1,014 research outputs found
Unifying Parsimonious Tree Reconciliation
Evolution is a process that is influenced by various environmental factors,
e.g. the interactions between different species, genes, and biogeographical
properties. Hence, it is interesting to study the combined evolutionary history
of multiple species, their genes, and the environment they live in. A common
approach to address this research problem is to describe each individual
evolution as a phylogenetic tree and construct a tree reconciliation which is
parsimonious with respect to a given event model. Unfortunately, most of the
previous approaches are designed only either for host-parasite systems, for
gene tree/species tree reconciliation, or biogeography. Hence, a method is
desirable, which addresses the general problem of mapping phylogenetic trees
and covering all varieties of coevolving systems, including e.g., predator-prey
and symbiotic relationships. To overcome this gap, we introduce a generalized
cophylogenetic event model considering the combinatorial complete set of local
coevolutionary events. We give a dynamic programming based heuristic for
solving the maximum parsimony reconciliation problem in time O(n^2), for two
phylogenies each with at most n leaves. Furthermore, we present an exact
branch-and-bound algorithm which uses the results from the dynamic programming
heuristic for discarding partial reconciliations. The approach has been
implemented as a Java application which is freely available from
http://pacosy.informatik.uni-leipzig.de/coresym.Comment: Peer-reviewed and presented as part of the 13th Workshop on
Algorithms in Bioinformatics (WABI2013
Exact reconciliation of undated trees
Reconciliation methods aim at recovering macro evolutionary events and at
localizing them in the species history, by observing discrepancies between gene
family trees and species trees. In this article we introduce an Integer Linear
Programming (ILP) approach for the NP-hard problem of computing a most
parsimonious time-consistent reconciliation of a gene tree with a species tree
when dating information on speciations is not available. The ILP formulation,
which builds upon the DTL model, returns a most parsimonious reconciliation
ranging over all possible datings of the nodes of the species tree. By studying
its performance on plausible simulated data we conclude that the ILP approach
is significantly faster than a brute force search through the space of all
possible species tree datings. Although the ILP formulation is currently
limited to small trees, we believe that it is an important proof-of-concept
which opens the door to the possibility of developing an exact, parsimony based
approach to dating species trees. The software (ILPEACE) is freely available
for download
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