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Volumn 10, Issue 2, 2014, Pages 273-285

Bayesian clustering analyses for genetic assignment and study of hybridization in oaks: Effects of asymmetric phylogenies and asymmetric sampling schemes

Author keywords

BAPS; Bayesian clustering; Microsatellites; Quercus; Simulation; STRUCTURE

Indexed keywords


EID: 84897024096     PISSN: 16142942     EISSN: 16142950     Source Type: Journal    
DOI: 10.1007/s11295-013-0680-2     Document Type: Article
Times cited : (49)

References (50)
  • 1
    • 1842766313 scopus 로고    scopus 로고
    • Whole-tree silvic identifications and the microsatellite genetic structure of a red oak species complex in an Indiana old-growth forest
    • Aldrich PR, Parker GR, Michler CH, Romero-Severson J (2003) Whole-tree silvic identifications and the microsatellite genetic structure of a red oak species complex in an Indiana old-growth forest. Can J Forest Res 33: 2228-2237.
    • (2003) Can J Forest Res , vol.33 , pp. 2228-2237
    • Aldrich, P.R.1    Parker, G.R.2    Michler, C.H.3    Romero-Severson, J.4
  • 4
    • 84872855883 scopus 로고    scopus 로고
    • Evaluating the ability of Bayesian clustering methods to detect hybridization and introgression using an empirical red wolf data set
    • Bohling JH, Adams JR, Waits LP (2013) Evaluating the ability of Bayesian clustering methods to detect hybridization and introgression using an empirical red wolf data set. Mol Ecol 22: 74-86.
    • (2013) Mol Ecol , vol.22 , pp. 74-86
    • Bohling, J.H.1    Adams, J.R.2    Waits, L.P.3
  • 6
    • 2242491935 scopus 로고    scopus 로고
    • Computational and inferential difficulties with mixture posterior distributions
    • Celeux G, Hurn M, Robert CP (2000) Computational and inferential difficulties with mixture posterior distributions. J Am Stat Assoc 95: 957-970.
    • (2000) J Am Stat Assoc , vol.95 , pp. 957-970
    • Celeux, G.1    Hurn, M.2    Robert, C.P.3
  • 7
    • 33747078134 scopus 로고    scopus 로고
    • Bayesian identification of admixture events using multilocus molecular markers
    • Corander J, Marttinen P (2006) Bayesian identification of admixture events using multilocus molecular markers. Mol Ecol 15: 2833-2843.
    • (2006) Mol Ecol , vol.15 , pp. 2833-2843
    • Corander, J.1    Marttinen, P.2
  • 8
    • 62349132559 scopus 로고    scopus 로고
    • Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations
    • Corander J, Marttinen P, Sirén J, Tang J (2008a) Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations. BMC Bioinforma 9: 539.
    • (2008) BMC Bioinforma , vol.9 , pp. 539
    • Corander, J.1    Marttinen, P.2    Sirén, J.3    Tang, J.4
  • 9
    • 38149124743 scopus 로고    scopus 로고
    • Bayesian spatial modeling of genetic population structure
    • Corander J, Sirén J, Arjas E (2008b) Bayesian spatial modeling of genetic population structure. Compu Stat 23: 111-129.
    • (2008) Compu Stat , vol.23 , pp. 111-129
    • Corander, J.1    Sirén, J.2    Arjas, E.3
  • 10
    • 38649137655 scopus 로고    scopus 로고
    • Evidence for hybridization and introgression within a species-rich oak (Quercus spp.) community
    • Curtu AL, Gailing O, Finkeldey R (2007) Evidence for hybridization and introgression within a species-rich oak (Quercus spp.) community. BMC Evol Biol 7: 218.
    • (2007) BMC Evol Biol , vol.7 , pp. 218
    • Curtu, A.L.1    Gailing, O.2    Finkeldey, R.3
  • 11
    • 83655181420 scopus 로고    scopus 로고
    • Comparison of measures of marker informativeness for ancestry and admixture mapping
    • Ding L, Wiener H, Abebe T et al (2011) Comparison of measures of marker informativeness for ancestry and admixture mapping. BMC Genomics 12: 622.
    • (2011) BMC Genomics , vol.12 , pp. 622
    • Ding, L.1    Wiener, H.2    Abebe, T.3
  • 12
    • 34249763755 scopus 로고
    • Characterization of highly variable (GA/CT) n microsatellites in the bur oak, Quercus macrocarpa
    • Dow B, Ashley M, Howe H (1995) Characterization of highly variable (GA/CT) n microsatellites in the bur oak, Quercus macrocarpa. Theor Appl Genet 91: 137-141.
    • (1995) Theor Appl Genet , vol.91 , pp. 137-141
    • Dow, B.1    Ashley, M.2    Howe, H.3
  • 13
    • 33749862708 scopus 로고    scopus 로고
    • Blind population genetics survey of tropical rainforest trees
    • Duminil J, Caron H, Scotti I, Cazal S-O, Petit RJ (2006) Blind population genetics survey of tropical rainforest trees. Mol Ecol 15: 3505-3513.
    • (2006) Mol Ecol , vol.15 , pp. 3505-3513
    • Duminil, J.1    Caron, H.2    Scotti, I.3    Cazal, S.-O.4    Petit, R.J.5
  • 14
    • 77957901667 scopus 로고    scopus 로고
    • A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study
    • Durand J, Bodénès C, Chancerel E et al (2010) A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study. BMC Genomics 11: 570.
    • (2010) BMC Genomics , vol.11 , pp. 570
    • Durand, J.1    Bodénès, C.2    Chancerel, E.3
  • 15
    • 84882759440 scopus 로고    scopus 로고
    • STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method
    • Earl DA, vonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4: 359-361.
    • (2012) Conserv Genet Resour , vol.4 , pp. 359-361
    • Earl, D.A.1    vonHoldt, B.M.2
  • 16
    • 21244479740 scopus 로고    scopus 로고
    • Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study
    • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14: 2611-2620.
    • (2005) Mol Ecol , vol.14 , pp. 2611-2620
    • Evanno, G.1    Regnaut, S.2    Goudet, J.3
  • 17
    • 0041817568 scopus 로고    scopus 로고
    • Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies
    • Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567-1587.
    • (2003) Genetics , vol.164 , pp. 1567-1587
    • Falush, D.1    Stephens, M.2    Pritchard, J.K.3
  • 18
    • 33748618441 scopus 로고    scopus 로고
    • Genetic structure and assignment tests demonstrate illegal translocation of red deer (Cervus elaphus) into a continuous population
    • Frantz AC, Pourtois JT, Heuertz M, Schley L, Flamand MC, Krier A, Bertouille S, Chaumont F, Burke T (2006) Genetic structure and assignment tests demonstrate illegal translocation of red deer (Cervus elaphus) into a continuous population. Mol Ecol 15: 3191-3203.
    • (2006) Mol Ecol , vol.15 , pp. 3191-3203
    • Frantz, A.C.1    Pourtois, J.T.2    Heuertz, M.3    Schley, L.4    Flamand, M.C.5    Krier, A.6    Bertouille, S.7    Chaumont, F.8    Burke, T.9
  • 19
    • 84875063186 scopus 로고    scopus 로고
    • Molecular and morphological support for a Florida origin of the Cuban oak
    • doi:10.1111/j.1365-2699.2011.02610.x
    • Gugger PF, Cavender-Bares J (2011) Molecular and morphological support for a Florida origin of the Cuban oak. J Biogeogr. doi: 10. 1111/j. 1365-2699. 2011. 02610. x.
    • (2011) J Biogeogr
    • Gugger, P.F.1    Cavender-Bares, J.2
  • 20
    • 79954603803 scopus 로고    scopus 로고
    • Two highly validated multiplexes (12-plex and 8-plex) for species delimitation and parentage analysis in oaks (Quercus spp.)
    • Guichoux E, Lagache L, Wagner S, Léger P, Petit RJ (2011) Two highly validated multiplexes (12-plex and 8-plex) for species delimitation and parentage analysis in oaks (Quercus spp.). Mol Ecol Resour 11: 578-585.
    • (2011) Mol Ecol Resour , vol.11 , pp. 578-585
    • Guichoux, E.1    Lagache, L.2    Wagner, S.3    Léger, P.4    Petit, R.J.5
  • 22
    • 67149119196 scopus 로고    scopus 로고
    • Hyper-recombination, diversity, and antibiotic resistance in Pneumococcus
    • Hanage WP, Fraser C, Tang J, Connor TR, Corander J (2009) Hyper-recombination, diversity, and antibiotic resistance in Pneumococcus. Science 324: 1454-1457.
    • (2009) Science , vol.324 , pp. 1454-1457
    • Hanage, W.P.1    Fraser, C.2    Tang, J.3    Connor, T.R.4    Corander, J.5
  • 23
    • 0032965634 scopus 로고    scopus 로고
    • Perspective: highly variable loci and their interpretation in evolution and conservation
    • Hedrick PW (1999) Perspective: highly variable loci and their interpretation in evolution and conservation. Evolution 53: 313.
    • (1999) Evolution , vol.53 , pp. 313
    • Hedrick, P.W.1
  • 24
    • 7044286389 scopus 로고    scopus 로고
    • Chloroplast DNA variation and postglacial recolonization of common ash (Fraxinus excelsior L.) in Europe
    • Heuertz M, Fineschi S, Anzidei M et al (2004) Chloroplast DNA variation and postglacial recolonization of common ash (Fraxinus excelsior L.) in Europe. Mol Ecol 13: 3437-3452.
    • (2004) Mol Ecol , vol.13 , pp. 3437-3452
    • Heuertz, M.1    Fineschi, S.2    Anzidei, M.3
  • 25
    • 84865488715 scopus 로고    scopus 로고
    • Die Artintegrität unserer heimischen Eichen Quercus robur L., Q. petraea (Matt.) Liebl. und Q. pubescens Willd. aus genetischer Sicht (in German)
    • Höltken A, Buschbom J, Kätzel R (2012) Die Artintegrität unserer heimischen Eichen Quercus robur L., Q. petraea (Matt.) Liebl. und Q. pubescens Willd. aus genetischer Sicht (in German). Allg Forst Jagdztg 183: 100-110.
    • (2012) Allg Forst Jagdztg , vol.183 , pp. 100-110
    • Höltken, A.1    Buschbom, J.2    Kätzel, R.3
  • 26
    • 34547861256 scopus 로고    scopus 로고
    • CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure
    • Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23: 1801-1806.
    • (2007) Bioinformatics , vol.23 , pp. 1801-1806
    • Jakobsson, M.1    Rosenberg, N.A.2
  • 27
    • 79953123367 scopus 로고    scopus 로고
    • The computer program STRUCTURE does not reliably identify the main genetic clusters within species: simulations and implications for human population structure
    • Kalinowski ST (2011) The computer program STRUCTURE does not reliably identify the main genetic clusters within species: simulations and implications for human population structure. Heredity 106: 625-632.
    • (2011) Heredity , vol.106 , pp. 625-632
    • Kalinowski, S.T.1
  • 28
    • 0032458261 scopus 로고    scopus 로고
    • Characterization of (GA) n microsatellite loci from Quercus robur
    • Kampfer S, Lexer C, Glössl J, Steinkellner H (1998) Characterization of (GA) n microsatellite loci from Quercus robur. Hereditas 129: 183-186.
    • (1998) Hereditas , vol.129 , pp. 183-186
    • Kampfer, S.1    Lexer, C.2    Glössl, J.3    Steinkellner, H.4
  • 29
    • 33748571508 scopus 로고    scopus 로고
    • Multilocus analyses of admixture and introgression among hybridizing Heliconius butterflies
    • Kronforst MR, Young LG, Blume LM, Gilbert LE (2006) Multilocus analyses of admixture and introgression among hybridizing Heliconius butterflies. Evolution 60: 1254-1268.
    • (2006) Evolution , vol.60 , pp. 1254-1268
    • Kronforst, M.R.1    Young, L.G.2    Blume, L.M.3    Gilbert, L.E.4
  • 32
    • 16344396105 scopus 로고    scopus 로고
    • Barrier to gene flow between two ecologically divergent Populus species, P. alba (white poplar) and P. tremula (European aspen): the role of ecology and life history in gene introgression
    • Lexer C, Fay MF, Joseph JA, Nica M-S, Heinze B (2005) Barrier to gene flow between two ecologically divergent Populus species, P. alba (white poplar) and P. tremula (European aspen): the role of ecology and life history in gene introgression. Mol Ecol 14: 1045-1057.
    • (2005) Mol Ecol , vol.14 , pp. 1045-1057
    • Lexer, C.1    Fay, M.F.2    Joseph, J.A.3    Nica, M.-S.4    Heinze, B.5
  • 33
    • 0033174343 scopus 로고    scopus 로고
    • Phylogeny, biogeography, and processes of molecular differentiation in Quercus Subgenus Quercus (Fagaceae)
    • Manos PS, Doyle JJ, Nixon KC (1999) Phylogeny, biogeography, and processes of molecular differentiation in Quercus Subgenus Quercus (Fagaceae). Mol Phylogenet Evol 12: 333-349.
    • (1999) Mol Phylogenet Evol , vol.12 , pp. 333-349
    • Manos, P.S.1    Doyle, J.J.2    Nixon, K.C.3
  • 34
    • 47649120138 scopus 로고    scopus 로고
    • Differentiating salmon populations at broad and fine geographical scales with microsatellites and single nucleotide polymorphisms
    • Narum SR, Banks M, Beacham TD et al (2008) Differentiating salmon populations at broad and fine geographical scales with microsatellites and single nucleotide polymorphisms. Mol Ecol 17: 3464-3477.
    • (2008) Mol Ecol , vol.17 , pp. 3464-3477
    • Narum, S.R.1    Banks, M.2    Beacham, T.D.3
  • 35
    • 77950025084 scopus 로고    scopus 로고
    • Detecting interspecific and geographic differentiation patterns in two interfertile oak species (Quercus petraea (Matt.) Liebl. and Q. robur L.) using small sets of microsatellite markers
    • Neophytou C, Aravanopoulos F, Fink S, Dounavi A (2010) Detecting interspecific and geographic differentiation patterns in two interfertile oak species (Quercus petraea (Matt.) Liebl. and Q. robur L.) using small sets of microsatellite markers. For Ecol Manag 259: 2026-2035.
    • (2010) For Ecol Manag , vol.259 , pp. 2026-2035
    • Neophytou, C.1    Aravanopoulos, F.2    Fink, S.3    Dounavi, A.4
  • 36
    • 79957922204 scopus 로고    scopus 로고
    • Interfertile oaks in an island environment: I. High nuclear genetic differentiation and high degree of chloroplast DNA sharing between Q. alnifolia and Q. coccifera in Cyprus. A multipopulation study
    • Neophytou C, Dounavi A, Fink S, Aravanopoulos F (2011) Interfertile oaks in an island environment: I. High nuclear genetic differentiation and high degree of chloroplast DNA sharing between Q. alnifolia and Q. coccifera in Cyprus. A multipopulation study. Eur J For Res 130: 543-555.
    • (2011) Eur J For Res , vol.130 , pp. 543-555
    • Neophytou, C.1    Dounavi, A.2    Fink, S.3    Aravanopoulos, F.4
  • 37
    • 33751320684 scopus 로고    scopus 로고
    • HYBRIDLAB (version 1.0): a program for generating simulated hybrids from population samples
    • Nielsen EE, Bach LA, Kotlicki P (2006) HYBRIDLAB (version 1. 0): a program for generating simulated hybrids from population samples. Mol Ecol Notes 6: 971-973.
    • (2006) Mol Ecol Notes , vol.6 , pp. 971-973
    • Nielsen, E.E.1    Bach, L.A.2    Kotlicki, P.3
  • 38
    • 66249125357 scopus 로고    scopus 로고
    • A genomewide comparison of population structure at STRPs and nearby SNPs in humans
    • Payseur BA, Jing P (2009) A genomewide comparison of population structure at STRPs and nearby SNPs in humans. Mol Biol Evol 26: 1369-1377.
    • (2009) Mol Biol Evol , vol.26 , pp. 1369-1377
    • Payseur, B.A.1    Jing, P.2
  • 39
    • 0034118493 scopus 로고    scopus 로고
    • Inference of population structure using multilocus genotype data
    • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
    • (2000) Genetics , vol.155 , pp. 945-959
    • Pritchard, J.K.1    Stephens, M.2    Donnelly, P.3
  • 40
    • 79952125428 scopus 로고    scopus 로고
    • Species delimitation under the general lineage concept: an empirical example using wild North American hops (Cannabaceae: Humulus lupulus)
    • Reeves PA, Richards CM (2011) Species delimitation under the general lineage concept: an empirical example using wild North American hops (Cannabaceae: Humulus lupulus). Syst Biol 60: 45-59.
    • (2011) Syst Biol , vol.60 , pp. 45-59
    • Reeves, P.A.1    Richards, C.M.2
  • 41
    • 1342331102 scopus 로고    scopus 로고
    • DISTRUCT: a program for the graphical display of population structure
    • Rosenberg NA (2004) DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes 4: 137-138.
    • (2004) Mol Ecol Notes , vol.4 , pp. 137-138
    • Rosenberg, N.A.1
  • 42
    • 28744455932 scopus 로고    scopus 로고
    • Algorithms for selecting informative marker panels for population assignment
    • Rosenberg NA (2005) Algorithms for selecting informative marker panels for population assignment. J Comput Biol 12: 1183-1201.
    • (2005) J Comput Biol , vol.12 , pp. 1183-1201
    • Rosenberg, N.A.1
  • 43
    • 0034759330 scopus 로고    scopus 로고
    • Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds
    • Rosenberg NA, Burke T, Elo K et al (2001) Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds. Genetics 159: 699-713.
    • (2001) Genetics , vol.159 , pp. 699-713
    • Rosenberg, N.A.1    Burke, T.2    Elo, K.3
  • 45
    • 0347362518 scopus 로고    scopus 로고
    • Informativeness of genetic markers for inference of ancestry
    • Rosenberg NA, Li LM, Ward R, Pritchard JK (2003) Informativeness of genetic markers for inference of ancestry. Am J Hum Genet 73: 1402-1422.
    • (2003) Am J Hum Genet , vol.73 , pp. 1402-1422
    • Rosenberg, N.A.1    Li, L.M.2    Ward, R.3    Pritchard, J.K.4
  • 47
    • 0031464387 scopus 로고    scopus 로고
    • Conservation of (GA)n microsatellite loci between Quercus species
    • Steinkellner H, Lexer C, Turetschek E, Glössl J (1997b) Conservation of (GA)n microsatellite loci between Quercus species. Mol Ecol 6: 1189-1194.
    • (1997) Mol Ecol , vol.6 , pp. 1189-1194
    • Steinkellner, H.1    Lexer, C.2    Turetschek, E.3    Glössl, J.4
  • 48
    • 77952307333 scopus 로고    scopus 로고
    • POPTREE2: software for constructing population trees from allele frequency data and computing other population statistics with windows interface
    • Takezaki N, Nei M, Tamura K (2010) POPTREE2: software for constructing population trees from allele frequency data and computing other population statistics with windows interface. Mol Biol Evol 27: 747-752.
    • (2010) Mol Biol Evol , vol.27 , pp. 747-752
    • Takezaki, N.1    Nei, M.2    Tamura, K.3
  • 49
    • 33645076280 scopus 로고    scopus 로고
    • Efficiency of model-based Bayesian methods for detecting hybrid individuals under different hybridization scenarios and with different numbers of loci
    • Vähä J-P, Primmer CR (2006) Efficiency of model-based Bayesian methods for detecting hybrid individuals under different hybridization scenarios and with different numbers of loci. Mol Ecol 15: 63-72.
    • (2006) Mol Ecol , vol.15 , pp. 63-72
    • Vähä, J.-P.1    Primmer, C.R.2
  • 50
    • 0021566877 scopus 로고
    • Estimating F-statistics for the analysis of population structure
    • Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38: 1358-1370.
    • (1984) Evolution , vol.38 , pp. 1358-1370
    • Weir, B.S.1    Cockerham, C.C.2


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