People involved: E. Caglioti, V. Loreto, A. Pagnani, S. Pompei, F. Tria
The first image we are used to associate to a phylogeny, is that of a tree (the tree of life, the genealogical tree of a family, the tree of languages..). What emerged in the last decade, and across different disciplines, is that this representation is too reductive in a wide number of cases. In biology, horizontal genes transfer is widely recognized to be a major mechanism of variation for many organisms. In linguistic, loans from a language to another play an important role in the evolution of a language. The identification of these phenomena induces a change in perspective with respect to the old idea of phylogenesis. In particular, in many cases, a clear hierarchy in the evolution lacks, so that phylogeny can no longer be represented as a tree and we have to consider some kind of network instead. This evidence uncovers the gap between the present and the needed analysis tools. While well established results are available for perfect phylogenies (i.e. evolutionary history that can be associated to a tree topology), when a deviation from a tree-like structure has to be considered very little is known, despite the efforts in this direction. Our project on phylogeny reconstruction aims at providing methods to identify and to correctly take into account deviations from perfect phylogenies and also at providing the community with suitable benchmarks to test the validity of inferred phylogenies. One crucial problem, once a tree or a network is reconstructed, is to determine how reliable it is, i.e. how well it represents the true evolutionary history.
