A method for measuring support for synapomorphy using character state distributions on phylogenetic trees

Cladistics

Volumn 28, Issue 6, 2012, Pages 627-638

  Turjak, Martin ^a   Trontelj, Peter ^a  

^a UNIVERSITY OF LJUBLJANA   (Slovenia)

Author keywords

[No Author keywords available]

Indexed keywords

CHARACTER DISPLACEMENT; CLADISTICS; EMPIRICAL ANALYSIS; HIERARCHICAL SYSTEM; PHYLOGENETICS; PROBABILITY; TOPOLOGY; TREE;

EID: 84869157613     PISSN: 07483007     EISSN: 10960031     Source Type: Journal    
DOI: 10.1111/j.1096-0031.2012.00403.x     Document Type: Article

References (40)

1. Assis, L., Brigandt, I., 2009. Homology: homeostatic property cluster kinds in systematics and evolution. Evol. Biol. 36, 248-255.
2. Assis, L.C., Rieppel, O., 2011. Are monophyly and synapomorphy the same or different? Revisiting the role of morphology in phylogenetics. Cladistics 27, 94-102.
3. Ax, P., 1987. The Phylogenetic System. The Systematization of Organisms on the Basis of Their Phylogenies. Wiley, Chichester, UK.
4. Bremer, K., 1994. Branch support and tree stability. Cladistics 10, 295-304.
5. Carine, M.A., Scotland, R.W., 1999. Taxic and transformational homology: different ways of seeing. Cladistics 15, 121-129.
6. Farris, J.S. 1983. The logical basis of phylogenetic analysis. In: Platnick, N.I., Funk, V.A., (Eds.), Advances in Cladistics, Vol. 2. NY Botanical Garden, New York, pp. 7-36.
7. Farris, J.S., 1989. The retention index and the re-scaled consistency index. Cladistics 5, 417-419.
8. Felsenstein, J. 2004. Inferring Phylogenies. Sinauer Associates, Sunderland, MA.
9. Fišer, C., Sket, B., Trontelj, P., 2008. A phylogenetic perspective on 160 years of troubled taxonomy of Niphargus (Crustacea: Amphipoda). Zool. Scr. 37, 665-680.
10. Fitch, W.M., 1971. Toward defining the course of evolution: minimum change for a specified tree topology. Syst. Zool. 20, 406-416.
11. Fuellen, G., Wägele, J.W., Giegerich, R., 2001. Minimum conflict: a divide-and-conquer approach to phylogeny estimation. Bioinformatics 17, 1168-1178.
12. Harvey, A.W., 1992. Three-taxon statements: more precisely, an abuse of parsimony. Cladistics 8, 345-354.
13. Hennig, W. 1950. Grundzüge einer Theorie der Phylogenetischen Systematik. Deutscher Zentralverlag, Berlin, Germany.
14. Hennig, W., 1953. Kritische Bemerkungen zum phylogenetischen System der Insekten. Beiträge zur Entomologie 3, 1-85.
15. Hennig, W. 1966. Phylogenetic Systematics. University of Illinois Press, Urbana, IL.
16. Kitching, I.J., Forey, P.L., Humphries, C.J., Williams, D.M. 1998. Cladistics, 2nd edn. Oxford University Press, Oxford.
17. Lyons-Weiler, J., Hoelzer, G.A., Tausch, R.J., 1996. Relative apparent synapomorphy analysis (RASA) I: the statistical measurement of phylogenetic signal. Mol. Biol. Evol. 13, 749-757.
18. Maddison, W.P., 1995. Calculating the probability distributions of ancestral states reconstructed by parsimony on phylogenetic trees. Syst. Biol. 44, 474-481.
19. Mooi, R.D., Gill, A.C., 2010. Phylogenies without synapomorphies-a crisis in fish systematics: time to show some character. Zootaxa 2450, 26-40.
20. Nelson, G.J., Platnick, N.I. 1981. Systematics and Biogeography. Columbia University Press, New York.
21. Nelson, G., Platnick, N.I., 1991. Three-taxon statements: a more precise use of parsimony? Cladistics 7, 351-366.
22. Nixon, K.C., Carpenter, J.M. 2012. On homology. Cladistics 28, 160-169.
23. Pagel, M., 1999. The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. Syst. Biol. 48, 612-622.
24. Patterson, C., 1982a. Classes and cladists or individuals and evolution. Syst. Zool. 31, 284-286.
25. Patterson, C. 1982b. Morphological characters and homology. In: Joysey, K.A., Friday, A.E., (Eds.), Problems of Phylogenetic Reconstruction. Academic Press, London, pp. 21-74.
26. de Pinna, M.C.C., 1991. Concepts and tests of homology in the cladistic paradigm. Cladistics 7, 367-394.
27. Ridley, M. 1986. Evolution and Classification: The Reformation of Cladism. Longman, London.
28. Rieppel, O., 2011. Willi Hennig's dichotomization of nature. Cladistics 27, 103-112.
29. Sankoff, D., 1975. Minimal mutation trees of sequences. SIAM J. Appl. Math. 28, 35-42.
30. Schluter, D., Price, T., Mooers, A.O., Ludwig, D., 1997. Likelihood of ancestral states in adaptive radiation. Evolution 51, 1699-1711.
31. Schuh, R.T., Brower, A.V.Z. 2009. Biological Systematics: Principles and Applications, 2nd edn. Cornell University Press, Ithaca, NY.
32. Scotland, R.W., 2000. Taxic homology and three-taxon statement analysis. Syst. Biol. 49, 480-500.
33. Scott-Ram, N.R. 1990. Transformed Cladistics, Taxonomy and Evolution. Cambridge University Press, Cambridge, UK.
34. Sharkey, M.J., 1999. Transition confidence and modified mean values: confidence measures for hypotheses of character state transition between nodes and ancestral state optimizations. Cladistics 15, 113-120.
35. Sober, E. 1988. Reconstructing the Past: Parsimony, Evolution, and Inference. MIT Press, Cambridge, MA.
36. Vergara-Silva, F., 2009. Pattern cladistics and the 'realism-antirealism debate' in the philosophy of biology. Acta. Biotheor. 57, 269-294.
37. Wägele, J.W. 2005. Foundations of Phylogenetic Systematics. Verlag Dr. Friedrich Pfeil, Munich, Germany.
38. Wägele, J.W., Rödding, F., 1998. A priori estimation of phylogenetic information conserved in aligned sequences. Mol. Phylogenet. Evol. 9, 358-365.
39. Williams, P., 1992. Confusion in cladism. Synthese 91, 135-152.
40. Williams, M.D., Ebach, M.C. 2008. Foundations of Systematics and Biogeography. Springer Science and Business Media, New York.