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Volumn 69, Issue 8, 2015, Pages 2154-2166

Evaluating methods for estimating local effective population size with and without migration

Author keywords

Effective population size; Gene flow; Genetic drift; Population genetics; Population structure

Indexed keywords

DATA SET; DEMOGRAPHIC TRANSITION; EFFECTIVE POPULATION SIZE; ESTIMATION METHOD; GENE FLOW; GENETIC DRIFT; METAPOPULATION; POPULATION MIGRATION; POPULATION STRUCTURE;

EID: 84940461333     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/evo.12713     Document Type: Article
Times cited : (146)

References (45)
  • 1
    • 22144499620 scopus 로고    scopus 로고
    • An efficient Monte Carlo method for estimating Ne from temporally spaced samples using a coalescent-based likelihood
    • Anderson, E. C. 2005. An efficient Monte Carlo method for estimating Ne from temporally spaced samples using a coalescent-based likelihood. Genetics 170:955-967.
    • (2005) Genetics , vol.170 , pp. 955-967
    • Anderson, E.C.1
  • 2
    • 84901493693 scopus 로고    scopus 로고
    • Effects of population characteristics and structure on estimates of effective population size in a house sparrow metapopulation
    • Baalsrud, H. T., B.-E. Saether, I. J. Hagen, A. M. Myhre, T. H. Ringsby, H. Pärn, and H. Jensen. 2014. Effects of population characteristics and structure on estimates of effective population size in a house sparrow metapopulation. Mol. Ecol. 23:2653-2668.
    • (2014) Mol. Ecol. , vol.23 , pp. 2653-2668
    • Baalsrud, H.T.1    Saether, B.-E.2    Hagen, I.J.3    Myhre, A.M.4    Ringsby, T.H.5    Pärn, H.6    Jensen, H.7
  • 3
    • 80054822935 scopus 로고    scopus 로고
    • Effective population size of natural populations of Drosophila buzzatii, with a comparative evaluation of nine methods of estimation
    • Barker, J. S. F. 2011. Effective population size of natural populations of Drosophila buzzatii, with a comparative evaluation of nine methods of estimation. Mol. Ecol. 20:4452-4471.
    • (2011) Mol. Ecol. , vol.20 , pp. 4452-4471
    • Barker, J.S.F.1
  • 4
    • 0043210659 scopus 로고    scopus 로고
    • Estimation of population growth or decline in genetically monitored populations
    • Beaumont, M. A. 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
  • 6
    • 0035836728 scopus 로고    scopus 로고
    • Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach
    • Beerli, P., and J. Felsenstein. 2001. Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proc. Natl. Acad. Sci. 98:4563-4568.
    • (2001) Proc. Natl. Acad. Sci. , vol.98 , pp. 4563-4568
    • Beerli, P.1    Felsenstein, J.2
  • 7
    • 0036191720 scopus 로고    scopus 로고
    • Likelihood-based estimation of the effective population size using temporal changes in allele frequencies: a genealogical approach
    • Berthier, P., M. A. Beaumont, J.-M. Cornuet, and G. Luikart. 2002. Likelihood-based 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
  • 8
    • 0028674867 scopus 로고
    • Developments in the prediction of effective population size
    • Caballero, A. 1994. Developments in the prediction of effective population size. Heredity 73:657-679.
    • (1994) Heredity , vol.73 , pp. 657-679
    • Caballero, A.1
  • 9
    • 84890151430 scopus 로고    scopus 로고
    • NeEstimator v2: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data
    • Do, C., R. S. Waples, D. Peel, G. M. Macbeth, B. J. Tillett, and J. R. Ovenden. 2014. NeEstimator v2: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Mol. Ecol. Res. 14:209-214.
    • (2014) Mol. Ecol. Res. , vol.14 , pp. 209-214
    • Do, C.1    Waples, R.S.2    Peel, D.3    Macbeth, G.M.4    Tillett, B.J.5    Ovenden, J.R.6
  • 11
    • 33749823781 scopus 로고    scopus 로고
    • Nemo: an evolutionary and population genetics programming framework
    • Guillaume, F., and J. Rougemont. 2006. Nemo: an evolutionary and population genetics programming framework. Bioinformatics 22:2556-2557.
    • (2006) Bioinformatics , vol.22 , pp. 2556-2557
    • Guillaume, F.1    Rougemont, J.2
  • 12
    • 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
  • 13
    • 0001099861 scopus 로고
    • A note on effective population size with overlapping generations
    • Hill, W. G. 1979. A note on effective population size with overlapping generations. Genetics 92:317-322.
    • (1979) Genetics , vol.92 , pp. 317-322
    • Hill, W.G.1
  • 14
    • 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
  • 15
    • 0014357408 scopus 로고
    • The effects of inbreeding at loci with heterozygote advantage
    • Hill, W. G., and A. Robertson. 1968. The effects of inbreeding at loci with heterozygote advantage. Genetics 60:615-628.
    • (1968) Genetics , vol.60 , pp. 615-628
    • Hill, W.G.1    Robertson, A.2
  • 16
    • 84892861467 scopus 로고    scopus 로고
    • Testing single-sample estimators of effective population size in genetically structured populations
    • Holleley, C. E., R. A. Nichols, M. R. Whitehead, A. T. Adamack, M. R. Gunn, and W. B. Sherwin. 2013. Testing single-sample estimators of effective population size in genetically structured populations. Cons. Genet. 15:23-35.
    • (2013) Cons. Genet. , vol.15 , pp. 23-35
    • Holleley, C.E.1    Nichols, R.A.2    Whitehead, M.R.3    Adamack, A.T.4    Gunn, M.R.5    Sherwin, W.B.6
  • 17
    • 35549004419 scopus 로고    scopus 로고
    • Unbiased estimator for genetic drift and effective population size
    • Jorde, P. E., and N. Ryman. 2007. Unbiased estimator for genetic drift and effective population size. Genetics 177:927-935.
    • (2007) Genetics , vol.177 , pp. 927-935
    • Jorde, P.E.1    Ryman, N.2
  • 18
    • 33645108873 scopus 로고    scopus 로고
    • LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters
    • Kuhner, M. K. 2006. LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics 22:768-770.
    • (2006) Bioinformatics , vol.22 , pp. 768-770
    • Kuhner, M.K.1
  • 19
    • 84883243555 scopus 로고    scopus 로고
    • Linkage disequilibrium estimation of effective population size with immigrants from divergent populations: a case study on Spanish mackerel (Scomberomorus commerson)
    • Macbeth, G. M., D. Broderick, R. C. Buckworth, and J. R. Ovenden. 2013. Linkage disequilibrium estimation of effective population size with immigrants from divergent populations: a case study on Spanish mackerel (Scomberomorus commerson). Genes Genom. Genet. 3:709-717.
    • (2013) Genes Genom. Genet. , vol.3 , pp. 709-717
    • Macbeth, G.M.1    Broderick, D.2    Buckworth, R.C.3    Ovenden, J.R.4
  • 20
    • 84882448979 scopus 로고    scopus 로고
    • Estimation of effective population size in continuously distributed populations: there goes the neighborhood
    • Neel, M. C., K. McKelvey, N. Ryman, M. W. Lloyd, R. S. Bull, F. W. Allendorf, M. K. Schwartz, and R. S. Waples. 2013. Estimation of effective population size in continuously distributed populations: there goes the neighborhood. Heredity 111:189-199.
    • (2013) Heredity , vol.111 , pp. 189-199
    • Neel, M.C.1    McKelvey, K.2    Ryman, N.3    Lloyd, M.W.4    Bull, R.S.5    Allendorf, F.W.6    Schwartz, M.K.7    Waples, R.S.8
  • 21
    • 0019776310 scopus 로고
    • Genetic drift and estimation of effective population size
    • Nei, M., and F. Tajima. 1981. Genetic drift and estimation of effective population size. Genetics 98:625-640.
    • (1981) Genetics , vol.98 , pp. 625-640
    • Nei, M.1    Tajima, F.2
  • 22
    • 65549150328 scopus 로고    scopus 로고
    • Estimation of effective number of breeders from molecular coancestry of single cohort sample
    • Nomura T. 2008. Estimation of effective number of breeders from molecular coancestry of single cohort sample. Evol. Appl. 1:462-474.
    • (2008) Evol. Appl. , vol.1 , pp. 462-474
    • Nomura, T.1
  • 23
    • 84876585105 scopus 로고    scopus 로고
    • Effective/census population size ratio estimation: a compendium and appraisal
    • Palstra, F. P., and D. J. Fraser. 2012. Effective/census population size ratio estimation: a compendium and appraisal. Ecol. Evol. 2:2357-2365.
    • (2012) Ecol. Evol. , vol.2 , pp. 2357-2365
    • Palstra, F.P.1    Fraser, D.J.2
  • 24
    • 0020960732 scopus 로고
    • A new method for estimating effective population size from allele frequency changes
    • Pollak, E. 1983. A new method for estimating effective population size from allele frequency changes. Genetics 104:531-548.
    • (1983) Genetics , vol.104 , pp. 531-548
    • Pollak, E.1
  • 25
    • 0029744513 scopus 로고    scopus 로고
    • On the potential for estimating the effective number of breeders from heterozygote-excess in progeny
    • Pudovkin, A. I., D. V. Zaykin, and D. Hedgecock. 1996. On the potential for estimating the effective number of breeders from heterozygote-excess in progeny. Genetics 144:383-387.
    • (1996) Genetics , vol.144 , pp. 383-387
    • Pudovkin, A.I.1    Zaykin, D.V.2    Hedgecock, D.3
  • 26
    • 0035166445 scopus 로고    scopus 로고
    • Effective population size and genetic conservation criteria for Bull trout
    • Rieman, B. E. 2001. Effective population size and genetic conservation criteria for Bull trout. N. Am. J. Fish. Manage. 21:756-764.
    • (2001) N. Am. J. Fish. Manage. , vol.21 , pp. 756-764
    • Rieman, B.E.1
  • 27
    • 84890150172 scopus 로고    scopus 로고
    • Samples from subdivided populations yield biased estimates of effective size that overestimate the rate of loss of genetic variation
    • Ryman, N., F. W. Allendorf, P. E. Jorde, L. Laikre, and O Hössjer. 2013. Samples from subdivided populations yield biased estimates of effective size that overestimate the rate of loss of genetic variation. Mol. Ecol. Res. 14:87-99.
    • (2013) Mol. Ecol. Res. , vol.14 , pp. 87-99
    • Ryman, N.1    Allendorf, F.W.2    Jorde, P.E.3    Laikre, L.4    Hössjer, O.5
  • 28
    • 33845599911 scopus 로고    scopus 로고
    • Genetic monitoring as a promising tool for conservation and management
    • Schwartz, M. K., G. Luikart, and R. S. Waples. 2007. Genetic monitoring as a promising tool for conservation and management. Trends Ecol. Evol. 22:25-33.
    • (2007) Trends Ecol. Evol. , vol.22 , pp. 25-33
    • Schwartz, M.K.1    Luikart, G.2    Waples, R.S.3
  • 29
    • 84862516405 scopus 로고    scopus 로고
    • Short-term genetic changes: evaluating effective population size estimates in a comprehensively described brown trout (Salmo trutta) population
    • Serbezov D., P. E. Jorde, L. Bernatchez, E. M. Olsen, and L. A. Vollestad. 2012. Short-term genetic changes: evaluating effective population size estimates in a comprehensively described brown trout (Salmo trutta) population. Genetics 191:579-592.
    • (2012) Genetics , vol.191 , pp. 579-592
    • Serbezov, D.1    Jorde, P.E.2    Bernatchez, L.3    Olsen, E.M.4    Vollestad, L.A.5
  • 30
    • 0000905848 scopus 로고
    • Minimum population sizes for species conservation
    • Shaffer, M. L. 1981. Minimum population sizes for species conservation. BioScience 31:131-134.
    • (1981) BioScience , vol.31 , pp. 131-134
    • Shaffer, M.L.1
  • 31
    • 3142749747 scopus 로고    scopus 로고
    • Comparative evaluation of a new effective population size estimator based on approximate Bayesian computation
    • Tallmon, D. A., G. Luikart, and M. A. Beaumont. 2004. Comparative evaluation of a new effective population size estimator based on approximate Bayesian computation. Genetics 167:977-988.
    • (2004) Genetics , vol.167 , pp. 977-988
    • Tallmon, D.A.1    Luikart, G.2    Beaumont, M.A.3
  • 32
    • 38949178372 scopus 로고    scopus 로고
    • ONeSAMP: a program to estimate effective population size using approximate Bayesian computation
    • Tallmon, D. A., A. Koyuk, G. Luikart, and M. A. Beaumont. 2008 ONeSAMP: a program to estimate effective population size using approximate Bayesian computation. Mol. Ecol. Res. 8:299-301.
    • (2008) Mol. Ecol. Res. , vol.8 , pp. 299-301
    • Tallmon, D.A.1    Koyuk, A.2    Luikart, G.3    Beaumont, M.A.4
  • 33
    • 84869076462 scopus 로고    scopus 로고
    • Inferring the history of population size change from genome-wide SNP data
    • Theunert C., K. Tang, M. Lachmann, S. Hu, and M. Stoneking. 2012. Inferring the history of population size change from genome-wide SNP data. Mol. Biol. Evol. 29:3653-3667.
    • (2012) Mol. Biol. Evol. , vol.29 , pp. 3653-3667
    • Theunert, C.1    Tang, K.2    Lachmann, M.3    Hu, S.4    Stoneking, M.5
  • 34
    • 0035108501 scopus 로고    scopus 로고
    • Estimation of effective population size and migration rate from one- and two-locus identity measures
    • Vitalis, R., and D. Couvet. 2001a. Estimation of effective population size and migration rate from one- and two-locus identity measures. Genetics 157:911-925.
    • (2001) Genetics , vol.157 , pp. 911-925
    • Vitalis, R.1    Couvet, D.2
  • 35
    • 0035106387 scopus 로고    scopus 로고
    • Two-locus identity probabilities and identity disequilibrium in a partially selfing subdivided population
    • Vitalis, R. 2001b. Two-locus identity probabilities and identity disequilibrium in a partially selfing subdivided population. Genet. Res. 77:67-81.
    • (2001) Genet. Res. , vol.77 , pp. 67-81
    • Vitalis, R.1
  • 36
    • 0011956582 scopus 로고    scopus 로고
    • Estim 1.0: a computer program to infer population parameters from one- and two-locus gene identity probabilities
    • Vitalis, R. 2001c. Estim 1.0: a computer program to infer population parameters from one- and two-locus gene identity probabilities. Mol. Ecol. Notes 1:354-356.
    • (2001) Mol. Ecol. Notes , vol.1 , pp. 354-356
    • Vitalis, R.1
  • 37
    • 31344454299 scopus 로고    scopus 로고
    • Estimation of effective population sizes from data on genetic markers
    • Wang, J. 2005. Estimation of effective population sizes from data on genetic markers. Philos. Trans. R. Soc. Lond. B Biol. Sci. 360:1395-1409.
    • (2005) Philos. Trans. R. Soc. Lond. B Biol. Sci. , vol.360 , pp. 1395-1409
    • Wang, J.1
  • 38
    • 65549163137 scopus 로고    scopus 로고
    • A new method for estimating effective population sizes from a single sample of multilocus genotypes
    • Wang, J. 2009. A new method for estimating effective population sizes from a single sample of multilocus genotypes. Mol. Ecol. 18:2148-2164.
    • (2009) Mol. Ecol. , vol.18 , pp. 2148-2164
    • Wang, J.1
  • 39
    • 0037280106 scopus 로고    scopus 로고
    • Estimating effective population size and migration rates from genetic samples over space and time
    • Wang, J., and M. C. Whitlock. 2003. Estimating effective population size and migration rates from genetic samples over space and time. Genetics 163:429-446.
    • (2003) Genetics , vol.163 , pp. 429-446
    • Wang, J.1    Whitlock, M.C.2
  • 40
    • 47249162403 scopus 로고    scopus 로고
    • LDNe: a program for estimating effective population size from data on linkage disequilibrium
    • Waples, R. S., and C. Do. 2008. LDNe: a program for estimating effective population size from data on linkage disequilibrium. Mol. Ecol. Res. 8:753-756.
    • (2008) Mol. Ecol. Res. , vol.8 , pp. 753-756
    • Waples, R.S.1    Do, C.2
  • 41
    • 80053967558 scopus 로고    scopus 로고
    • Estimating contemporary effective population size on the basis of linkage disequilibrium in the face of migration
    • Waples, R. S., and P. R. England. 2011. Estimating contemporary effective population size on the basis of linkage disequilibrium in the face of migration. Genetics 189:633-644.
    • (2011) Genetics , vol.189 , pp. 633-644
    • Waples, R.S.1    England, P.R.2
  • 42
    • 65549125297 scopus 로고    scopus 로고
    • Modelling evolutionary processes in small populations: not as ideal as you think
    • Waples, R. S., and J. S. Faulkner. 2009. Modelling evolutionary processes in small populations: not as ideal as you think. Mol. Ecol. 18:1834-1847.
    • (2009) Mol. Ecol. , vol.18 , pp. 1834-1847
    • Waples, R.S.1    Faulkner, J.S.2
  • 43
    • 0026540733 scopus 로고
    • Temporal fluctuations in demographic parameters and the genetic variance among populations
    • Whitlock, M. C. 1992. Temporal fluctuations in demographic parameters and the genetic variance among populations. Evolution 46:608-615.
    • (1992) Evolution , vol.46 , pp. 608-615
    • Whitlock, M.C.1
  • 44
    • 0001024012 scopus 로고
    • Isolation by distance
    • Wright, S. 1943. Isolation by distance. Genetics 28:114-138.
    • (1943) Genetics , vol.28 , pp. 114-138
    • Wright, S.1
  • 45
    • 0001771498 scopus 로고
    • Evolution in Mendelian populations
    • Wright, S. 1931. Evolution in Mendelian populations. Genetics 16:97-159.
    • (1931) Genetics , vol.16 , pp. 97-159
    • Wright, S.1


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