Papers by Ran Libeskind-Hadas
Life, 2022
Phylogenetic reconciliation is a fundamental method in the study of pairs of coevolving species. ... more Phylogenetic reconciliation is a fundamental method in the study of pairs of coevolving species. This paper provides an overview of the underlying theory of reconciliation in the context of host-symbiont cophylogenetics, identifying some of the major challenges to users of these methods, such as selecting event costs and selecting representative reconciliations. Next, recent advances to address these challenges are discussed followed by a discussion of several established and recent software tools.
Motivation: Phylogenetic tree reconciliation is a widely used method for reconstructing the evolu... more Motivation: Phylogenetic tree reconciliation is a widely used method for reconstructing the evolutionary histories of gene families and species, hosts and parasites and other dependent pairs of entities. Reconciliation is typically performed using maximum parsimony, in which each evolutionary event type is assigned a cost and the objective is to find a reconciliation of minimum total cost. It is generally understood that reconciliations are sensitive to event costs, but little is understood about the relationship between event costs and solutions. Moreover, choosing appropriate event costs is a notoriously difficult problem. Results: We address this problem by giving an efficient algorithm for computing Pareto-optimal sets of reconciliations, thus providing the first systematic method for understanding the relationship between event costs and reconciliations. This, in turn, results in new techniques for computing event support values and, for cophylogenetic analyses, performing robust statistical tests. We provide new software tools and demonstrate their use on a number of datasets from evolutionary genomic and cophylogenetic studies.
The maximum parsimony phylogenetic reconciliation problem seeks to explain incongruity between a ... more The maximum parsimony phylogenetic reconciliation problem seeks to explain incongruity between a gene phylogeny and a species phylogeny with respect to a set of evolutionary events. While the reconciliation problem is well-studied for species and gene trees subject to events such as duplication, transfer, loss, and deep coalescence, recent work has examined species phylogenies that incorporate hybridization and are thus represented by networks rather than trees. In this paper, we show that the problem of computing a maximum parsimony reconciliation for a gene tree and species network is NP-hard even when only considering deep coalescence. This result suggests that future work on maximum parsimony reconciliation for species networks should explore approximation algorithms and heuristics.
Kolmogorov complexity is a theory based on the premise that the complexity of a binary string can... more Kolmogorov complexity is a theory based on the premise that the complexity of a binary string can be measured by its compressibility; that is, a string’s complexity is the length of the shortest program that produces that string. We explore applications of this measure to graph theory.
BMC Bioinformatics, 2021
Background Analyses of microbial evolution often use reconciliation methods. However, the standar... more Background Analyses of microbial evolution often use reconciliation methods. However, the standard duplication-transfer-loss (DTL) model does not account for the fact that species trees are often not fully sampled and thus, from the perspective of reconciliation, a gene family may enter the species tree from the outside. Moreover, within the genome, genes are often rearranged, causing them to move to new syntenic regions. Results We extend the DTL model to account for two events that commonly arise in the evolution of microbes: origin of a gene from outside the sampled species tree and rearrangement of gene syntenic regions. We describe an efficient algorithm for maximum parsimony reconciliation in this new DTLOR model and then show how it can be extended to account for non-binary gene trees to handle uncertainty in gene tree topologies. Finally, we describe preliminary experimental results from the integration of our algorithm into the existing xenoGI tool for reconstructing the hi...
BMC Bioinformatics, 2019
Background Maximum parsimony reconciliation in the duplication-transfer-loss model is a widely-us... more Background Maximum parsimony reconciliation in the duplication-transfer-loss model is a widely-used method for analyzing the evolutionary histories of pairs of entities such as hosts and parasites, symbiont species, and species and genes. While efficient algorithms are known for finding maximum parsimony reconciliations, the number of such reconciliations can be exponential in the size of the trees. Since these reconciliations can differ substantially from one another, making inferences from any one reconciliation may lead to conclusions that are not supported, or may even be contradicted, by other maximum parsimony reconciliations. Therefore, there is a need to find small sets of best representative reconciliations when the space of solutions is large and diverse. Results We provide a general framework for hierarchical clustering the space of maximum parsimony reconciliations. We demonstrate this framework for two specific linkage criteria, one that seeks to maximize the average su...
BMC Bioinformatics, 2019
Background Maximum parsimony reconciliation in the duplication-transfer-loss model is widely used... more Background Maximum parsimony reconciliation in the duplication-transfer-loss model is widely used in studying the evolutionary histories of genes and species and in studying coevolution of parasites and their hosts and pairs of symbionts. While efficient algorithms are known for finding maximum parsimony reconciliations, the number of reconciliations can grow exponentially in the size of the trees. An understanding of the space of maximum parsimony reconciliations is necessary to determine whether a single reconciliation can adequately represent the space or whether multiple representative reconciliations are needed. Results We show that for any instance of the reconciliation problem, the distribution of pairwise distances can be computed exactly by an efficient polynomial-time algorithm with respect to several different distance metrics. We describe the algorithm, analyze its asymptotic worst-case running time, and demonstrate its utility and viability on a large biological dataset...
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2019
Gene trees can differ from species trees due to a variety of biological phenomena, the most preva... more Gene trees can differ from species trees due to a variety of biological phenomena, the most prevalent being gene duplication, horizontal gene transfer, gene loss, and coalescence. To explain topological incongruence between the two trees, researchers apply reconciliation methods, often relying on a maximum parsimony framework. However, while several studies have investigated the space of maximum parsimony reconciliations (MPRs) under the duplication-loss and duplication-transfer-loss models, the space of MPRs under the duplication-loss-coalescence (DLC) model remains poorly understood. To address this problem, we present new algorithms for computing the size of MPR space under the DLC model and sampling from this space uniformly at random. Our algorithms are efficient in practice, with runtime polynomial in the size of the species and gene tree when the number of genes that map to any given species is fixed, thus proving that the MPR problem is fixed-parameter tractable. We have applied our methods to a biological data set of 16 fungal species to provide the first key insights in the space of MPRs under the DLC model. Our results show that a plurality reconciliation, and underlying events, are likely to be representative of MPR space.
BMC Bioinformatics, 2017
Background: Maximum parsimony phylogenetic tree reconciliation is an important technique for reco... more Background: Maximum parsimony phylogenetic tree reconciliation is an important technique for reconstructing the evolutionary histories of hosts and parasites, genes and species, and other interdependent pairs. Since the problem of finding temporally feasible maximum parsimony reconciliations is NP-complete, current methods use either exact algorithms with exponential worst-case running time or heuristics that do not guarantee optimal solutions. Results: We offer an efficient new approach that begins with a potentially infeasible maximum parsimony reconciliation and iteratively "repairs" it until it becomes temporally feasible. Conclusions: In a non-trivial number of cases, this approach finds solutions that are better than those found by the widely-used Jane heuristic.
Proceedings of the 1989 26th ACM/IEEE conference on Design automation conference - DAC '89, 1989
In this paper we study two strategies for modifying a given placement of modules in order to impr... more 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 miniize 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.
Proceedings of the First Merged International Parallel Processing Symposium and Symposium on Parallel and Distributed Processing
A unicast-based multicasting algorithm is presented for arbitrary interconnection networks arisin... more A unicast-based multicasting algorithm is presented for arbitrary interconnection networks arising in switchbased networks of workstations. The algorithm is optimal with respect to the number of startups incurred and is provably free from depth contention. Specically, no two constituent unicasts for the same multicast contend for a common channel, even if some unicasts are delayed due to unpredictable variations in latencies. The algorithm uses an underlying partially adaptive deadlock-free unicast routing algorithm. Simulation results indicate that the algorithm behaves as predicted by its theoretical properties and provides a promising approach to unicast-based multicasting.
Proceedings. Second International Symposium on High-Performance Computer Architecture
2008 IEEE International Conference on Communications, 2008
This paper addresses the problem of on-line traffic grooming in WDM paths. Each request consists ... more This paper addresses the problem of on-line traffic grooming in WDM paths. Each request consists of a source node, a destination node, and the desired bandwidth for the connection. Connections may be multi-hop, permitting the use of multiple lightpaths. We describe a new distributed on-line algorithm for this problem that is provably wide-sense non-blocking under certain assumptions. Moreover, we use simulations to demonstrate that the algorithm is extremely effective even when some of these assumptions are relaxed. This full text paper was peer reviewed at the direction of IEEE Communications Society subject matter experts for publication in the ICC 2008 proceedings.
2009 IEEE International Conference on Communications, 2009
This paper addresses the problem of traffic grooming in WDM rings in which all traffic emanates f... more This paper addresses the problem of traffic grooming in WDM rings in which all traffic emanates from a single node and all other nodes are destination nodes. This "one-to-many" scenario arises in metropolitan access networks in which one node serves as a "hub" connecting the ring to a larger network as well as in video-on-demand and other multimedia services where a single source node serves a collection of subscriber nodes. The ring comprises a given number of wavelengths of uniform capacity and a variable number of tunable Add-Drop Multiplexers (ADMs) at each node. Given a set of requests at the destination nodes, where each request comprises a bandwidth demand and a profit for fulfilling the request, our objective is to select a subset of the requests and pack ("groom") them onto the wavelengths such that no wavelength's capacity is exceeded and the total profit of the selected requests is maximized. Although this problem is NP-complete, we give polynomial time approximation algorithms with excellent theoretical performance validated with experimental results.
Bioinformatics, 2014
Motivation: Phylogenetic tree reconciliation is a widely used method for reconstructing the evolu... more Motivation: Phylogenetic tree reconciliation is a widely used method for reconstructing the evolutionary histories of gene families and species, hosts and parasites and other dependent pairs of entities. Reconciliation is typically performed using maximum parsimony, in which each evolutionary event type is assigned a cost and the objective is to find a reconciliation of minimum total cost. It is generally understood that reconciliations are sensitive to event costs, but little is understood about the relationship between event costs and solutions. Moreover, choosing appropriate event costs is a notoriously difficult problem. Results: We address this problem by giving an efficient algorithm for computing Pareto-optimal sets of reconciliations, thus providing the first systematic method for understanding the relationship between event costs and reconciliations. This, in turn, results in new techniques for computing event support values and, for cophylogenetic analyses, performing robu...
Proceedings 2000. International Workshop on Parallel Processing
This paper studies the problem of eficient multicast in heterogeneous networks of workstations (H... more This paper studies the problem of eficient multicast in heterogeneous networks of workstations (HNO W s) using a parameterized communication model [3]. This model associates a sending overhead and a receiving overhead with each node as well as a network latency parameter. The problem of finding optimal multicasts in this model is known to be NP-complete in the strong sense. Nevertheless, we show that for two different properties that arise in typical HNO Ws, provably near-optimal and optimal solutions, respectively, can be found in polynomial time. Specifically, we show the following two results: When the ratios of receiving overhead to sending overhead among the nodes is bounded by constants, solutions within a bounded ratio of optimal can be found in time O(n1ogn). Secondly, i f the number of distinct types of workstations is fixed then optimal solutions can be found in polynomial time. These results provide a practical means of finding optimal and provably near-optimal multicast schedules in a large class of frequently occurring heterogeneous networks of workstations.
Bioinformatics for Biologists
I can understand how a flower and a bee might slowly become, either simultaneously or one after t... more I can understand how a flower and a bee might slowly become, either simultaneously or one after the other, modified and adapted in the most perfect manner to each other, by the continued preservation of individuals presenting mutual and slightly favourable deviations of structure. Charles Darwin, The Origin of Species
Systematic Biology, 2012
It is thought that speciation in phytophagous insects is often due to colonization of novel host ... more 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.
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Papers by Ran Libeskind-Hadas