Phyloloc

Teisaire Emmanuel1, Domé Damián1, Bombau Nicolás1, Castro Carlos1, Gutson Daniel2, Jones Leandro3
1
Instituto Tecnológico de Buenos Aires, Buenos Aires, Argentina
2
FuDePAN, Córdoba, Argentina
3
Division of Molecular Biology, Estación de Fotobiología Playa Unión, Chubut, Argentina

Background

Emergent viruses and other pathogens spread out by means of chains of infection in which, basically, one
host passes the pathogen to another one. In this way, pathogens gradually spread along a geographic
range that usually corresponds to its host distribution. Hosts capable of moving long distances can
therefore largely drive pathogen dispersal.
Despite the obvious interest in the problem of tracing the geographic origin and dynamics of emerging
diseases, a formal optimality criterion capable of integrating phylogenetic and geographic data is lacking.
Here, we describe a method to estimate the geographic origin of any given clade in a rooted tree.

Conclusion

The method described here produces, for each node in a given tree, a vector of potential ancestral
locations. Each location present in this vector has an associated value, that reflects the plausibility, for the
corresponding location, of being the geographic origin of the node’s child.
In order to estimate the vectors of locations of the internal nodes, two passes are performed across the
tree: an initial down-pass (i.e. from tips to root), where the internal nodes’ vectors are given transitory
states, followed by an up-pass, where we obtain a higher level of integration among subtrees information.
The method considers the following three factors for the information integration:
• Topology
• Branch Length of every node, including terminals and non-terminals
• Geographical Information of terminal nodes, and geographical dispersion of their locations

Result

The algorithms previously presented, shall be part of a software product called Phyloloc, which shall also
let the user perform several operations on trees and well as provide phylogenetic analysis tools, including
the following:
• Tree Propagation: Execution of the algorithm introduced in the previous section
• Tree Consensus: Obtain a consensed tree from a set of trees, that contains information from all the set,
but in a way that is easier to analyze
• Tree Visualization: Provide a user friendly tool for visualizing phylogenetic trees
• Node Selection and Coloring: Point-and-click selection and coloring of nodes
• Node Collapsing and Expanding: Point-and-click collapsing and expanding of nodes
• Node Descendants and Ancestors Selection: Select all the descendants and ancestors of a certain node
• Tree Importing and Exporting: Import and export trees from and to text files
Phyloloc’s source shall be public under GPL V3 license, and work on newest Windows and Linux
distributions.

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