Results 1  10
of
27
Comparison of treechild phylogenetic networks,
 IEEE/ACM Transactions on Computational Biology and Bioinformatics
, 2009
"... ..."
(Show Context)
Evolutionary Phylogenetic Networks: Models and Issues
"... Abstract Phylogenetic networks are special graphs that generalize phylogenetic trees to allow for modeling of nontreelike evolutionary histories. The ability to sequence multiple genetic markers from a set of organisms and the conflicting evolutionary signals that these markers provide in many case ..."
Abstract

Cited by 18 (5 self)
 Add to MetaCart
(Show Context)
Abstract Phylogenetic networks are special graphs that generalize phylogenetic trees to allow for modeling of nontreelike evolutionary histories. The ability to sequence multiple genetic markers from a set of organisms and the conflicting evolutionary signals that these markers provide in many cases, have propelled research and interest in phylogenetic networks to the forefront in computational phylogenetics. Nonetheless, the term ‘phylogenetic network ’ has been generically used to refer to a class of models whose core shared property is tree generalization. Several excellent surveys of the different flavors of phylogenetic networks and methods for their reconstruction have been written recently. However, unlike these surveys, this chapter focuses specifically on one type of phylogenetic networks, namely evolutionary phylogenetic networks, which explicitly model reticulate evolutionary events. Further, this chapter focuses less on surveying existing tools, and addresses in more detail issues that are central to the accurate reconstruction of phylogenetic networks. 1
Tripartitions do not always discriminate phylogenetic networks,”Mathematical Biosciences,
, 2008
"... ..."
(Show Context)
Parsimony score of phylogenetic networks: Hardness results and a lineartime heuristic
 IEEE/ACM TRANS. COMPUT. BIOLOGY BIOINFORM
, 2009
"... Phylogenies—the evolutionary histories of groups of organisms—play a major role in representing the interrelationships among biological entities. Many methods for reconstructing and studying such phylogenies have been proposed, almost all of which assume that the underlying history of a given set o ..."
Abstract

Cited by 13 (5 self)
 Add to MetaCart
(Show Context)
Phylogenies—the evolutionary histories of groups of organisms—play a major role in representing the interrelationships among biological entities. Many methods for reconstructing and studying such phylogenies have been proposed, almost all of which assume that the underlying history of a given set of species can be represented by a binary tree. Although many biological processes can be effectively modeled and summarized in this fashion, others cannot: recombination, hybrid speciation, and horizontal gene transfer result in networks of relationships rather than trees of relationships. In previous works, we formulated a maximum parsimony (MP) criterion for reconstructing and evaluating phylogenetic networks, and demonstrated its quality on biological as well as synthetic data sets. In this paper, we provide further theoretical results as well as a very fast heuristic algorithm for the MP criterion of phylogenetic networks. In particular, we provide a novel combinatorial definition of phylogenetic networks in terms of “forbidden cycles, ” and provide detailed hardness and hardness of approximation proofs for the “small ” MP problem. We demonstrate the performance of our heuristic in terms of time and accuracy on both biological and synthetic data sets. Finally, we explain the difference between our model and a similar one formulated by Nguyen et al., and describe the implications of this difference on the hardness and approximation results.
A new lineartime heuristic algorithm for computing the parsimony score of phylogenetic networks: Theoretical bounds and empirical performance
, 2007
"... Phylogenies play a major role in representing the interrelationships among biological entities. Many methods for reconstructing and studying such phylogenies have been proposed, almost all of which assume that the underlying history of a given set of species can be represented by a binary tree. Al ..."
Abstract

Cited by 11 (5 self)
 Add to MetaCart
(Show Context)
Phylogenies play a major role in representing the interrelationships among biological entities. Many methods for reconstructing and studying such phylogenies have been proposed, almost all of which assume that the underlying history of a given set of species can be represented by a binary tree. Although many biological processes can be effectively modeled and summarized in this fashion, others cannot: recombination, hybrid speciation, and horizontal gene transfer result in networks, rather than trees, of relationships. In a series of papers, we have extended the maximum parsimony (MP) criterion to phylogenetic networks, demonstrated its appropriateness, and established the intractability of the problem of scoring the parsimony of a phylogenetic network. In this work we show the hardness of approximation for the general case of the problem, devise a very fast (lineartime) heuristic algorithm for it, and implement it on simulated as well as biological data.
SEEING THE TREES AND THEIR BRANCHES IN THE NETWORK IS HARD
, 2007
"... Phylogenetic networks are a restricted class of directed acyclic graphs that model evolutionary histories in the presence of reticulate evolutionary events, such as horizontal gene transfer, hybrid speciation, and recombination. Characterizing a phylogenetic network as a collection of trees and thei ..."
Abstract

Cited by 9 (1 self)
 Add to MetaCart
Phylogenetic networks are a restricted class of directed acyclic graphs that model evolutionary histories in the presence of reticulate evolutionary events, such as horizontal gene transfer, hybrid speciation, and recombination. Characterizing a phylogenetic network as a collection of trees and their branches has long been the basis for several methods of reconstructing and evaluating phylogenetic networks. Further, these characterizations have been used to understand molecular sequence evolution on phylogenetic networks. In this paper, we address theoretical questions with regard to phylogenetic networks, their characterizations, and sequence evolution on them. In particular, we prove that the problem of deciding whether a given tree is contained inside a network is NPcomplete. Further, we prove that the problem of deciding whether a branch of a given tree is also a branch of a given network is polynomially equivalent to that of deciding whether the evolution of a molecular character (site) on a network is governed by the infinite site model. Exploiting this equivalence, we establish the NPcompleteness of both problems, and provide a parameterized algorithm that runs in time O(2 k/2 n 2), where n is the total number of nodes and k is the number of recombination nodes in the network, which significantly improves upon the trivial bruteforce O(2 k n) time algorithm for the problem. This reduction in time is significant, particularly when analyzing recombination hotspots.
Properties of normal phylogenetic networks
, 2009
"... Abstract. A phylogenetic network is a rooted acyclic digraph with vertices corresponding to taxa. Let X denote a set of vertices containing the root, the leaves, and all vertices of outdegree 1. Regard X as the set of vertices on which measurements such as DNA can be made. A vertex is called normal ..."
Abstract

Cited by 7 (3 self)
 Add to MetaCart
(Show Context)
Abstract. A phylogenetic network is a rooted acyclic digraph with vertices corresponding to taxa. Let X denote a set of vertices containing the root, the leaves, and all vertices of outdegree 1. Regard X as the set of vertices on which measurements such as DNA can be made. A vertex is called normal if it has one parent, and hybrid if it has more than one parent. The network is called normal if it has no redundant arcs and also from every vertex there is a directed path to a member of X such that all vertices after the first are normal. This paper studies properties of normal networks. Under a simple model of inheritance that allows homoplasies only at hybrid vertices, there is essentially unique determination of the genomes at all vertices by the genomes at members of X if and only if the network is normal. This model is a limiting case of more standard models of inheritance when the substitution rate is sufficiently low. Various mathematical properties of normal networks are described. These properties include that the number of vertices grows at most quadratically with the number of leaves and that the number of hybrid vertices grows at most linearly with the number of leaves. Key words: normal network; hybrid; recombination; speciation; genome; ancestral reconstruction. 1
Integrating sequence and topology for efficient and accurate detection of horizontal gene transfer
 PROCEEDINGS OF THE SIXTH RECOM COMPARATIVE GENOMICS SATELLITE WORKSHOP
, 2008
"... One phylogenybased approach to horizontal gene transfer (HGT) detection entails comparing the topology of a gene tree to that of the species tree, and using their differences to locate HGT events. Another approach is based on augmenting a species tree into a phylogenetic network to improve the fit ..."
Abstract

Cited by 5 (2 self)
 Add to MetaCart
One phylogenybased approach to horizontal gene transfer (HGT) detection entails comparing the topology of a gene tree to that of the species tree, and using their differences to locate HGT events. Another approach is based on augmenting a species tree into a phylogenetic network to improve the fitness of the evolution of the gene sequence data under an optimization criterion, such as maximum parsimony (MP). One major problem with the first approach is that gene tree estimates may have wrong branches, which result in false positive estimates of HGT events, and the second approach is accurate, yet suffers from the computational complexity of searching through the space of possible phylogenetic networks. The contributions of this paper are twofold. First, we present a measure that computes the support of HGT events inferred from pairs of species and gene trees. The measure uses the bootstrap values of the gene tree branches. Second, we present an integrative method to speed up the approaches for augmenting species trees into phylogenetic networks. We conducted data analysis and performance study of our methods on a data set of 20 genes from the Amborella mitochondrial genome, in which Jeffrey Palmer and his coworkers postulated a massive amount of horizontal gene transfer. As expected, we found that including poorly supported gene tree branches in the analysis results in a high rate of false positive gene transfer events. Further, the bootstrapbased support measure assessed, with high accuracy, the support of the inferred gene transfer events. Further, we obtained very promising results, in terms of both speed and accuracy, when applying our integrative method on these data sets (we are currently studying the performance in extensive simulations). All methods have been implemented in the PhyloNet and NEPAL tools, which are available in the form of executable code
TreeSibling Time Consistent Phylogenetic Networks Are Graph IsomorphismComplete,” http://arxiv.org/abs/0902.4640
, 2009
"... Several polynomial time computable metrics on the class of semibinary treesibling time consistent phylogenetic networks are available in the literature; in particular, the problem of deciding if two networks of this kind are isomorphic is in P. In this paper, we show that if we remove the semibina ..."
Abstract

Cited by 2 (1 self)
 Add to MetaCart
(Show Context)
Several polynomial time computable metrics on the class of semibinary treesibling time consistent phylogenetic networks are available in the literature; in particular, the problem of deciding if two networks of this kind are isomorphic is in P. In this paper, we show that if we remove the semibinarity condition, then the problem becomes much harder. More precisely, we prove that the isomorphism problem for generic treesibling time consistent phylogenetic networks is polynomially equivalent to the graph isomorphism problem. Since the latter is believed not to belong to P, the chances are that it is impossible to define a metric on the class of all treesibling time consistent phylogenetic networks that can be computed in polynomial time.