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

Hymenopterous parasites associated with Phyllonorycter blancardella [Lepidoptera: Gracillariidae] in Nova Scotia and Quebec

Une étude a été effectuée dans des vergers commerciaux et non-traités du Québec et de la Nouvelle-Écosse pour déterminer l’abondance et la diversité des parasites de la mineuse marbrée, Phyllonorycter blancardella [Lepidoptera : Gracillariidae]. Au Québec, 29 espèces de parasites ont été retrouvées et elles appartenaient à 7 familles, soit Aphelinidae, Braconidae, Chalcidae, Eulophidae, Ichneumonidae, Pteromalidae et Scelionidae. Les espèces les plus fréquentes étaient : Pholetesor ornigis (67 %), Sympiesis marylandensis (11 %), S. serviceicornis (7 %), Pnigalio maculipes (1,5 %), Tetrasticus spp. (1,2 %). Toutes les autres espèces représentaient moins de 1 % des espèces trouvées. Pholetesor pedias, une espèce braconide relâchée à Frelighsburg, Québec en 1983 n’a pas été détectée en 1984 et 1985. En Nouvelle-Écosse, 19 espèces ont été trouvées et elles appartenaient à 5 familles, soit Braconidae, Chalcidae, Eulophidae, Ichneumonidae et Pteromalidae. Les espèces les plus fréquentes étaient : Pholetesor ornigis (52 %), Pnigalio maculipes (14 %), Sympiesis serviceicornis (12 %), S. marylandensis (9,5 %), Sympiesis spp. (5 %), Horismenus fraternus (1,8 %), Paraleurocerus sp. (1,3 %), Stictopisthus flaviceps (1,1 %); toutes les autres espèces représentaient moins de 1 % des espèces trouvées. Sept et cinq espèces d’hyperparasites ont été retrouvées en Nouvelle-Écosse et au Québec, respectivement. Sticopisthus bilineatus, S. flaviceps, Euderis sp., Pnigalio epilobii, P. pallipes and Paraleurocerus bicoloripes constituent des nouvelles mentions comme parasites de la mineuse marbrée pour l’Amérique du Nord.Mined leaves were collected in commercial and unsprayed (no insecticides) apple orchards of Quebec and Nova Scotia to determine the relative abundance and diversity of parasites of the spotted tentiform leafminer, Phyllonorycter blancardella [Lepidoptera: Gracillariidae]. In Quebec, 29 species of leafminer parasites were recovered, belonging to 7 families: Aphelinidae, Braconidae, Chalcidae, Eulophidae, Ichneumonidae, Pteromalidae and Scelionidae. The most prevalent species were Pholetesor ornigis (67%), Sympiesis marylandensis (11%), S. serviceicornis (7%), Pnigalio maculipes (1.5%), Tetrasticus spp. (1.2%), while all other species accounted for < 1.0%. Pholetesor pedias, a braconid released in 1983 at Frelighsburg, Quebec, was not found in the 1984 and 1985 surveys. In Nova Scotia, 19 parasite species were recovered, belonging to 5 families : Braconidae, Encyrtidae, Eulophidae, Ichneumonidae and Pteromalidae. The most prevalent species were: Pholetesor ornigis (52%), Pnigalio maculipes (14%), Sympiesis serviceicornis (12%), S. marylandensis (9.5%), Sympiesis spp. (5%), Horismenus fraternus (1.8%), Paraleurocerus sp. (1.3%), Stictopisthus flaviceps (1.1%), while all other species accounted for < 1%. Seven and five species of hyperparasites were recovered in Nova Scotia and Quebec, respectively. New records for North America for the spotted tentiform leafminer as a host are : Sticopisthus bilineatus, S. flaviceps, Euderis sp., Pnigalio epilobii, P. pallipes and Paraleurocerus bicoloripes

Software for Computing and Annotating Genomic Ranges

We describe Bioconductor infrastructure for representing and computing on annotated genomic ranges and integrating genomic data with the statistical computing features of R and its extensions. At the core of the infrastructure are three packages: IRanges, GenomicRanges, and GenomicFeatures. These packages provide scalable data structures for representing annotated ranges on the genome, with special support for transcript structures, read alignments and coverage vectors. Computational facilities include efficient algorithms for overlap and nearest neighbor detection, coverage calculation and other range operations. This infrastructure directly supports more than 80 other Bioconductor packages, including those for sequence analysis, differential expression analysis and visualization

Quarnet Inference Rules for Level-1 Networks

An important problem in phylogenetics is the construction of phylogenetic trees. One way to approach this problem, known as the supertree method, involves inferring a phylogenetic tree with leaves consisting of a set X of species from a collection of trees, each having leaf-set some subset of X. In the 1980s, Colonius and Schulze gave certain inference rules for deciding when a collection of 4-leaved trees, one for each 4-element subset of X, can be simultaneously displayed by a single supertree with leaf-set X. Recently, it has become of interest to extend this and related results to phylogenetic networks. These are a generalization of phylogenetic trees which can be used to represent reticulate evolution (where species can come together to form a new species). It has recently been shown that a certain type of phylogenetic network, called a (unrooted) level-1 network, can essentially be constructed from 4-leaved trees. However, the problem of providing appropriate inference rules for such networks remains unresolved. Here, we show that by considering 4-leaved networks, called quarnets, as opposed to 4-leaved trees, it is possible to provide such rules. In particular, we show that these rules can be used to characterize when a collection of quarnets, one for each 4-element subset of X, can all be simultaneously displayed by a level-1 network with leaf-set X. The rules are an intriguing mixture of tree inference rules, and an inference rule for building up a cyclic ordering of X from orderings on subsets of X of size 4. This opens up several new directions of research for inferring phylogenetic networks from smaller ones, which could yield new algorithms for solving the supernetwork problem in phylogenetics

Recognizing Treelike k-Dissimilarities

A k-dissimilarity D on a finite set X, |X| >= k, is a map from the set of size k subsets of X to the real numbers. Such maps naturally arise from edge-weighted trees T with leaf-set X: Given a subset Y of X of size k, D(Y) is defined to be the total length of the smallest subtree of T with leaf-set Y . In case k = 2, it is well-known that 2-dissimilarities arising in this way can be characterized by the so-called "4-point condition". However, in case k > 2 Pachter and Speyer recently posed the following question: Given an arbitrary k-dissimilarity, how do we test whether this map comes from a tree? In this paper, we provide an answer to this question, showing that for k >= 3 a k-dissimilarity on a set X arises from a tree if and only if its restriction to every 2k-element subset of X arises from some tree, and that 2k is the least possible subset size to ensure that this is the case. As a corollary, we show that there exists a polynomial-time algorithm to determine when a k-dissimilarity arises from a tree. We also give a 6-point condition for determining when a 3-dissimilarity arises from a tree, that is similar to the aforementioned 4-point condition.Comment: 18 pages, 4 figure

Pretreatment with a novel aquaporin 4 inhibitor, TGN-020, significantly reduces ischemic cerebral edema

We investigated the in vivo effects of a novel aquaporin 4 (AQP4) inhibitor 2-(nicotinamide)-1,3,4-thiadiazole, TGN-020, in a mouse model of focal cerebral ischemia using 7.0-T magnetic resonance imaging (MRI). Pretreatment with TGN-020 significantly reduced brain edema associated with brain ischemia, as reflected by percentage of brain swelling volume (%BSV), 12.1 ± 6.3% in the treated group, compared to (20.8 ± 5.9%) in the control group (p < 0.05), and in the size of cortical infarction as reflected by the percentage of hemispheric lesion volume (%HLV), 20.0 ± 7.6% in the treated group, compared to 30.0 ± 9.1% in the control group (p < 0.05). The study indicated the potential pharmacological use of AQP4 inhibition in reducing brain edema associated with focal ischemia

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

Binets: fundamental building blocks for phylogenetic networks

Phylogenetic networks are a generalization of evolutionary trees that are used by biologists to represent the evolution of organisms which have undergone reticulate evolution. Essentially, a phylogenetic network is a directed acyclic graph having a unique root in which the leaves are labelled by a given set of species. Recently, some approaches have been developed to construct phylogenetic networks from collections of networks on 2- and 3-leaved networks, which are known as binets and trinets, respectively. Here we study in more depth properties of collections of binets, one of the simplest possible types of networks into which a phylogenetic network can be decomposed. More speci_cally, we show that if a collection of level-1 binets is compatible with some binary network, then it is also compatible with a binary level-1 network. Our proofs are based on useful structural results concerning lowest stable ancestors in networks. In addition, we show that, although the binets do not determine the topology of the network, they do determine the number of reticulations in the network, which is one of its most important parameters. We also consider algorithmic questions concerning binets. We show that deciding whether an arbitrary set of binets is compatible with some network is at least as hard as the well-known Graph Isomorphism problem. However, if we restrict to level-1 binets, it is possible to decide in polynomial time whether there exists a binary network that displays all the binets. We also show that to _nd a network that displays a maximum number of the binets is NP-hard, but that there exists a simple polynomial-time 1/3-approximation algorithm for this problem. It is hoped that these results will eventually assist in the development of new methods for constructing phylogenetic networks from collections of smaller networks