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Volumn 3, Issue 1, 2011, Pages 246-258

Detecting phylogenetic breakpoints and discordance from genome-wide alignments for species tree reconstruction

Author keywords

Bayesian concordance analysis; Horizontal transfer; Incomplete lineage sorting; Minimum description length; Phylogenomics; Recombination

Indexed keywords

ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; BIOLOGY; CHROMOSOME BREAKAGE; COMPUTER SIMULATION; DNA SEQUENCE; GENETIC ASSOCIATION; GENETIC DATABASE; GENETIC RECOMBINATION; HORIZONTAL GENE TRANSFER; HUMAN; METHODOLOGY; MOLECULAR EVOLUTION; PHYLOGENY; SEQUENCE ALIGNMENT;

EID: 79960041437     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evr013     Document Type: Article
Times cited : (27)

References (63)
  • 1
    • 0016355478 scopus 로고
    • A new look at the statistical model identification
    • Akaike H. 1974. A new look at the statistical model identification. IEEE Trans Automat Contr. 19:716-723.
    • (1974) IEEE Trans Automat Contr , vol.19 , pp. 716-723
    • Akaike, H.1
  • 2
    • 17444424295 scopus 로고    scopus 로고
    • Serial SimCoal: A population genetics model for data from multiple populations and points in time
    • DOI 10.1093/bioinformatics/bti154
    • Anderson CNK, Ramakrishnan U, Chan YL, Hadly EA. 2005. Serial SimCoal: a population genetics model for data from multiple populations and points in time. Bioinformatics. 21:1733-1734. (Pubitemid 40542747)
    • (2005) Bioinformatics , vol.21 , Issue.8 , pp. 1733-1734
    • Anderson, C.N.K.1    Ramakrishnan, U.2    Chan, Y.L.3    Hadly, E.A.4
  • 3
    • 79955439952 scopus 로고    scopus 로고
    • Reconstructing concordance trees and testing the coalescent model from genome-wide data sets
    • Knowles LL, Kubatko LS, editors. Hoboken (NJ): Wiley-Blackwell
    • Ané C. 2010. Reconstructing concordance trees and testing the coalescent model from genome-wide data sets. In: Knowles LL, Kubatko LS, editors. Estimating species trees: practical and theoretical aspects. Hoboken (NJ): Wiley-Blackwell. pp. 35-52.
    • (2010) Estimating Species Trees: Practical and Theoretical Aspects , pp. 35-52
    • Ané, C.1
  • 5
    • 15944396106 scopus 로고    scopus 로고
    • Missing the forest for the trees: Phylogenetic compression and its implications for inferring complex evolutionary histories
    • Ané C, Sanderson MJ. 2005. Missing the forest for the trees: phylogenetic compression and its implications for inferring complex evolutionary histories. Syst Biol. 54:146.
    • (2005) Syst Biol , vol.54 , pp. 146
    • Ané, C.1    Sanderson, M.J.2
  • 6
    • 33846839295 scopus 로고    scopus 로고
    • Concordance trees, concordance factors, and the exploration of reticulate genealogy
    • Baum DA. 2007. Concordance trees, concordance factors, and the exploration of reticulate genealogy. Taxon. 56:417-426. (Pubitemid 47025837)
    • (2007) Taxon , vol.56 , Issue.2 , pp. 417-426
    • Baum, D.A.1
  • 7
    • 57749113806 scopus 로고    scopus 로고
    • StepBrothers: Inferring partially shared ancestries among recombinant viral sequences
    • DOI 10.1093/biostatistics/kxn019
    • Bloomquist EW, Dorman KS, Suchard MA. 2009. StepBrothers: inferring partially shared ancestries among recombinant viral sequences. Biostatistics. 10:106-120. (Pubitemid 352847910)
    • (2009) Biostatistics , vol.10 , Issue.1 , pp. 106-120
    • Bloomquist, E.W.1    Dorman, K.S.2    Suchard, M.A.3
  • 8
    • 68149165460 scopus 로고    scopus 로고
    • A mixture model and a hidden markov model to simultaneously detect recombination breakpoints and reconstruct phylogenies
    • Boussau B, Gué guen L, Gouy M. 2009. A mixture model and a hidden markov model to simultaneously detect recombination breakpoints and reconstruct phylogenies. Evol Bioinform Online. 5:67-79.
    • (2009) Evol Bioinform Online , vol.5 , pp. 67-79
    • Boussau, B.1    Guéguen, L.2    Gouy, M.3
  • 9
    • 34249700809 scopus 로고    scopus 로고
    • Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: An example from melanoplus grasshoppers
    • DOI 10.1080/10635150701405560, PII 778979727
    • Carstens BC, Knowles LL. 2007. Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers. Syst Biol. 56:400-411. (Pubitemid 46826903)
    • (2007) Systematic Biology , vol.56 , Issue.3 , pp. 400-411
    • Carstens, B.C.1    Knowles, L.L.2
  • 10
    • 33749613832 scopus 로고    scopus 로고
    • Detecting recombination in evolving nucleotide sequences
    • Chan C, Beiko R, Ragan M. 2006. Detecting recombination in evolving nucleotide sequences. BMC Bioinformatics. 7:412.
    • (2006) BMC Bioinformatics , vol.7 , pp. 412
    • Chan, C.1    Beiko, R.2    Ragan, M.3
  • 11
    • 50349088009 scopus 로고    scopus 로고
    • Phylogenetic detection of recombination with a Bayesian prior on the distance between trees
    • de Oliveira Martins L, Leal E, Kishino H. 2008. Phylogenetic detection of recombination with a Bayesian prior on the distance between trees. PLoS One. 3:e2651.
    • (2008) PLoS One , vol.3
    • De Oliveira Martins, L.1    Leal, E.2    Kishino, H.3
  • 13
    • 84959798530 scopus 로고
    • Cases in which parsimony or compatibility methods will be positively misleading
    • Felsenstein J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool. 27:401-410.
    • (1978) Syst Zool , vol.27 , pp. 401-410
    • Felsenstein, J.1
  • 14
    • 38449096427 scopus 로고    scopus 로고
    • A model of horizontal gene transfer and the bacterial phylogeny problem
    • Galtier N. 2007. A model of horizontal gene transfer and the bacterial phylogeny problem. Syst Biol. 56:633-642.
    • (2007) Syst Biol , vol.56 , pp. 633-642
    • Galtier, N.1
  • 15
    • 0031041347 scopus 로고    scopus 로고
    • A likelihood method for the detection of selection and recombination using nucleotide sequences
    • Grassly N, Holmes E. 1997. A likelihood method for the detection of selection and recombination using nucleotide sequences. Mol Biol Evol. 14:239-247. (Pubitemid 27102670)
    • (1997) Molecular Biology and Evolution , vol.14 , Issue.3 , pp. 239-247
    • Grassly, N.C.1    Holmes, E.C.2
  • 17
    • 79960091789 scopus 로고    scopus 로고
    • Minimum description length model selection criteria for generalized linear models
    • Goldstein DR, editor. Beachwood (OH): Institute of Mathematical Statistics
    • Hansen MH, Yu B. 2003. Minimum description length model selection criteria for generalized linear models. In: Goldstein DR, editor. Statistics and science: A festschrift for terry speed. Beachwood (OH): Institute of Mathematical Statistics. pp. 145-163.
    • (2003) Statistics and Science: A Festschrift for Terry Speed , pp. 145-163
    • Hansen, M.H.1    Yu, B.2
  • 18
    • 0027471670 scopus 로고
    • A heuristic method to reconstruct the history of sequences subject to recombination
    • Hein J. 1993. A heuristic method to reconstruct the history of sequences subject to recombination. J Mol Evol. 36:396-406.
    • (1993) J Mol Evol , vol.36 , pp. 396-406
    • Hein, J.1
  • 20
    • 45849120228 scopus 로고    scopus 로고
    • A Bayesian perspective on a non-parsimonious parsimony model
    • DOI 10.1080/10635150802166046, PII 794012413
    • Huelsenbeck JP, Ané C, Larget B, Ronquist F. 2008. A Bayesian perspective on a non-parsimonious parsimony model. Syst Biol. 57:406-419. (Pubitemid 351882204)
    • (2008) Systematic Biology , vol.57 , Issue.3 , pp. 406-419
    • Huelsenbeck, J.P.1    Ane, C.2    Larget, B.3    Ronquist, F.4
  • 21
    • 27544493059 scopus 로고    scopus 로고
    • Discriminating between rate heterogeneity and interspecific recombination in DNA sequence alignments with phylogenetic factorial hidden Markov models
    • DOI 10.1093/bioinformatics/bti1127
    • Husmeier D. 2005. Discriminating between rate heterogeneity and interspecific recombination in DNA sequence alignments with phylogenetic factorial hidden Markov models. Bioinformatics. 21:ii166-172. (Pubitemid 41535444)
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 2
    • Husmeier, D.1
  • 22
    • 57349190314 scopus 로고    scopus 로고
    • Addressing the shortcomings of three recent Bayesian methods for detecting interspecific recombination in DNA sequence alignments
    • Husmeier D, Mantzaris AV. 2008. Addressing the shortcomings of three recent Bayesian methods for detecting interspecific recombination in DNA sequence alignments. Stat Appl Genet Mol Biol. 7:
    • (2008) Stat Appl Genet Mol Biol , vol.7
    • Husmeier, D.1    Mantzaris, A.V.2
  • 23
    • 0037358827 scopus 로고    scopus 로고
    • Detecting recombination in 4-taxa DNA sequence alignments with bayesian hidden markov models and Markov chain Monte Carlo
    • DOI 10.1093/molbev/msg039
    • Husmeier D, McGuire G. 2003. Detecting recombination in 4- axa DNA sequence alignments with Bayesian hidden Markov models and Markov Chain Monte Carlo. Mol Biol Evol. 20:315-337. (Pubitemid 36427167)
    • (2003) Molecular Biology and Evolution , vol.20 , Issue.3 , pp. 315-337
    • Husmeier, D.1    McGuire, G.2
  • 24
    • 37649007931 scopus 로고    scopus 로고
    • Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns
    • Jansen RK, et al. 2007. Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc Natl Acad Sci U S A. 104:19369-19374.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 19369-19374
    • Jansen, R.K.1
  • 25
    • 70450233546 scopus 로고    scopus 로고
    • Estimating species trees: Methods of phylogenetic analysis when there is incongruence across genes
    • Knowles LL. 2009. Estimating species trees: methods of phylogenetic analysis when there is incongruence across genes. Syst Biol. 58:463-467.
    • (2009) Syst Biol , vol.58 , pp. 463-467
    • Knowles, L.L.1
  • 27
    • 77949525939 scopus 로고    scopus 로고
    • Long-branch attraction bias and inconsistency in Bayesian phylogenetics
    • Kolaczkowski B, Thornton JW. 2009. Long-branch attraction bias and inconsistency in Bayesian phylogenetics. PLoS One. 4:e7891.
    • (2009) PLoS One , vol.4
    • Kolaczkowski, B.1    Thornton, J.W.2
  • 30
    • 78149256307 scopus 로고    scopus 로고
    • BUCKy: Gene tree/ species tree reconciliation with Bayesian concordance analysis
    • Larget BR, Kotha SK, Dewey CN, Ané C. 2010. BUCKy: gene tree/ species tree reconciliation with Bayesian concordance analysis. Bioinformatics. 26:2910-2911.
    • (2010) Bioinformatics , vol.26 , pp. 2910-2911
    • Larget, B.R.1    Kotha, S.K.2    Dewey, C.N.3    Ané, C.4
  • 31
    • 34248159030 scopus 로고    scopus 로고
    • Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model
    • Lartillot N, Brinkmann H, Philippe H. 2007. Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evol Biol. 7(Suppl 4):S4.
    • (2007) BMC Evol Biol , vol.7 , Issue.SUPPL. 4
    • Lartillot, N.1    Brinkmann, H.2    Philippe, H.3
  • 32
    • 0031504952 scopus 로고    scopus 로고
    • Gene trees in species trees
    • Maddison WP. 1997. Gene trees in species trees. Syst Biol. 46:523-536.
    • (1997) Syst Biol , vol.46 , pp. 523-536
    • Maddison, W.P.1
  • 33
    • 33644606488 scopus 로고    scopus 로고
    • Inferring phylogeny despite incomplete lineage sorting
    • Maddison WP, Knowles LL. 2006. Inferring phylogeny despite incomplete lineage sorting. Syst Biol. 55:21-30.
    • (2006) Syst Biol , vol.55 , pp. 21-30
    • Maddison, W.P.1    Knowles, L.L.2
  • 34
    • 38449104891 scopus 로고    scopus 로고
    • Phylogenetic mixtures on a single tree can mimic a tree of another topology
    • Matsen FA, Steel M. 2007. Phylogenetic mixtures on a single tree can mimic a tree of another topology. Syst Biol. 56:767-775.
    • (2007) Syst Biol , vol.56 , pp. 767-775
    • Matsen, F.A.1    Steel, M.2
  • 35
    • 33646154660 scopus 로고    scopus 로고
    • Recco: Recombination analysis using cost optimization
    • Maydt J, Lengauer T. 2006. Recco: recombination analysis using cost optimization. Bioinformatics. 22:1064-1071.
    • (2006) Bioinformatics , vol.22 , pp. 1064-1071
    • Maydt, J.1    Lengauer, T.2
  • 36
    • 0034097468 scopus 로고    scopus 로고
    • TOPAL 2.0: Improved detection of mosaic sequences within multiple alignments
    • McGuire G, Wright F. 2000. TOPAL 2.0: improved detection of mosaic sequences within multiple alignments. Bioinformatics. 16:130-134. (Pubitemid 30248589)
    • (2000) Bioinformatics , vol.16 , Issue.2 , pp. 130-134
    • McGuire, G.1    Wright, F.2
  • 37
    • 21444455535 scopus 로고    scopus 로고
    • Dual multiple change-point model leads to more accurate recombination detection
    • DOI 10.1093/bioinformatics/bti459
    • Minin VN, Dorman KS, Fang F, Suchard MA. 2005. Dual multiple change-point model leads to more accurate recombination detection. Bioinformatics. 21:3034-3042. (Pubitemid 40916429)
    • (2005) Bioinformatics , vol.21 , Issue.13 , pp. 3034-3042
    • Minin, V.N.1    Dorman, K.S.2    Fang, F.3    Suchard, M.A.4
  • 38
    • 44149123106 scopus 로고    scopus 로고
    • An information-theoretic method for the treatment of plural ancestry in phylogenetics
    • Munshaw S, Kepler TB. 2008. An information-theoretic method for the treatment of plural ancestry in phylogenetics. Mol Biol Evol. 25:1199-1208.
    • (2008) Mol Biol Evol , vol.25 , pp. 1199-1208
    • Munshaw, S.1    Kepler, T.B.2
  • 39
    • 0031774059 scopus 로고    scopus 로고
    • GeneTree: Comparing gene and species phylogenies using reconciled trees
    • Page RD. 1998. GeneTree: comparing gene and species phylogenies using reconciled trees. Bioinformatics. 14:819-820. (Pubitemid 28552117)
    • (1998) Bioinformatics , vol.14 , Issue.9 , pp. 819-820
    • Page, R.D.M.1
  • 40
    • 57149106289 scopus 로고    scopus 로고
    • Modelling heterotachy in phylogenetic inference by reversible-jump Markov chain Monte Carlo
    • Pagel M, Meade A. 2008. Modelling heterotachy in phylogenetic inference by reversible-jump Markov chain Monte Carlo. Philos Trans R Soc Lond B Biol Sci. 363:3955-3964.
    • (2008) Philos Trans R Soc Lond B Biol Sci , vol.363 , pp. 3955-3964
    • Pagel, M.1    Meade, A.2
  • 42
    • 33750437728 scopus 로고    scopus 로고
    • Widespread discordance of gene trees with species tree in Drosophila: Evidence for incomplete lineage sorting
    • Pollard D, Iyer VN, Moses AM, Eisen MB. 2006. Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting. PLoS Genet. 2:e173.
    • (2006) PLoS Genet , vol.2
    • Pollard, D.1    Iyer, V.N.2    Moses, A.M.3    Eisen, M.B.4
  • 44
    • 68149093715 scopus 로고    scopus 로고
    • Search for a "tree of Life" in the thicket of the phylogenetic forest
    • Puigbo P, Wolf Y, Koonin E. 2009. Search for a "Tree of Life" in the thicket of the phylogenetic forest. J Biol. 8:59.
    • (2009) J Biol , vol.8 , pp. 59
    • Puigbo, P.1    Wolf, Y.2    Koonin, E.3
  • 45
    • 0018015137 scopus 로고
    • Modeling by shortest data description
    • Rissanen J. 1978. Modeling by shortest data description. Automatica. 14:465-471.
    • (1978) Automatica , vol.14 , pp. 465-471
    • Rissanen, J.1
  • 46
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • DOI 10.1016/0025-5564(81)90043-2
    • Robinson DR, Foulds LR. 1981. Comparison of phylogenetic trees. Math Biosci. 53:131-147. (Pubitemid 11129084)
    • (1981) Mathematical Biosciences , vol.53 , Issue.1-2 , pp. 131-147
    • Robinson, D.F.1    Foulds, L.R.2
  • 47
    • 84857002599 scopus 로고    scopus 로고
    • RECOMP: A parsimony-based method for detecting recombination
    • 2006 Feb 13-16; Taipei, Taiwan. London: Imperial College Press
    • Ruths D, Nakhleh L. 2006. RECOMP: a parsimony-based method for detecting recombination. Proceedings of the 4th Asia Pacific Bioinformatics Conference; 2006 Feb 13-16; Taipei, Taiwan. London: Imperial College Press.
    • (2006) Proceedings of the 4th Asia Pacific Bioinformatics Conference
    • Ruths, D.1    Nakhleh, L.2
  • 49
    • 0000120766 scopus 로고
    • Estimating the dimension of a model
    • Schwarz G. 1978. Estimating the dimension of a model. Ann Statist. 6:461-464.
    • (1978) Ann Statist , vol.6 , pp. 461-464
    • Schwarz, G.1
  • 50
    • 33645234370 scopus 로고    scopus 로고
    • The concordance of gene trees and species trees at two linked loci
    • Slatkin M, Pollack JL. 2006. The concordance of gene trees and species trees at two linked loci. Genetics. 172:1979-1984.
    • (2006) Genetics , vol.172 , pp. 1979-1984
    • Slatkin, M.1    Pollack, J.L.2
  • 51
    • 79952174584 scopus 로고    scopus 로고
    • Can we avoid "sIN" in the house of "no CommonMechanism"?
    • Steel M. 2010. Can we avoid "SIN" in the house of "No CommonMechanism"? Syst Biol. 60(1):96-109.
    • (2010) Syst Biol , vol.60 , Issue.1 , pp. 96-109
    • Steel, M.1
  • 52
    • 0242404116 scopus 로고    scopus 로고
    • Hierarchical phylogenetic models for analyzing multipartite sequence data
    • DOI 10.1080/10635150390238879
    • Suchard MA, Kitchen CMR, Sinsheimer JS, Weiss RE. 2003. Hierarchicalphylogenetic models for analyzing multipartite sequence data. Syst Biol. 52:649-664. (Pubitemid 37365046)
    • (2003) Systematic Biology , vol.52 , Issue.5 , pp. 649-664
    • Suchard, M.A.1    Kitchen, C.M.R.2    Sinsheimer, J.S.3    Weiss, R.E.4
  • 55
    • 0031149251 scopus 로고    scopus 로고
    • Links between maximum likelihood and maximum parsimony under a simple model of site substitution
    • Tuffley C, Steel M. 1997. Links between maximum likelihood and maximum parsimony under a simple model of site substitution. Bull Math Biol. 59:581-607. (Pubitemid 27208833)
    • (1997) Bulletin of Mathematical Biology , vol.59 , Issue.3 , pp. 581-607
    • Tuffley, C.1    Steel, M.2
  • 56
    • 57349156628 scopus 로고    scopus 로고
    • Phylogenetic inference under recombination using Bayesian stochastic topology selection
    • Webb A, Hancock JM, Holmes CC. 2009. Phylogenetic inference under recombination using Bayesian stochastic topology selection. Bioinformatics. 25:197-203.
    • (2009) Bioinformatics , vol.25 , pp. 197-203
    • Webb, A.1    Hancock, J.M.2    Holmes, C.C.3
  • 57
    • 46249126320 scopus 로고    scopus 로고
    • DupTree: A program for large-scale phylogenetic analyses using gene tree parsimony
    • DOI 10.1093/bioinformatics/btn230
    • Wehe A, Bansal MS, Burleigh JG, Eulenstein O. 2008. DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony. Bioinformatics. 24:1540-1541. (Pubitemid 351911710)
    • (2008) Bioinformatics , vol.24 , Issue.13 , pp. 1540-1541
    • Wehe, A.1    Bansal, M.S.2    Burleigh, J.G.3    Eulenstein, O.4
  • 58
    • 47649095950 scopus 로고    scopus 로고
    • Spatial and temporal heterogeneity in nucleotide sequence evolution
    • DOI 10.1093/molbev/msn119
    • Whelan S. 2008. Spatial and temporal heterogeneity in nucleotide sequence evolution. Mol Biol Evol. 25:1683-1694. (Pubitemid 352019854)
    • (2008) Molecular Biology and Evolution , vol.25 , Issue.8 , pp. 1683-1694
    • Whelan, S.1
  • 60
    • 77951062024 scopus 로고    scopus 로고
    • Phylogeny of gammaproteobacteria
    • Williams KP, et al. 2010. Phylogeny of gammaproteobacteria. J Bacteriol. 192:2305-2314.
    • (2010) J Bacteriol , vol.192 , pp. 2305-2314
    • Williams, K.P.1
  • 61
  • 62
    • 0028064845 scopus 로고
    • Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
    • Yang ZT. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J Mol Evol. 39:306-314.
    • (1994) J Mol Evol , vol.39 , pp. 306-314
    • Yang, Z.T.1
  • 63
    • 74549146721 scopus 로고    scopus 로고
    • A Dirichlet process covarion mixture model and its assessments using posterior predictive discrepancy tests
    • Zhou Y, Brinkmann H, Rodrigue N, Lartillot N, Philippe H. 2010. A Dirichlet process covarion mixture model and its assessments using posterior predictive discrepancy tests. Mol Biol Evol. 27:371-384.
    • (2010) Mol Biol Evol , vol.27 , pp. 371-384
    • Zhou, Y.1    Brinkmann, H.2    Rodrigue, N.3    Lartillot, N.4    Philippe, H.5


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