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Volumn 104, Issue , 2015, Pages 46-58

Demographic inference using genetic data from a single individual: Separating population size variation from population structure

Author keywords

Coalescence time; Demographic history; Maximum likelihood estimation; Population size change; Symmetric island model

Indexed keywords

COALESCENCE; DATA SET; DEMOGRAPHIC HISTORY; ECOLOGICAL MODELING; GENETIC ANALYSIS; GENOMICS; PARAMETERIZATION; POLYPLOIDY; POPULATION BOTTLENECK; POPULATION DISTRIBUTION; POPULATION GENETICS; POPULATION SIZE; POPULATION STRUCTURE; RECOMBINATION; RECONSTRUCTION;

EID: 84938719094     PISSN: 00405809     EISSN: 10960325     Source Type: Journal    
DOI: 10.1016/j.tpb.2015.06.003     Document Type: Article
Times cited : (65)

References (44)
  • 1
    • 0016355478 scopus 로고
    • A new look at the statistical model identification
    • Akaike H. A new look at the statistical model identification. IEEE Trans. Automat. Control 1974, 19(6):716-723.
    • (1974) IEEE Trans. Automat. Control , vol.19 , Issue.6 , pp. 716-723
    • Akaike, H.1
  • 2
    • 0032713236 scopus 로고    scopus 로고
    • Detecting population expansion and decline using microsatellites
    • Beaumont M.A. Detecting population expansion and decline using microsatellites. Genetics 1999, 153(4):2013-2029.
    • (1999) Genetics , vol.153 , Issue.4 , pp. 2013-2029
    • Beaumont, M.A.1
  • 3
    • 78149388939 scopus 로고    scopus 로고
    • Approximate Bayesian computation in evolution and ecology
    • Beaumont M.A. Approximate Bayesian computation in evolution and ecology. Annu. Rev. Ecol. Evol. Syst. 2010, 41:379-406.
    • (2010) Annu. Rev. Ecol. Evol. Syst. , vol.41 , pp. 379-406
    • Beaumont, M.A.1
  • 4
    • 0036964474 scopus 로고    scopus 로고
    • Approximate Bayesian computation in population genetics
    • Beaumont M.A., Zhang W., Balding D.J. Approximate Bayesian computation in population genetics. Genetics 2002, 162(4):2025-2035.
    • (2002) Genetics , vol.162 , Issue.4 , pp. 2025-2035
    • Beaumont, M.A.1    Zhang, W.2    Balding, D.J.3
  • 6
    • 34547883224 scopus 로고    scopus 로고
    • Bayesian clustering algorithms ascertaining spatial population structure: a new computer program and a comparison study
    • Chen C., Durand E., Forbes F., François O. Bayesian clustering algorithms ascertaining spatial population structure: a new computer program and a comparison study. Mol. Ecol. Notes 2007, 7(5):747-756.
    • (2007) Mol. Ecol. Notes , vol.7 , Issue.5 , pp. 747-756
    • Chen, C.1    Durand, E.2    Forbes, F.3    François, O.4
  • 7
    • 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 V.C., Luisi P., Goossens B., Beaumont M.A. The confounding effects of population structure, genetic diversity and the sampling scheme on the detection and quantification of population size changes. Genetics 2010, 186(3):983-995.
    • (2010) Genetics , vol.186 , Issue.3 , pp. 983-995
    • Chikhi, L.1    Sousa, V.C.2    Luisi, P.3    Goossens, B.4    Beaumont, M.A.5
  • 8
    • 7244224987 scopus 로고    scopus 로고
    • BAPS 2: enhanced possibilities for the analysis of genetic population structure
    • Corander J., Waldmann P., Marttinen P., Sillanpää M.J. BAPS 2: enhanced possibilities for the analysis of genetic population structure. Bioinformatics 2004, 20(15):2363-2369.
    • (2004) Bioinformatics , vol.20 , Issue.15 , pp. 2363-2369
    • Corander, J.1    Waldmann, P.2    Marttinen, P.3    Sillanpää, M.J.4
  • 10
    • 33746456056 scopus 로고    scopus 로고
    • Comment on "Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens" and "Microcephalin, a gene regulating brain size, continues to evolve adaptively in humans"
    • Currat M., Excoffier L., Maddison W., Otto S.P., Ray N., Whitlock M.C., Yeaman S. Comment on "Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens" and "Microcephalin, a gene regulating brain size, continues to evolve adaptively in humans". Science 2006, 313(5784):172.
    • (2006) Science , vol.313 , Issue.5784 , pp. 172
    • Currat, M.1    Excoffier, L.2    Maddison, W.3    Otto, S.P.4    Ray, N.5    Whitlock, M.C.6    Yeaman, S.7
  • 11
    • 0029559462 scopus 로고
    • Coalescents and genealogical structure under neutrality
    • Donnelly P., Tavaré S. Coalescents and genealogical structure under neutrality. Annu. Rev. Genet. 1995, 29(1):401-421.
    • (1995) Annu. Rev. Genet. , vol.29 , Issue.1 , pp. 401-421
    • Donnelly, P.1    Tavaré, S.2
  • 13
    • 79955937119 scopus 로고    scopus 로고
    • Inferring population decline and expansion from microsatellite data: A simulation-based evaluation of the msvar method
    • Girod C., Vitalis R., Leblois R., Fréville H. Inferring population decline and expansion from microsatellite data: A simulation-based evaluation of the msvar method. Genetics 2011, 188(1):165-179. URL: http://www.genetics.org/content/188/1/165.abstract.
    • (2011) Genetics , vol.188 , Issue.1 , pp. 165-179
    • Girod, C.1    Vitalis, R.2    Leblois, R.3    Fréville, H.4
  • 15
    • 0019827394 scopus 로고
    • The number of heterozygous loci between two randomly chosen completely linked sequences of loci in two subdivided population models
    • Griffiths R. The number of heterozygous loci between two randomly chosen completely linked sequences of loci in two subdivided population models. J. Math. Biol. 1981, 12(2):251-261.
    • (1981) J. Math. Biol. , vol.12 , Issue.2 , pp. 251-261
    • Griffiths, R.1
  • 16
    • 28344432025 scopus 로고    scopus 로고
    • GENELAND: a computer package for landscape genetics
    • Guillot G., Mortier F., Estoup A. GENELAND: a computer package for landscape genetics. Mol. Ecol. Notes 2005, 5(3):712-715.
    • (2005) Mol. Ecol. Notes , vol.5 , Issue.3 , pp. 712-715
    • Guillot, G.1    Mortier, F.2    Estoup, A.3
  • 17
    • 84911926943 scopus 로고    scopus 로고
    • Acceleration of evolutionary spread by long-range dispersal
    • Hallatschek O., Fisher D.S. Acceleration of evolutionary spread by long-range dispersal. Proc. Natl. Acad. Sci. 2014, 111(46):E4911-E4919.
    • (2014) Proc. Natl. Acad. Sci. , vol.111 , Issue.46 , pp. E4911-E4919
    • Hallatschek, O.1    Fisher, D.S.2
  • 18
    • 84877134593 scopus 로고    scopus 로고
    • The confounding effect of population structure on Bayesian skyline plot inferences of demographic history
    • Heller R., Chikhi L., Siegismund H.R. The confounding effect of population structure on Bayesian skyline plot inferences of demographic history. PLoS One 2013, 8(5):e62992.
    • (2013) PLoS One , vol.8 , Issue.5
    • Heller, R.1    Chikhi, L.2    Siegismund, H.R.3
  • 20
    • 0036184745 scopus 로고    scopus 로고
    • Generating samples under a Wright-Fisher neutral model of genetic variation
    • Hudson R.R. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 2002, 18(2):337-338. URL: http://bioinformatics.oxfordjournals.org/content/18/2/337.abstract.
    • (2002) Bioinformatics , vol.18 , Issue.2 , pp. 337-338
    • Hudson, R.R.1
  • 21
    • 0001935493 scopus 로고
    • Gene genealogies and the coalescent process
    • Hudson R.R., et al. Gene genealogies and the coalescent process. Oxf. Surv. Evol. Biol. 1990, 7(1):44.
    • (1990) Oxf. Surv. Evol. Biol. , vol.7 , Issue.1 , pp. 44
    • Hudson, R.R.1
  • 22
    • 23744500479 scopus 로고    scopus 로고
    • SciPy: Open source scientific tools for Python
    • [Online; accessed 18.11.14]
    • Jones, E., Oliphant, T., Peterson, P., et al. 2001. SciPy: Open source scientific tools for Python. [Online; accessed 18.11.14]. http://www.scipy.org/.
    • (2001)
    • Jones, E.1    Oliphant, T.2    Peterson, P.3
  • 23
    • 0001358930 scopus 로고
    • The stepping stone model of population structure and the decrease of genetic correlation with distance
    • Kimura M., Weiss G.H. The stepping stone model of population structure and the decrease of genetic correlation with distance. Genetics 1964, 49(4):561-576.
    • (1964) Genetics , vol.49 , Issue.4 , pp. 561-576
    • Kimura, M.1    Weiss, G.H.2
  • 24
    • 33749828614 scopus 로고    scopus 로고
    • Genetics of recent habitat contraction and reduction in population size: does isolation by distance matter?
    • Leblois R., Estoup A., Streiff R. Genetics of recent habitat contraction and reduction in population size: does isolation by distance matter?. Mol. Ecol. 2006, 15(12):3601-3615.
    • (2006) Mol. Ecol. , vol.15 , Issue.12 , pp. 3601-3615
    • Leblois, R.1    Estoup, A.2    Streiff, R.3
  • 25
    • 33749828614 scopus 로고    scopus 로고
    • Genetics of recent habitat contraction and reduction in population size: does isolation by distance matter?
    • Leblois R., Estoup A., Streiff R. Genetics of recent habitat contraction and reduction in population size: does isolation by distance matter?. Mol. Ecol. 2006, 15(12):3601-3615.
    • (2006) Mol. Ecol. , vol.15 , Issue.12 , pp. 3601-3615
    • Leblois, R.1    Estoup, A.2    Streiff, R.3
  • 26
    • 79960914105 scopus 로고    scopus 로고
    • Inference of human population history from individual whole-genome sequences
    • Li H., Durbin R. Inference of human population history from individual whole-genome sequences. Nature 2011, 475(7357):493-496.
    • (2011) Nature , vol.475 , Issue.7357 , pp. 493-496
    • Li, H.1    Durbin, R.2
  • 28
    • 0027237436 scopus 로고
    • Effective population size, genetic diversity, and coalescence time in subdivided populations
    • Nei M., Takahata N. Effective population size, genetic diversity, and coalescence time in subdivided populations. J. Mol. Evol. 1993, 37(3):240-244.
    • (1993) J. Mol. Evol. , vol.37 , Issue.3 , pp. 240-244
    • Nei, M.1    Takahata, N.2
  • 29
    • 0000238336 scopus 로고
    • A simplex method for function minimization
    • Nelder J.A., Mead R. A simplex method for function minimization. Comput. J. 1965, 7(4):308-313.
    • (1965) Comput. J. , vol.7 , Issue.4 , pp. 308-313
    • Nelder, J.A.1    Mead, R.2
  • 30
    • 61649119281 scopus 로고    scopus 로고
    • Statistical inferences in phylogeography
    • Nielsen R., Beaumont M.A. Statistical inferences in phylogeography. Mol. Ecol. 2009, 18(6):1034-1047.
    • (2009) Mol. Ecol. , vol.18 , Issue.6 , pp. 1034-1047
    • Nielsen, R.1    Beaumont, M.A.2
  • 31
    • 44149100979 scopus 로고    scopus 로고
    • From genetic diversity and structure to conservation: genetic signature of recent population declines in three mouse lemur species (Microcebus spp.)
    • Olivieri G.L., Sousa V., Chikhi L., Radespiel U. From genetic diversity and structure to conservation: genetic signature of recent population declines in three mouse lemur species (Microcebus spp.). Biol. Conserv. 2008, 141(5):1257-1271.
    • (2008) Biol. Conserv. , vol.141 , Issue.5 , pp. 1257-1271
    • Olivieri, G.L.1    Sousa, V.2    Chikhi, L.3    Radespiel, U.4
  • 32
    • 84879016166 scopus 로고    scopus 로고
    • The demographic history of populations experiencing asymmetric gene flow: combining simulated and empirical data
    • Paz-Vinas I., Quéméré E., Chikhi L., Loot G., Blanchet S. The demographic history of populations experiencing asymmetric gene flow: combining simulated and empirical data. Mol. Ecol. 2013, 22(12):3279-3291.
    • (2013) Mol. Ecol. , vol.22 , Issue.12 , pp. 3279-3291
    • Paz-Vinas, I.1    Quéméré, E.2    Chikhi, L.3    Loot, G.4    Blanchet, S.5
  • 33
    • 78149423210 scopus 로고    scopus 로고
    • Distinguishing between population bottleneck and population subdivision by a Bayesian model choice procedure
    • Peter B.M., Wegmann D., Excoffier L. Distinguishing between population bottleneck and population subdivision by a Bayesian model choice procedure. Mol. Ecol. 2010, 19(21):4648-4660.
    • (2010) Mol. Ecol. , vol.19 , Issue.21 , pp. 4648-4660
    • Peter, B.M.1    Wegmann, D.2    Excoffier, L.3
  • 34
    • 0034118493 scopus 로고    scopus 로고
    • Inference of population structure using multilocus genotype data
    • Pritchard J.K., Stephens M., Donnelly P. Inference of population structure using multilocus genotype data. Genetics 2000, 155(2):945-959.
    • (2000) Genetics , vol.155 , Issue.2 , pp. 945-959
    • Pritchard, J.K.1    Stephens, M.2    Donnelly, P.3
  • 35
    • 84864703849 scopus 로고    scopus 로고
    • Genetic data suggest a natural prehuman origin of open habitats in northern Madagascar and question the deforestation narrative in this region
    • Quéméré E., Amelot X., Pierson J., Crouau-Roy B., Chikhi L. Genetic data suggest a natural prehuman origin of open habitats in northern Madagascar and question the deforestation narrative in this region. Proc. Natl. Acad. Sci. 2012, 109(32):13028-13033.
    • (2012) Proc. Natl. Acad. Sci. , vol.109 , Issue.32 , pp. 13028-13033
    • Quéméré, E.1    Amelot, X.2    Pierson, J.3    Crouau-Roy, B.4    Chikhi, L.5
  • 36
    • 0026548159 scopus 로고
    • Population growth makes waves in the distribution of pairwise genetic differences
    • Rogers A.R., Harpending H. Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 1992, 9(3):552-569.
    • (1992) Mol. Biol. Evol. , vol.9 , Issue.3 , pp. 552-569
    • Rogers, A.R.1    Harpending, H.2
  • 38
    • 84905572361 scopus 로고    scopus 로고
    • Inferring human population size and separation history from multiple genome sequences
    • Schiffels S., Durbin R. Inferring human population size and separation history from multiple genome sequences. Nature Genet. 2014.
    • (2014) Nature Genet.
    • Schiffels, S.1    Durbin, R.2
  • 39
    • 84859974526 scopus 로고    scopus 로고
    • Population divergence with or without admixture: selecting models using an ABC approach
    • Sousa V.C., Beaumont M.A., Fernandes P., Coelho M.M., Chikhi L. Population divergence with or without admixture: selecting models using an ABC approach. Heredity 2012, 108(5):521-530. URL: http://dx.doi.org/10.1038/hdy.2011.116.
    • (2012) Heredity , vol.108 , Issue.5 , pp. 521-530
    • Sousa, V.C.1    Beaumont, M.A.2    Fernandes, P.3    Coelho, M.M.4    Chikhi, L.5
  • 40
    • 67849119548 scopus 로고    scopus 로고
    • The impact of sampling schemes on the site frequency spectrum in nonequilibrium subdivided populations
    • Städler T., Haubold B., Merino C., Stephan W., Pfaffelhuber P. The impact of sampling schemes on the site frequency spectrum in nonequilibrium subdivided populations. Genetics 2009, 182(1):205-216.
    • (2009) Genetics , vol.182 , Issue.1 , pp. 205-216
    • Städler, T.1    Haubold, B.2    Merino, C.3    Stephan, W.4    Pfaffelhuber, P.5
  • 43
    • 0032736182 scopus 로고    scopus 로고
    • Nonequilibrium migration in human history
    • Wakeley J. Nonequilibrium migration in human history. Genetics 1999, 153(4):1863-1871.
    • (1999) Genetics , vol.153 , Issue.4 , pp. 1863-1871
    • Wakeley, J.1
  • 44
    • 0001771498 scopus 로고
    • Evolution in Mendelian populations
    • Wright S. Evolution in Mendelian populations. Genetics 1931, 16(2):97.
    • (1931) Genetics , vol.16 , Issue.2 , pp. 97
    • Wright, S.1


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