Orthology Relations and the Reconciliation of Gene and Species Trees
Presented by Peter STADLER
Type: Oral presentation
Track: Graphs and Networks in Biology
The evolution of a family of genes is represented by a "gene tree" T, whose leafs are labeled by the genes. The internal vertices of T represent the evolutionary events that lead to the separation of lineages: gene duplications and speciation events. Genes to no occur in isolation but have been determined from known species. The evolutionary history of the species is encoded by a species tree S. The reconstruction of the history of a gene family is an important problem in the field of molecular evolution. Given S and T, one has to determine the event labels of the internal vertices of T and a mapping of the vertices from S to T so that 'speciation events' in T map to internal vertices of S and 'duplication events' map to edges of S. Two genes are co-orthologs if their last common ancestor in T is a speciation event; they are strict orthologs if all events along the path in T between them are speciation event, and in-paralogs if all events are duplications. Interestingly, it is possible to estimate the co-orthology relation (at least in part) directly from sequence data . We investigate here to what extent the co-orthology relation together with the assignment of genes to species constrains of even determines the trees S and T and the reconciliation map between them. To this end we build on results from the theory of symbolic ultrametrics  and on the reconstructibility of trees from sets of triples .  M. Lechner, S. Findeiß, L. Steiner, M. Marz, P.F. Stadler, S.J. Prohaska. Proteinortho: Detection of (Co-)Orthologs in Large-Scale Analysis. BMC Bioinformatics 12:124, 2011.  S. Böcker and A.W.M. Dress. Recovering symbolically dated, rooted trees from symbolic ultrametrics. Advances in Mathematics, 138:105–125, 1998.  A.V. Aho, T.G. Sagiv, T.G. Szymanski, J.D. Ullman, Inferring a tree from lowest common ancestors with an application to the optimization of relational expressions, SIAM J. Comput. 10:405–421, 1981.