46,472 research outputs found
Trinets encode tree-child and level-2 phylogenetic networks
Phylogenetic networks generalize evolutionary trees, and are commonly used to represent evolutionary histories of species that undergo reticulate evolutionary processes such as hybridization, recombination and lateral gene transfer. Recently, there has been great interest in trying to develop methods to construct rooted phylogenetic networks from triplets, that is rooted trees on three species. However, although triplets determine or encode rooted phylogenetic trees, they do not in general encode rooted phylogenetic networks, which is a potential issue for any such method. Motivated by this fact, Huber and Moulton recently introduced trinets as a natural extension of rooted triplets to networks. In particular, they showed that level-1 level-1 phylogenetic networks are encoded by their trinets, and also conjectured that all “recoverable” rooted phylogenetic networks are encoded by their trinets. Here we prove that recoverable binary level-2 networks and binary tree-child networks are also encoded by their trinets. To do this we prove two decomposition theorems based on trinets which hold for all recoverable binary rooted phylogenetic networks. Our results provide some additional evidence in support of the conjecture that trinets encode all recoverable rooted phylogenetic networks, and could also lead to new approaches to construct phylogenetic networks from trinets
Trinets encode tree-child and level-2 phylogenetic networks
Phylogenetic networks generalize evolutionary trees, and are commonly used to
represent evolutionary histories of species that undergo reticulate
evolutionary processes such as hybridization, recombination and lateral gene
transfer. Recently, there has been great interest in trying to develop methods
to construct rooted phylogenetic networks from triplets, that is rooted trees
on three species. However, although triplets determine or encode rooted
phylogenetic trees, they do not in general encode rooted phylogenetic networks,
which is a potential issue for any such method. Motivated by this fact, Huber
and Moulton recently introduced trinets as a natural extension of rooted
triplets to networks. In particular, they showed that level-1 phylogenetic
networks are encoded by their trinets, and also conjectured that all
"recoverable" rooted phylogenetic networks are encoded by their trinets. Here
we prove that recoverable binary level-2 networks and binary tree-child
networks are also encoded by their trinets. To do this we prove two
decomposition theorems based on trinets which hold for all recoverable binary
rooted phylogenetic networks. Our results provide some additional evidence in
support of the conjecture that trinets encode all recoverable rooted
phylogenetic networks, and could also lead to new approaches to construct
phylogenetic networks from trinets
Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets
Binets and trinets are phylogenetic networks with two and three leaves, respectively. Here we consider the problem of deciding if there exists a binary level-1 phylogenetic network displaying a given set T of binary binets or trinets over a taxon set X, and constructing such a network whenever it exists. We show that this is NP-hard for trinets but polynomial-time solvable for binets. Moreover, we show that the problem is still polynomial-time solvable for inputs consisting of binets and trinets as long as the cycles in the trinets have size three. Finally, we present an O(3^{|X|} poly(|X|)) time algorithm for general sets of binets and trinets. The latter two algorithms generalise to instances containing level-1 networks with arbitrarily many leaves, and thus provide some of the first supernetwork algorithms for computing networks from a set of rooted 1 phylogenetic networks
A first step towards computing all hybridization networks for two rooted binary phylogenetic trees
Recently, considerable effort has been put into developing fast algorithms to
reconstruct a rooted phylogenetic network that explains two rooted phylogenetic
trees and has a minimum number of hybridization vertices. With the standard
approach to tackle this problem being combinatorial, the reconstructed network
is rarely unique. From a biological point of view, it is therefore of
importance to not only compute one network, but all possible networks. In this
paper, we make a first step towards approaching this goal by presenting the
first algorithm---called allMAAFs---that calculates all
maximum-acyclic-agreement forests for two rooted binary phylogenetic trees on
the same set of taxa.Comment: 21 pages, 5 figure
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Lowest common ancestor interconnection networks
Lowest Common Ancestor (LCA) networks are built using switches capable of connecting u + d inputs/outputs in a permutation pattern. For n source nodes and I stages of switches, n/d switches are used in stage l - n/d - u/d in stage l - 2, and in general , n-u^l-i-l/d^l-i switches in stage i. The resulting hierarchical structure possesses interesting connectivity and permutational properties. A full characterization of LCA networks is presented together with a permutation routing algorithm for a family of LCA networks. The algorithm uses the network itself to collect and disseminate information about the permutation. A schedule of O(dp log_d/u n) passes is obtained with a switch set-up cost factor of O(log_d/u n) (p is the minimum number of passes that an algorithm with global knowledge schedules)
Lower Bounds in the Preprocessing and Query Phases of Routing Algorithms
In the last decade, there has been a substantial amount of research in
finding routing algorithms designed specifically to run on real-world graphs.
In 2010, Abraham et al. showed upper bounds on the query time in terms of a
graph's highway dimension and diameter for the current fastest routing
algorithms, including contraction hierarchies, transit node routing, and hub
labeling. In this paper, we show corresponding lower bounds for the same three
algorithms. We also show how to improve a result by Milosavljevic which lower
bounds the number of shortcuts added in the preprocessing stage for contraction
hierarchies. We relax the assumption of an optimal contraction order (which is
NP-hard to compute), allowing the result to be applicable to real-world
instances. Finally, we give a proof that optimal preprocessing for hub labeling
is NP-hard. Hardness of optimal preprocessing is known for most routing
algorithms, and was suspected to be true for hub labeling
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