Formalizing reliability in the taxonomic congruence approach

Zoologica Scripta

Volumn 38, Issue 1, 2009, Pages 101-112

  Li, Blaise ^b   Lecointre, Guillaume ^a  

^a Département Systématique et Évolution ^*  (France)

^b SORBONNE UNIVERSITÉ   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ACANTHOMORPHA;

EID: 57649236247     PISSN: 03003256     EISSN: 14636409     Source Type: Journal    
DOI: 10.1111/j.1463-6409.2008.00361.x     Document Type: Article

References (45)

1. Bandelt, H.-J. Dress, A. (1992). Split decomposition: a new useful approach to phylogenetic analysis of distance data. Molecular Phylogenetics and Evolution, 3, 242 252.
2. Baum, B. Ragan, M. (2004). The MRP method. In O. Bininda-Edmonds (Ed.) Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life (pp. 17 34). Dordrecht, the Netherlands : Kluver Academic.
3. Berry, V. Gascuel, O. (2000). Inferring evolutionary trees with strong combinatorial evidence. Theoretical Computer Science, 240, 271 298.
4. Bininda-Edmonds, O. (2003). Novel versus unsupported clades: assessing the qualitative support for clades in MRP supertrees. Systematic Biology, 52 (6 839 848.
5. Brinkmann, H., Van der Giezen, M., Zhou, Y., Poncelin de Raucourt, G. Philippe, H. (2005). An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics. Systematic Biology, 54 (5 743 757.
6. Bryant, D. (2003). A classification of consensus methods for phylogenetics. In M. Janowitz, F. Lapointe, F. McMorris, B. Mirkin F. Roberts (Eds) Bioconsensus (pp. 1 21). Piscataway, NJ : American Mathematical Society Publications-DIMACS.
7. Carnap, R. (1950). Logical Foundations of Probability. Chicago : University of Chicago press.
8. Chen, W.-J., Bonillo, C. Lecointre, G. (2000). Taxonomic congruence as a tool to discover new clades in the acanthomorph (Teleostei) radiation. In Program Book and Abstracts, 80th Annual Meeting ASIH, La Paz, México, June 14-20, 2000 (p. 369). American Society of Ichthyologists and Herpetologists, American Society of Ichthyologists and Herpetologists.
9. Chen, W.-J., Bonillo, C. Lecointre, G. (2003). Repeatability of clades as a criterion of reliability: a case study for molecular phylogeny of Acanthomorpha (Teleostei) with larger number of taxa. Molecular Phylogenetics and Evolution, 26, 262 288.
10. Cotton, J., Slater, C. Wilkinson, M. (2006). Discriminating supported and unsupported relationships in supertrees using triplets. Systematic Biology, 55 (2 345 350.
11. Dettaï, A. (2004). La phylogénie des Acanthomorpha (Teleostei) inférée par l'étude de la congruence taxinomique. PhD Thesis. Université Paris VI Pierre et Marie Curie.
12. Dettaï, A. Lecointre, G. (2004). In search of nothothenioid (Teleostei) relatives. Antarctic Science, 16 (1 71 85.
13. Dettaï, A. Lecointre, G. (2005). Further support for the clades obtained by multiple molecular phylogenies in the acanthomorph bush. Comptes Rendus Biologies, 328, 674 689.
14. Douady, C., Delsuc, F., Boucher, Y., Doolittle, F. Douzery, E. (2003). Comparison of bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Molecular Biology and Evolution, 20 (2 248 254.
15. Felsenstein, J. (2004). PHYLIP. Phylogeny Inference Package, Version3.6. Seattle : Department of Genome Sciences and Departement of Biology, University of Washington.
16. Froese, R. Pauly, D. (2006). Fishbase. World Wide Web electronic publication. Available Via http://www.fishbase.org.
17. Grande, L. (1994). Repeating patterns in nature, predictability, and 'impact' in science. In L. Grande O. Rieppel (Eds) Interpreting the Hierarchy of Nature, 1st edn (pp. 61 84). New York : Academic Press.
18. Hempel, C. (1965). Aspects of Scientific Explanation, and Other Essays in the Philosophy of Science. New York : Free press.
19. Hillis, D. Bull, J. (1993). An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systematic Biology, 42 (2 182 192.
20. Kearney, M. Rieppel, O. (2006). Rejecting 'the given' in systematics. Cladistics, 22, 369 377.
21. Lecointre, G. Deleporte, P. (2005). Total evidence requires exclusion of phylogenetically misleading data. Zoologica Scripta, 34 (1 101 117.
22. Lecointre, G., Philippe, H., Lê, H. L. V. Le Guyader, H. (1994). How many nucleotides are required to resolve a phylogenetic problem? The use of a new statistical method applicable to available sequences. Molecular Phylogenetics and Evolution, 3 (4 292 309.
23. Lockhart, P., Penny, D. Meyer, A. (1995). Testing the phylogeny of swordtail fishes using split decomposition and spectral analysis. Journal of Molecular Evolution, 41, 666 674.
24. Maddison, W. (1997). Gene trees in species trees. Systematic Biology, 46 (3 523 536.
25. Mahner, M. Bunge, M. (1997). Foundations of Biophilosophy. Berlin : Springer.
26. Miya, M., Takeshima, H., Endo, H., Ishiguro, N., Inoue, J., Mukai, T., Satoh, T., Yamaguchi, M., Kawaguchi, A., Mabuchi, K., Shirai, S. Nishida, M. (2003). Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Molecular Phylogenetics and Evolution, 26, 121 138.
27. Miyamoto, M. Fitch, W. (1995). Testing species phylogenies and phylogenetic methods with congruence. Systematic Biology, 44 (1 64 75.
28. Moore, B., Smith, S. Donoghue, M. (2006). Increasing data transparency and estimating phylogenetic uncertainty in supertrees: approaches using nonparametric bootstrapping. Systematic Biology, 55 (4 662 676.
29. Müller, J. Müller, K. (2004). TreeGraph: automated drawing of complex tree figures using an extensible tree description format. Molecular Ecology Notes, 4, 786 788.
30. Phillips, M., Delsuc, F. Penny, D. (2004). Genome-scale phylogeny and the detection of systematic biases. Molecular Biology and Evolution, 21 (7 1455 1458.
31. Phillips, C. Warnow, T. (1996). The asymetric median tree: a new model for building consensus trees. Discrete Applied Mathematics, 71, 311 335.
32. Pisani, D. Wilkinson, M. (2002). Matrix representation with parsimony, taxonomic congruence, and total evidence. Systematic Biology, 51 (1 151 155.
33. Rambaut, A. (2002). Se-Al, Sequence Alignment Editor, Version, 2.0a11. Oxford, OX1 3PS, UK : Department of Zoology, University of Oxford, South Parks Road.
34. Rieppel, O. (2004a). The language of systematics, and the philosophy of 'total evidence'. Systematics and Biodiversity, 2 (1 9 19.
35. Rieppel, O. (2004b). What happens when the language of science threatens to break down in systematics: a popperian perspective. In D. Williams P. Forey (Eds) Milestones in Systematics (pp. 57 100). CRC Press.
36. Rodrigo, A. (1996). On combining cladograms. Taxon, 45 (2 267 274.
37. Rodrigo, A., Kelly-Borges, M., Bergquist, P. Bergquist, P. (1993). A randomisation test of the null hypothesis that two cladograms are sample estimates of a parametric phylogenetic tree. New Zealand Journal of Botany, 31, 257 268.
38. Ross, H. Rodrigo, A. (2004). An assessment of matrix representation with compatibility in supertree construction. In O. Bininda-Edmonds (Ed.) Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life (pp. 35 63). Dordrecht, the Netherlands : Kluver Academic.
39. Seo, T.-K., Hirohisa, K. Thorne, J. (2005). Incorporating gene-specific variation when inferring and evaluating optimal evolutionary tree topologies from multilocus sequence data. Proceedings of the National Academy of Sciences of the United States of America, 102 (12 4436 4441.
40. Struck, T., Purschke, G. Halanych, K. (2006). Phylogeny of Eunicida (Annelida) and exploring data congruence using a partition addition bootstrap alteration (PABA) approach. Systematic Biology, 55 (1 1 20.
41. Swofford, D. (2002). paup*. Phylogenetic Analysis Using Parsimony (* and other methods), Version 4.0b10. Sunderland, Massachusetts : Sinauer Associates.
42. Wilkinson, M. (1994). Common cladistic information and its consensus representation: reduced Adams and reduced cladistic consensus trees and profiles. Systematic Biology, 43 (3 343 368.
43. Wilkinson, M. (1996). Majority-rule reduced consensus trees and their use in bootstrapping. Molecular Biology and Evolution, 13 (3 437 444.
44. Wilkinson, M., Lapointe, F.-J. Gower, D. (2003). Branch lengths and support. Systematic Biology, 52 (1 127 130.
45. Wilkinson, M., Pisani, D., Cotton, J. Corfe, I. (2005). Measuring support and finding unsupported relationships in supertrees. Systematic Biology, 54 (5 823 831.