
Stefan Grünewald,
Katharina Huber,
Vincent Moulton,
Charles Semple and
Andreas Spillner. Characterizing weak compatibility in terms of weighted quartets. In Advances in Applied Mathematics, Vol. 42(3):329341, 2009. Keywords: abstract network, characterization, from quartets, split network, weak hierarchy. Note: http://www.math.canterbury.ac.nz/~c.semple/papers/GHMSS08.pdf, slides at http://www.lirmm.fr/miep08/slides/12_02_huber.pdf.





Stefan Grünewald,
Jacobus Koolen and
WooSun Lee. Quartets in maximal weakly compatible split systems. In Applied Mathematics Letters, Vol. 22(6):16041608, 2009. Note: http://dx.doi.org/10.1016/j.aml.2009.05.006.
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"Weakly compatible split systems are a generalization of unrooted evolutionary trees and are commonly used to display reticulate evolution or ambiguity in biological data. They are collections of bipartitions of a finite set X of taxa (e.g. species) with the property that, for every four taxa, at least one of the three bipartitions into two pairs (quartets) is not induced by any of the Xsplits. We characterize all split systems where exactly two quartets from every quadruple are induced by some split. On the other hand, we construct maximal weakly compatible split systems where the number of induced quartets per quadruple tends to 0 with the number of taxa going to infinity. © 2009."



Martin Lott,
Andreas Spillner,
Katharina Huber and
Vincent Moulton. PADRE: A Package for Analyzing and Displaying Reticulate Evolution. In BIO, Vol. 25(9):11991200, 2009. Keywords: duplication, explicit network, from multilabeled tree, phylogenetic network, phylogeny, Program PADRE, reconstruction, software. Note: http://dx.doi.org/10.1093/bioinformatics/btp133.
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"Recent advances in gene sequencing for polyploid species, coupled with standard phylogenetic tree reconstruction, leads to gene trees in which the same species can label several leaves. Such multilabeled trees are then used to reconstruct the evolutionary history of the polyploid species in question. However, this reconstruction process requires new techniques that are not available in current phylogenetic software packages. Here, we describe the software package PADRE (Package for Analyzing and Displaying Reticulate Evolution) that implements such techniques, allowing the reconstruction of complex evolutionary histories for polyploids in the form of phylogenetic networks. © The Author 2009. Published by Oxford University Press. All rights reserved."



Mark A. Ragan. Trees and networks before and after Darwin. In Biology Direct, Vol. 4(43), 2009. Keywords: abstract network, explicit network, phylogenetic network, phylogeny, survey, visualization. Note: http://dx.doi.org/10.1186/17456150443.
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"It is wellknown that Charles Darwin sketched abstract trees of relationship in his 1837 notebook, and depicted a tree in the Origin of Species (1859). Here I attempt to place Darwin's trees in historical context. By the midEighteenth century the Great Chain of Being was increasingly seen to be an inadequate description of order in nature, and by about 1780 it had been largely abandoned without a satisfactory alternative having been agreed upon. In 1750 Donati described aquatic and terrestrial organisms as forming a network, and a few years later Buffon depicted a network of genealogical relationships among breeds of dogs. In 1764 Bonnet asked whether the Chain might actually branch at certain points, and in 1766 Pallas proposed that the gradations among organisms resemble a tree with a compound trunk, perhaps not unlike the tree of animal life later depicted by Eichwald. Other trees were presented by Augier in 1801 and by Lamarck in 1809 and 1815, the latter two assuming a transmutation of species over time. Elaborate networks of affinities among plants and among animals were depicted in the late Eighteenth and very early Nineteenth centuries. In the two decades immediately prior to 1837, socalled affinities and/or analogies among organisms were represented by diverse geometric figures. Series of plant and animal fossils in successive geological strata were represented as trees in a popular textbook from 1840, while in 1858 Bronn presented a system of animals, as evidenced by the fossil record, in a form of a tree. Darwin's 1859 tree and its subsequent elaborations by Haeckel came to be accepted in many but not all areas of biological sciences, while network diagrams were used in others. Beginning in the early 1960s trees were inferred from protein and nucleic acid sequences, but networks were reintroduced in the mid1990s to represent lateral genetic transfer, increasingly regarded as a fundamental mode of evolution at least for bacteria and archaea. In historical context, then, the Network of Life preceded the Tree of Life and might again supersede it. Reviewers: This article was reviewed by Eric Bapteste, Patrick Forterre and Dan Graur. © 2009 Ragan; licensee BioMed Central Ltd."



Laxmi Parida,
Asif Javed,
Marta Melé,
Francesc Calafell,
Jaume Bertranpetit and
Genographic Consortium. Minimizing recombinations in consensus networks for phylogeographic studies. In BMCB, Vol. 10(Suppl 1):S72, 2009. Note: Selected papers from the Seventh AsiaPacific Bioinformatics Conference (APBC 2009), http://dx.doi.org/10.1186/1471210510S1S72.
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"Background: We address the problem of studying recombinational variations in (human) populations. In this paper, our focus is on one computational aspect of the general task: Given two networks G1 and G2, with both mutation and recombination events, defined on overlapping sets of extant units the objective is to compute a consensus network G3 with minimum number of additional recombinations. We describe a polynomial time algorithm with a guarantee that the number of computed new recombination events is within = sz(G1, G2) (function sz is a wellbehaved function of the sizes and topologies of G1 and G2) of the optimal number of recombinations. To date, this is the best known result for a network consensus problem. Results: Although the network consensus problem can be applied to a variety of domains, here we focus on structure of human populations. With our preliminary analysis on a segment of the human Chromosome X data we are able to infer ancient recombinations, populationspecific recombinations and more, which also support the widely accepted 'Out of Africa' model. These results have been verified independently using traditional manual procedures. To the best of our knowledge, this is the first recombinationsbased characterization of human populations. Conclusion: We show that our mathematical model identifies recombination spots in the individual haplotypes; the aggregate of these spots over a set of haplotypes defines a recombinational landscape that has enough signal to detect continental as well as population divide based on a short segment of Chromosome X. In particular, we are able to infer ancient recombinations, populationspecific recombinations and more, which also support the widely accepted 'Out of Africa' model. The agreement with mutationbased analysis can be viewed as an indirect validation of our results and the model. Since the model in principle gives us more information embedded in the networks, in our future work, we plan to investigate more nontraditional questions via these structures computed by our methodology. © 2009 Parida et al; licensee BioMed Central Ltd."



Sarah C. Ayling and
Terence A. Brown. Novel methodology for construction and pruning of quasimedian networks. In BMCB, Vol. 9:115, 2009. Keywords: abstract network, from sequences, median network, phylogenetic network, phylogeny, quasimedian network, reconstruction. Note: http://dx.doi.org/10.1186/147121059115.
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"BACKGROUND: Visualising the evolutionary history of a set of sequences is a challenge for molecular phylogenetics. One approach is to use undirected graphs, such as median networks, to visualise phylogenies where reticulate relationships such as recombination or homoplasy are displayed as cycles. Median networks contain binary representations of sequences as nodes, with edges connecting those sequences differing at one character; hypothetical ancestral nodes are invoked to generate a connected network which contains all most parsimonious trees. Quasimedian networks are a generalisation of median networks which are not restricted to binary data, although phylogenetic information contained within the multistate positions can be lost during the preprocessing of data. Where the history of a set of samples contain frequent homoplasies or recombination events quasimedian networks will have a complex topology. Graph reduction or pruning methods have been used to reduce network complexity but some of these methods are inapplicable to datasets in which recombination has occurred and others are procedurally complex and/or result in disconnected networks. RESULTS: We address the problems inherent in construction and reduction of quasimedian networks. We describe a novel method of generating quasimedian networks that uses all characters, both binary and multistate, without imposing an arbitrary ordering of the multistate partitions. We also describe a pruning mechanism which maintains at least one shortest path between observed sequences, displaying the underlying relations between all pairs of sequences while maintaining a connected graph. CONCLUSION: Application of this approach to 5S rDNA sequence data from sea beet produced a pruned network within which genetic isolation between populations by distance was evident, demonstrating the value of this approach for exploration of evolutionary relationships."



Martin Lott,
Andreas Spillner,
Katharina Huber,
Anna Petri,
Bengt Oxelman and
Vincent Moulton. Inferring polyploid phylogenies from multiplylabeled gene trees. In BMCEB, Vol. 9:216, 2009. Keywords: duplication, explicit network, from multilabeled tree, phylogenetic network, phylogeny, Program PADRE, reconstruction. Note: http://dx.doi.org/10.1186/147121489216.
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"Background : Gene trees that arise in the context of reconstructing the evolutionary history of polyploid species are often multiplylabeled, that is, the same leaf label can occur several times in a single tree. This property considerably complicates the task of forming a consensus of a collection of such trees compared to usual phylogenetic trees. Results. We present a method for computing a consensus tree of multiplylabeled trees. As with the wellknown greedy consensus tree approach for phylogenetic trees, our method first breaks the given collection of gene trees into a set of clusters. It then aims to insert these clusters one at a time into a tree, starting with the clusters that are supported by most of the gene trees. As the problem to decide whether a cluster can be inserted into a multiplylabeled tree is computationally hard, we have developed a heuristic method for solving this problem. Conclusion. We illustrate the applicability of our method using two collections of trees for plants of the genus Silene, that involve several allopolyploids at different levels. © 2009 Lott et al; licensee BioMed Central Ltd."



Stefan Grünewald,
Vincent Moulton and
Andreas Spillner. Consistency of the QNet algorithm for generating planar split networks from weighted quartets. In DAM, Vol. 157(10):23252334, 2009. Keywords: abstract network, consistency, from quartets, phylogenetic network, phylogeny, Program QNet, reconstruction, software. Note: http://dx.doi.org/10.1016/j.dam.2008.06.038.
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"Phylogenetic networks are a generalization of evolutionary or phylogenetic trees that allow the representation of conflicting signals or alternative evolutionary histories in a single diagram. Recently the QuartetNet or "QNet" method was introduced, a method for computing a special kind of phylogenetic network called a split network from a collection of weighted quartet trees (i.e. phylogenetic trees with 4 leaves). This can be viewed as a quartet analogue of the distancebased NeighborNet (NNet) method for constructing outerlabeled planar split networks. In this paper, we prove that QNet is a consistent method, that is, we prove that if QNet is applied to a collection of weighted quartets arising from a circular split weight function, then it will return precisely this function. This key property of QNet not only ensures that it is guaranteed to produce a tree if the input corresponds to a tree, and an outerlabeled planar split network if the input corresponds to such a network, but also provides the main guiding principle for the design of the method. © 2008 Elsevier B.V. All rights reserved."



Ulrik Brandes and
Sabine Cornelsen. Phylogenetic Graph Models Beyond Trees. In DAM, Vol. 157(10):23612369, 2009. Keywords: abstract network, cactus graph, from splits, phylogenetic network, phylogeny, polynomial, reconstruction. Note: http://www.inf.unikonstanz.de/~cornelse/Papers/bcpgmbt07.pdf.
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"A graph model for a set S of splits of a set X consists of a graph and a map from X to the vertices of the graph such that the inclusionminimal cuts of the graph represent S. Phylogenetic trees are graph models in which the graph is a tree. We show that the model can be generalized to a cactus (i.e. a tree of edges and cycles) without losing computational efficiency. A cactus can represent a quadratic rather than linear number of splits in linear space. We show how to decide in linear time in the size of a succinct representation of S whether a set of splits has a cactus model, and if so construct it within the same time bounds. As a byproduct, we show how to construct the subset of all compatible splits and a maximal compatible set of splits in linear time. Note that it is N Pcomplete to find a compatible subset of maximum size. Finally, we briefly discuss further generalizations of tree models. © 2008 Elsevier B.V. All rights reserved."





Leo van Iersel,
Steven Kelk and
Matthias Mnich. Uniqueness, intractability and exact algorithms: reflections on levelk phylogenetic networks. In JBCB, Vol. 7(4):597623, 2009. Keywords: explicit network, from triplets, galled tree, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, reconstruction, uniqueness. Note: http://arxiv.org/pdf/0712.2932v2.



Sagi Snir and
Tamir Tuller. The NETHMM approach: Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. In JBCB, Vol. 7(4):625644, 2009. Keywords: explicit network, from sequences, HMM, lateral gene transfer, likelihood, phylogenetic network, phylogeny, statistical model. Note: http://research.haifa.ac.il/~ssagi/published%20papers/SnirNETHMMJBCB2009.pdf.
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"Horizontal gene transfer (HGT) is the event of transferring genetic material from one lineage in the evolutionary tree to a different lineage. HGT plays a major role in bacterial genome diversification and is a significant mechanism by which bacteria develop resistance to antibiotics. Although the prevailing assumption is of complete HGT, cases of partial HGT (which are also named chimeric HGT) where only part of a gene is horizontally transferred, have also been reported, albeit less frequently. In this work we suggest a new probabilistic model, the NETHMM, for analyzing and modeling phylogenetic networks. This new model captures the biologically realistic assumption that neighboring sites of DNA or amino acid sequences are not independent, which increases the accuracy of the inference. The model describes the phylogenetic network as a Hidden Markov Model (HMM), where each hidden state is related to one of the network's trees. One of the advantages of the NETHMM is its ability to infer partial HGT as well as complete HGT. We describe the properties of the NETHMM, devise efficient algorithms for solving a set of problems related to it, and implement them in software. We also provide a novel complementary significance test for evaluating the fitness of a model (NETHMM) to a given dataset. Using NETHMM, we are able to answer interesting biological questions, such as inferring the length of partial HGT's and the affected nucleotides in the genomic sequences, as well as inferring the exact location of HGT events along the tree branches. These advantages are demonstrated through the analysis of synthetical inputs and three different biological inputs. © 2009 Imperial College Press."



Ran LibeskindHadas and
Michael A. Charleston. On the Computational Complexity of the Reticulate Cophylogeny Reconstruction Problem. In JCB, Vol. 16(1):105117, 2009. Keywords: cophylogeny, heuristic, NP complete, parsimony, phylogenetic network, reconstruction. Note: http://dx.doi.org/10.1089/cmb.2008.0084.
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"The cophylogeny reconstruction problem is that of finding minimal cost explanations of differences between evolutionary histories of ecologically linked groups of biological organisms. We present a proof that shows that the general problem of reconciling evolutionary histories is NPcomplete and provide a sharp boundary where this intractability begins. We also show that a related problem, that of finding Pareto optimal solutions, is NPhard. As a byproduct of our results, we give a framework by which metaheuristics can be applied to find good solutions to this problem. © Mary Ann Liebert, Inc. 2009."



Francesc Rosselló and
Gabriel Valiente. All that Glisters is not Galled. In MBIO, Vol. 221(1):5459, 2009. Keywords: galled tree, phylogenetic network, phylogeny. Note: http://arxiv.org/abs/0904.2448.
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"Galled trees, evolutionary networks with isolated reticulation cycles, have appeared under several slightly different definitions in the literature. In this paper, we establish the actual relationships between the main four such alternative definitions: namely, the original galled trees, level1 networks, nested networks with nesting depth 1, and evolutionary networks with arcdisjoint reticulation cycles. © 2009 Elsevier Inc. All rights reserved."



Laura S. Kubatko. Identifying Hybridization Events in the Presence of Coalescence via Model Selection. In Systematic Biology, Vol. 58(5):478488, 2009. Keywords: AIC, BIC, branch length, coalescent, explicit network, from rooted trees, from species tree, hybridization, lineage sorting, model selection, phylogenetic network, phylogeny, statistical model. Note: http://dx.doi.org/10.1093/sysbio/syp055.



Bui Quang Minh,
Steffen Klaere and
Arndt von Haeseler. Taxon Selection under Split Diversity. In Systematic Biology, Vol. 58(6):586594, 2009. Keywords: abstract network, circular split system, diversity, from network, phylogenetic network, split network. Note: http://dx.doi.org/10.1093/sysbio/syp058.
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"The phylogenetic diversity (PD) measure of biodiversity is evaluated using a phylogenetic tree, usually inferred from morphological or molecular data. Consequently, it is vulnerable to errors in that tree, including those resulting from sampling error, model misspecification, or conflicting signals. To improve the robustness of PD, we can evaluate the measure using either a collection (or distribution) of trees or a phylogenetic network. Recently, it has been shown that these 2 approaches are equivalent but that the problem of maximizing PD in the general concept is NPhard. In this study, we provide an efficient dynamic programming algorithm for maximizing PD when splits in the trees or network form a circular split system. We illustrate our method using a case study of game birds (Galliformes) and discuss the different choices of taxa based on our approach and PD."



Daniel H. Huson. Drawing Rooted Phylogenetic Networks. In TCBB, Vol. 6(1):103109, 2009. Keywords: explicit network, phylogenetic network, phylogeny, Program Dendroscope, Program SplitsTree, visualization. Note: http://dx.doi.org/10.1109/TCBB.2008.58.
Toggle abstract
"The evolutionary history of a collection of species is usually represented by a phylogenetic tree. Sometimes, phylogenetic networks are used as a means of representing reticulate evolution or of showing uncertainty and incompatibilities in evolutionary datasets. This is often done using unrooted phylogenetic networks such as split networks, due in part, to the availability of software (SplitsTree) for their computation and visualization. In this paper we discuss the problem of drawing rooted phylogenetic networks as cladograms or phylograms in a number of different views that are commonly used for rooted trees. Implementations of the algorithms are available in new releases of the Dendroscope and SplitsTree programs. © 2006 IEEE."



Bui Quang Minh,
Fabio Pardi,
Steffen Klaere and
Arndt von Haeseler. Budgeted Phylogenetic Diversity on Circular Split Systems. In TCBB, Vol. 6(1):2229, 2009. Keywords: abstract network, circular split system, dynamic programming, from network, phylogenetic network, polynomial, split, split network. Note: http://dx.doi.org/10.1109/TCBB.2008.54.
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"In the last 15 years, Phylogenetic Diversity (PD) has gained interest in the community of conservation biologists as a surrogate measure for assessing biodiversity. We have recently proposed two approaches to select taxa for maximizing PD, namely PD with budget constraints and PD on split systems. In this paper, we will unify these two strategies and present a dynamic programming algorithm to solve the unified framework of selecting taxa with maximal PD under budget constraints on circular split systems. An improved algorithm will also be given if the underlying split system is a tree. © 2006 IEEE."





Gabriel Cardona,
Mercè Llabrés,
Francesc Rosselló and
Gabriel Valiente. Metrics for phylogenetic networks I: Generalizations of the RobinsonFoulds metric. In TCBB, Vol. 6(1):4661, 2009. Keywords: distance between networks, explicit network, phylogenetic network, phylogeny, time consistent network, treechild network, tripartition distance. Note: http://dx.doi.org/10.1109/TCBB.2008.70.
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"The assessment of phylogenetic network reconstruction methods requires the ability to compare phylogenetic networks. This is the first in a series of papers devoted to the analysis and comparison of metrics for treechild time consistent phylogenetic networks on the same set of taxa. In this paper, we study three metrics that have already been introduced in the literature: the RobinsonFoulds distance, the tripartitions distance and the $mu$distance. They generalize to networks the classical RobinsonFoulds or partition distance for phylogenetic trees. We analyze the behavior of these metrics by studying their least and largest values and when they achieve them. As a byproduct of this study, we obtain tight bounds on the size of a treechild time consistent phylogenetic network. © 2006 IEEE."



Gabriel Cardona,
Mercè Llabrés,
Francesc Rosselló and
Gabriel Valiente. Metrics for phylogenetic networks II: Nodal and triplets metrics. In TCBB, Vol. 6(3):454469, 2009. Keywords: distance between networks, phylogenetic network, phylogeny. Note: http://dx.doi.org/10.1109/TCBB.2008.127.
Toggle abstract
"The assessment of phylogenetic network reconstruction methods requires the ability to compare phylogenetic networks. This is the second in a series of papers devoted to the analysis and comparison of metrics for treechild time consistent phylogenetic networks on the same set of taxa. In this paper, we generalize to phylogenetic networks two metrics that have already been introduced in the literature for phylogenetic trees: the nodal distance and the triplets distance. We prove that they are metrics on any class of tree child time consistent phylogenetic networks on the same set of taxa, as well as some basic properties for them. To prove these results, we introduce a reduction/expansion procedure that can be used not only to establish properties of treechild time consistent phylogenetic networks by induction, but also to generate all treechild time consistent phylogenetic networks with a given number of leaves. © 2009 IEEE."





Gabriel Cardona,
Francesc Rosselló and
Gabriel Valiente. Comparison of treechild phylogenetic networks. In TCBB, Vol. 6(4):552569, 2009. Keywords: explicit network, phylogenetic network, phylogeny, Program Bio PhyloNetwork, Program PhyloNetwork, tree sibling network, treechild network. Note: http://arxiv.org/abs/0708.3499.
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"Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of nontreelike evolutionary events, like recombination, hybridization, or lateral gene transfer. While much progress has been made to find practical algorithms for reconstructing a phylogenetic network from a set of sequences, all attempts to endorse a class of phylogenetic networks (strictly extending the class of phylogenetic trees) with a wellfounded distance measure have, to the best of our knowledge and with the only exception of the bipartition distance on regular networks, failed so far. In this paper, we present and study a new meaningful class of phylogenetic networks, called treechild phylogenetic networks, and we provide an injective representation of these networks as multisets of vectors of natural numbers, their path multiplicity vectors. We then use this representation to define a distance on this class that extends the wellknown RobinsonFoulds distance for phylogenetic trees and to give an alignment method for pairs of networks in this class. Simple polynomial algorithms for reconstructing a treechild phylogenetic network from its path multiplicity vectors, for computing the distance between two treechild phylogenetic networks and for aligning a pair of treechild phylogenetic networks, are provided. They have been implemented as a Perl package and a Java applet, which can be found at http://bioinfo.uib.es/~recerca/ phylonetworks/mudistance/. © 2009 IEEE."



Gabriel Cardona,
Mercè Llabrés,
Francesc Rosselló and
Gabriel Valiente. On Nakhleh's metric for reduced phylogenetic networks. In TCBB, Vol. 6(4):629638, 2009. Keywords: distance between networks, phylogenetic network, phylogeny. Note: Preliminary versions: http://arxiv.org/abs/0809.0110 and http://arxiv.org/abs/0801.2354v1.
Toggle abstract
"We prove that Nakhleh's metric for reduced phylogenetic networks is also a metric on the classes of treechild phylogenetic networks, semibinary treesibling time consistent phylogenetic networks, and multilabeled phylogenetic trees. We also prove that it separates distinguishable phylogenetic networks. In this way, it becomes the strongest dissimilarity measure for phylogenetic networks available so far. Furthermore, we propose a generalization of that metric that separates arbitrary phylogenetic networks. © 2009 IEEE."





Simon Joly,
Patricia A. McLenachan and
Peter J. Lockhart. A Statistical Approach for Distinguishing Hybridization and Incomplete Lineage Sorting. In The American Naturalist, Vol. 174(2):E54E70, 2009. Keywords: hybridization, lineage sorting, phylogenetic network, phylogeny, reconstruction, statistical model. Note: http://www.plantevolution.org/pdf/Joly&al_2009_AmNat.pdf.
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"The extent and evolutionary significance of hybridization is difficult to evaluate because of the difficulty in distinguishing hybridization from incomplete lineage sorting. Here we present a novel parametric approach for statistically distinguishing hybridization from incomplete lineage sorting based on minimum genetic distances of a nonrecombining locus. It is based on the idea that the expected minimum genetic distance between sequences from two species is smaller for some hybridization events than for incomplete lineage sorting scenarios. When applied to empirical data sets, distributions can be generated for the minimum interspecies distances expected under incomplete lineage sorting using coalescent simulations. If the observed distance between sequences from two species is smaller than its predicted distribution, incomplete lineage sorting can be rejected and hybridization inferred. We demonstrate the power of the method using simulations and illustrate its application on New Zealand alpine buttercups (Ranunculus). The method is robust and complements existing approaches. Thus it should allow biologists to assess with greater accuracy the importance of hybridization in evolution. © 2009 by The University of Chicago."



Chen Meng and
Laura S. Kubatko. Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model. In Theoretical Population Biology, Vol. 75(1):3545, 2009. Keywords: bayesian, coalescent, from network, from rooted trees, hybridization, likelihood, lineage sorting, phylogenetic network, phylogeny, statistical model. Note: http://dx.doi.org/10.1016/j.tpb.2008.10.004.
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"The application of phylogenetic inference methods, to data for a set of independent genes sampled randomly throughout the genome, often results in substantial incongruence in the singlegene phylogenetic estimates. Among the processes known to produce discord between singlegene phylogenies, two of the best studied in a phylogenetic context are hybridization and incomplete lineage sorting. Much recent attention has focused on the development of methods for estimating species phylogenies in the presence of incomplete lineage sorting, but phylogenetic models that allow for hybridization have been more limited. Here we propose a model that allows incongruence in singlegene phylogenies to be due to both hybridization and incomplete lineage sorting, with the goal of determining the contribution of hybridization to observed gene tree incongruence in the presence of incomplete lineage sorting. Using our model, we propose methods for estimating the extent of the role of hybridization in both a likelihood and a Bayesian framework. The performance of our methods is examined using both simulated and empirical data. © 2008 Elsevier Inc. All rights reserved."







ThuHien To and
Michel Habib. Levelk Phylogenetic Networks Are Constructable from a Dense Triplet Set in Polynomial Time. In CPM09, (5577):275288, springer, 2009. Keywords: explicit network, from triplets, level k phylogenetic network, minimum number, phylogenetic network, phylogeny, polynomial, reconstruction. Note: http://arxiv.org/abs/0901.1657.
Toggle abstract
"For a given dense triplet set Τ there exist two natural questions [7]: Does there exist any phylogenetic network consistent with Τ? In case such networks exist, can we find an effective algorithm to construct one? For cases of networks of levels k = 0, 1 or 2, these questions were answered in [1,6,7,8,10] with effective polynomial algorithms. For higher levels k, partial answers were recently obtained in [11] with an O(/Τ/k+1)time algorithm for simple networks. In this paper, we give a complete answer to the general case, solving a problem proposed in [7]. The main idea of our proof is to use a special property of SNsets in a levelk network. As a consequence, for any fixed k, we can also find a levelk network with the minimum number of reticulations, if one exists, in polynomial time. © 2009 Springer Berlin Heidelberg."



Philippe Gambette,
Vincent Berry and
Christophe Paul. The structure of levelk phylogenetic networks. In CPM09, Vol. 5577:289300 of LNCS, springer, 2009. Keywords: coalescent, explicit network, galled tree, level k phylogenetic network, phylogenetic network, Program Recodon. Note: http://hallirmm.ccsd.cnrs.fr/lirmm00371485/en/.
Toggle abstract
"Evolution is usually described as a phylogenetic tree, but due to some exchange of genetic material, it can be represented as a phylogenetic network which has an underlying tree structure. The notion of level was recently introduced as a parameter on realistic kinds of phylogenetic networks to express their complexity and treelikeness. We study the structure of levelk networks, and how they can be decomposed into levelk generators. We also provide a polynomial time algorithm which takes as input the set of levelk generators and builds the set of level(k + 1) generators. Finally, with a simulation study, we evaluate the proportion of levelk phylogenetic networks among networks generated according to the coalescent model with recombination. © 2009 Springer Berlin Heidelberg."



Lichen Bao and
Sergey Bereg. Counting Faces in Split Networks. In ISBRA09, Vol. 5251:284295 of LNCS, 2009. Note: http://dx.doi.org/10.1007/9783642015519_12.
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SplitsTree is a popular program for inferring and visualizing various phylogenetic networks including split networks. Split networks are useful for realizing metrics that are linear combinations of split metrics. We show that the realization is not unique in some cases and design an algorithm for computing split networks with minimum number of faces. We also prove that the minimum number of faces in a split network is equal to the number of pairs of incompatible splits.



Daniel H. Huson,
Regula Rupp,
Vincent Berry,
Philippe Gambette and
Christophe Paul. Computing Galled Networks from Real Data. In ISMBECCB09, Vol. 25(12):i85i93 of BIO, 2009. Keywords: abstract network, cluster containment, explicit network, FPT, from clusters, from rooted trees, galled network, NP complete, phylogenetic network, phylogeny, polynomial, Program Dendroscope, reconstruction. Note: http://hallirmm.ccsd.cnrs.fr/lirmm00368545/en/.
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"Motivation: Developing methods for computing phylogenetic networks from biological data is an important problem posed by molecular evolution and much work is currently being undertaken in this area. Although promising approaches exist, there are no tools available that biologists could easily and routinely use to compute rooted phylogenetic networks on real datasets containing tens or hundreds of taxa. Biologists are interested in clades, i.e. groups of monophyletic taxa, and these are usually represented by clusters in a rooted phylogenetic tree. The problem of computing an optimal rooted phylogenetic network from a set of clusters, is hard, in general. Indeed, even the problem of just determining whether a given network contains a given cluster is hard. Hence, some researchers have focused on topologically restricted classes of networks, such as galled trees and levelk networks, that are more tractable, but have the practical drawback that a given set of clusters will usually not possess such a representation. Results: In this article, we argue that galled networks (a generalization of galled trees) provide a good tradeoff between level of generality and tractability. Any set of clusters can be represented by some galled network and the question whether a cluster is contained in such a network is easy to solve. Although the computation of an optimal galled network involves successively solving instances of two different NPcomplete problems, in practice our algorithm solves this problem exactly on large datasets containing hundreds of taxa and many reticulations in seconds, as illustrated by a dataset containing 279 prokaryotes. © 2009 The Author(s)."



Chris Whidden and
Norbert Zeh. A Unifying View on Approximation and FPT of Agreement Forests. In WABI09, Vol. 5724:390402 of LNCS, Springer, 2009. Keywords: agreement forest, approximation, explicit network, FPT, minimum number, phylogenetic network, phylogeny, reconstruction. Note: https://www.cs.dal.ca/sites/default/files/technical_reports/CS200902.pdf.
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"We provide a unifying view on the structure of maximum (acyclic) agreement forests of rooted and unrooted phylogenies. This enables us to obtain linear or O(n log n)time 3approximation and improved fixedparameter algorithms for the subtree prune and regraft distance between two rooted phylogenies, the tree bisection and reconnection distance between two unrooted phylogenies, and the hybridization number of two rooted phylogenies. © 2009 Springer Berlin Heidelberg."



