410-418.
    • (2012) Methods Ecol Evol. , vol.25 , pp. 410-418
    • Csillery, K.1    Francois, O.2    Blum, M.G.B.3
  • 12
    • 84873583931 scopus 로고    scopus 로고
    • Geographic sampling scheme as a determinant of the major axis of genetic variation in principal components analysis
    • DeGiorgio M, Rosenberg NA. 2013. Geographic sampling scheme as a determinant of the major axis of genetic variation in principal components analysis. Mol Biol Evol. 30:480-488.
    • (2013) Mol Biol Evol. , vol.30 , pp. 480-488
    • Degiorgio, M.1    Rosenberg, N.A.2
  • 13
    • 65849346286 scopus 로고    scopus 로고
    • Using classical population genetics tools with heterochroneous data: Time matters!
    • Depaulis F, Orlando L, Hanni C. 2009. Using classical population genetics tools with heterochroneous data: time matters! PLoS One 4: e5541.
    • (2009) PLoS One , vol.4
    • Depaulis, F.1    Orlando, L.2    Hanni, C.3
  • 14
    • 38649110663 scopus 로고    scopus 로고
    • BEAST: Bayesian evolutionary analysis by sampling trees
    • Drummond A, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 7:214.
    • (2007) BMC Evol Biol. , vol.7 , pp. 214
    • Drummond, A.1    Rambaut, A.2
  • 15
    • 17744381574 scopus 로고    scopus 로고
    • Bayesian coalescent inference of past population dynamics from molecular sequences
    • Drummond AJ, Rambaut A, Shapiro B, Pybus OG. 2005. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol. 22:1185-1192.
    • (2005) Mol Biol Evol. , vol.22 , pp. 1185-1192
    • Drummond, A.J.1    Rambaut, A.2    Shapiro, B.3    Pybus, O.G.4
  • 16
    • 79961039058 scopus 로고    scopus 로고
    • Testing for ancient admixture between closely related populations
    • Durand EY, Patterson N, Reich D, Slatkin M. 2011. Testing for ancient admixture between closely related populations. Mol Biol Evol. 28: 2239-2252.
    • (2011) Mol Biol Evol. , vol.28 , pp. 2239-2252
    • Durand, E.Y.1    Patterson, N.2    Reich, D.3    Slatkin, M.4
  • 17
    • 78049415423 scopus 로고    scopus 로고
    • Analysis of population structure: A unifying framework and novel methods based on sparse factor analysis
    • Engelhardt BE, Stephens M. 2010. Analysis of population structure: a unifying framework and novel methods based on sparse factor analysis. PLoS Genet. 6:e1001117.
    • (2010) PLoS Genet. , vol.6
    • Engelhardt, B.E.1    Stephens, M.2
  • 18
    • 79954469204 scopus 로고    scopus 로고
    • Fastsimcoal: A continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios
    • Excoffier L, Foll M. 2011. Fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios. Bioinformatics 27:1332-1334.
    • (2011) Bioinformatics , vol.27 , pp. 1332-1334
    • Excoffier, L.1    Foll, M.2
  • 21
    • 0021688630 scopus 로고
    • DNA sequence from the quagga, an extinct member of the horse family
    • Higuchi R, Bowman B, Freiberg M, Ryder OA, Wilson AC. 1984. DNA sequence from the quagga, an extinct member of the horse family. Nature 312:282-284.
    • (1984) Nature , vol.312 , pp. 282-284
    • Higuchi, R.1    Bowman, B.2    Freiberg, M.3    Ryder, O.A.4    Wilson, A.C.5
  • 22
    • 79954569160 scopus 로고    scopus 로고
    • Skyline-plot methods for estimating demographic history from nucleotide sequences
    • Ho SY, Shapiro B. 2011. Skyline-plot methods for estimating demographic history from nucleotide sequences. Mol Ecol Resour. 11: 423-434.
    • (2011) Mol Ecol Resour. , vol.11 , pp. 423-434
    • Ho, S.Y.1    Shapiro, B.2
  • 24
    • 0036184745 scopus 로고    scopus 로고
    • Generating samples under a Wright-Fisher neutral model of genetic variation
    • Hudson RR. 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
  • 25
    • 70350700909 scopus 로고    scopus 로고
    • COMPASS: A program for generating serial samples under an infinite sites model
    • Jakobsson M. 2009. COMPASS: a program for generating serial samples under an infinite sites model. Bioinformatics 25:2845-2847.
    • (2009) Bioinformatics , vol.25 , pp. 2845-2847
    • Jakobsson, M.1
  • 26
    • 0035614380 scopus 로고    scopus 로고
    • Coalescent theory for seed bank models
    • Kaj I, Krone SM, Lascoux M. 2001. Coalescent theory for seed bank models. J Appl Probab. 38:285-300.
    • (2001) J Appl Probab. , vol.38 , pp. 285-300
    • Kaj, I.1    Krone, S.M.2    Lascoux, M.3
  • 30
    • 0001330047 scopus 로고
    • The genetics of Dacus oleae. V. Changes of esterase polymorphism in a natural population following insecticide control-selection or drift?
    • Krimbas CB, Tsakas S. 1971. The genetics of Dacus oleae. V. Changes of esterase polymorphism in a natural population following insecticide control-selection or drift? Evolution 25:454-460.
    • (1971) Evolution , vol.25 , pp. 454-460
    • Krimbas, C.B.1    Tsakas, S.2
  • 31
    • 79960914105 scopus 로고    scopus 로고
    • Inference of human population history from individual whole-genome sequences
    • Li H, Durbin R. 2011. Inference of human population history from individual whole-genome sequences. Nature 475:493-496.
    • (2011) Nature , vol.475 , pp. 493-496
    • Li, H.1    Durbin, R.2
  • 32
    • 73349108482 scopus 로고    scopus 로고
    • A genealogical interpretation of principal components analysis
    • McVean G. 2009. A genealogical interpretation of principal components analysis. PLoS Genet. 5:e1000686.
    • (2009) PLoS Genet. , vol.5
    • McVean, G.1
  • 35
    • 84865503238 scopus 로고    scopus 로고
    • Statistical guidelines for detecting past population shifts using ancient DNA
    • Mourier T, Ho SY, Gilbert MTP, Willerslev E, Orlando L. 2012. Statistical guidelines for detecting past population shifts using ancient DNA. Mol Biol Evol. 29:2241-2251.
    • (2012) Mol Biol Evol. , vol.29 , pp. 2241-2251
    • Mourier, T.1    Ho, S.Y.2    Gilbert, M.T.P.3    Willerslev, E.4    Orlando, L.5
  • 36
    • 77955730964 scopus 로고    scopus 로고
    • Combining contemporary and ancient DNA in population genetic and phylogeographical studies
    • Navascues M, Depaulis F, Emerson BC. 2010. Combining contemporary and ancient DNA in population genetic and phylogeographical studies. Mol Ecol Resour. 10:760-772.
    • (2010) Mol Ecol Resour. , vol.10 , pp. 760-772
    • Navascues, M.1    Depaulis, F.2    Emerson, B.C.3
  • 37
    • 0006919926 scopus 로고
    • Analysis of gene diversity in subdivided populations
    • Nei M. 1973. Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci U S A. 70:3321-3323.
    • (1973) Proc Natl Acad Sci U S A. , vol.70 , pp. 3321-3323
    • Nei, M.1
  • 38
    • 0034967295 scopus 로고    scopus 로고
    • Distinguishing migration from isolation: A Markov chain Monte Carlo approach
    • Nielsen R, Wakeley J. 2001. Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics 158:885-896.
    • (2001) Genetics , vol.158 , pp. 885-896
    • Nielsen, R.1    Wakeley, J.2
  • 39
    • 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.
    • (1998) Am J Hum Genet. , vol.63 , pp. 1237
    • Nordborg, M.1
  • 40
    • 42649093791 scopus 로고    scopus 로고
    • Interpreting principal component analyses of spatial population genetic variation
    • Novembre J, Stephens M. 2008. Interpreting principal component analyses of spatial population genetic variation. Nat Genet. 40:646-649.
    • (2008) Nat Genet. , vol.40 , pp. 646-649
    • Novembre, J.1    Stephens, M.2
  • 44
    • 0021802416 scopus 로고
    • Molecular cloning of ancient Egyptian mummy DNA
    • Pääbo S. 1985. Molecular cloning of ancient Egyptian mummy DNA. Nature 314:644-645.
    • (1985) Nature , vol.314 , pp. 644-645
    • Pääbo, S.1
  • 47
    • 84869026948 scopus 로고    scopus 로고
    • Inference of population splits and mixtures from genome-wide allele frequency data
    • Pickrell JK, Pritchard JK. 2012. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 8:e1002967.
    • (2012) PLoS Genet. , vol.8
    • Pickrell, J.K.1    Pritchard, J.K.2
  • 48
    • 0032735986 scopus 로고    scopus 로고
    • Population growth of human y chromosomes: A study of y chromosome microsatellites
    • Pritchard JK, Seielstad MT, Perez-Lezaun A, Feldman MW. 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    Perez-Lezaun, A.3    Feldman, M.W.4
  • 52
    • 26944492704 scopus 로고    scopus 로고
    • Detecting past population bottlenecks using temporal genetic data
    • Ramakrishnan U, Hadly EA, Mountain JL. 2005. Detecting past population bottlenecks using temporal genetic data. Mol Ecol. 14: 2915-2922.
    • (2005) Mol Ecol. , vol.14 , pp. 2915-2922
    • Ramakrishnan, U.1    Hadly, E.A.2    Mountain, J.L.3
  • 53
    • 62849103887 scopus 로고    scopus 로고
    • Using phylochronology to reveal cryptic population histories: Review and synthesis of 29 ancient DNA studies
    • Ramakrishnan UMA, Hadly EA. 2009. Using phylochronology to reveal cryptic population histories: review and synthesis of 29 ancient DNA studies. Mol Ecol. 18:1310-1330.
    • (2009) Mol Ecol. , vol.18 , pp. 1310-1330
    • Ramakrishnan, U.M.A.1    Hadly, E.A.2
  • 62
    • 4644240756 scopus 로고    scopus 로고
    • Evidence for gradients of human genetic diversity within and among continents
    • Serre D, Pääbo S. 2004. Evidence for gradients of human genetic diversity within and among continents. Genome Res. 14:1679-1685.
    • (2004) Genome Res. , vol.14 , pp. 1679-1685
    • Serre, D.1    Pääbo, S.2
  • 63
    • 84892911863 scopus 로고    scopus 로고
    • A Paleogenomic perspective on evolution and gene function: New insights from ancient DNA
    • Shapiro B, Hofreiter M. 2014. A Paleogenomic perspective on evolution and gene function: new insights from ancient DNA. Science 343: 1236573.
    • (2014) Science , vol.343 , pp. 1236573
    • Shapiro, B.1    Hofreiter, M.2
  • 64
    • 84879621036 scopus 로고    scopus 로고
    • Estimating variable effective population sizes from multiple genomes: A sequentially Markov conditional sampling distribution approach
    • Sheehan S, Harris K, Song YS. 2013. Estimating variable effective population sizes from multiple genomes: a sequentially Markov conditional sampling distribution approach. Genetics 194:647-662.
    • (2013) Genetics , vol.194 , pp. 647-662
    • Sheehan, S.1    Harris, K.2    Song, Y.S.3
  • 65
    • 84899580461 scopus 로고    scopus 로고
    • Assessing the maximum contribution from ancient populations
    • Sjödin P, Skoglund P, Jakobsson M. 2014. Assessing the maximum contribution from ancient populations. Mol Biol Evol. 31:1248-1260.
    • (2014) Mol Biol Evol. , vol.31 , pp. 1248-1260
    • Sjödin, P.1    Skoglund, P.2    Jakobsson, M.3
  • 66
    • 79952846662 scopus 로고    scopus 로고
    • Estimation of population divergence times from non-overlapping genomic sequences: Examples from dogs and wolves
    • Skoglund P, Götherström A, Jakobsson M. 2011. Estimation of population divergence times from non-overlapping genomic sequences: examples from dogs and wolves. Mol Biol Evol. 28:1505-1517.
    • (2011) Mol Biol Evol. , vol.28 , pp. 1505-1517
    • Skoglund, P.1    Götherström, A.2    Jakobsson, M.3
  • 69
    • 0026050476 scopus 로고
    • Inbreeding coefficients and coalescence times
    • Slatkin M. 1991. Inbreeding coefficients and coalescence times. Genet Res. 58:167-175.
    • (1991) Genet Res. , vol.58 , pp. 167-175
    • Slatkin, M.1
  • 70
  • 71
    • 0027498622 scopus 로고
    • Holocene dwarf mammoths from Wrangel Island in the Siberian Arctic
    • Vartanyan SL, Garutt VE, Sher AV. 1993. Holocene dwarf mammoths from Wrangel Island in the Siberian Arctic. Nature 362:337-340.
    • (1993) Nature , vol.362 , pp. 337-340
    • Vartanyan, S.L.1    Garutt, V.E.2    Sher, A.V.3
  • 72
    • 29444451610 scopus 로고    scopus 로고
    • Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes
    • Voight BF, Adams AM, Frisse LA, Qian Y, Hudson RR, Di Rienzo A. 2005. Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes. Proc Natl Acad Sci U S A. 102:18508-18513.
    • (2005) Proc Natl Acad Sci U S A. , vol.102 , pp. 18508-18513
    • Voight, B.F.1    Adams, A.M.2    Frisse, L.A.3    Qian, Y.4    Hudson, R.R.5    Di Rienzo, A.6
  • 73
    • 0035704882 scopus 로고    scopus 로고
    • A pseudo-likelihood method for estimating effective population size from temporally spaced samples
    • Wang J. 2001. A pseudo-likelihood method for estimating effective population size from temporally spaced samples. Genet Res. 78:243-258.
    • (2001) Genet Res. , vol.78 , pp. 243-258
    • Wang, J.1
  • 74
    • 0001162795 scopus 로고
    • Temporal variation in allele frequencies: Testing the right hypothesis
    • Waples RS. 1989. Temporal variation in allele frequencies: testing the right hypothesis. Evolution 43:1236-1251.
    • (1989) Evolution , vol.43 , pp. 1236-1251
    • Waples, R.S.1
  • 75
    • 0003752712 scopus 로고    scopus 로고
    • Sunderland (MA): Sinauer Associates, Inc.
    • Weir BS. 1996. Genetic data analysis II. Sunderland (MA): Sinauer Associates, Inc.
    • (1996) Genetic Data Analysis II
    • Weir, B.S.1
  • 76
    • 0000439372 scopus 로고
    • Breeding structure of populations in relation to speciation
    • Wright S. 1940. Breeding structure of populations in relation to speciation. Am Nat. 74:232-248.
    • (1940) Am Nat. , vol.74 , pp. 232-248
    • Wright, S.1
  • 77
    • 0000948495 scopus 로고
    • Population structure in evolution
    • Wright S. 1949. Population structure in evolution. Proc Am Philos Soc. 93:471-478.
    • (1949) Proc Am Philos Soc. , vol.93 , pp. 471-478
    • Wright, S.1
  • 78
    • 84890417804 scopus 로고
    • The genetical structure of populations
    • Wright S. 1951. The genetical structure of populations. Ann Eugen. 15: 323-354.
    • (1951) Ann Eugen. , vol.15 , pp. 323-354
    • Wright, S.1


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