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New Algorithmic and Mathematical Tools to Construct a Net of Life

Objective

Phylogenetics, the study of evolutionary relationships among groups of species, is a well-established interdisciplinary scientific field. Until today, phylogeneticists put a lot of effort into the precise reconstruction of evolutionary trees. However, in recent years, the research focus on reconstructing phylogenetic trees is turning towards the reconstruction of phylogenetic networks because evolution cannot be properly represented as a tree. For example, a comparison of several trees that all represent a given set of present-day species and have been reconstructed for different genetic loci often reveals conflicting tree topologies. These discrepancies are not always due to missampling or uncertainty in the tree reconstruction method, but rather due to reticulation (e.g. horizontal gene transfer, hybridization, or recombination).

Since phylogenetic networks are far more complex than phylogenetic trees, new mathematical and computational tools are needed. This proposal suggests new directions of research within the broad area of phylogenetic networks. First, we will develop new (fixed-parameter) algorithms to analyze intrahost recombination in viruses and apply them to biological data sets. This will provide new insight into the evolution of RNA viruses (e.g. HIV), which is essential in the development of any medication. Second, noting that many questions that are polynomial-time solvable for phylogenetic trees are NP-hard for when stated in terms of networks, we will tackle these harder questions by using novel methodology. Instead of directly solving a problem for a network, we will transform a given network into a tree by using the concept of tree-decompositions, and then solve an `easier' problem for the obtained tree. In particular, we will investigate problems related to the parsimony score of a phylogenetic network and supernetworks.

Call for proposal

FP7-PEOPLE-2011-IOF
See other projects for this call

Coordinator

EBERHARD KARLS UNIVERSITAET TUEBINGEN
Address
Geschwister-scholl-platz
72074 Tuebingen
Germany
Activity type
Higher or Secondary Education Establishments
EU contribution
€ 192 461,62
Administrative Contact
Marine Gaudefroy Bergmann (Ms.)