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Volumn 141, Issue 1-3, 2013, Pages 119-131

Tests of two methods for identifying founder effects in metapopulations reveal substantial type II error

Author keywords

Bottleneck; Decomposed pairwise regression; Equilibrium nonequilibrium; Extinction colonization; Historical demography; Metapopulation

Indexed keywords


EID: 84875656870     PISSN: 00166707     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10709-013-9711-z     Document Type: Article
Times cited : (10)

References (55)
  • 1
    • 0032713236 scopus 로고    scopus 로고
    • Detecting population expansion and decline using microsatellites
    • Beaumont MA (1999) Detecting population expansion and decline using microsatellites. Genetics 153: 2013-2029.
    • (1999) Genetics , vol.153 , pp. 2013-2029
    • Beaumont, M.A.1
  • 2
    • 0030467524 scopus 로고    scopus 로고
    • Evaluating loci for use in the genetic analysis of population structure
    • Beaumont MA, Nichols RA (1996) Evaluating loci for use in the genetic analysis of population structure. Proc R Soc Lond B 263: 1619-1626.
    • (1996) Proc R Soc Lond B , vol.263 , pp. 1619-1626
    • Beaumont, M.A.1    Nichols, R.A.2
  • 3
    • 0032979748 scopus 로고    scopus 로고
    • Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach
    • Beerli P, Felsenstein J (1999) Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics 152: 763-773.
    • (1999) Genetics , vol.152 , pp. 763-773
    • Beerli, P.1    Felsenstein, J.2
  • 4
    • 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, Felsenstein J (2001) Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proc Natl Acad Sci USA 98: 4563-4568.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 4563-4568
    • Beerli, P.1    Felsenstein, J.2
  • 5
    • 77953065916 scopus 로고    scopus 로고
    • 2BAD: an application to estimate the parental contributions during two independent admixture events
    • Bray TC, Parreira B, Bruford MW, Chikhi L (2010) 2BAD: an application to estimate the parental contributions during two independent admixture events. Mol Ecol Resour 3: 538-541.
    • (2010) Mol Ecol Resour , vol.3 , pp. 538-541
    • Bray, T.C.1    Parreira, B.2    Bruford, M.W.3    Chikhi, L.4
  • 6
    • 8744307994 scopus 로고    scopus 로고
    • Multimodal inference: understanding AIC and BIC in model selection
    • Burnham KP, Anderson DR (2004) Multimodal inference: understanding AIC and BIC in model selection. Sociol Methods Res 33: 261-304.
    • (2004) Sociol Methods Res , vol.33 , pp. 261-304
    • Burnham, K.P.1    Anderson, D.R.2
  • 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 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
  • 9
    • 0030478757 scopus 로고    scopus 로고
    • Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data
    • Cornuet JM, Luikart G (1996) Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144: 2001-2014.
    • (1996) Genetics , vol.144 , pp. 2001-2014
    • Cornuet, J.M.1    Luikart, G.2
  • 10
    • 77955493069 scopus 로고    scopus 로고
    • Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0)
    • Cornuet JM, Ravigné V, Estoup A (2010) Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1. 0). BMC Bioinform 11: 401.
    • (2010) BMC Bioinform , vol.11 , pp. 401
    • Cornuet, J.M.1    Ravigné, V.2    Estoup, A.3
  • 11
    • 77952878806 scopus 로고    scopus 로고
    • Detecting bottlenecks using BOTTLENECK 1.2.02 in wild populations: the importance of the microsatellite structure
    • Cristescu R, Sherwin WB, Handasyde K, Cahill V, Cooper DW (2010) Detecting bottlenecks using BOTTLENECK 1. 2. 02 in wild populations: the importance of the microsatellite structure. Conserv Genet 11: 1043-1049.
    • (2010) Conserv Genet , vol.11 , pp. 1043-1049
    • Cristescu, R.1    Sherwin, W.B.2    Handasyde, K.3    Cahill, V.4    Cooper, D.W.5
  • 13
    • 0027453041 scopus 로고    scopus 로고
    • Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection
    • Fu YX (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 133: 693-709.
    • (1997) Genetics , vol.133 , pp. 693-709
    • Fu, Y.X.1
  • 15
    • 0002261251 scopus 로고    scopus 로고
    • The metapopulation approach, its history, conceptual domain, and application to conservation
    • I. Hanski and M. E. Gilpin (Eds.), San Diego: Academic Press
    • Hanski I, Simberloff D (1997) The metapopulation approach, its history, conceptual domain, and application to conservation. In: Hanski I, Gilpin ME (eds) Metapopulation biology. Academic Press, San Diego, pp 5-26.
    • (1997) Metapopulation Biology , pp. 5-26
    • Hanski, I.1    Simberloff, D.2
  • 16
    • 74749093505 scopus 로고    scopus 로고
    • Founder effect and bottleneck signatures in an introduced, insular population of elk
    • Hundertmark KJ, van Daele LJ (2010) Founder effect and bottleneck signatures in an introduced, insular population of elk. Conserv Genet 11: 139-147.
    • (2010) Conserv Genet , vol.11 , pp. 139-147
    • Hundertmark, K.J.1    van Daele, L.J.2
  • 17
    • 0033427602 scopus 로고    scopus 로고
    • Correlation of pairwise genetic and geographic distance measures: inferring the relative influences of gene flow and drift on the distribution of genetic variability
    • Hutchinson DW, Templeton AR (1999) Correlation of pairwise genetic and geographic distance measures: inferring the relative influences of gene flow and drift on the distribution of genetic variability. Evolution 53: 1898-1914.
    • (1999) Evolution , vol.53 , pp. 1898-1914
    • Hutchinson, D.W.1    Templeton, A.R.2
  • 18
    • 0001358930 scopus 로고
    • The stepping stone model of population structure and the decrease of genetic correlations with distance
    • Kimura M, Weiss G (1964) The stepping stone model of population structure and the decrease of genetic correlations with distance. Genetics 49: 561-576.
    • (1964) Genetics , vol.49 , pp. 561-576
    • Kimura, M.1    Weiss, G.2
  • 19
    • 33748614325 scopus 로고    scopus 로고
    • Decomposed pairwise regression analysis of genetic and geographic distances reveals a metapopulation structure of stream-dwelling Dolly Varden char
    • Koizumi I, Yamamoto S, Maekawa K (2006) Decomposed pairwise regression analysis of genetic and geographic distances reveals a metapopulation structure of stream-dwelling Dolly Varden char. Mol Ecol 15: 3175-3189.
    • (2006) Mol Ecol , vol.15 , pp. 3175-3189
    • Koizumi, I.1    Yamamoto, S.2    Maekawa, K.3
  • 20
    • 7244221627 scopus 로고    scopus 로고
    • simcoal version 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history
    • Laval G, Excoffier L (2004) simcoal version 2. 0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history. Bioinformatics 20: 2485-2487.
    • (2004) Bioinformatics , vol.20 , pp. 2485-2487
    • Laval, G.1    Excoffier, L.2
  • 21
    • 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 (2006) Genetics of recent habitat contraction and reduction in population size: does isolation by distance matter? Mol Ecol 15: 3601-3615.
    • (2006) Mol Ecol , vol.15 , pp. 3601-3615
    • Leblois, R.1    Estoup, A.2    Streiff, R.3
  • 22
    • 0000065728 scopus 로고
    • Some demographic and genetic consequences of environmental heterogeneity for biological control
    • Levins R (1969) Some demographic and genetic consequences of environmental heterogeneity for biological control. Bull Entomol Soc Am 15: 237-240.
    • (1969) Bull Entomol Soc Am , vol.15 , pp. 237-240
    • Levins, R.1
  • 23
    • 0037854449 scopus 로고    scopus 로고
    • Genetic diversity and population history of golden monkeys (Rhinopithecus roxellana)
    • Li H, Meng SJ, Men ZM, Fu YX, Zhang YP (2006) Genetic diversity and population history of golden monkeys (Rhinopithecus roxellana). Genetics 164: 269-275.
    • (2006) Genetics , vol.164 , pp. 269-275
    • Li, H.1    Meng, S.J.2    Men, Z.M.3    Fu, Y.X.4    Zhang, Y.P.5
  • 24
    • 0031866781 scopus 로고    scopus 로고
    • Distortion of allele frequency distributions provides a test for recent bottlenecks
    • Luikart G, Allendorf FW, Cornuet JM, Sherwin WB (1998) Distortion of allele frequency distributions provides a test for recent bottlenecks. J Hered 89: 238-247.
    • (1998) J Hered , vol.89 , pp. 238-247
    • Luikart, G.1    Allendorf, F.W.2    Cornuet, J.M.3    Sherwin, W.B.4
  • 25
    • 33646199080 scopus 로고    scopus 로고
    • Population genetic analysis identifies source-sink dynamics for two sympatric garter snake species (Thamnophis elegans and Thamnophis sirtalis)
    • Manier MK, Arnold SJ (2005) Population genetic analysis identifies source-sink dynamics for two sympatric garter snake species (Thamnophis elegans and Thamnophis sirtalis). Mol Ecol 14: 3965-3976.
    • (2005) Mol Ecol , vol.14 , pp. 3965-3976
    • Manier, M.K.1    Arnold, S.J.2
  • 26
    • 1642282195 scopus 로고    scopus 로고
    • The allele frequency spectrum in genome-wide human variation data reveals signals of different demographic history in three large world populations
    • Marth GT, Czabarka E, Murvai J, Sherry ST (2004) The allele frequency spectrum in genome-wide human variation data reveals signals of different 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
  • 27
    • 0022352290 scopus 로고
    • Population bottlenecks and non-equilibrium models in population genetics. II. Number of alleles in a small population that was formed by a recent bottleneck
    • Maruyama T, Fuerst PA (1985) Population bottlenecks and non-equilibrium models in population genetics. II. Number of alleles in a small population that was formed by a recent bottleneck. Genetics 111: 675-689.
    • (1985) Genetics , vol.111 , pp. 675-689
    • Maruyama, T.1    Fuerst, P.A.2
  • 28
    • 0000655270 scopus 로고
    • Genetic distance between populations
    • Nei M (1972) Genetic distance between populations. Am Nat 106: 283-292.
    • (1972) Am Nat , vol.106 , pp. 283-292
    • Nei, M.1
  • 31
    • 0016629918 scopus 로고
    • The bottleneck effect and genetic variability in populations
    • Nei M, Maruyama T, Chakraborty R (1975) The bottleneck effect and genetic variability in populations. Evolution 29: 1-10.
    • (1975) Evolution , vol.29 , pp. 1-10
    • Nei, M.1    Maruyama, T.2    Chakraborty, R.3
  • 32
    • 61649119281 scopus 로고    scopus 로고
    • Statistical inferences in phylogeography
    • Nielsen R, Beaumont MA (2009) Statistical inferences in phylogeography. Mol Ecol 18: 1034-1047.
    • (2009) Mol Ecol , vol.18 , pp. 1034-1047
    • Nielsen, R.1    Beaumont, M.A.2
  • 33
    • 0038650624 scopus 로고    scopus 로고
    • Coalescence in a metapopulation with recurrent local extinction and recolonization
    • Pannell JR (2003) Coalescence in a metapopulation with recurrent local extinction and recolonization. Evolution 57: 949-961.
    • (2003) Evolution , vol.57 , pp. 949-961
    • Pannell, J.R.1
  • 34
    • 0032809938 scopus 로고    scopus 로고
    • Neutral genetic diversity in a metapopulation with recurrent local extinction and recolonization
    • Pannell JR, Charlesworth B (1999) Neutral genetic diversity in a metapopulation with recurrent local extinction and recolonization. Evolution 53: 664-676.
    • (1999) Evolution , vol.53 , pp. 664-676
    • Pannell, J.R.1    Charlesworth, B.2
  • 35
    • 33644871292 scopus 로고    scopus 로고
    • Population genetic software for teaching and research
    • Peakall R, Smouse PE (2006) Population genetic software for teaching and research. Mol Ecol Notes 6: 288-295.
    • (2006) Mol Ecol Notes , vol.6 , pp. 288-295
    • Peakall, R.1    Smouse, P.E.2
  • 36
    • 78149423210 scopus 로고    scopus 로고
    • Distinguishing between population bottleneck and population subdivision by a Bayesian model choice procedure
    • Peter BM, Wegmann D, Excoffier L (2010) Distinguishing between population bottleneck and population subdivision by a Bayesian model choice procedure. Mol Ecol 19: 4648-4660.
    • (2010) Mol Ecol , vol.19 , pp. 4648-4660
    • Peter, B.M.1    Wegmann, D.2    Excoffier, L.3
  • 37
    • 0032880393 scopus 로고    scopus 로고
    • bottleneck: a computer program for detecting recent reductions in the effective population size using allele frequency data
    • Piry S, Luikart G, Cornuet JM (1999) bottleneck: a computer program for detecting recent reductions in the effective population size using allele frequency data. J Hered 90: 502-503.
    • (1999) J Hered , vol.90 , pp. 502-503
    • Piry, S.1    Luikart, G.2    Cornuet, J.M.3
  • 38
    • 79951480123 scopus 로고    scopus 로고
    • R Development Core Team, Vienna: R Foundation for Statistical Computing
    • R Development Core Team (2010) r: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna.
    • (2010) R: A Language and Environment for Statistical Computing
  • 39
    • 0036897674 scopus 로고    scopus 로고
    • Statistical properties of new neutrality tests against population growth
    • Ramos-Onsins SE, Rozas J (2002) Statistical properties of new neutrality tests against population growth. Mol Biol Evol 19: 2092-2100.
    • (2002) Mol Biol Evol , vol.19 , pp. 2092-2100
    • Ramos-Onsins, S.E.1    Rozas, J.2
  • 40
    • 0000262278 scopus 로고
    • genepop version 1.2: population genetics software for exact tests and ecumenicism
    • Raymond M, Rousset F (1995) genepop version 1. 2: population genetics software for exact tests and ecumenicism. J Hered 86: 248-249.
    • (1995) J Hered , vol.86 , pp. 248-249
    • Raymond, M.1    Rousset, F.2
  • 41
    • 0030888985 scopus 로고    scopus 로고
    • Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance
    • Rousset F (1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145: 1219-1228.
    • (1997) Genetics , vol.145 , pp. 1219-1228
    • Rousset, F.1
  • 42
    • 0000392112 scopus 로고
    • Isolation by distance in equilibrium and non-equilibrium populations
    • Slatkin M (1993) Isolation by distance in equilibrium and non-equilibrium populations. Evolution 47: 264-279.
    • (1993) Evolution , vol.47 , pp. 264-279
    • Slatkin, M.1
  • 43
    • 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 (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
  • 45
    • 0024313579 scopus 로고
    • Statistical methods for testing the neutral mutation hypothesis by DNA polymorphism
    • Tajima F (1989) Statistical methods for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
    • (1989) Genetics , vol.123 , pp. 585-595
    • Tajima, F.1
  • 46
    • 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
  • 47
    • 1642277697 scopus 로고    scopus 로고
    • Metapopulation models for historical inference
    • Wakeley J (2004) Metapopulation models for historical inference. Mol Ecol 13: 865-875.
    • (2004) Mol Ecol , vol.13 , pp. 865-875
    • Wakeley, J.1
  • 48
    • 77954978722 scopus 로고    scopus 로고
    • Natural distributions of mitochondrial sequence diversity support new null hypotheses
    • Wares JP (2009) Natural distributions of mitochondrial sequence diversity support new null hypotheses. Evolution 64: 1136-1142.
    • (2009) Evolution , vol.64 , pp. 1136-1142
    • Wares, J.P.1
  • 49
    • 0016491430 scopus 로고
    • On the number of segregating sites in genetical models without recombination
    • Watterson GA (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
  • 50
    • 0000200459 scopus 로고
    • Allele frequencies after a bottleneck
    • Watterson GA (1984) Allele frequencies after a bottleneck. Theor Popul Biol 26: 387-407.
    • (1984) Theor Popul Biol , vol.26 , pp. 387-407
    • Watterson, G.A.1
  • 51
    • 28444493739 scopus 로고    scopus 로고
    • Combining probability from independent tests: the weighted Z-method is superior to Fisher's approach
    • Whitlock MC (2005) Combining probability from independent tests: the weighted Z-method is superior to Fisher's approach. J Evol Biol 18: 1368-1373.
    • (2005) J Evol Biol , vol.18 , pp. 1368-1373
    • Whitlock, M.C.1
  • 52
    • 0025599681 scopus 로고
    • Some population genetic consequences of colony formation and extinction: genetic correlations within founding groups
    • Whitlock MC, McCauley MJ (1990) Some population genetic consequences of colony formation and extinction: genetic correlations within founding groups. Evolution 44: 1717-1724.
    • (1990) Evolution , vol.44 , pp. 1717-1724
    • Whitlock, M.C.1    McCauley, M.J.2
  • 53
    • 0003822814 scopus 로고
    • Actualites scientifiques et industrielles 802. Exposes de biometrie et de la statistique biologique XIII. Hermann et Cie, Paris
    • Wright S (1939) Statistical genetics in relation to evolution. Actualites scientifiques et industrielles 802. Exposes de biometrie et de la statistique biologique XIII. Hermann et Cie, Paris.
    • (1939) Statistical genetics in relation to evolution
    • Wright, S.1
  • 54
    • 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
  • 55
    • 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


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