When and How the Perfect Phylogeny Model Explains Evolution
Character-based parsimony models have been among the most studied notions in computational evolution, but research in the field stagnated until some important, recent applications, such as the analysis of data from protein domains, protein networks, and genetic markers, as well as haplotyping, brought new life into this sector. The focus of this survey is to present the perfect phylogeny model and some of its generalizations. In particular, we develop the use of persistency in the perfect phylogeny model as a new promising computational approach to analyzing and reconstructing evolution. We show that, in this setting, some graph-theoretical notions can provide a characterization of the relationships between characters (or attributes), playing a crucial role in developing algorithmic solutions to the problem of reconstructing a maximum parsimony tree.
PB and APC are supported by the Fondo di Ateneo 2011 grant “Metodi algoritmici per l’analisi di strutture combinatorie in bioinformatica”. GDV is supported by the Fondo di Ateneo 2011 grant “Tecniche algoritmiche avanzate in Biologia Computazionale”. PB, GDV and RD are supported by the MIUR PRIN 2010–2011 grant “Automi e Linguaggi Formali: Aspetti Matematici e Applicativi”, code H41J12000190001. TMP is supported by the Intramural Research Program of the National Institutes of Health, National Library of Medicine.
- 6.L.L. Cavalli-Sforza, A.W.F. Edwards, Phylogenetic analysis. Models and estimation procedures. Am. J. Hum. Genet. 19(3 Pt 1), 233 (1967)Google Scholar
- 10.A.W.F. Edwards, L.L. Cavalli-Sforza, The reconstruction of evolution. Heredity 18, 553 (1963)Google Scholar
- 11.J. Felsenstein, Inferring Phylogenies (Sinauer Associates, Sunderland, 2004)Google Scholar
- 15.M. Garey, D. Johnson, Computer and Intractability: A Guide to the Theory of NP-Completeness (W.H. Freeman, San Francisco, 1979)Google Scholar
- 18.D. Gusfield, Haplotyping as perfect phylogeny: conceptual framework and efficient solutions, in Proceedings of the 6th Annual Conference on Research in Computational Molecular Biology (RECOMB), Washington, DC, 2002, pp. 166–175Google Scholar
- 23.T.M. Przytycka, An important connection between network motifs and parsimony models, in Proceedings of the 10th Annual Conference on Research in Computational Molecular Biology (RECOMB), Venice, 2006, pp. 321–335Google Scholar
- 25.R.V. Satya, A. Mukherjee, G. Alexe, L. Parida, G. Bhanot, Constructing near-perfect phylogenies with multiple homoplasy events, in ISMB (Supplement of Bioinformatics), Fortaleza, 2006, pp. 514–522Google Scholar
- 26.C. Semple, M. Steel, Phylogenetics. Oxford Lecture Series in Mathematics and Its Applications (Oxford University Press, Oxford, 2003)Google Scholar
- 28.A. Subramanian, S. Shackney, R. Schwartz, Inference of tumor phylogenies from genomic assays on heterogeneous samples. J. Biomed. Biotechnol. 2012, 1–16 (2012)Google Scholar
- 31.E. Zotenko, K.S. Guimarães, R. Jothi, T.M. Przytycka, Decomposition of overlapping protein complexes: a graph theoretical method for analyzing static and dynamic protein associations. Algorithms Mol. Biol. 7(1), 1–11 (2006)Google Scholar