172 research outputs found
Treewidth of display graphs: bounds, brambles and applications
Phylogenetic trees and networks are leaf-labelled graphs used to model evolution. Display graphs are created by identifying common leaf labels in two or more phylogenetic trees or networks. The treewidth of such graphs is bounded as a function of many common dissimilarity measures between phylogenetic trees and this has been leveraged in fixed parameter tractability results. Here we further elucidate the properties of display graphs and their interaction with treewidth. We show that it is NP-hard to recognize display graphs, but that display graphs of bounded treewidth can be recognized in linear time. Next we show that if a phylogenetic network displays (i.e. topologically embeds) a phylogenetic tree, the treewidth of their display graph is bounded by a function of the treewidth of the original network (and also by various other parameters). In fact, using a bramble argument we show that this treewidth bound is sharp up to an additive term of 1. We leverage this bound to give an FPT algorithm, parameterized by treewidth, for determining whether a network displays a tree, which is an intensively-studied problem in the field. We conclude with a discussion on the future use of display graphs and treewidth in phylogenetics
The Complexity of Rooted Phylogeny Problems
Several computational problems in phylogenetic reconstruction can be
formulated as restrictions of the following general problem: given a formula in
conjunctive normal form where the literals are rooted triples, is there a
rooted binary tree that satisfies the formula? If the formulas do not contain
disjunctions, the problem becomes the famous rooted triple consistency problem,
which can be solved in polynomial time by an algorithm of Aho, Sagiv,
Szymanski, and Ullman. If the clauses in the formulas are restricted to
disjunctions of negated triples, Ng, Steel, and Wormald showed that the problem
remains NP-complete. We systematically study the computational complexity of
the problem for all such restrictions of the clauses in the input formula. For
certain restricted disjunctions of triples we present an algorithm that has
sub-quadratic running time and is asymptotically as fast as the fastest known
algorithm for the rooted triple consistency problem. We also show that any
restriction of the general rooted phylogeny problem that does not fall into our
tractable class is NP-complete, using known results about the complexity of
Boolean constraint satisfaction problems. Finally, we present a pebble game
argument that shows that the rooted triple consistency problem (and also all
generalizations studied in this paper) cannot be solved by Datalog
Evolution through segmental duplications and losses : A Super-Reconciliation approach
The classical gene and species tree reconciliation, used to infer the history of gene gain and loss explaining the evolution of gene families, assumes an independent evolution for each family. While this assumption is reasonable for genes that are far apart in the genome, it is not appropriate for genes grouped into syntenic blocks, which are more plausibly the result of a concerted evolution. Here, we introduce the Super-Reconciliation problem which consists in inferring a history of segmental duplication and loss events (involving a set of neighboring genes) leading to a set of present-day syntenies from a single ancestral one. In other words, we extend the traditional Duplication-Loss reconciliation problem of a single gene tree, to a set of trees, accounting for segmental duplications and losses. Existency of a Super-Reconciliation depends on individual gene tree consistency. In addition, ignoring rearrangements implies that existency also depends on gene order consistency. We first show that the problem of reconstructing a most parsimonious Super-Reconciliation, if any, is NP-hard and give an exact exponential-time algorithm to solve it. Alternatively, we show that accounting for rearrangements in the evolutionary model, but still only minimizing segmental duplication and loss events, leads to an exact polynomial-time algorithm. We finally assess time efficiency of the former exponential time algorithm for the Duplication-Loss model on simulated datasets, and give a proof of concept on the opioid receptor genes
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