Abstract
In this paper we present an extended model related to reconciliation concepts. It is based on gene duplications, gene losses and speciation events. We define an evolutionary scenario (called a DLS-tree) which informally can represent an evolution of genes in species. We are interested in all scenarios – not only parsimonious ones. We propose a system of rules for transforming the scenarios. We prove that the system is confluent, sound and strongly normalizing. We show that a scenario in normal form (i.e. non-reducible) is unique and minimal in the sense of the cost computed as the total number of gene duplications and losses. Moreover, we present a classification of the scenarios and analyze their hierarchy. Finally, we prove that the tree in normal form could be easily transformed into the reconciled tree [12] in duplication-loss model. This solves some open problems stated in [13].
Keywords
Financial support is provided by KBN Grant 4 T11F 020 25.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Arvestad, L., Berglund, A.-C., Lagergren, J., Sennblad, B.: Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution. In: RECOMB 2004 (2004)
Bonizzoni, P., Vedova, G.D., Dondi, R.: Reconciling gene trees to a species tree. Algorithms and Complexity. In: Petreschi, R., Persiano, G., Silvestri, R. (eds.) CIAC 2003. LNCS, vol. 2653, pp. 120–131. Springer, Heidelberg (2003)
Charleston, M.A.: Jungles: A new solution to the host/parasite phylogeny reconciliation problem. Mathematical Biosciences 149, 191–223 (1998)
Eulenstein, Vingron: On the equivalence of two tree mapping measures. DAMATH: Discrete Applied Mathematics and Combinatorial Operations Research and Computer Science 88 (1998)
Eulenstein, O., Mirkin, B., Vingron, M.: Duplication-based measures of difference between gene and species trees. Journal of Computational Biology 1, 135–148 (1998)
Goodman, M., Czelusniak, J., Moore, G.W., Romero-Harrera, A.E., Matsuda, G.: Fitting the gene lineage into its species lineage. A parsimony strategy illustrated by cladograms constructed from globin sequences. Syst. Zool. 28, 132–163 (1979)
Hallett, M.T., Lagergren, J.: New algorithms for the duplication-loss model. In: Proceedings of RECOMB 2000, Tokyo, pp. 138–146. ACM Press, New York (2000)
Ma, B., Li, M., Zhang, L.: On Reconstructing Species Trees from Gene Trees in Term of Duplications and Losses. In: RECOMB 1998, pp. 182–191 (1998)
Ma, B., Li, M., Zhang, L.: From gene trees to species trees. SIAM Journal of Comput. 30, 792–852 (2000)
Górecki, P.: Reconciliation problems for duplication, loss and horizontal gene transfer. In: RECOMB 2004, San Diego (2004)
Mirkin, B., Muchnik, I., Smith, T.F.: A biologically meaningful model for comparing molecular phylogenies. J. of Comput. Biol. 2, 492–507 (1995)
Page, R.D.M.: Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas. Systematic Biology 43, 58–77 (1994)
Page, R.D.M., Charleston, M.A.: Reconciled trees and incogruent gene and species trees. Mathematical Hierarchies and Biology. DIMACS Series in Mathematics and Theoretical Computers Science, vol. 37(57–70) (1997)
Page, R.D.M.: Component analysis: A valiant failure? Cladistics 6, 119–136 (1990)
Muchnik, I., Guigo, R., Smith, T.: Reconstruction of ancient molecular phylogeny. Mol. Phy. and Evol. 6, 189–213 (1996)
Zhang, L.: On a mirkin-muchnik-smith conjecture for comparing molecular phylog enies. Journal of Computational Biology 4(2), 177–188 (1997)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Górecki, P., Tiuryn, J. (2005). On the Structure of Reconciliations. In: Lagergren, J. (eds) Comparative Genomics. RCG 2004. Lecture Notes in Computer Science(), vol 3388. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-32290-0_4
Download citation
DOI: https://doi.org/10.1007/978-3-540-32290-0_4
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-24455-4
Online ISBN: 978-3-540-32290-0
eBook Packages: Computer ScienceComputer Science (R0)