Ran Libeskind-Hadas

Jane: a new tool for the cophylogeny reconstruction problem

BackgroundThis paper describes the theory and implementation of a new software tool, called Jane, for the study of historical associations. This problem arises in parasitology (associations of hosts and parasites), molecular systematics (associations of orderings and genes), and biogeography (associations of regions and orderings). The underlying problem is that of reconciling pairs of trees subject to biologically plausible events and costs associated with these events. Existing software tools for this problem have strengths and limitations, and the new Jane tool described here provides functionality that complements existing tools.ResultsThe Jane software tool uses a polynomial time dynamic programming algorithm in conjunction with a genetic algorithm to find very good, and often optimal, solutions even for relatively large pairs of trees. The tool allows the user to provide rich timing information on both the host and parasite trees. In addition the user can limit host switch distance and specify multiple host switch costs by specifying regions in the host tree and costs for host switches between pairs of regions. Jane also provides a graphical user interface that allows the user to interactively experiment with modifications to the solutions found by the program.ConclusionsJane is shown to be a useful tool for cophylogenetic reconstruction. Its functionality complements existing tools and it is therefore likely to be of use to researchers in the areas of parasitology, molecular systematics, and biogeography.

An Extreme Case of Plant-Insect Codiversification: Figs and Fig-Pollinating Wasps

It is thought that speciation in phytophagous insects is often due to colonization of novel host plants, because radiations of plant and insect lineages are typically asynchronous. Recent phylogenetic comparisons have supported this model of diversification for both insect herbivores and specialized pollinators. An exceptional case where contemporaneous plant-insect diversification might be expected is the obligate mutualism between fig trees (Ficus species, Moraceae) and their pollinating wasps (Agaonidae, Hymenoptera). The ubiquity and ecological significance of this mutualism in tropical and subtropical ecosystems has long intrigued biologists, but the systematic challenge posed by >750 interacting species pairs has hindered progress toward understanding its evolutionary history. In particular, taxon sampling and analytical tools have been insufficient for large-scale cophylogenetic analyses. Here, we sampled nearly 200 interacting pairs of fig and wasp species from across the globe. Two supermatrices were assembled: on an average, wasps had sequences from 77% of 6 genes (5.6 kb), figs had sequences from 60% of 5 genes (5.5 kb), and overall 850 new DNA sequences were generated for this study. We also developed a new analytical tool, Jane 2, for event-based phylogenetic reconciliation analysis of very large data sets. Separate Bayesian phylogenetic analyses for figs and fig wasps under relaxed molecular clock assumptions indicate Cretaceous diversification of crown groups and contemporaneous divergence for nearly half of all fig and pollinator lineages. Event-based cophylogenetic analyses further support the codiversification hypothesis. Biogeographic analyses indicate that the present-day distribution of fig and pollinator lineages is consistent with a Eurasian origin and subsequent dispersal, rather than with Gondwanan vicariance. Overall, our findings indicate that the fig-pollinator mutualism represents an extreme case among plant-insect interactions of coordinated dispersal and long-term codiversification. [Biogeography; coevolution; cospeciation; host switching; long-branch attraction; phylogeny.].

Multicast routing and wavelength assignment in multihop optical networks

This paper addresses multicast routing in circuit-switched multihop optical networks employing wavelength-division multiplexing. We consider a model in which multicast communication requests are made and released dynamically over time. A multicast connection is realized by constructing a multicast tree which distributes the message from the source node to all destination nodes such that the wavelengths used on each link and the receivers and transmitters used at each node are not used by existing circuits. We show that the problem of routing and wavelength assignment in this model is, in general, NP-complete. However, we also show that for any given multicast tree, the wavelength assignment problem can be solved in linear time.

On Multicast Algorithms for Heterogeneous Networks of Workstations

Networks of workstations (NOWs) provide an economical platform for high performance parallel computing. Such networks may comprise a variety of different types of workstations and network devices. This paper addresses the problem of efficient multicast in a heterogeneous communication model. Although the problem of finding optimal multicast schedules is known to be NP-complete in this model, a greedy algorithm has been shown experimentally to find good solutions in practice. In this paper we show that the greedy algorithm finds provably near-optimal schedules in polynomial time and that optimal schedules can be found in polynomial time when the number of distinct types of workstations is bounded by a constant. Specifically, this paper presents three results. First, when there are n workstations of some constant k distinct types, the greedy algorithm is shown to find schedules that complete at most a constant additive term later than optimal. Second, an algorithm is given that finds optimal schedules in time O(n2k). Finally, it is shown that for the general problem, the greedy algorithm finds solutions that complete the multicast in at most twice the optimal time.

The Cophylogeny Reconstruction Problem is NP-Complete

The co phylogeny reconstruction problem is that of finding minimum cost explanations of differences between historical associations. The problem arises in parasitology, molecular systematics, and biogeography. Existing software tools for this problem either have worst-case exponential time or use heuristics that do not guarantee optimal solutions. To date, no polynomial time optimal algorithms have been found for this problem. In this article, we prove that the problem is NP-complete, suggesting that future research on algorithms for this problem should seek better polynomial-time approximation algorithms and heuristics rather than optimal solutions.

Origin-based fault-tolerant routing in the mesh

The ability to tolerate faults is critical in multi-computers employing large numbers of processors. This paper describes a class of fault-tolerant routing algorithms for n-dimensional meshes that can tolerate large numbers of faults without using virtual channels. We show that these routing algorithms prevent livelock and deadlock while remaining highly adaptive. >

Discordant phylogenies suggest repeated host shifts in the Fusarium-Euwallacea ambrosia beetle mutualism.

The mutualism between xyleborine beetles in the genus Euwallacea (Coleoptera: Curculionidae: Scolytinae) and members of the Ambrosia Fusarium Clade (AFC) represents one of 11 known evolutionary origins of fungiculture by ambrosia beetles. Female Euwallacea beetles transport fusarial symbionts in paired mandibular mycangia from their natal gallery to woody hosts where they are cultivated in galleries as a source of food. Native to Asia, several exotic Euwallacea species were introduced into the United States and Israel within the past two decades and they now threaten urban landscapes, forests and avocado production. To assess species limits and to date the evolutionary diversification of the mutualists, we reconstructed the evolutionary histories of key representatives of the Fusarium and Euwallacea clades using maximum parsimony and maximum likelihood methods. Twelve species-level lineages, termed AF 1-12, were identified within the monophyletic AFC and seven among the Fusarium-farming Euwallacea. Bayesian diversification-time estimates placed the origin of the Euwallacea-Fusarium mutualism near the Oligocene-Miocene boundary ∼19-24 Mya. Most Euwallacea spp. appear to be associated with one species of Fusarium, but two species farmed two closely related fusaria. Euwallacea sp. #2 in Miami-Dade County, Florida cultivated Fusarium spp. AF-6 and AF-8 on avocado, and Euwallacea sp. #4 farmed Fusarium ambrosium AF-1 and Fusarium sp. AF-11 on Chinese tea in Sri Lanka. Cophylogenetic analyses indicated that the Euwallacea and Fusarium phylogenies were largely incongruent, apparently due to the beetles switching fusarial symbionts (i.e., host shifts) at least five times during the evolution of this mutualism. Three cospeciation events between Euwallacea and their AFC symbionts were detected, but randomization tests failed to reject the null hypothesis that the putative parallel cladogenesis is a stochastic pattern. Lastly, two collections of Euwallacea sp. #2 from Miami-Dade County, Florida shared an identical cytochrome oxidase subunit 1 (CO1) allele with Euwallacea validus, suggesting introgressive hybridization between these species and/or pseudogenous nature of this marker. Results of the present study highlight the importance of understanding the potential for and frequency of host-switching between Euwallacea and members of the AFC, and that these shifts may bring together more aggressive and virulent combinations of these invasive mutualists.

Solutions to the Module Orientation and Rotation Problems by Neural Computation Networks

In this paper we study two strategies for modifying a given placement of modules in order to improve the quality of the routing results in the next stage of design. We assume that the modules have already been placed. The first strategy seeks to minimize the total wire length by flipping each module about its vertical and/or horizontal axes of symmetry. The second strategy seeks to minimize the total wire length by rotating each module by a multiple of 90 degrees. We introduce a new algorithm based on the Hopfield-Tank neuralnet model to solve these problems. Our algorithm performs better than the best algorithms known for these problems. Both problems are shown to be NP-Complete.

On edge-disjoint spanning trees in hypercubes

In this note we give a construction for obtaining the maximum number of edge-disjoint spanning trees in a hypercube. The result has applications to multicast communication in wormhole-routed parallel computers.

Tree-based multicasting in wormhole-routed irregular topologies

A deadlock-free tree-based multicast routing algorithm is presented for all direct networks, regardless of interconnection topology. The algorithm delivers a message to any number of destinations using only a single start up phase. In contrast to existing tree-based schemes, this algorithm applies to all interconnection topologies, requires only fixed-sized input buffers that are independent of maximum message length, and uses a simple asynchronous flit replication mechanism. The theoretical basis of the technique used here is sufficiently general to develop other tree-based multicasting algorithms for regular and irregular topologies. Simulation results demonstrate that this tree-based algorithm provides a very promising means of achieving very low latency multicast.