메뉴 건너뛰기




Volumn 174, Issue 2, 2009, Pages

A statistical approach for distinguishing hybridization and incomplete lineage sorting

Author keywords

Coalescence theory; Hybridization; Incomplete lineage sorting; Nonmonophyletic species; Predictive posterior distribution; Ranunculus

Indexed keywords

COALESCENCE; DATA SET; EVOLUTIONARY BIOLOGY; GENETIC ANALYSIS; HERB; HYBRIDIZATION; POPULATION DISTRIBUTION; SIMULATION; STATISTICAL ANALYSIS;

EID: 70149100417     PISSN: 00030147     EISSN: None     Source Type: Journal    
DOI: 10.1086/600082     Document Type: Article
Times cited : (338)

References (62)
  • 1
  • 4
    • 1542752643 scopus 로고    scopus 로고
    • Transfer and origin of adaptations through natural hybridization: Were Anderson and Stebbins right?
    • -. 2004. Transfer and origin of adaptations through natural hybridization: were Anderson and Stebbins right? Plant Cell 16: 562-570.
    • (2004) Plant Cell , vol.16 , pp. 562-570
  • 5
    • 0035043379 scopus 로고    scopus 로고
    • The role of hybridization in evolution
    • Barton, N. H. 2001. The role of hybridization in evolution. Molecular Ecology 10:551-568.
    • (2001) Molecular Ecology , vol.10 , pp. 551-568
    • Barton, N.H.1
  • 6
    • 84879887848 scopus 로고    scopus 로고
    • Thermochronological analysis of the dynamics of the Southern Alps, New Zealand
    • Batt, G. E., J. Braun, B. P. Kohn, and I. McDougall. 2000. Thermochronological analysis of the dynamics of the Southern Alps, New Zealand. Geological Society of America Bulletin 112:250-266. (Pubitemid 32828198)
    • (2000) Bulletin of the Geological Society of America , vol.112 , Issue.2 , pp. 250-266
    • Batt, G.E.1    Braun, J.2    Kohn, B.3    McDougall, I.4
  • 7
    • 32144440085 scopus 로고    scopus 로고
    • Comparison of Bayesian and maximum-likelihood inference of population genetic parameters
    • DOI 10.1093/bioinformatics/bti803
    • Beerli, P. 2006. Comparison of Bayesian and maximum likelihood inference of population genetic parameters. Bioinformatics 22: 341-345. (Pubitemid 43205381)
    • (2006) Bioinformatics , vol.22 , Issue.3 , pp. 341-345
    • Beerli, P.1
  • 8
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini, Y., and Y. Hochberg. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing Journal of the Royal Statistical Society B 57:289-300.
    • (1995) Journal of the Royal Statistical Society B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 11
    • 33646167864 scopus 로고    scopus 로고
    • A simple robust statistical test for detecting the presence of recombination
    • Bruen, T. C., H. Philippe, and D. Bryant. 2006. A simple robust statistical test for detecting the presence of recombination. Genetics 172:2665-2681.
    • (2006) Genetics , vol.172 , pp. 2665-2681
    • Bruen, T.C.1    Philippe, H.2    Bryant, D.3
  • 12
    • 33747338447 scopus 로고    scopus 로고
    • Differentiating between hypotheses of lineage sorting and introgression in New Zealand alpine cicadas (Maoricicada Dugdale)
    • Buckley, T. R., M. Cordeiro, D. C. Marshall, and C. Simon. 2006. Differentiating between hypotheses of lineage sorting and introgression in New Zealand alpine cicadas (Maoricicada Dugdale). Systematic Biology 55:411-425.
    • (2006) Systematic Biology , vol.55 , pp. 411-425
    • Buckley, T.R.1    Cordeiro, M.2    Marshall, D.C.3    Simon, C.4
  • 13
    • 49749142953 scopus 로고    scopus 로고
    • Estimation of hominoid ancestral population sizes under Bayesian coalescent models incorporating mutation rate variation and sequencing errors
    • Burgess, R., and Z. Yang. 2008. Estimation of hominoid ancestral population sizes under Bayesian coalescent models incorporating mutation rate variation and sequencing errors. Molecular Biology and Evolution 25:1979-1994.
    • (2008) Molecular Biology and Evolution , vol.25 , pp. 1979-1994
    • Burgess, R.1    Yang, Z.2
  • 14
    • 33646928341 scopus 로고    scopus 로고
    • Discordance of species trees with their most likely gene trees
    • Degnan, J. H., and N. A. Rosenberg. 2006. Discordance of species trees with their most likely gene trees. PLoS Genetics 2:e68.
    • (2006) PLoS Genetics , vol.2
    • Degnan, J.H.1    Rosenberg, N.A.2
  • 15
    • 0034496840 scopus 로고    scopus 로고
    • Gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies
    • Edwards, S. V., and P. Beerli. 2000. Gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 54:1839-1854.
    • (2000) Evolution , vol.54 , pp. 1839-1854
    • Edwards, S.V.1    Beerli, P.2
  • 19
    • 0842322955 scopus 로고    scopus 로고
    • Species-level paraphyly and polyphyly: Frequency, causes, and consequences, with insights from animal mitochondrial DNA
    • Funk, D. J., and K. E. Omland. 2003. Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annual Review of Ecology, Evolution, and Systematics 34:397-423.
    • (2003) Annual Review of Ecology, Evolution, and Systematics , vol.34 , pp. 397-423
    • Funk, D.J.1    Omland, K.E.2
  • 20
    • 0030390387 scopus 로고    scopus 로고
    • High survival of Darwin's finch hybrids: Effects of beak morphology and diets
    • Grant, B. R., and P. R. Grant. 1996. High survival of Darwin's finch hybrids: effects of beak morphology and diets. Ecology 77:500-509.
    • (1996) Ecology , vol.77 , pp. 500-509
    • Grant, B.R.1    Grant, P.R.2
  • 22
    • 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
    • DOI 10.1534/genetics.103.024182
    • 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. (Pubitemid 38931862)
    • (2004) Genetics , vol.167 , Issue.2 , pp. 747-760
    • Hey, J.1    Nielsen, R.2
  • 25
    • 0020744702 scopus 로고
    • Properties of a neutral allele model with intragenic recombination
    • Hudson, R. R. 1983. Properties of a neutral allele model with intragenic recombination. Theoretical Population Biology 23:182-201.
    • (1983) Theoretical Population Biology , vol.23 , pp. 182-201
    • Hudson, R.R.1
  • 27
    • 33845886105 scopus 로고    scopus 로고
    • Inferring phylogenetic networks by the maximum parsimony criterion: A case study
    • DOI 10.1093/molbev/msl163
    • Jin, G., L. Nakhleh, S. Snir, and T. Tuller. 2006. Inferring phylogenetic networks by the maximum parsimony criterion: a case study. Molecular Biology and Evolution 24:324-337. (Pubitemid 46026305)
    • (2007) Molecular Biology and Evolution , vol.24 , Issue.1 , pp. 324-337
    • Jin, G.1    Nakhleh, L.2    Snir, S.3    Tuller, T.4
  • 28
    • 34447297637 scopus 로고    scopus 로고
    • Incorporating allelic variation for reconstructing the evolutionary history of organisms from multiple genes: An example from Rosa in North
    • Joly, S., and A. Bruneau. 2006. Incorporating allelic variation for reconstructing the evolutionary history of organisms from multiple genes: an example from Rosa in North America. Systematic Biology 55:623-636.
    • (2006) America Systematic Biology , vol.55 , pp. 623-636
    • Joly, S.1    Bruneau, A.2
  • 29
    • 33644749147 scopus 로고    scopus 로고
    • Polyploid and hybrid evolution in roses east of the Rocky Mountains
    • Joly, S., J. R. Starr, W. H. Lewis, and A. Bruneau. 2006. Polyploid and hybrid evolution in roses east of the Rocky Mountains. American Journal of Botany 93:412-425. (Pubitemid 43346721)
    • (2006) American Journal of Botany , vol.93 , Issue.3 , pp. 412-425
    • Joly, S.1    Starr, J.R.2    Lewis, W.H.3    Bruneau, A.4
  • 30
    • 0000732090 scopus 로고
    • H. N. Munro, ed. Mammalian protein metabolism. Academic Press, New York
    • Jukes, T. H., and C. R. Cantor. 1969. Evolution of protein molecules. Pages 21-123 in H. N. Munro, ed. Mammalian protein metabolism. Academic Press, New York.
    • (1969) Evolution of Protein Molecules. , pp. 21-123
    • Jukes, T.H.1    Cantor, C.R.2
  • 32
    • 0002556819 scopus 로고
    • On the genealogy of large populations
    • -. 1982b. On the genealogy of large populations. Journal of Applied Probability 19:27-43.
    • (1982) Journal of Applied Probability , vol.19 , pp. 27-43
  • 33
    • 2442562566 scopus 로고    scopus 로고
    • Phylogeny of Panax using chloroplast trnC-trnD intergenic region and the utility of trnC-trriD in interspecific studies of plants
    • Lee, C., and J. Wen. 2004. Phylogeny of Panax using chloroplast trnC-trnD intergenic region and the utility of trnC-trriD in interspecific studies of plants. Molecular Phylogenetics and Evolution 31:894-903.
    • (2004) Molecular Phylogenetics and Evolution , vol.31 , pp. 894-903
    • Lee, C.1    Wen, J.2
  • 34
    • 0036554652 scopus 로고    scopus 로고
    • Reconstruction of biogeographic and evolutionary networks using reticulograms
    • DOI 10.1080/10635150252899725
    • Legendre, P., and V. Makarenkov. 2002. Reconstruction of biogeographic and evolutionary networks using reticulograms. Systematic Biology 51:199-216. (Pubitemid 35180704)
    • (2002) Systematic Biology , vol.51 , Issue.2 , pp. 199-216
    • Legendre, P.1    Makarenkov, V.2
  • 35
    • 17044416291 scopus 로고    scopus 로고
    • Reconstructing patterns of reticulate evolution in plants
    • Linder, C. R., and L. H. Rieseberg. 2004. Reconstructing patterns of reticulate evolution in plants. American Journal of Botany 91: 1700-1708.
    • (2004) American Journal of Botany , vol.91 , pp. 1700-1708
    • Linder, C.R.1    Rieseberg, L.H.2
  • 36
    • 0034792017 scopus 로고    scopus 로고
    • Phylogeny, radiation, and transoceanic dispersal of New Zealand alpine buttercups: Molecular evidence under split decomposition
    • Lockhart, P. J., P. A. McLenachan, D. Havell, D. Gleny, D. Huson, and U. Jensen. 2001. Phylogeny, radiation, and transoceanic dispersal of New Zealand alpine buttercups: molecular evidence under split decomposition. Annals of the Missouri Botanical Garden 88: 458-477.
    • (2001) Annals of the Missouri Botanical Garden , vol.88 , pp. 458-477
    • Lockhart, P.J.1    McLenachan, P.A.2    Havell, D.3    Gleny, D.4    Huson, D.5    Jensen, U.6
  • 37
    • 0036215045 scopus 로고    scopus 로고
    • Inferring the history of speciation from multilocus DNA sequence data: The case of Drosophila pseudoobscura and close relatives
    • Machado, C. A., R. M. Kliman, J. A. Markert, and J. Hey. 2002. Inferring the history of speciation from multilocus DNA sequence data: the case of Drosophila pseudoobscura and close relatives. Molecular Biology and Evolution 19:472-488.
    • (2002) Molecular Biology and Evolution , vol.19 , pp. 472-488
    • Machado, C.A.1    Kliman, R.M.2    Markert, J.A.3    Hey, J.4
  • 38
    • 0031504952 scopus 로고    scopus 로고
    • Gene trees in species trees
    • Maddison, W. P. 1997. Gene trees in species trees. Systematic Biology 46:523-536.
    • (1997) Systematic Biology , vol.46 , pp. 523-536
    • Maddison, W.P.1
  • 39
    • 33644606488 scopus 로고    scopus 로고
    • Inferring phylogeny despite incomplete lineage sorting
    • Maddison, W. P., and L. L. Knowles. 2006. Inferring phylogeny despite incomplete lineage sorting. Systematic Biology 55:21-30.
    • (2006) Systematic Biology , vol.55 , pp. 21-30
    • Maddison, W.P.1    Knowles, L.L.2
  • 41
    • 0034923452 scopus 로고    scopus 로고
    • The genetics of reproductive isolation and the potential for gene exchange between Drosophila pseudoobscura and D. persimilis via backcross hybrid males
    • Noor, M. A. F., K. L. Grams, L. A. Bertucci, Y. Almendarez, J. Reiland, and K. R. Smith. 2001. The genetics of reproductive isolation and the potential for gene exchange between Drosophila pseudoobscura and D. persimilis via backcross hybrid males. Evolution 55:512521.
    • (2001) Evolution , vol.55 , pp. 512521
    • Noor, M.A.F.1    Grams, K.L.2    Bertucci, L.A.3    Almendarez, Y.4    Reiland, J.5    Smith, K.R.6
  • 42
    • 0023822631 scopus 로고
    • Relationships between gene trees and species trees
    • Pamilo, P., and M. Nei. 1988. Relationships between gene trees and species trees. Molecular Biology and Evolution 5:568-583.
    • (1988) Molecular Biology and Evolution , vol.5 , pp. 568-583
    • Pamilo, P.1    Nei, M.2
  • 43
    • 30744441926 scopus 로고    scopus 로고
    • Phylogenetic relationships and biogeography of Ranunculus and allied genera (Ranunculaceae) in the Mediterranean region and in the European Alpine system
    • Paun, O., C. Lehnebach, J. T. Johansson, P. J. Lockhart, and E. Hörandl. 2005. Phylogenetic relationships and biogeography of Ranunculus and allied genera (Ranunculaceae) in the Mediterranean region and in the European Alpine system. Taxon 54:911-930.
    • (2005) Taxon , vol.54 , pp. 911-930
    • Paun, O.1    Lehnebach, C.2    Johansson, J.T.3    Lockhart, P.J.4    Hörandl, E.5
  • 44
    • 0031773680 scopus 로고    scopus 로고
    • MODELTEST: Testing the model of DNA substitution
    • Posada, D., and K. A. Crandall. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14:817-818. (Pubitemid 28552116)
    • (1998) Bioinformatics , vol.14 , Issue.9 , pp. 817-818
    • Posada, D.1    Crandall, K.A.2
  • 46
    • 0030928378 scopus 로고    scopus 로고
    • Seq-gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
    • Rambaut, A., and N. C. Grassly. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Computer Applications in the Biosciences 13: 235-238. (Pubitemid 27249927)
    • (1997) Computer Applications in the Biosciences , vol.13 , Issue.3 , pp. 235-238
    • Rambaut, A.1    Grassly, N.C.2
  • 47
    • 0041817551 scopus 로고    scopus 로고
    • Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci
    • Rannala, B., and Z. Yang. 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164:1645-1656. (Pubitemid 37102224)
    • (2003) Genetics , vol.164 , Issue.4 , pp. 1645-1656
    • Rannala, B.1    Yang, Z.2
  • 50
    • 0036245438 scopus 로고    scopus 로고
    • Genealogical trees, coalescent theory and the analysis of genetic polymorphisms
    • Rosenberg, N. A., and M. Nordborg. 2002. Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nature Reviews 3:380-390.
    • (2002) Nature Reviews , vol.3 , pp. 380-390
    • Rosenberg, N.A.1    Nordborg, M.2
  • 51
    • 0034350321 scopus 로고    scopus 로고
    • Testing hybridization hypotheses based on incongruent gene trees
    • Sang, T, and Y. Zhong. 2000. Testing hybridization hypotheses based on incongruent gene trees. Systematic Biology 49:422-434.
    • (2000) Systematic Biology , vol.49 , pp. 422-434
    • Sang, T.1    Zhong, Y.2
  • 52
    • 0031406079 scopus 로고    scopus 로고
    • Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae)
    • Sang, T., D. J. Crawford, and T. F. Stuessy. 1997. Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae). American Journal of Botany 84:1120-1136.
    • (1997) American Journal of Botany , vol.84 , pp. 1120-1136
    • Sang, T.1    Crawford, D.J.2    Stuessy, T.F.3
  • 53
    • 1642375725 scopus 로고    scopus 로고
    • Hybridization and adaptive radiation
    • Seehausen, O. 2004. Hybridization and adaptive radiation. Trends in Ecology & Evolution 19:198-207.
    • (2004) Trends in Ecology & Evolution , vol.19 , pp. 198-207
    • Seehausen, O.1
  • 54
    • 0032229478 scopus 로고    scopus 로고
    • The tortoise and the hare: Choosing between noncoding plastome and nuclear Adh sequences for phylogeny reconstruction in a recently diverged plant group
    • Small, R. L., J. A. Ryburn, R. C. Cronn, T. Seelanan, and J. F. Wendel. 1998. The tortoise and the hare: choosing between noncoding plastome and nuclear Adh sequences for phylogeny reconstruction in a recently diverged plant group. American Journal of Botany 85:1301-1315.
    • (1998) American Journal of Botany , vol.85 , pp. 1301-1315
    • Small, R.L.1    Ryburn, J.A.2    Cronn, R.C.3    Seelanan, T.4    Wendel, J.F.5
  • 55
    • 0346091308 scopus 로고    scopus 로고
    • Use of nuclear genes for phylogeny reconstruction in plants
    • DOI 10.1071/SB03015
    • Small, R. L., R. Cronn, and J. F. Wendel. 2004. Use of nuclear genes for phylogeny reconstruction in plants. Australian Systematic Botany 17:145-170. (Pubitemid 38600714)
    • (2004) Australian Systematic Botany , vol.17 , Issue.2 , pp. 145-170
    • Small, R.L.1    Cronn, R.C.2    Wendel, J.F.3
  • 58
    • 0026261665 scopus 로고
    • Universal primers for amplification of three non-coding regions of chloroplast DNA
    • Taberlet, P., L. Gielly, G. Pautou, and J. Bouvet. 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology 17:1105-1109.
    • (1991) Plant Molecular Biology , vol.17 , pp. 1105-1109
    • Taberlet, P.1    Gielly, L.2    Pautou, G.3    Bouvet, J.4
  • 59
    • 0345393289 scopus 로고    scopus 로고
    • Paraphyly of Tarasa (Malvaceae) and diverse origins of the polyploid species
    • Tate, J. A., and B. B. Simpson. 2003. Paraphyly of Tarasa (Malvaceae) and diverse origins of the polyploid species. Systematic Botany 28: 723-737.
    • (2003) Systematic Botany , vol.28 , pp. 723-737
    • Tate, J.A.1    Simpson, B.B.2
  • 60
    • 0003243515 scopus 로고    scopus 로고
    • Gene flow and natural selection in the origin of Drosophila pseudoobscura and close relatives
    • Wang, R. L., J. Wakeley, and J. Hey. 1997. Gene flow and natural selection in the origin of Drosophila pseudoobscura and close relatives. Genetics 147:1091-1106.
    • (1997) Genetics , vol.147 , pp. 1091-1106
    • Wang, R.L.1    Wakeley, J.2    Hey, J.3
  • 61
    • 0023462635 scopus 로고
    • Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs
    • Wolfe, K. H., W.-H. Li, and P. M. Sharp. 1987. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proceedings of the National Academy of Sciences of the USA 84:9054-9058.
    • (1987) Proceedings of the National Academy of Sciences of the USA , vol.84 , pp. 9054-9058
    • Wolfe, K.H.1    Li, W.-H.2    Sharp, P.M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.