Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta)
Müller T, Rahmann S, Dandekar T, Wolf M (2004)
BMC Evolutionary Biology 4(1): 20.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
Download
Autor*in
Müller, Tobias;
Rahmann, Sven;
Dandekar, Thomas;
Wolf, Matthias
Einrichtung
Abstract / Bemerkung
Background: In phylogenetic analysis we face the problem that several subclade topologies are known or easily inferred and well supported by bootstrap analysis, but basal branching patterns cannot be unambiguously estimated by the usual methods (maximum parsimony (MP), neighbor-joining (NJ), or maximum likelihood (ML)), nor are they well supported. We represent each subclade by a sequence profile and estimate evolutionary distances between profiles to obtain a matrix of distances between subclades. Results: Our estimator of profile distances generalizes the maximum likelihood estimator of sequence distances. The basal branching pattern can be estimated by any distance-based method, such as neighbor-joining. Our method (profile neighbor-joining, PNJ) then inherits the accuracy and robustness of profiles and the time efficiency of neighbor-joining. Conclusions: Phylogenetic analysis of Chlorophyceae with traditional methods (MP, NJ, ML and MrBayes) reveals seven well supported subclades, but the methods disagree on the basal branching pattern. The tree reconstructed by our method is better supported and can be confirmed by known morphological characters. Moreover the accuracy is significantly improved as shown by parametric bootstrap.
Erscheinungsjahr
2004
Zeitschriftentitel
BMC Evolutionary Biology
Band
4
Ausgabe
1
Art.-Nr.
20
ISSN
1471-2148
Page URI
https://pub.uni-bielefeld.de/record/1773761
Zitieren
Müller T, Rahmann S, Dandekar T, Wolf M. Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta). BMC Evolutionary Biology. 2004;4(1): 20.
Müller, T., Rahmann, S., Dandekar, T., & Wolf, M. (2004). Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta). BMC Evolutionary Biology, 4(1), 20. https://doi.org/10.1186/1471-2148-4-20
Müller, Tobias, Rahmann, Sven, Dandekar, Thomas, and Wolf, Matthias. 2004. “Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta)”. BMC Evolutionary Biology 4 (1): 20.
Müller, T., Rahmann, S., Dandekar, T., and Wolf, M. (2004). Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta). BMC Evolutionary Biology 4:20.
Müller, T., et al., 2004. Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta). BMC Evolutionary Biology, 4(1): 20.
T. Müller, et al., “Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta)”, BMC Evolutionary Biology, vol. 4, 2004, : 20.
Müller, T., Rahmann, S., Dandekar, T., Wolf, M.: Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta). BMC Evolutionary Biology. 4, : 20 (2004).
Müller, Tobias, Rahmann, Sven, Dandekar, Thomas, and Wolf, Matthias. “Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta)”. BMC Evolutionary Biology 4.1 (2004): 20.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Copyright Statement:
Dieses Objekt ist durch das Urheberrecht und/oder verwandte Schutzrechte geschützt. [...]
Volltext(e)
Name
Access Level

Zuletzt Hochgeladen
2019-09-06T08:48:09Z
MD5 Prüfsumme
a277ed3bab8ef785ce09acfff16170aa
Daten bereitgestellt von European Bioinformatics Institute (EBI)
28 Zitationen in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
Assessing intragenomic variation of the internal transcribed spacer two: Adapting the Illumina metagenomics protocol.
Alanagreh L, Pegg C, Harikumar A, Buchheim M., PLoS One 12(7), 2017
PMID: 28719667
Alanagreh L, Pegg C, Harikumar A, Buchheim M., PLoS One 12(7), 2017
PMID: 28719667
Widespread green algae Chlorella and Stichococcus exhibit polar-temperate and tropical-temperate biogeography.
Hodač L, Hallmann C, Spitzer K, Elster J, Faßhauer F, Brinkmann N, Lepka D, Diwan V, Friedl T., FEMS Microbiol Ecol 92(8), 2016
PMID: 27279416
Hodač L, Hallmann C, Spitzer K, Elster J, Faßhauer F, Brinkmann N, Lepka D, Diwan V, Friedl T., FEMS Microbiol Ecol 92(8), 2016
PMID: 27279416
A non‐toxigenic but morphologically and phylogenetically distinct new species of Pseudo‐nitzschia, P. sabit sp. nov. (Bacillariophyceae)
Teng ST, Lim PT, Lim HC, Rivera‐Vilarelle M, Quijano‐Scheggia S, Takata Y, Quilliam MA, Wolf M, Bates SS, Leaw CP, Lin S., J Phycol 51(4), 2015
PMID: IND603566542
Teng ST, Lim PT, Lim HC, Rivera‐Vilarelle M, Quijano‐Scheggia S, Takata Y, Quilliam MA, Wolf M, Bates SS, Leaw CP, Lin S., J Phycol 51(4), 2015
PMID: IND603566542
Internal transcribed spacer 1 secondary structure analysis reveals a common core throughout the anaerobic fungi (Neocallimastigomycota).
Koetschan C, Kittelmann S, Lu J, Al-Halbouni D, Jarvis GN, Müller T, Wolf M, Janssen PH., PLoS One 9(3), 2014
PMID: 24663345
Koetschan C, Kittelmann S, Lu J, Al-Halbouni D, Jarvis GN, Müller T, Wolf M, Janssen PH., PLoS One 9(3), 2014
PMID: 24663345
Tracing evolutionary footprints to identify novel gene functional linkages.
Chen Y, Yang L, Ding Y, Zhang S, He T, Mao F, Zhang C, Zhang H, Huo C, Liu P., PLoS One 8(6), 2013
PMID: 23825567
Chen Y, Yang L, Ding Y, Zhang S, He T, Mao F, Zhang C, Zhang H, Huo C, Liu P., PLoS One 8(6), 2013
PMID: 23825567
Predicting function from sequence in a large multifunctional toxin family.
Malhotra A, Creer S, Harris JB, Stöcklin R, Favreau P, Thorpe RS., Toxicon 72(), 2013
PMID: 23831284
Malhotra A, Creer S, Harris JB, Stöcklin R, Favreau P, Thorpe RS., Toxicon 72(), 2013
PMID: 23831284
Phylogeny of Oedogoniales, Chaetophorales and Chaetopeltidales (Chlorophyceae): inferences from sequence-structure analysis of ITS2.
Buchheim MA, Sutherland DM, Schleicher T, Förster F, Wolf M., Ann Bot 109(1), 2012
PMID: 22028463
Buchheim MA, Sutherland DM, Schleicher T, Förster F, Wolf M., Ann Bot 109(1), 2012
PMID: 22028463
Morphology evolution and molecular phylogeny of Pestalotiopsis (Coelomycetes) based on ITS2 secondary structure
Watanabe K, Nakazono T, Ono Y., Mycoscience 53(3), 2012
PMID: IND44736254
Watanabe K, Nakazono T, Ono Y., Mycoscience 53(3), 2012
PMID: IND44736254
'Y'Scenedesmus (Chlorophyta, Chlorophyceae): the internal transcribed spacer 2 rRNA secondary structure re-revisited.
Markert SM, Müller T, Koetschan C, Friedl T, Wolf M., Plant Biol (Stuttg) 14(6), 2012
PMID: 22639929
Markert SM, Müller T, Koetschan C, Friedl T, Wolf M., Plant Biol (Stuttg) 14(6), 2012
PMID: 22639929
Lineage-specific fragmentation and nuclear relocation of the mitochondrial cox2 gene in chlorophycean green algae (Chlorophyta).
Rodríguez-Salinas E, Riveros-Rosas H, Li Z, Fucíková K, Brand JJ, Lewis LA, González-Halphen D., Mol Phylogenet Evol 64(1), 2012
PMID: 22724135
Rodríguez-Salinas E, Riveros-Rosas H, Li Z, Fucíková K, Brand JJ, Lewis LA, González-Halphen D., Mol Phylogenet Evol 64(1), 2012
PMID: 22724135
MORPHOLOGY AND MOLECULAR CHARACTERIZATION OF PSEUDO-NITZSCHIA (BACILLARIOPHYCEAE) FROM MALAYSIAN BORNEO, INCLUDING THE NEW SPECIES PSEUDO-NITZSCHIA CIRCUMPORA SP. NOV.
Lim HC, Leaw CP, Su SN, Teng ST, Usup G, Mohammad-Noor N, Lundholm N, Kotaki Y, Lim PT., J Phycol 48(5), 2012
PMID: 27011282
Lim HC, Leaw CP, Su SN, Teng ST, Usup G, Mohammad-Noor N, Lundholm N, Kotaki Y, Lim PT., J Phycol 48(5), 2012
PMID: 27011282
Probing the Monophyly of the Sphaeropleales (Chlorophyceae) Using Data From Five Genes.
Tippery NP, Fučíková K, Lewis PO, Lewis LA., J Phycol 48(6), 2012
PMID: 27009998
Tippery NP, Fučíková K, Lewis PO, Lewis LA., J Phycol 48(6), 2012
PMID: 27009998
Cleaning up the 'Bigmessidae': molecular phylogeny of scleractinian corals from Faviidae, Merulinidae, Pectiniidae and Trachyphylliidae.
Huang D, Licuanan WY, Baird AH, Fukami H., BMC Evol Biol 11(), 2011
PMID: 21299898
Huang D, Licuanan WY, Baird AH, Fukami H., BMC Evol Biol 11(), 2011
PMID: 21299898
Internal transcribed spacer 2 (nu ITS2 rRNA) sequence-structure phylogenetics: towards an automated reconstruction of the green algal tree of life.
Buchheim MA, Keller A, Koetschan C, Förster F, Merget B, Wolf M., PLoS One 6(2), 2011
PMID: 21347329
Buchheim MA, Keller A, Koetschan C, Förster F, Merget B, Wolf M., PLoS One 6(2), 2011
PMID: 21347329
Atypical subunit composition of the chlorophycean mitochondrial F1FO-ATP synthase and role of Asa7 protein in stability and oligomycin resistance of the enzyme.
Lapaille M, Escobar-Ramírez A, Degand H, Baurain D, Rodríguez-Salinas E, Coosemans N, Boutry M, Gonzalez-Halphen D, Remacle C, Cardol P., Mol Biol Evol 27(7), 2010
PMID: 20156838
Lapaille M, Escobar-Ramírez A, Degand H, Baurain D, Rodríguez-Salinas E, Coosemans N, Boutry M, Gonzalez-Halphen D, Remacle C, Cardol P., Mol Biol Evol 27(7), 2010
PMID: 20156838
Microevolution and speciation in Thalassiosira weissflogii (Bacillariophyta).
Sorhannus U, Ortiz JD, Wolf M, Fox MG., Protist 161(2), 2010
PMID: 20018562
Sorhannus U, Ortiz JD, Wolf M, Fox MG., Protist 161(2), 2010
PMID: 20018562
The analysis of rRNA sequence-structure in phylogenetics: An application to the family Pectinidae (Mollusca: Bivalvia).
Salvi D, Bellavia G, Cervelli M, Mariottini P., Mol Phylogenet Evol 56(3), 2010
PMID: 20416386
Salvi D, Bellavia G, Cervelli M, Mariottini P., Mol Phylogenet Evol 56(3), 2010
PMID: 20416386
The exceptionally large chloroplast genome of the green alga Floydiella terrestris illuminates the evolutionary history of the Chlorophyceae.
Brouard JS, Otis C, Lemieux C, Turmel M., Genome Biol Evol 2(), 2010
PMID: 20624729
Brouard JS, Otis C, Lemieux C, Turmel M., Genome Biol Evol 2(), 2010
PMID: 20624729
A molecular phylogeny of Hypnales (Bryophyta) inferred from ITS2 sequence-structure data.
Merget B, Wolf M., BMC Res Notes 3(), 2010
PMID: 21108782
Merget B, Wolf M., BMC Res Notes 3(), 2010
PMID: 21108782
Evolutionary distances in the twilight zone--a rational kernel approach.
Schwarz RF, Fletcher W, Förster F, Merget B, Wolf M, Schultz J, Markowetz F., PLoS One 5(12), 2010
PMID: 21209825
Schwarz RF, Fletcher W, Förster F, Merget B, Wolf M, Schultz J, Markowetz F., PLoS One 5(12), 2010
PMID: 21209825
FastTree: computing large minimum evolution trees with profiles instead of a distance matrix.
Price MN, Dehal PS, Arkin AP., Mol Biol Evol 26(7), 2009
PMID: 19377059
Price MN, Dehal PS, Arkin AP., Mol Biol Evol 26(7), 2009
PMID: 19377059
ITS2 secondary structure improves phylogeny estimation in a radiation of blue butterflies of the subgenus Agrodiaetus (Lepidoptera: Lycaenidae: Polyommatus ).
Wiemers M, Keller A, Wolf M., BMC Evol Biol 9(), 2009
PMID: 20035628
Wiemers M, Keller A, Wolf M., BMC Evol Biol 9(), 2009
PMID: 20035628
Deep division in the chlorophyceae (chlorophyta) revealed by chloroplast phylogenomic analyses
Turmel M, Brouard JS, Gagnon C, Otis C, Lemieux C., J Phycol 44(3), 2008
PMID: IND44059346
Turmel M, Brouard JS, Gagnon C, Otis C, Lemieux C., J Phycol 44(3), 2008
PMID: IND44059346
Chloroplast DNA sequence of the green alga Oedogonium cardiacum (Chlorophyceae): unique genome architecture, derived characters shared with the Chaetophorales and novel genes acquired through horizontal transfer.
Brouard JS, Otis C, Lemieux C, Turmel M., BMC Genomics 9(), 2008
PMID: 18558012
Brouard JS, Otis C, Lemieux C, Turmel M., BMC Genomics 9(), 2008
PMID: 18558012
ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales).
Keller A, Schleicher T, Förster F, Ruderisch B, Dandekar T, Müller T, Wolf M., BMC Evol Biol 8(), 2008
PMID: 18655698
Keller A, Schleicher T, Förster F, Ruderisch B, Dandekar T, Müller T, Wolf M., BMC Evol Biol 8(), 2008
PMID: 18655698
ProfDistS: (profile-) distance based phylogeny on sequence--structure alignments.
Wolf M, Ruderisch B, Dandekar T, Schultz J, Müller T., Bioinformatics 24(20), 2008
PMID: 18723521
Wolf M, Ruderisch B, Dandekar T, Schultz J, Müller T., Bioinformatics 24(20), 2008
PMID: 18723521
ProfDist: a tool for the construction of large phylogenetic trees based on profile distances.
Friedrich J, Dandekar T, Wolf M, Müller T., Bioinformatics 21(9), 2005
PMID: 15677706
Friedrich J, Dandekar T, Wolf M, Müller T., Bioinformatics 21(9), 2005
PMID: 15677706
Genomic multiple sequence alignments: refinement using a genetic algorithm.
Wang C, Lefkowitz EJ., BMC Bioinformatics 6(), 2005
PMID: 16086841
Wang C, Lefkowitz EJ., BMC Bioinformatics 6(), 2005
PMID: 16086841
24 References
Daten bereitgestellt von Europe PubMed Central.
The neighbor-joining method: a new method for reconstructing phylogenetic trees
Saitou N, Nei M., 1987
Saitou N, Nei M., 1987
Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction.
Bruno WJ, Socci ND, Halpern AL., Mol. Biol. Evol. 17(1), 2000
PMID: 10666718
Bruno WJ, Socci ND, Halpern AL., Mol. Biol. Evol. 17(1), 2000
PMID: 10666718
BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
Gascuel O., Mol. Biol. Evol. 14(7), 1997
PMID: 9254330
Gascuel O., Mol. Biol. Evol. 14(7), 1997
PMID: 9254330
Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle.
Desper R, Gascuel O., J. Comput. Biol. 9(5), 2002
PMID: 12487758
Desper R, Gascuel O., J. Comput. Biol. 9(5), 2002
PMID: 12487758
Improvement of distance-based phylogenetic methods by a local maximum likelihood approach using triplets.
Ranwez V, Gascuel O., Mol. Biol. Evol. 19(11), 2002
PMID: 12411604
Ranwez V, Gascuel O., Mol. Biol. Evol. 19(11), 2002
PMID: 12411604
A method for deducing branching sequences in phylogeny
Camin J, Sokal R., 1965
Camin J, Sokal R., 1965
Evolutionary trees from DNA sequences: a maximum likelihood approach.
Felsenstein J., J. Mol. Evol. 17(6), 1981
PMID: 7288891
Felsenstein J., J. Mol. Evol. 17(6), 1981
PMID: 7288891
Phylogeny of the Chlorophyceae with special reference to the Sphaeropleales: A study of 18S and 26S rDNA data
Buchheim MA, Michalopulos EA, Buchheim JA., 2001
Buchheim MA, Michalopulos EA, Buchheim JA., 2001
Phylogenetic position of the Sphaeropleaceae (Chlorophyta)
Wolf M, Buchheim M, Hegewald E, Krienitz L, Hepperle D., 2002
Wolf M, Buchheim M, Hegewald E, Krienitz L, Hepperle D., 2002
MRBAYES: Bayesian inference of phylogenetic trees.
Huelsenbeck JP, Ronquist F., Bioinformatics 17(8), 2001
PMID: 11524383
Huelsenbeck JP, Ronquist F., Bioinformatics 17(8), 2001
PMID: 11524383
Polyphyletic origin of parallel basal bodies in swimming cells of chlorophycean green algae (Chlorophyta)
Shoup S, Lewis L., 2003
Shoup S, Lewis L., 2003
Profile analysis: detection of distantly related proteins.
Gribskov M, McLachlan AD, Eisenberg D., Proc. Natl. Acad. Sci. U.S.A. 84(13), 1987
PMID: 3474607
Gribskov M, McLachlan AD, Eisenberg D., Proc. Natl. Acad. Sci. U.S.A. 84(13), 1987
PMID: 3474607
Robust estimation of the phylogeny of Chlorophyceae (Chlorophyta) based on profile distances
Müller T, Rahmann S, Dandekar T, Wolf M., 2003
Müller T, Rahmann S, Dandekar T, Wolf M., 2003
TreeBASE: the roots of phylogeny
Morell V., 1996
Morell V., 1996
TreeBASE
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
Phylogeny estimation: traditional and Bayesian approaches.
Holder M, Lewis PO., Nat. Rev. Genet. 4(4), 2003
PMID: 12671658
Holder M, Lewis PO., Nat. Rev. Genet. 4(4), 2003
PMID: 12671658
An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis
Hillis D, Bull J., 1993
Hillis D, Bull J., 1993
Rose: generating sequence families.
Stoye J, Evers D, Meyer F., Bioinformatics 14(2), 1998
PMID: 9545448
Stoye J, Evers D, Meyer F., Bioinformatics 14(2), 1998
PMID: 9545448
BiBiServ
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
Comparison of phylogenetic trees
Robinson D, Foulds L., 1981
Robinson D, Foulds L., 1981
A new method for calculating evolutionary substitution rates.
Lanave C, Preparata G, Saccone C, Serio G., J. Mol. Evol. 20(1), 1984
PMID: 6429346
Lanave C, Preparata G, Saccone C, Serio G., J. Mol. Evol. 20(1), 1984
PMID: 6429346
Bootstrap confidence levels for phylogenetic trees.
Efron B, Halloran E, Holmes S., Proc. Natl. Acad. Sci. U.S.A. 93(14), 1996
PMID: 8692949
Efron B, Halloran E, Holmes S., Proc. Natl. Acad. Sci. U.S.A. 93(14), 1996
PMID: 8692949
Confidence limits on phylogenies: an approach using the bootstrap
Felsenstein J., 1985
Felsenstein J., 1985
Export
Markieren/ Markierung löschen
Markierte Publikationen
Web of Science
Dieser Datensatz im Web of Science®Quellen
PMID: 15222898
PubMed | Europe PMC
Suchen in