LIFENET

New Algorithmic and Mathematical Tools to Construct a Net of Life

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 Obiettivo del progetto (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.'

Introduzione (Teaser)

The classic evolutionary tree is challenged in the face of new genomic data. Using mathematical and computational tools, the more complex phylogenetic network is better suited to accurately represent complex evolutionary relationships.

Descrizione progetto (Article)

Phylogenetics uses a tree to depict the evolutionary links between groups of species. However, an evolutionary tree cannot adequately represent all genetic processes occurring throughout evolution. The use of different genetic loci, for example, will give conflicting species interrelationships due to processes such as horizontal gene transfer and recombination.

The LIFENET (New algorithmic and mathematical tools to construct a net of life) project has developed algorithms to construct phylogenetic networks. The team studied gene recombination events in viruses to provide new insight into evolution of viruses such as HIV.

The research group has established an algorithm to quantify hybridisation for an arbitrary number of trees that was previously limited to two trees. Furthermore, parsimony analyses for trees were extended to networks. Previously used parsimony frameworks produce networks with reduced biological relevance. LIFENET has therefore proposed a new definition of parsimony for networks.

LIFENET also settled questions related to the computational complexity of several decision problems related to phylogenetic networks. For example, it was shown that counting the number of trees that a phylogenetic network simultaneously embeds is a computationally hard problem.

Research results have been published in several peer-reviewed journals. The work also helped to establish fruitful collaborations between researchers in Germany, the Netherlands, New Zealand and the United States.

LIFENET has enabled the incorporation of a variety of genetic events into a phylogenetic network or tree. Complex interactions are common through evolution and their incorporation is necessary for the application of disease therapy.