Abstract
BackgroundMaximum parsimony phylogenetic tree reconciliation is an important technique for reconstructing the evolutionary histories of hosts and parasites, genes and species, and other interdependent pairs. Since the problem of finding temporally feasible maximum parsimony reconciliations is NP-complete, current methods use either exact algorithms with exponential worst-case running time or heuristics that do not guarantee optimal solutions.ResultsWe offer an efficient new approach that begins with a potentially infeasible maximum parsimony reconciliation and iteratively “repairs” it until it becomes temporally feasible.ConclusionsIn a non-trivial number of cases, this approach finds solutions that are better than those found by the widely-used Jane heuristic.
Highlights
Maximum parsimony phylogenetic tree reconciliation is an important technique for reconstructing the evolutionary histories of hosts and parasites, genes and species, and other interdependent pairs
Phylogenetic tree reconciliation is a fundamental technique for studying the evolution of pairs of entities such as gene families and species, parasites and their hosts, and species and their geographical habitats
The reconciliation problem takes as input two trees and the associations between their leaves and seeks to find a mapping between the trees that accounts for their incongruence
Summary
Phylogenetic tree reconciliation is a fundamental technique for studying the evolution of pairs of entities such as gene families and species, parasites and their hosts, and species and their geographical habitats. We propose a new approach for finding temporally feasible reconciliations This approach runs in polynomial time and, in a non-trivial number of cases (11% in our experiments using the Tree of Life dataset [5]), gives more parsimonious solutions than those found by Jane. We note that seminal work by Tofigh et al [7] explores repairing temporally infeasible reconciliations in the Duplication-Transfer model They give an exact algorithm that runs in time exponential in the cost of the reconciliation. An instance of the maximum parsimony reconciliation problem comprises a gene tree G, a species tree S, a leaf mapping L : Le(G) → Le(S), and positive costs C , C , and C for duplication, transfer, and loss events, respectively. For each v ∈ V such that its corresponding node in S or G is the parent of a leaf, there is an edge (v, ) ∈ E
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