
JeanChristophe Aude,
Yolande DiazLazcoz,
JeanJacques Codani and
JeanLoup Risler. Applications of the Pyramidal Clustering Method to Biological Objects. In CC, Vol. 23(34):303315, 1999. Keywords: from distances, phylogenetic network, phylogeny, Program Pyramids, pyramid, reconstruction, software, visualization. Note: http://dx.doi.org/10.1016/S00978485(99)000066.



Vineet Bafna and
Vikas Bansal. The Number of Recombination Events in a Sample History: Conflict Graph and Lower Bounds. In TCBB, Vol. 1(2):7890, 2004. Keywords: ARG, bound, minimum number, phylogeny, recombination. Note: http://wwwcse.ucsd.edu/users/vbafna/pub/tcbb04.pdf.
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"We consider the following problem: Given a set of binary sequences, determine lower bounds on the minimum number of recombinations required to explain the history of the sample, under the infinitesites model of mutation. The problem has implications for finding recombination hotspots and for the Ancestral Recombination Graph reconstruction problem. Hudson and Kaplan gave a lower bound based on the fourgamete test. In practice, their bound R m often greatly underestimates the minimum number of recombinations. The problem was recently revisited by Myers and Griffiths, who introduced two new lower bounds R h and R s which are provably better, and also yield good bounds in practice. However, the worstcase complexities of their procedures for computing R h and R s are exponential and superexponential, respectively. In this paper, we show that the number of nontrivial connected components, Rc, in the conflict graph for a given set of sequences, computable in time O(nm 2), is also a lower bound on the minimum number of recombination events. We show that in many cases, R c is a better bound than R h. The conflict graph was used by Gusfield et al. to obtain a polynomial time algorithm for the galled tree problem, which is a special case of the Ancestral Recombination Graph (ARG) reconstruction problem. Our results also offer some insight into the structural properties of this graph and are of interest for the general Ancestral Recombination Graph reconstruction problem."





HansJürgen Bandelt and
Andreas W. M. Dress. Weak hierarchies associated with similarity measures: an additive clustering technique. In BMB, Vol. 51:113166, 1989. Keywords: abstract network, clustering, from distances, from trees, phylogenetic network, phylogeny, Program WeakHierarchies, reconstruction, weak hierarchy. Note: http://dx.doi.org/10.1007/BF02458841.
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"A new and apparently rather useful and natural concept in cluster analysis is studied: given a similarity measure on a set of objects, a subset is regarded as a cluster if any two objects a, b inside this subset have greater similarity than any third object outside has to at least one of a, b. These clusters then form a closure system which can be described as a hypergraph without triangles. Conversely, given such a system, one may attach some weight to each cluster and then compose a similarity measure additively, by letting the similarity of a pair be the sum of weights of the clusters containing that particular pair. The original clusters can be reconstructed from the obtained similarity measure. This clustering model is thus located between the general additive clustering model of Shepard and Arabie (1979) and the standard hierarchical model. Potential applications include fitting dendrograms with few additional nonnested clusters and simultaneous representation of some families of multiple dendrograms (in particular, twodendrogram solutions), as well as assisting the search for phylogenetic relationships by proposing a somewhat larger system of possibly relevant "family groups", from which an appropriate choice (based on additional insight or individual preferences) remains to be made. © 1989 Society for Mathematical Biology."





Mihaela Baroni,
Stefan Grünewald,
Vincent Moulton and
Charles Semple. Bounding the number of hybridization events for a consistent evolutionary history. In JOMB, Vol. 51(2):171182, 2005. Keywords: agreement forest, bound, explicit network, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction, SPR distance. Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BGMS05.pdf.
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"Evolutionary processes such as hybridisation, lateral gene transfer, and recombination are all key factors in shaping the structure of genes and genomes. However, since such processes are not always best represented by trees, there is now considerable interest in using more general networks instead. For example, in recent studies it has been shown that networks can be used to provide lower bounds on the number of recombination events and also for the number of lateral gene transfers that took place in the evolutionary history of a set of molecular sequences. In this paper we describe the theoretical performance of some related bounds that result when merging pairs of trees into networks. © SpringerVerlag 2005."



Jaroslaw Byrka,
Pawel Gawrychowski,
Katharina Huber and
Steven Kelk. Worstcase optimal approximation algorithms for maximizing triplet consistency within phylogenetic networks. In Journal of Discrete Algorithms, Vol. 8(1):6575, 2010. Keywords: approximation, explicit network, from triplets, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction. Note: http://arxiv.org/abs/0710.3258.
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"The study of phylogenetic networks is of great interest to computational evolutionary biology and numerous different types of such structures are known. This article addresses the following question concerning rooted versions of phylogenetic networks. What is the maximum value of p ∈ [0, 1] such that for every input set T of rooted triplets, there exists some network N such that at least p  T  of the triplets are consistent with N? We call an algorithm that computes such a network (where p is maximum) worstcase optimal. Here we prove that the set containing all triplets (the full triplet set) in some sense defines p. Moreover, given a network N that obtains a fraction p′ for the full triplet set (for any p′), we show how to efficiently modify N to obtain a fraction ≥ p′ for any given triplet set T. We demonstrate the power of this insight by presenting a worstcase optimal result for level1 phylogenetic networks improving considerably upon the 5/12 fraction obtained recently by Jansson, Nguyen and Sung. For level2 phylogenetic networks we show that p ≥ 0.61. We emphasize that, because we are taking  T  as a (trivial) upper bound on the size of an optimal solution for each specific input T, the results in this article do not exclude the existence of approximation algorithms that achieve approximation ratio better than p. Finally, we note that all the results in this article also apply to weighted triplet sets. © 2009 Elsevier B.V. All rights reserved."



Magnus Bordewich,
Simone Linz,
Katherine St. John and
Charles Semple. A reduction algorithm for computing the hybridization number of two trees. In EBIO, Vol. 3:8698, 2007. Keywords: agreement forest, FPT, from rooted trees, hybridization, phylogenetic network, phylogeny, Program HybridNumber. Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BLSS07.pdf.



HansJürgen Bandelt,
Vincent Macaulay and
Martin Richards. Median networks: speedy construction and greedy reduction, one simulation, and two case studies from human mtDNA. In MPE, Vol. 16:828, 2000. Keywords: from sequences, from splits, median network, phylogenetic network, phylogeny, reconstruction. Note: http://www.stats.gla.ac.uk/~vincent/papers/speedy.pdf.
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"Molecular data sets characterized by few phylogenetically informative characters with a broad spectrum of mutation rates, such as intraspecific controlregion sequence variation of human mitochondrial DNA (mtDNA), can be usefully visualized in the form of median networks. Here we provide a stepbystep guide to the construction of such networks by hand. We improve upon a previously implemented algorithm by outlining an efficient parametrized strategy amenable to large data sets, greedy reduction, which makes it possible to reconstruct some of the confounding recurrent mutations. This entails some postprocessing as well, which assists in capturing more parsimonious solutions. To simplify the creation of the resulting network by hand, we describe a speedy approach to network construction, based on a careful planning of the processing order. A coalescent simulation tailored to human mtDNA variation in Eurasia testifies to the usefulness of reduced median networks, while highlighting notorious problems faced by all phylogenetic methods in this context. Finally, we discuss two case studies involving the comparison of characters in the two hypervariable segments of the human mtDNA control region in the light of the worldwide controlregion sequence database, as well as additional restriction fragment length polymorphism information. We conclude that only a minority of the mutations that hit the second segment occur at sites that would have a mutation rate comparable to those at most sites in the first segment. Discarding the known 'noisy' sites of the second segment enhances the analysis. (C) 2000 Academic Press."



Magnus Bordewich and
Charles Semple. Computing the minimum number of hybridization events for a consistent evolutionary history. In DAM, Vol. 155:914918, 2007. Keywords: agreement forest, approximation, APX hard, explicit network, from rooted trees, hybridization, inapproximability, NP complete, phylogenetic network, phylogeny, SPR distance. Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BS06a.pdf.



David Bryant and
Vincent Moulton. NeighborNet: An Agglomerative Method for the Construction of Phylogenetic Networks. In MBE, Vol. 21(2):255265, 2004. Keywords: phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network. Note: http://www.math.auckland.ac.nz/~bryant/Papers/04NeighborNet.pdf.
Toggle abstract
"We present NeighborNet, a distance based method for constructing phylogenetic networks that is based on the NeighborJoining (NJ) algorithm of Saitou and Nei. NeighborNet provides a snapshot of the data that can guide more detailed analysis. Unlike split decomposition, NeighborNet scales well and can quickly produce detailed and informative networks for several hundred taxa. We illustrate the method by reanalyzing three published data sets: a collection of 110 highly recombinant Salmonella multilocus sequence typing sequences, the 135 "African Eve" human mitochondrial sequences published by Vigilant et al., and a collection of 12 Archeal chaperonin sequences demonstrating strong evidence for gene conversion. NeighborNet is available as part of the SplitsTree4 software package."



Mihaela Baroni,
Charles Semple and
Mike Steel. A framework for representing reticulate evolution. In ACOM, Vol. 8:398401, 2004. Keywords: explicit network, from clusters, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction, regular network, SPR distance. Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BSS04.pdf.
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"Acyclic directed graphs (ADGs) are increasingly being viewed as more appropriate for representing certain evolutionary relationships, particularly in biology, than rooted trees. In this paper, we develop a framework for the analysis of these graphs which we call hybrid phylogenies. We are particularly interested in the problem whereby one is given a set of phylogenetic trees and wishes to determine a hybrid phylogeny that 'embeds' each of these trees and which requires the smallest number of hybridisation events. We show that this quantity can be greatly reduced if additional species are involved, and investigate other combinatorial aspects of this and related questions."



Mihaela Baroni,
Charles Semple and
Mike Steel. Hybrids in Real Time. In Systematic Biology, Vol. 55(1):4656, 2006. Keywords: agreement forest, from rooted trees, phylogenetic network, phylogeny, polynomial, reconstruction, time consistent network. Note: http://www.math.canterbury.ac.nz/~m.steel/Non_UC/files/research/hybrids.pdf.
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"We describe some new and recent results that allow for the analysis and representation of reticulate evolution by nontree networks. In particular, we (1) present a simple result to show that, despite the presence of reticulation, there is always a welldefined underlying tree that corresponds to those parts of life that do not have a history of reticulation; (2) describe and apply new theory for determining the smallest number of hybridization events required to explain conflicting gene trees; and (3) present a new algorithm to determine whether an arbitrary rooted network can be realized by contemporaneous reticulation events. We illustrate these results with examples. Copyright © Society of Systematic Biologists."



HoLeung Chan,
Jesper Jansson,
TakWah Lam and
SiuMing Yiu. Reconstructing an Ultrametric Galled Phylogenetic Network from a Distance Matrix. In JBCB, Vol. 4(4):807832, 2006. Keywords: explicit network, from distances, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction. Note: http://www.df.lth.se/~jj/Publications/dist_ugn7_JBCB2006.pdf.
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"Given a distance matrix M that specifies the pairwise evolutionary distances between n species, the phylogenetic tree reconstruction problem asks for an edgeweighted phylogenetic tree that satisfies M, if one exists. We study some extensions of this problem to rooted phylogenetic networks. Our main result is an O(n2 log n)time algorithm for determining whether there is an ultrametric galled network that satisfies M, and if so, constructing one. In fact, if such an ultrametric galled network exists, our algorithm is guaranteed to construct one containing the minimum possible number of nodes with more than one parent (hybrid nodes). We also prove that finding a largest possible submatrix M′ of M such that there exists an ultrametric galled network that satisfies M′ is NPhard. Furthermore, we show that given an incomplete distance matrix (i.e. where some matrix entries are missing), it is also NPhard to determine whether there exists an ultrametric galled network which satisfies it. © 2006 Imperial College Press."



Charles Choy,
Jesper Jansson,
Kunihiko Sadakane and
WingKin Sung. Computing the maximum agreement of phylogenetic networks. In TCS, Vol. 335(1):93107, 2005. Keywords: dynamic programming, FPT, level k phylogenetic network, MASN, NP complete, phylogenetic network, phylogeny. Note: http://www.df.lth.se/~jj/Publications/masn8_TCS2005.pdf.
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"We introduce the maximum agreement phylogenetic subnetwork problem (MASN) for finding branching structure shared by a set of phylogenetic networks. We prove that the problem is NPhard even if restricted to three phylogenetic networks and give an O(n2)time algorithm for the special case of two level1 phylogenetic networks, where n is the number of leaves in the input networks and where N is called a levelf phylogenetic network if every biconnected component in the underlying undirected graph induces a subgraph of N containing at most f nodes with indegree 2. We also show how to extend our technique to yield a polynomialtime algorithm for any two levelf phylogenetic networks N1,N2 satisfying f=O(logn); more precisely, its running time is O(V(N1)·V(N2)·2f1+f2), where V(Ni) and fi denote the set of nodes in Ni and the level of Ni, respectively, for i∈{1,2}. © 2005 Elsevier B.V. All rights reserved."



Mark Clement,
David Posada and
Keith A. Crandall. TCS: a computer program to estimate gene genealogies. In MOLE, Vol. 9:16571659, 2000. Keywords: from sequences, parsimony, phylogenetic network, phylogeny, Program TCS, reconstruction, software, statistical parsimony. Note: http://darwin.uvigo.es/download/papers/08.tcs00.pdf.
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[No abstract available]



Gabriel Cardona,
Francesc Rosselló and
Gabriel Valiente. Tripartitions do not always discriminate phylogenetic networks. In MBIO, Vol. 211(2):356370, 2008. Keywords: distance between networks, phylogenetic network, phylogeny, Program Bio PhyloNetwork, tree child network, tripartition distance. Note: http://arxiv.org/abs/0707.2376, slides available at http://www.newton.cam.ac.uk/webseminars/pg+ws/2007/plg/plgw01/0904/valiente/.
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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. In a recent series of papers devoted to the study of reconstructibility of phylogenetic networks, Moret, Nakhleh, Warnow and collaborators introduced the socalled tripartition metric for phylogenetic networks. In this paper we show that, in fact, this tripartition metric does not satisfy the separation axiom of distances (zero distance means isomorphism, or, in a more relaxed version, zero distance means indistinguishability in some specific sense) in any of the subclasses of phylogenetic networks where it is claimed to do so. We also present a subclass of phylogenetic networks whose members can be singled out by means of their sets of tripartitions (or even clusters), and hence where the latter can be used to define a meaningful metric. © 2007 Elsevier Inc. All rights reserved."



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 child network, tree sibling network. Note: http://arxiv.org/abs/0708.3499.
Toggle abstract
"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."





Andreas W. M. Dress,
Daniel H. Huson and
Vincent Moulton. Analyzing and visualizing distance data using SplitsTree. In DAM, Vol. 71(1):95109, 1996. Keywords: abstract network, from distances, phylogenetic network, phylogeny, Program SplitsTree, software, split network, visualization. Note: http://bibiserv.techfak.unibielefeld.de/splits/splits.pdf.



Andreas W. M. Dress and
Daniel H. Huson. Constructing splits graphs. In TCBB, Vol. 1(3):109115, 2004. Keywords: abstract network, circular split system, from trees, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network, visualization. Note: http://scilib.kiev.ua/ieee/tcbb/2004/03/n3/n0109.pdf.
Toggle abstract
"Phylogenetic trees correspond onetoone to compatible systems of splits and so splits play an important role in theoretical and computational aspects of phylogeny. Whereas any tree reconstruction method can be thought of as producing a compatible system of splits, an increasing number of phylogenetlc algorithms are available that compute split systems that are not necessarily compatible and, thus, cannot always be represented by a tree. Such methods include the split decomposition, NeighborNet, consensus networks, and the Zclosure method. A more general split system of this kind can be represented graphically by a socalled splits graph, which generalizes the concept of a phylogenetic tree. This paper addresses the problem of computing a splits graph for a given set of splits. We have implemented all presented algorithms in a new program called SplitsTree4. © 2004 IEEE."





Philippe Gambette and
Daniel H. Huson. Improved Layout of Phylogenetic Networks. In TCBB, Vol. 5(3):472479, 2008. Keywords: abstract network, heuristic, phylogenetic network, phylogeny, Program SplitsTree, software, split network, visualization. Note: http://hallirmm.ccsd.cnrs.fr/lirmm00309694/en/.
Toggle abstract
"Split networks are increasingly being used in phylogenetic analysis. Usually, a simple equalangle algorithm is used to draw such networks, producing layouts that leave much room for improvement. Addressing the problem of producing better layouts of split networks, this paper presents an algorithm for maximizing the area covered by the network, describes an extension of the equaldaylight algorithm to networks, looks into using a spring embedder, and discusses how to construct rooted split networks. © 2008 IEEE."



Olivier Gauthier and
FrançoisJoseph Lapointe. Hybrids and Phylogenetics Revisited: A Statistical Test of Hybridization Using Quartets. In Systematic Botany, Vol. 32(1):815, 2007. Keywords: explicit network, from quartets, hybridization, phylogenetic network, phylogeny, reconstruction, reticulogram, split decomposition. Note: http://dx.doi.org/10.1600/036364407780360238.
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"The occurrence of reticulations in the evolutionary history of species poses serious challenges for all modern practitioners of phylogenetic analysis. Such events, including hybridization, introgression, and lateral gene transfer, lead to evolutionary histories that cannot be adequately represented in the form of phylogenetic trees. Although numerous methods that allow for the reconstruction of phylogenetic networks have been proposed in recent years, the detection of reticulations still remains problematic. In this paper we present a Hybrid Detection Criterion (HDC) along with a statistical procedure that allows for the identification of hybrid taxa. The test assesses whether a putative hybrid is consistently intermediate between its postulated parents, with respect to the other taxa. The performance of the statistical method is evaluated using known hybrids of the genus Aphelandra (Acanthaceae) using two network methods: reticulograms and split decomposition graphs. Our results indicate that the HDC test is reliable when used jointly with split decomposition. On the other hand, the test lacks power and provides misleading results when using reticulograms. We then show how the procedure can be used as a tool to identify putative hybrids. © Copyright 2007 by the American Society of Plant Taxonomists."



Dan Gusfield,
Satish Eddhu and
Charles Langley. Optimal, Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination. In JBCB, Vol. 2(1):173213, 2004. Keywords: explicit network, from sequences, galled tree, phylogenetic network, phylogeny, recombination, reconstruction. Note: http://wwwcsif.cs.ucdavis.edu/~gusfield/exfinalrec.pdf.
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"A phylogenetic network is a generalization of a phylogenetic tree, allowing structural properties that are not treelike. In a seminal paper, Wang et al.1 studied the problem of constructing a phylogenetic network, allowing recombination between sequences, with the constraint that the resulting cycles must be disjoint. We call such a phylogenetic network a "galledtree". They gave a polynomialtime algorithm that was intended to determine whether or not a set of sequences could be generated on galledtree. Unfortunately, the algorithm by Wang et al.1 is incomplete and does not constitute a necessary test for the existence of a galledtree for the data. In this paper, we completely solve the problem. Moreover, we prove that if there is a galledtree, then the one produced by our algorithm minimizes the number of recombinations over all phylogenetic networks for the data, even allowing multiplecrossover recombinations. We also prove that when there is a galledtree for the data, the galledtree minimizing the number of recombinations is "essentially unique" . We. also note two additional results: first, any set of sequences that can be derived on a galled tree can be derived on a true tree (without recombination cycles), where at most one back mutation per site is allowed; second, the site compatibility problem (which is NPhard in general) can be solved in polynomial time for any set of sequences that can be derived on a galled tree. Perhaps more important than the specific results about galledtrees, we introduce an approach that can be used to study recombination in general phylogenetic networks. This paper greatly extends the conference version that appears in an earlier work.8 PowerPoint slides of the conference talk can be found at our website. © Imperial College Press."



Dan Gusfield,
Satish Eddhu and
Charles Langley. The fine structure of galls in phylogenetic networks. In INCOMP, Vol. 16(4):459469, 2004. Keywords: explicit network, from sequences, galled tree, phylogenetic network, phylogeny, reconstruction. Note: http://wwwcsif.cs.ucdavis.edu/~gusfield/informs.pdf.
Toggle abstract
"A phylogenetic network is a generalization of a phylogenetic tree, allowing properties that are not treelike. With the growth of genomic data, much of which does not fit ideal tree models, there is greater need to understand the algorithmics and combinatorics of phylogenetic networks (Posada and Crandall 2001, Schierup and Hein 2000). Wang et al. (2001) studied the problem of constructing a phylogenetic network for a set of n binary sequences derived from the allzero ancestral sequence, when each site in the sequence can mutate from zero to one at most once in the network, and recombination between sequences is allowed. They showed that the problem of minimizing the number of recombinations in such networks is NPhard, but introduced a special case of the problem, i.e., to determine whether the sequences could be derived on a phylogenetic network where the recombination cycles are nodedisjoint. Wang et al. (2001) provide a sufficient, but not a necessary test, for such solutions. Gusfield et al. (2003, 2004) gave a polynomialtime algorithm that is both a necessary and sufficient test. In this paper, we study in much more detail the fine combinatorial structure of nodedisjoint cycles in phylogenetic networks, both for purposes of insight into phylogenetic networks and to speed up parts of the previous algorithm. We explicitly characterize all the ways in which mutations can be arranged on a disjoint cycle, and prove a strong necessary condition for a set of mutations to be on a disjoint cycle. The main contribution here is to show how structure in the phylogenetic network is reflected in the structure of an efficientlycomputable graph, called the conflict graph. The success of this approach suggests that additional insight into the structure of phylogenetic networks can be obtained by exploring structural properties of the conflict graph."



Stefan Grünewald,
Kristoffer Forslund,
Andreas W. M. Dress and
Vincent Moulton. QNet: An agglomerative method for the construction of phylogenetic networks from weighted quartets. In MBE, Vol. 24(2):532538, 2007. Keywords: abstract network, circular split system, from quartets, phylogenetic network, phylogeny, Program QNet, reconstruction, software. Note: http://mbe.oxfordjournals.org/cgi/content/abstract/24/2/532.
Toggle abstract
"We present QNet, a method for constructing split networks from weighted quartet trees. QNet can be viewed as a quartet analogue of the distancebased NeighborNet (NNet) method for network construction. Just as NNet, QNet works by agglomeratively computing a collection of circular weighted splits of the taxa set which is subsequently represented by a planar split network. To illustrate the applicability of QNet, we apply it to a previously published Salmonella data set. We conclude that QNet can provide a useful alternative to NNet if distance data are not available or a characterbased approach is preferred. Moreover, it can be used as an aid for determining when a quartetbased treebuilding method may or may not be appropriate for a given data set. QNet is freely available for download. © The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved."



Stefan Grünewald,
Katharina Huber and
Qiong Wu. Two novel closure rules for constructing phylogenetic supernetworks. In BMB, Vol. 70(7):19061924, 2008. Keywords: abstract network, from splits, from unrooted trees, phylogenetic network, phylogeny, Program MY CLOSURE, reconstruction, supernetwork. Note: http://arxiv.org/abs/0709.0283, slides available at http://www.newton.cam.ac.uk/webseminars/pg+ws/2007/plg/plgw01/0904/huber/.
Toggle abstract
"A contemporary and fundamental problem faced by many evolutionary biologists is how to puzzle together a collection P of partial trees (leaflabeled trees whose leaves are bijectively labeled by species or, more generally, taxa, each supported by, e.g., a gene) into an overall parental structure that displays all trees in P. This already difficult problem is complicated by the fact that the trees in P regularly support conflicting phylogenetic relationships and are not on the same but only overlapping taxa sets. A desirable requirement on the sought after parental structure, therefore, is that it can accommodate the observed conflicts. Phylogenetic networks are a popular tool capable of doing precisely this. However, not much is known about how to construct such networks from partial trees, a notable exception being the Zclosure supernetwork approach, which is based on the Zclosure rule, and the Qimputation approach. Although attractive approaches, they both suffer from the fact that the generated networks tend to be multidimensional making it necessary to apply some kind of filter to reduce their complexity. To avoid having to resort to a filter, we follow a different line of attack in this paper and develop closure rules for generating circular phylogenetic networks which have the attractive property that they can be represented in the plane. In particular, we introduce the novel Y(closure) rule and show that this rule on its own or in combination with one of Meacham's closure rules (which we call the Mrule) has some very desirable theoretical properties. In addition, we present a case study based on Rivera et al. "ring of life" to explore the reconstructive power of the M and Yrule and also reanalyze an Arabidopsis thaliana data set. © 2008 Society for Mathematical Biology."



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.
Toggle abstract
"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."





Barbara R. Holland,
Glenn Conner,
Katharina Huber and
Vincent Moulton. Imputing Supertrees and Supernetworks from Quartets. In Systematic Biology, Vol. 56(1):5767, 2007. Keywords: abstract network, from unrooted trees, phylogenetic network, phylogeny, Program Quartet, reconstruction, split network, supernetwork. Note: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.99.3215.
Toggle abstract
"Inferring species phylogenies is an important part of understanding molecular evolution. Even so, it is well known that an accurate phylogenetic tree reconstruction for a single gene does not always necessarily correspond to the species phylogeny. One commonly accepted strategy to cope with this problem is to sequence many genes; the way in which to analyze the resulting collection of genes is somewhat more contentious. Supermatrix and supertree methods can be used, although these can suppress conflicts arising from true differences in the gene trees caused by processes such as lineage sorting, horizontal gene transfer, or gene duplication and loss. In 2004, Huson et al. (IEEE/ACM Trans. Comput. Biol. Bioinformatics 1:151158) presented the Zclosure method that can circumvent this problem by generating a supernetwork as opposed to a supertree. Here we present an alternative way for generating supernetworks called Qimputation. In particular, we describe a method that uses quartet information to add missing taxa into gene trees. The resulting trees are subsequently used to generate consensus networks, networks that generalize strict and majorityrule consensus trees. Through simulations and application to real data sets, we compare Qimputation to the matrix representation with parsimony (MRP) supertree method and Zclosure, and demonstrate that it provides a useful complementary tool. Copyright © Society of Systematic Biologists."



Daniel H. Huson,
Tobias Dezulian,
Tobias Kloepper and
Mike Steel. Phylogenetic SuperNetworks from Partial Trees. In TCBB, Vol. 1(4):151158, 2004. Keywords: abstract network, from unrooted trees, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, supernetwork. Note: http://hdl.handle.net/10092/3177.
Toggle abstract
"In practice, one is often faced with incomplete phylogenetic data, such as a collection of partial trees or partial splits. This paper poses the problem of Inferring a phylogenetic supernetwork from such data and provides an efficient algorithm for doing so, called the Zclosure method. Additionally, the questions of assigning lengths to the edges of the network and how to restrict the "dimensionality" of the network are addressed. Applications to a set of five published partial gene trees relating different fungal species and to six published partial gene trees relating different grasses illustrate the usefulness of the method and an experimental study confirms Its potential. The method Is implemented as a plugin for the program SplitsTree4. © 2004 IEEE."



Jotun Hein. A heuristic method to reconstruct the history of sequences subject to recombination. In JME, Vol. 36(4):396405, 1993. Keywords: explicit network, from sequences, heuristic, parsimony, phylogenetic network, phylogeny, Program RecPars, recombination, recombination detection, software. Note: http://dx.doi.org/10.1007/BF00182187.





Katharina Huber,
Michael Langton,
David Penny,
Vincent Moulton and
Mike Hendy. Spectronet: A package for computing spectra and median networks. In ABIO, Vol. 1(3):159161, 2004. Keywords: from splits, median network, phylogenetic network, phylogeny, Program Spectronet, software, split, visualization. Note: http://citeseer.ist.psu.edu/631776.html.
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Spectronet is a package that uses various methods for exploring and visualising complex evolutionary signals. Given an alignment in NEXUS format, the package works by computing a collection of weighted splits or bipartitions of the taxa and then allows the user to interactively analyse the resulting collection using tools such as Lentoplots and median networks. The package is highly interactive and available for PCs.



Katharina Huber,
Vincent Moulton,
Peter J. Lockhart and
Andreas W. M. Dress. Pruned Median Networks: A Technique for Reducing the Complexity of Median Networks. In MPE, Vol. 19(2):302310, 2001. Keywords: abstract network, median network, phylogenetic network, phylogeny, split. Note: http://dx.doi.org/10.1006/mpev.2001.0935.
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"Observations from molecular marker studies on recently diverged species indicate that substitution patterns in DNA sequences can often be complex and poorly described by treelike bifurcating evolutionary models. These observations might result from processes of species diversification and/or processes of sequence evolution that are not treelike. In these cases, bifurcating tree representations provide poor visualization of phylogenetic signals in sequence data. In this paper, we use median networks to study DNA sequence substitution patterns in plant nuclear and chloroplast markers. We describe how to prune median networks to obtain so called pruned median networks. These simpler networks may help to provide a useful framework for investigating the phylogenetic complexity of recently diverged taxa with hybrid origins. © 2001 Academic Press."



Katharina Huber,
Bengt Oxelman,
Martin Lott and
Vincent Moulton. Reconstructing the Evolutionary History of Polyploids from Multilabeled Trees. In MBE, Vol. 23(9):17841791, 2007. Keywords: duplication, explicit network, from multilabeled tree, from trees, phylogenetic network, phylogeny, Program PADRE, reconstruction, software. Note: http://mbe.oxfordjournals.org/cgi/content/full/23/9/1784.
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"In recent studies, phylogenetic networks have been derived from socalled multilabeled trees in order to understand the origins of certain polyploids. Although the trees used in these studies were constructed using sophisticated techniques in phylogenetic analysis, the presented networks were inferred using ad hoc arguments that cannot be easily extended to larger, more complicated examples. In this paper, we present a general method for constructing such networks, which takes as input a multilabeled phylogenetic tree and outputs a phylogenetic network with certain desirable properties. To illustrate the applicability of our method, we discuss its use in reconstructing the evolutionary history of plant allopolyploids. We conclude with a discussion concerning possible future directions. The network construction method has been implemented and is freely available for use from http://www.uea.ac.uk/ ∼a043878/padre.html. © The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved."



Vincent Moulton and
Katharina Huber. Phylogenetic networks from multilabelled trees. In JOMB, Vol. 52(5):613632, 2006. Keywords: duplication, explicit network, from multilabeled tree, phylogenetic network, phylogeny, Program PADRE, reconstruction. Note: http://www.uea.ac.uk/~a043878/jmb.pdf.
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"It is now quite well accepted that the evolutionary past of certain species is better represented by phylogenetic networks as opposed to trees. For example, polyploids are typically thought to have resulted through hybridization and duplication, processes that are probably not best represented as bifurcating speciation events. Based on the knowledge of a multilabelled tree relating collection of polyploids, we present a canonical construction of a phylogenetic network that exhibits the tree. In addition, we prove that the resulting network is in some welldefined sense a minimal network having this property. © SpringerVerlag 2006."





Daniel H. Huson and
David Bryant. Application of Phylogenetic Networks in Evolutionary Studies. In MBE, Vol. 23(2):254267, 2006. Keywords: abstract network, phylogenetic network, phylogeny, Program SplitsTree, software, survey. Note: http://dx.doi.org/10.1093/molbev/msj030, software available from www.splitstree.org.
Toggle abstract
"The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, even when evolution proceeds in a treelike manner, analysis of the data may not be best served by using methods that enforce a tree structure but rather by a richer visualization of the data to evaluate its properties, at least as an essential first step. Thus, phylogenetic networks should be employed when reticulate events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved, and, even in the absence of such events, phylogenetic networks have a useful role to play. This article reviews the terminology used for phylogenetic networks and covers both split networks and reticulate networks, how they are defined, and how they can be interpreted. Additionally, the article outlines the beginnings of a comprehensive statistical framework for applying split network methods. We show how split networks can represent confidence sets of trees and introduce a conservative statistical test for whether the conflicting signal in a network is treelike. Finally, this article describes a new program, SplitsTree4, an interactive and comprehensive tool for inferring different types of phylogenetic networks from sequences, distances, and trees. © The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved."



Jesper Jansson and
WingKin Sung. Inferring a level1 phylogenetic network from a dense set of rooted triplets. In TCS, Vol. 363(1):6068, 2006. 1 comment Keywords: explicit network, from triplets, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, polynomial, reconstruction. Note: http://www.df.lth.se/~jj/Publications/ipnrt8_TCS2006.pdf.
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"We consider the following problem: Given a set T of rooted triplets with leaf set L, determine whether there exists a phylogenetic network consistent with T, and if so, construct one. We show that if no restrictions are placed on the hybrid nodes in the solution, the problem is trivially solved in polynomial time by a simple sorting networkbased construction. For the more interesting (and biologically more motivated) case where the solution is required to be a level1 phylogenetic network, we present an algorithm solving the problem in O ( T 2) time when T is dense, i.e., when T contains at least one rooted triplet for each cardinality three subset of L. We also give an O ( T 5 / 3)time algorithm for finding the set of all phylogenetic networks having a single hybrid node attached to exactly one leaf (and having no other hybrid nodes) that are consistent with a given dense set of rooted triplets. © 2006 Elsevier B.V. All rights reserved."



Jesper Jansson,
Nguyen Bao Nguyen and
WingKin Sung. Algorithms for Combining Rooted Triplets into a Galled Phylogenetic Network. In SICOMP, Vol. 35(5):10981121, 2006. 1 comment Keywords: approximation, explicit network, from triplets, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction. Note: http://www.df.lth.se/~jj/Publications/triplets_to_gn7_SICOMP2006.pdf.
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"This paper considers the problem of determining whether a given set Τ of rooted triplets can be merged without conflicts into a galled phylogenetic network and, if so, constructing such a network. When the input Τ is dense, we solve the problem in O(Τ) time, which is optimal since the size of the input is Θ(Τ). In comparison, the previously fastest algorithm for this problem runs in O(Τ2) time. We also develop an optimal O(Τ)time algorithm for enumerating all simple phylogenetic networks leaflabeled by L that are consistent with Τ, where L is the set of leaf labels in Τ, which is used by our main algorithm. Next, we prove that the problem becomes NPhard if extended to nondense inputs, even for the special case of simple phylogenetic networks. We also show that for every positive integer n, there exists some set Τ of rooted triplets on n leaves such that any galled network can be consistent with at most 0.4883 ·Τ of the rooted triplets in Τ. On the other hand, we provide a polynomialtime approximation algorithm that always outputs a galled network consistent with at least a factor of 5/12 (> 0.4166) of the rooted triplets in Τ. © 2006 Society for Industrial and Applied Mathematics."



Guohua Jin,
Luay Nakhleh,
Sagi Snir and
Tamir Tuller. Maximum Likelihood of Phylogenetic Networks. In BIO, Vol. 22(21):26042611, 2006. Keywords: explicit network, likelihood, phylogenetic network, phylogeny, Program Nepal, reconstruction. Note: http://www.cs.rice.edu/~nakhleh/Papers/NetworksML06.pdf, supplementary material: http://www.cs.rice.edu/~nakhleh/Papers/SuppML.pdf.





Martyn Kennedy,
Barbara R. Holland,
Russel D. Gray and
Hamish G. Spencer. Untangling Long Branches: Identifying Conflicting Phylogenetic Signals Using Spectral Analysis, NeighborNet, and Consensus Networks. In Systematic Biology, Vol. 54(4):620633, 2005. Keywords: abstract network, consensus, NeighborNet, phylogenetic network, phylogeny. Note: http://awcmee.massey.ac.nz/people/bholland/pdf/Kennedy_etal_2005.pdf.













Bernard M. E. Moret,
Luay Nakhleh,
Tandy Warnow,
C. Randal Linder,
Anna Tholse,
Anneke Padolina,
Jerry Sun and
Ruth Timme. Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy. In TCBB, Vol. 1(1):1323, 2004. Keywords: distance between networks, evaluation, phylogenetic network, phylogeny, time consistent network, tripartition distance. Note: http://www.cs.rice.edu/~nakhleh/Papers/tcbb04.pdf.



David A. Morrison. Networks in phylogenetic analysis: new tools for population biology. In IJP, Vol. 35:567582, 2005. Keywords: median network, NeighborNet, phylogenetic network, phylogeny, population genetics, Program Network, Program Spectronet, Program SplitsTree, Program T REX, Program TCS, reconstruction, reticulogram, split decomposition, survey. Note: http://hem.fyristorg.com/acacia/papers/networks.pdf.



Cam Thach Nguyen,
Nguyen Bao Nguyen and
WingKin Sung. Fast Algorithms for computing the Tripartitionbased Distance between Phylogenetic Networks. In JCO, Vol. 13(3), 2007. Keywords: distance between networks, phylogenetic network, phylogeny, tripartition distance. Note: http://dx.doi.org/10.1007/s1087800690255.
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"Consider two phylogenetic networks N and N′ of size n. The tripartitionbased distance finds the proportion of tripartitions which are not shared by N and N′. This distance is proposed by Moret et al. (2004) and is a generalization of RobinsonFoulds distance, which is orginally used to compare two phylogenetic trees. This paper gives an O(min {kn log n, n log n + hn} time algorithm to compute this distance, where h is the number of hybrid nodes in N and N′ while k is the maximum number of hybrid nodes among all biconnected components in N and N′. Note that k ≪ h ≪ n in a phylogenetic network. In addition, we propose algorithms for comparing galledtrees, which are an important, biological meaningful special case of phylogenetic network. We give an O(n)time algorithm for comparing two galledtrees. We also give an O(n + kh)time algorithm for comparing a galledtree with another general network, where h and k are the number of hybrid nodes in the latter network and its biggest biconnected component respectively. © Springer Science+Business Media, LLC 2007."



Cam Thach Nguyen,
Nguyen Bao Nguyen,
WingKin Sung and
Louxin Zhang. Reconstructing Recombination Network from Sequence Data: The Small Parsimony Problem. In TCBB, Vol. 4(3):394402, 2007. Keywords: explicit network, from sequences, labeling, NP complete, parsimony, phylogenetic network, phylogeny. Note: http://www.cs.washington.edu/homes/ncthach/Papers/TCBB2007.pdf.





Luay Nakhleh,
Tandy Warnow,
C. Randal Linder and
Katherine St. John. Reconstructing reticulate evolution in species  theory and practice. In JCB, Vol. 12(6):796811, 2005. Keywords: from rooted trees, galled tree, phylogenetic network, phylogeny, polynomial, Program SPNet, reconstruction, software. Note: http://www.cs.rice.edu/~nakhleh/Papers/NWLSjcb.pdf.



David Posada,
Keith A. Crandall and
Edward C. Holmes. Recombination in Evolutionary Genomics. In ARG, Vol. 36:7597, 2002. Keywords: phylogenetic network, phylogeny, recombination, recombination detection, survey. Note: http://dx.doi.org/10.1146/annurev.genet.36.040202.111115.
Toggle abstract
"Recombination can be a dominant force in shaping genomes and associated phenotypes. To better understand the impact of recombination on genomic evolution, we need to be able to identify recombination in aligned sequences. We review bioinformatic approaches for detecting recombination and measuring recombination rates. We also examine the impact of recombination on the reconstruction of evolutionary histories and the estimation of population genetic parameters. Finally, we review the role of recombination in the evolutionary history of bacteria, viruses, and human mitochondria. We conclude by highlighting a number of areas for future development of tools to help quantify the role of recombination in genomic evolution."



David Posada and
Keith A. Crandall. Intraspecific gene genealogies: trees grafting into networks. In TEE, Vol. 16(1):3745, 2001. Keywords: likelihood, median network, netting, parsimony, phylogenetic network, phylogeny, Program Arlequin, Program SplitsTree, Program T REX, Program TCS, pyramid, reticulogram, split decomposition, statistical parsimony, survey. Note: http://darwin.uvigo.es/download/papers/09.networks01.pdf.





Andreas Spillner,
Binh T. Nguyen and
Vincent Moulton. Computing phylogenetic diversity for split systems. In TCBB, Vol. 5(2):235244, 2008. Keywords: abstract network, diversity, phylogenetic network, phylogeny, split. Note: http://dx.doi.org/10.1109/TCBB.2007.70260, slides available at http://www.newton.cam.ac.uk/webseminars/pg+ws/2007/plg/plgw01/0906/spillner/.
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"In conservation biology it is a central problem to measure, predict, and preserve biodiversity as species face extinction. In 1992 Faith proposed measuring the diversity of a collection of species in terms of their relationships on a phylogenetic tree, and to use this information to identify collections of species with high diversity. Here we are interested in some variants of the resulting optimization problem that arise when considering species whose evolution is better represented by a network rather than a tree. More specifically, we consider the problem of computing phylogenetic diversity relative to a split system on a collection of species of size $n$. We show that for general split systems this problem is NPhard. In addition we provide some efficient algorithms for some special classes of split systems, in particular presenting an optimal $O(n)$ time algorithm for phylogenetic trees and an $O(nlog n + n k)$ time algorithm for choosing an optimal subset of size $k$ relative to a circular split system. © 2006 IEEE."



Alan R. Templeton,
Keith A. Crandall and
Charles F. Sing. A Cladistic Analysis of Phenotypic Associations With Haplotypes Inferred From Restriction Endonuclease Mapping and DNA Sequence Data. III. Cladogram Estimation. In GEN, Vol. 132:619633, 2000. Keywords: from sequences, parsimony, phylogenetic network, phylogeny, Program TCS, recombination, reconstruction, statistical parsimony. Note: http://www.genetics.org/cgi/content/abstract/132/2/619.



Richard C. Winkworth,
David Bryant,
Peter J. Lockhart,
David Havell and
Vincent Moulton. Biogeographic Interpretation of Splits Graphs: Least Squares Optimization of Branch Lengths. In Systematic Biology, Vol. 54(1):5665, 2005. Keywords: abstract network, from distances, from network, phylogenetic network, phylogeny, reconstruction, split, split network. Note: http://www.math.auckland.ac.nz/~bryant/Papers/05Biogeographic.pdf.











Bhaskar DasGupta,
Sergio Ferrarini,
Uthra Gopalakrishnan and
Nisha Raj Paryani. Inapproximability results for the lateral gene transfer problem. In JCO, Vol. 11(4):387405, 2006. Keywords: approximation, from rooted trees, from species tree, inapproximability, lateral gene transfer, parsimony, phylogenetic network, phylogeny. Note: http://www.cs.uic.edu/~dasgupta/resume/publ/papers/tscenario3reviewed3.pdf.



Dave MacLeod,
Robert L. Charlebois,
W. Ford Doolittle and
Eric Bapteste. Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement. In BMCEB, Vol. 5(27), 2005. Keywords: explicit network, from rooted trees, lateral gene transfer, phylogenetic network, phylogeny, Program HorizStory, reconstruction, software. Note: http://dx.doi.org/10.1186/14712148527.
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"Background: When organismal phylogenies based on sequences of single marker genes are poorly resolved, a logical approach is to add more markers, on the assumption that weak but congruent phylogenetic signal will be reinforced in such multigene trees. Such approaches are valid only when the several markers indeed have identical phylogenies, an issue which many multigene methods (such as the use of concatenated gene sequences or the assembly of supertrees) do not directly address. Indeed, even when the true history is a mixture of vertical descent for some genes and lateral gene transfer (LGT) for others, such methods produce unique topologies. Results: We have developed software that aims to extract evidence for vertical and lateral inheritance from a set of gene trees compared against an arbitrary reference tree. This evidence is then displayed as a synthesis showing support over the tree for vertical inheritance, overlaid with explicit lateral gene transfer (LGT) events inferred to have occurred over the history of the tree. Like splitstree methods, one can thus identify nodes at which conflict occurs. Additionally one can make reasonable inferences about vertical and lateral signal, assigning putative donors and recipients. Conclusion: A tool such as ours can serve to explore the reticulated dimensionality of molecular evolution, by dissecting vertical and lateral inheritance at high resolution. By this, we mean that individual nodes can be examined not only for congruence, but also for coherence in light of LGT. We assert that our tools will facilitate the comparison of phylogenetic trees, and the interpretation of conflicting data. © 2005 MacLeod et al; licensee BioMed Central Ltd."



Daniel H. Huson,
Daniel C. Richter,
Christian Rausch,
Tobias Dezulian,
Markus Franz and
Regula Rupp. Dendroscope: An interactive viewer for large phylogenetic trees. In BMCB, Vol. 8:460, 2007. Keywords: phylogeny, Program Dendroscope, software, visualization. Note: http://dx.doi.org/10.1186/147121058460, slides available at http://www.newton.cam.ac.uk/webseminars/pg+ws/2007/plg/plgw01/0903/huson/, software freely available from http://www.dendroscope.org.
Toggle abstract
"Background: Research in evolution requires software for visualizing and editing phylogenetic trees, for increasingly very large datasets, such as arise in expression analysis or metagenomics, for example. It would be desirable to have a program that provides these services in an effcient and userfriendly way, and that can be easily installed and run on all major operating systems. Although a large number of tree visualization tools are freely available, some as a part of more comprehensive analysis packages, all have drawbacks in one or more domains. They either lack some of the standard tree visualization techniques or basic graphics and editing features, or they are restricted to small trees containing only tens of thousands of taxa. Moreover, many programs are diffcult to install or are not available for all common operating systems. Results: We have developed a new program, Dendroscope, for the interactive visualization and navigation of phylogenetic trees. The program provides all standard tree visualizations and is optimized to run interactively on trees containing hundreds of thousands of taxa. The program provides tree editing and graphics export capabilities. To support the inspection of large trees, Dendroscope offers a magnification tool. The software is written in Java 1.4 and installers are provided for Linux/Unix, MacOS X and Windows XP. Conclusion: Dendroscope is a userfriendly program for visualizing and navigating phylogenetic trees, for both small and large datasets. © 2007 Huson et al; licensee BioMed Central Ltd."



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."



Katharina Huber,
Elizabeth E. Watson and
Mike Hendy. An Algorithm for Constructing Local Regions in a Phylogenetic Network. In MPE, Vol. 19(1):18, 2000. Keywords: abstract network, median network, phylogenetic network, phylogeny, reconstruction, split. Note: http://dx.doi.org/10.1006/mpev.2000.0891.
Toggle abstract
"The groupings of taxa in a phylogenetic tree cannot represent all the conflicting signals that usually occur among site patterns in aligned homologous genetic sequences. Hence a treebuilding program must compromise by reporting a subset of the patterns, using some discriminatory criterion. Thus, in the worst case, out of possibly a large number of equally good trees, only an arbitrarily chosen tree might be reported by the treebuilding program as" The Tree." This tree might then be used as a basis for phylogenetic conclusions. One strategy to represent conflicting patterns in the data is to construct a network. The Buneman graph is a theoretically very attractive example of such a network. In particular, a characterization for when this network will be a tree is known. Also the Buneman graph contains each of the most parsimonious trees indicated by the data. In this paper we describe a new method for constructing the Buneman graph that can be used for a generalization of Hadamard conjugation to networks. This new method differs from previous methods by allowing us to focus on local regions of the graph without having to first construct the full graph. The construction is illustrated by an example. © 2001 Academic Press."







Dan Gusfield,
Vikas Bansal,
Vineet Bafna and
Yun S. Song. A Decomposition Theory for Phylogenetic Networks and Incompatible Characters. In JCB, Vol. 14(10):12471272, 2007. Keywords: explicit network, from sequences, galled tree, phylogenetic network, phylogeny, Program Beagle, Program GalledTree, recombination, reconstruction, software. Note: http://www.eecs.berkeley.edu/~yss/Pub/decomposition.pdf.





Gabriel Cardona,
Francesc Rosselló and
Gabriel Valiente. A Perl Package and an Alignment Tool for Phylogenetic Networks. In BMCB, Vol. 9:175, 2008. Keywords: distance between networks, phylogenetic network, phylogeny, Program Bio PhyloNetwork, tree child network, tree sibling network. Note: http://dx.doi.org/10.1186/147121059175.
Toggle abstract
"Background: Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of evolutionary events acting at the population level, like recombination between genes, hybridization between lineages, and lateral gene transfer. While most phylogenetics tools implement a wide range of algorithms on phylogenetic trees, there exist only a few applications to work with phylogenetic networks, none of which are opensource libraries, and they do not allow for the comparative analysis of phylogenetic networks by computing distances between them or aligning them. Results: In order to improve this situation, we have developed a Perl package that relies on the BioPerl bundle and implements many algorithms on phylogenetic networks. We have also developed a Java applet that makes use of the aforementioned Perl package and allows the user to make simple experiments with phylogenetic networks without having to develop a program or Perl script by him or herself. Conclusion: The Perl package is available as part of the BioPerl bundle, and can also be downloaded. A webbased application is also available (see availability and requirements). The Perl package includes full documentation of all its features. © 2008 Cardona et al; licensee BioMed Central Ltd."



Yun S. Song,
Zhihong Ding,
Dan Gusfield,
Charles Langley and
Yufeng Wu. Algorithms to Distinguish the Role of GeneConversion from SingleCrossover Recombination in the Derivation of SNP Sequences in Populations. In JCB, Vol. 14(10):12731286, 2007. Keywords: ARG, from sequences, phylogenetic network, phylogeny, Program SHRUB, reconstruction. Note: http://dx.doi.org/10.1089/cmb.2007.0096.
Toggle abstract
"Meiotic recombination is a fundamental biological event and one of the principal evolutionary forces responsible for shaping genetic variation within species. In addition to its fundamental role, recombination is central to several critical applied problems. The most important example is "association mapping" in populations, which is widely hoped to help find genes that influence genetic diseases (Carlson et al., 2004; Clark, 2003). Hence, a great deal of recent attention has focused on problems of inferring the historical derivation of sequences in populations when both mutations and recombinations have occurred. In the algorithms literature, most of that recent work has been directed to singlecrossover recombination. However, geneconversion is an important, and more common, form of (twocrossover) recombination which has been much less investigated in the algorithms literature. In this paper, we explicitly incorporate geneconversion into discrete methods to study historical recombination. We are concerned with algorithms for identifying and locating the extent of historical crossingover and geneconversion (along with singlenucleotide mutation), and problems of constructing full putative histories of those events. The novel technical issues concern the incorporation of geneconversion into recently developed discrete methods (Myers and Griffiths, 2003; Song et al., 2005) that compute lower and upperbound information on the amount of needed recombination without geneconversion. We first examine the most natural extension of the lower bound methods from Myers and Griffiths (2003), showing that the extension can be computed efficiently, but that this extension can only yield weak lower bounds. We then develop additional ideas that lead to higher lower bounds, and show how to solve, via integerlinear programming, a more biologically realistic version of the lower bound problem. We also show how to compute effective upper bounds on the number of needed singlecrossovers and geneconversions, along with explicit networks showing a putative history of mutations, singlecrossovers and geneconversions. Both lower and upper bound methods can handle data with missing entries, and the upper bound method can be used to infer missing entries with high accuracy. We validate the significance of these methods by showing that they can be effectively used to distinguish simulationderived sequences generated without geneconversion from sequences that were generated with geneconversion. We apply the methods to recently studied sequences of Arabidopsis thaliana, identifying many more regions in the sequences than were previously identified (Plagnol et al., 2006), where geneconversion may have played a significant role. Demonstration software is available at www.csif.cs.ucdavis.edu/∼gusfield. © 2007 Mary Ann Liebert, Inc."





Patricia Buendia and
Giri Narasimhan. Serial NetEvolve: A flexible utility for generating seriallysampled sequences along a tree or recombinant network. In BIO, Vol. 18(22):23132314, 2006. Keywords: generation, phylogenetic network, phylogeny, Program Serial NetEvolve, Program Treevolve, recombination, software. Note: http://dx.doi.org/10.1093/bioinformatics/btl387.
Toggle abstract
"Summary: Serial NetEvolve is a flexible simulation program that generates DNA sequences evolved along a tree or recombinant network. It offers a userfriendly Windows graphical interface and a Windows or Linux simulator with a diverse selection of parameters to control the evolutionary model. Serial NetEvolve is a modification of the Treevolve program with the following additional features: simulation of seriallysampled data, the choice of either a clocklike or a variable rate model of sequence evolution, sampling from the internal nodes and the output of the randomly generated tree or network in our newly proposed NeTwick format. © 2006 Oxford University Press."



Patricia Buendia and
Giri Narasimhan. Sliding MinPD: Building evolutionary networks of serial samples via an automated recombination detection approach. In BIO, Vol. 23(22):29933000, 2007. Keywords: from sequences, phylogenetic network, phylogeny, Program Sliding MinPD, recombination, recombination detection, serial evolutionary networks, software. Note: http://dx.doi.org/10.1093/bioinformatics/btm413.
Toggle abstract
"Motivation: Traditional phylogenetic methods assume treelike evolutionary models and are likely to perform poorly when provided with sequence data from fastevolving, recombining viruses. Furthermore, these methods assume that all the sequence data are from contemporaneous taxa, which is not valid for seriallysampled data. A more general approach is proposed here, referred to as the Sliding MinPD method, that reconstructs evolutionary networks for seriallysampled sequences in the presence of recombination. Results: Sliding MinPD combines distancebased phylogenetic methods with automated recombination detection based on the bestknown sliding window approaches to reconstruct serial evolutionary networks. Its performance was evaluated through comprehensive simulation studies and was also applied to a set of seriallysampled HIV sequences from a single patient. The resulting network organizations reveal unique patterns of viral evolution and may help explain the emergence of diseaseassociated mutants and drugresistant strains with implications for patient prognosis and treatment strategies. © The Author 2007. Published by Oxford University Press. All rights reserved."



Insa Cassens,
Patrick Mardulyn and
Michel C. Milinkovitch. Evaluating Intraspecific Network Construction Methods Using Simulated Sequence Data: Do Existing Algorithms Outperform the Global Maximum Parsimony Approach? In Systematic Biology, Vol. 54(3):363372, 2005. Keywords: abstract network, evaluation, from unrooted trees, haplotype network, parsimony, phylogenetic network, phylogeny, Program Arlequin, Program CombineTrees, Program Network, Program TCS, reconstruction, software. Note: http://www.lanevol.org/LANE/publications_files/Cassens_etal_SystBio_2005.pdf.





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.



Andreas W. M. Dress,
Katharina Huber,
Jacobus Koolen and
Vincent Moulton. Compatible decompositions and block realizations of finite metrics. In EJC, Vol. 29(7):16171633, 2008. Keywords: abstract network, block realization, from distances, phylogenetic network, phylogeny, realization, reconstruction. Note: http://www.ims.nus.edu.sg/preprints/200721.pdf.
Toggle abstract
"Given a metric D defined on a finite set X, we define a finite collection D of metrics on X to be a compatible decomposition of D if any two distinct metrics in D are linearly independent (considered as vectors in RX × X), D = ∑d ∈ D d holds, and there exist points x, x′ ∈ X for any two distinct metrics d, d′ in D such that d (x, y) d′ (x′, y) = 0 holds for every y ∈ X. In this paper, we show that such decompositions are in onetoone correspondence with (isomorphism classes of) block realizations of D, that is, graph realizations G of D for which G is a block graph and for which every vertex in G not labelled by X has degree at least 3 and is a cut point of G. This generalizes a fundamental result in phylogenetic combinatorics that states that a metric D defined on X can be realized by a tree if and only if there exists a compatible decomposition D of D such that all metrics d ∈ D are split metrics, and lays the foundation for a more general theory of metric decompositions that will be explored in future papers. © 2007 Elsevier Ltd. All rights reserved."



Tobias Kloepper and
Daniel H. Huson. Drawing explicit phylogenetic networks and their integration into SplitsTree. In BMCEB, Vol. 8(22), 2008. Keywords: explicit network, phylogenetic network, phylogeny, Program SplitsTree, software, split network, visualization. Note: http://dx.doi.org/10.1186/14712148822.
Toggle abstract
"Background. SplitsTree provides a framework for the calculation of phylogenetic trees and networks. It contains a wide variety of methods for the import/export, calculation and visualization of phylogenetic information. The software is developed in Java and implements a command line tool as well as a graphical user interface. Results. In this article, we present solutions to two important problems in the field of phylogenetic networks. The first problem is the visualization of explicit phylogenetic networks. To solve this, we present a modified version of the equal angle algorithm that naturally integrates reticulations into the layout process and thus leads to an appealing visualization of these networks. The second problem is the availability of explicit phylogenetic network methods for the general user. To advance the usage of explicit phylogenetic networks by biologists further, we present an extension to the SplitsTree framework that integrates these networks. By addressing these two problems, SplitsTree is among the first programs that incorporates implicit and explicit network methods together with standard phylogenetic tree methods in a graphical user interface environment. Conclusion. In this article, we presented an extension of SplitsTree 4 that incorporates explicit phylogenetic networks. The extension provides a set of core classes to handle explicit phylogenetic networks and a visualization of these networks. © 2008 Kloepper and Huson; licensee BioMed Central Ltd."



Luay Nakhleh. A Metric on the Space of Reduced Phylogenetic Networks. In TCBB, Vol. 7(2), 2010. Keywords: distance between networks, phylogenetic network, phylogeny. Note: http://www.cs.rice.edu/~nakhleh/Papers/tcbbMetric.pdf.
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"Phylogenetic networks are leaflabeled, rooted, acyclic, and directed graphs that are used to model reticulate evolutionary histories. Several measures for quantifying the topological dissimilarity between two phylogenetic networks have been devised, each of which was proven to be a metric on certain restricted classes of phylogenetic networks. A biologically motivated class of phylogenetic networks, namely, reduced phylogenetic networks, was recently introduced. None of the existing measures is a metric on the space of reduced phylogenetic networks. In this paper, we provide a metric on the space of reduced phylogenetic networks that is computable in time polynomial in the size of the networks. © 2006 IEEE."



Dan Levy and
Lior Pachter. The NeighborNet Algorithm. In Advances in Applied Mathematics, Vol. 47(2):240258, 2011. Keywords: abstract network, circular split system, evaluation, from distances, NeighborNet, phylogenetic network, phylogeny, split network. Note: http://arxiv.org/abs/math/0702515.
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"The neighborjoining algorithm is a popular phylogenetics method for constructing trees from dissimilarity maps. The neighbornet algorithm is an extension of the neighborjoining algorithm and is used for constructing split networks. We begin by describing the output of neighbornet in terms of the tessellation of M̄0n(R) by associahedra. This highlights the fact that neighbornet outputs a tree in addition to a circular ordering and we explain when the neighbornet tree is the neighborjoining tree. A key observation is that the tree constructed in existing implementations of neighbornet is not a neighborjoining tree. Next, we show that neighbornet is a greedy algorithm for finding circular split systems of minimal balanced length. This leads to an interpretation of neighbornet as a greedy algorithm for the traveling salesman problem. The algorithm is optimal for Kalmanson matrices, from which it follows that neighbornet is consistent and has optimal radius 12. We also provide a statistical interpretation for the balanced length for a circular split system as the length based on weighted least squares estimates of the splits. We conclude with applications of these results and demonstrate the implications of our theorems for a recently published comparison of Papuan and Austronesian languages. © 2010 Elsevier Inc. All rights reserved."



Steven M. Woolley,
David Posada and
Keith A. Crandall. A Comparison of Phylogenetic Network Methods Using Computer Simulation. In PLoSONE, Vol. 3(4):e1913, 2008. Keywords: abstract network, distance between networks, evaluation, median network, MedianJoining, minimum spanning network, NeighborNet, parsimony, phylogenetic network, phylogeny, Program Arlequin, Program CombineTrees, Program Network, Program SHRUB, Program SplitsTree, Program TCS, split decomposition. Note: http://dx.doi.org/10.1371/journal.pone.0001913.
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"Background: We present a series of simulation studies that explore the relative performance of several phylogenetic network approaches (statistical parsimony, split decomposition, union of maximum parsimony trees, neighbornet, simulated history recombination upper bound, medianjoining, reduced median joining and minimum spanning network) compared to standard tree approaches (neighborjoining and maximum parsimony) in the presence and absence of recombination. Principal Findings: In the absence of recombination, all methods recovered the correct topology and branch lengths nearly all of the time when the subtitution rate was low, except for minimum spanning networks, which did considerably worse. At a higher substitution rate, maximum parsimony and union of maximum parsimony trees were the most accurate. With recombination, the ability to infer the correct topology was halved for all methods and no method could accurately estimate branch lengths. Conclusions: Our results highlight the need for more accurate phylogenetic network methods and the importance of detecting and accounting for recombination in phylogenetic studies. Furthermore, we provide useful information for choosing a network algorithm and a framework in which to evaluate improvements to existing methods and novel algorithms developed in the future. © 2008 Woolley et al."





Gabriel Cardona,
Mercè Llabrés,
Francesc Rosselló and
Gabriel Valiente. A Distance Metric for a Class of TreeSibling Phylogenetic Networks. In BIO, Vol. 24(13):14811488, 2008. Keywords: distance between networks, phylogenetic network, phylogeny, polynomial, tree sibling network. Note: http://dx.doi.org/10.1093/bioinformatics/btn231.
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"Motivation: The presence of reticulate evolutionary events in phylogenies turn phylogenetic trees into phylogenetic networks. These events imply in particular that there may exist multiple evolutionary paths from a nonextant species to an extant one, and this multiplicity makes the comparison of phylogenetic networks much more difficult than the comparison of phylogenetic trees. In fact, all attempts to define a sound distance measure on the class of all phylogenetic networks have failed so far. Thus, the only practical solutions have been either the use of rough estimates of similarity (based on comparison of the trees embedded in the networks), or narrowing the class of phylogenetic networks to a certain class where such a distance is known and can be efficiently computed. The first approach has the problem that one may identify two networks as equivalent, when they are not; the second one has the drawback that there may not exist algorithms to reconstruct such networks from biological sequences. Results: We present in this articlea distance measure on the class of semibinary treesibling time consistent phylogenetic networks, which generalize treechild time consistent phylogenetic networks, and thus also galledtrees. The practical interest of this distance measure is 2fold: it can be computed in polynomial time by means of simple algorithms, and there also exist polynomialtime algorithms for reconstructing networks of this class from DNA sequence data. © 2008 The Author(s)."



James B. Whitfield,
Sydney A. Cameron,
Daniel H. Huson and
Mike Steel. Filtered ZClosure Supernetworks for Extracting and Visualizing Recurrent Signal from Incongruent Gene Trees. In Systematic Biology, Vol. 57(6):939947, 2008. Keywords: abstract network, from unrooted trees, phylogenetic network, phylogeny, Program SplitsTree, split, split network, supernetwork. Note: http://www.life.uiuc.edu/scameron/pdfs/Filtered%20Zclosure%20SystBiol.pdf.





Joanna L. Davies,
Frantisek Simancík,
Rune Lyngsø,
Thomas Mailund and
Jotun Hein. On RecombinationInduced Multiple and Simultaneous Coalescent Events. In GEN, Vol. 177:21512160, 2007. Keywords: coalescent, phylogenetic network, phylogeny, recombination, statistical model. Note: http://dx.doi.org/10.1534/genetics.107.071126.
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"Coalescent theory deals with the dynamics of how sampled genetic material has spread through a population from a single ancestor over many generations and is ubiquitous in contemporary molecular population genetics. Inherent in most applications is a continuoustime approximation that is derived under the assumption that sample size is small relative to the actual population size. In effect, this precludes multiple and simultaneous coalescent events that take place in the history of large samples. If sequences do not recombine, the number of sequences ancestral to a large sample is reduced sufficiently after relatively few generations such that use of the continuoustime approximation is justified. However, in tracing the history of large chromosomal segments, a large recombination rate per generation will consistently maintain a large number of ancestors. This can create a major disparity between discretetime and continuoustime models and we analyze its importance, illustrated with model parameters typical of the human genome. The presence of gene conversion exacerbates the disparity and could seriously undermine applications of coalescent theory to complete genomes. However, we show that multiple and simultaneous coalescent events influence global quantities, such as total number of ancestors, but have negligible effect on local quantities, such as linkage disequilibrium. Reassuringly, most applications of the coalescent model with recombination (including association mapping) focus on local quantities. Copyright © 2007 by the Genetics Society of America."



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.
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"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."



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, tree child 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.
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"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,
Mercè Llabrés,
Francesc Rosselló and
Gabriel Valiente. Path lengths in treechild time consistent hybridization networks. In Information Sciences, Vol. 180(3):366383, 2010. Keywords: distance between networks, phylogenetic network, phylogeny, time consistent network, tree child network. Note: http://arxiv.org/abs/0807.0087?context=cs.CE.
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"Hybridization networks are representations of evolutionary histories that allow for the inclusion of reticulate events like recombinations, hybridizations, or lateral gene transfers. The recent growth in the number of hybridization network reconstruction algorithms has led to an increasing interest in the definition of metrics for their comparison that can be used to assess the accuracy or robustness of these methods. In this paper we establish some basic results that make it possible the generalization to treechild time consistent (TCTC) hybridization networks of some of the oldest known metrics for phylogenetic trees: those based on the comparison of the vectors of path lengths between leaves. More specifically, we associate to each hybridization network a suitably defined vector of 'splitted' path lengths between its leaves, and we prove that if two TCTC hybridization networks have the same such vectors, then they must be isomorphic. Thus, comparing these vectors by means of a metric for realvalued vectors defines a metric for TCTC hybridization networks. We also consider the case of fully resolved hybridization networks, where we prove that simpler, 'nonsplitted' vectors can be used. © 2009 Elsevier Inc. All rights reserved."



Iyad A. Kanj,
Luay Nakhleh,
Cuong Than and
Ge Xia. Seeing the Trees and Their Branches in the Network is Hard. In TCS, Vol. 401:153164, 2008. Keywords: evaluation, from network, from rooted trees, NP complete, phylogenetic network, phylogeny, tree containment. Note: http://www.cs.rice.edu/~nakhleh/Papers/tcs08.pdf.



Barbara R. Holland,
Steffi Benthin,
Peter J. Lockhart,
Vincent Moulton and
Katharina Huber. Using supernetworks to distinguish hybridization from lineagesorting. In BMCEB, Vol. 8(202), 2008. Keywords: explicit network, from unrooted trees, hybridization, lineage sorting, phylogenetic network, phylogeny, reconstruction, supernetwork. Note: http://dx.doi.org/10.1186/147121488202.
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"Background. A simple and widely used approach for detecting hybridization in phylogenies is to reconstruct gene trees from independent gene loci, and to look for gene tree incongruence. However, this approach may be confounded by factors such as poor taxonsampling and/or incomplete lineagesorting. Results. Using coalescent simulations, we investigated the potential of supernetwork methods to differentiate between gene tree incongruence arising from taxon sampling and incomplete lineagesorting as opposed to hybridization. For few hybridization events, a large number of independent loci, and wellsampled taxa across these loci, we found that it was possible to distinguish incomplete lineagesorting from hybridization using the filtered Zclosure and Qimputation supernetwork methods. Moreover, we found that the choice of supernetwork method was less important than the choice of filtering, and that countbased filtering was the most effective filtering technique. Conclusion. Filtered supernetworks provide a tool for detecting and identifying hybridization events in phylogenies, a tool that should become increasingly useful in light of current genome sequencing initiatives and the ease with which large numbers of independent gene loci can be determined using new generation sequencing technologies. © 2008 Holland et al; licensee BioMed Central Ltd."



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.
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"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."



Miguel Arenas,
Gabriel Valiente and
David Posada. Characterization of reticulate networks based on the coalescent with recombination. In MBE, Vol. 25(12):25172520, 2008. Keywords: coalescent, evaluation, explicit network, galled tree, phylogenetic network, phylogeny, Program Recodon, regular network, simulation, tree child network, tree sibling network. Note: http://dx.doi.org/10.1093/molbev/msn219.
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"Phylogenetic networks aim to represent the evolutionary history of taxa. Within these, reticulate networks are explicitly able to accommodate evolutionary events like recombination, hybridization, or lateral gene transfer. Although several metrics exist to compare phylogenetic networks, they make several assumptions regarding the nature of the networks that are not likely to be fulfilled by the evolutionary process. In order to characterize the potential disagreement between the algorithms and the biology, we have used the coalescent with recombination to build the type of networks produced by reticulate evolution and classified them as regular, tree sibling, tree child, or galled trees. We show that, as expected, the complexity of these reticulate networks is a function of the population recombination rate. At small recombination rates, most of the networks produced are already more complex than regular or tree sibling networks, whereas with moderate and large recombination rates, no network fit into any of the standard classes. We conclude that new metrics still need to be devised in order to properly compare two phylogenetic networks that have arisen from reticulating evolutionary process. © 2008 The Authors."





Galina Glazko,
Vladimir Makarenkov,
Jing Liu and
Arcady Mushegian. Evolutionary history of bacteriophages with doublestranded DNA genomes. In Biology Direct, Vol. 2(36), 2007. Keywords: explicit network, from sequences, phylogenetic network, phylogeny, Program T REX. Note: http://dx.doi.org/10.1186/17456150236.
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"Background: Reconstruction of evolutionary history of bacteriophages is a difficult problem because of fast sequence drift and lack of omnipresent genes in phage genomes. Moreover, losses and recombinational exchanges of genes are so pervasive in phages that the plausibility of phylogenetic inference in phage kingdom has been questioned. Results: We compiled the profiles of presence and absence of 803 orthologous genes in 158 completely sequenced phages with doublestranded DNA genomes and used these gene content vectors to infer the evolutionary history of phages. There were 18 wellsupported clades, mostly corresponding to accepted genera, but in some cases appearing to define new taxonomic groups. Conflicts between this phylogeny and trees constructed from sequence alignments of phage proteins were exploited to infer 294 specific acts of intergenome gene transfer. Conclusion: A notoriously reticulate evolutionary history of fastevolving phages can be reconstructed in considerable detail by quantitative comparative genomics. © 2007 Glazko et al; licensee BioMed Central Ltd."



Roderic D.M. Page and
Michael A. Charleston. Trees within trees: phylogeny and historical associations. In TEE, Vol. 13(9):356359, 1998. Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, reconstruction, survey. Note: http://taxonomy.zoology.gla.ac.uk/rod/papers/tree.pdf.



Cuong Than,
Derek Ruths,
Hideki Innan and
Luay Nakhleh. Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions. In JCB, Vol. 14(4):517535, 2007. Keywords: enumeration, explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, Program LatTrans, Program PhyloNet. Note: http://www.cs.rice.edu/~nakhleh/Papers/recombcg06jcb.pdf.



Bin Ma,
Lusheng Wang and
Ming Li. Fixed topology alignment with recombination. In DAM, Vol. 104:281300, 2000. Keywords: approximation, explicit network, from network, from sequences, galled tree, inapproximability, phylogenetic network, phylogeny, recombination. Note: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.40.7759.
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"Background: Reticulate events play an important role in determining evolutionary relationships. The problem of computing the minimum number of such events to explain discordance between two phylogenetic trees is a hard computational problem. Even for binary trees, exact solvers struggle to solve instances with reticulation number larger than 4050.Results: Here we present CycleKiller and NonbinaryCycleKiller, the first methods to produce solutions verifiably close to optimality for instances with hundreds or even thousands of reticulations.Conclusions: Using simulations, we demonstrate that these algorithms run quickly for large and difficult instances, producing solutions that are very close to optimality. As a spinoff from our simulations we also present TerminusEst, which is the fastest exact method currently available that can handle nonbinary trees: this is used to measure the accuracy of the NonbinaryCycleKiller algorithm. All three methods are based on extensions of previous theoretical work (SIDMA 26(4):16351656, TCBB 10(1):1825, SIDMA 28(1):4966) and are publicly available. We also apply our methods to real data. © 2014 van Iersel et al.; licensee BioMed Central Ltd."



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."



Stephen J. Willson. Regular Networks Can Be Uniquely Constructed from Their Trees. In TCBB, Vol. 8(3):785796, 2010. Keywords: explicit network, from rooted trees, phylogenetic network, phylogeny, reconstruction, regular network. Note: http://www.public.iastate.edu/~swillson/RegularNetsFromTrees5.pdf.
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"A rooted acyclic digraph N with labeled leaves displays a tree T when there exists a way to select a unique parent of each hybrid vertex resulting in the tree T. Let Tr(N) denote the set of all trees displayed by the network N. In general, there may be many other networks M, such that Tr(M) = Tr(N). A network is regular if it is isomorphic with its cover digraph. If N is regular and D is a collection of trees displayed by N, this paper studies some procedures to try to reconstruct N given D. If the input is D=Tr(N), one procedure is described, which will reconstruct N. Hence, if N and M are regular networks and Tr(N) = Tr(M), it follows that N = M, proving that a regular network is uniquely determined by its displayed trees. If D is a (usually very much smaller) collection of displayed trees that satisfies certain hypotheses, modifications of the procedure will still reconstruct N given D. © 2011 IEEE."



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."





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."



Stephen J. Willson. Properties of normal phylogenetic networks. In BMB, Vol. 72(2):340358, 2010. Keywords: normal network, phylogenetic network, phylogeny, regular network. Note: http://www.public.iastate.edu/~swillson/RestrictionsOnNetworkspap9.pdf, slides available at http://www.newton.cam.ac.uk/webseminars/pg+ws/2007/plg/plgw01/0904/willson/.
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"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. © 2009 Society for Mathematical Biology."



Katharina Huber,
Leo van Iersel,
Steven Kelk and
Radoslaw Suchecki. A Practical Algorithm for Reconstructing Level1 Phylogenetic Networks. In TCBB, Vol. 8(3):607620, 2011. Keywords: explicit network, from triplets, galled tree, generation, heuristic, phylogenetic network, phylogeny, Program LEV1ATHAN, Program Lev1Generator, reconstruction, software. Note: http://arxiv.org/abs/0910.4067.
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"Recently, much attention has been devoted to the construction of phylogenetic networks which generalize phylogenetic trees in order to accommodate complex evolutionary processes. Here, we present an efficient, practical algorithm for reconstructing level1 phylogenetic networksa type of network slightly more general than a phylogenetic treefrom triplets. Our algorithm has been made publicly available as the program Lev1athan. It combines ideas from several known theoretical algorithms for phylogenetic tree and network reconstruction with two novel subroutines. Namely, an exponentialtime exact and a greedy algorithm both of which are of independent theoretical interest. Most importantly, Lev1athan runs in polynomial time and always constructs a level1 network. If the data are consistent with a phylogenetic tree, then the algorithm constructs such a tree. Moreover, if the input triplet set is dense and, in addition, is fully consistent with some level1 network, it will find such a network. The potential of Lev1athan is explored by means of an extensive simulation study and a biological data set. One of our conclusions is that Lev1athan is able to construct networks consistent with a high percentage of input triplets, even when these input triplets are affected by a low to moderate level of noise. © 2011 IEEE."



Josh Voorkamp né Collins,
Simone Linz and
Charles Semple. Quantifying hybridization in realistic time. In JCB, Vol. 18(10):13051318, 2011. Keywords: explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, software. Note: http://wwwcsif.cs.ucdavis.edu/~linzs/CLS10_interleave.pdf, software available at http://www.math.canterbury.ac.nz/~c.semple/software.shtml.
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"Recently, numerous practical and theoretical studies in evolutionary biology aim at calculating the extent to which reticulationfor example, horizontal gene transfer, hybridization, or recombinationhas influenced the evolution for a set of presentday species. It has been shown that inferring the minimum number of hybridization events that is needed to simultaneously explain the evolutionary history for a set of trees is an NPhard and also fixedparameter tractable problem. In this article, we give a new fixedparameter algorithm for computing the minimum number of hybridization events for when two rooted binary phylogenetic trees are given. This newly developed algorithm is based on interleavinga technique using repeated kernelization steps that are applied throughout the exhaustive search part of a fixedparameter algorithm. To show that our algorithm runs efficiently to be applicable to a wide range of practical problem instances, we apply it to a grass data set and highlight the significant improvements in terms of running times in comparison to an algorithm that has previously been implemented. © 2011, Mary Ann Liebert, Inc."



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."



Joel Velasco and
Elliott Sober. Testing for Treeness: Lateral Gene Transfer, Phylogenetic Inference, and Model Selection. In Biology and Philosophy, Vol. 25(4):675687, 2010. Keywords: explicit network, model selection, phylogenetic network, phylogeny, reconstruction, statistical model. Note: http://joelvelasco.net/Papers/velascosobertestingfortreeness.pdf.
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"A phylogeny that allows for lateral gene transfer (LGT) can be thought of as a strictly branching tree (all of whose branches are vertical) to which lateral branches have been added. Given that the goal of phylogenetics is to depict evolutionary history, we should look for the best supported phylogenetic network and not restrict ourselves to considering trees. However, the obvious extensions of popular treebased methods such as maximum parsimony and maximum likelihood face a serious problemif we judge networks by fit to data alone, networks that have lateral branches will always fit the data at least as well as any network that restricts itself to vertical branches. This is analogous to the wellstudied problem of overfitting data in the curvefitting problem. Analogous problems often have analogous solutions and we propose to treat network inference as a case of model selection and use the Akaike Information Criterion (AIC). Strictly treelike networks are more parsimonious than those that postulate lateral as well as vertical branches. This leads to the conclusion that we should not always infer LGT events whenever it would improve our fittodata, but should do so only when the improved fit is larger than the penalty for adding extra lateral branches. © 2010 Springer Science+Business Media B.V."











Leo van Iersel and
Steven Kelk. Constructing the Simplest Possible Phylogenetic Network from Triplets. In ALG, Vol. 60(2):207235, 2011. Keywords: explicit network, from triplets, galled tree, level k phylogenetic network, minimum number, phylogenetic network, phylogeny, polynomial, Program Marlon, Program Simplistic. Note: http://dx.doi.org/10.1007/s0045300993330.
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"A phylogenetic network is a directed acyclic graph that visualizes an evolutionary history containing socalled reticulations such as recombinations, hybridizations or lateral gene transfers. Here we consider the construction of a simplest possible phylogenetic network consistent with an input set T, where T contains at least one phylogenetic tree on three leaves (a triplet) for each combination of three taxa. To quantify the complexity of a network we consider both the total number of reticulations and the number of reticulations per biconnected component, called the level of the network. We give polynomialtime algorithms for constructing a level1 respectively a level2 network that contains a minimum number of reticulations and is consistent with T (if such a network exists). In addition, we show that if T is precisely equal to the set of triplets consistent with some network, then we can construct such a network with smallest possible level in time O(T k+1), if k is a fixed upper bound on the level of the network. © 2009 The Author(s)."



Simone Linz,
Charles Semple and
Tanja Stadler. Analyzing and reconstructing reticulation networks under timing constraints. In JOMB, Vol. 61(5):715737, 2010. Keywords: explicit network, from rooted trees, hybridization, lateral gene transfer, NP complete, phylogenetic network, phylogeny, reconstruction, time consistent network. Note: http://dx.doi.org/10.1007/s002850090319y..
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"Reticulation networks are now frequently used to model the history of life for various groups of species whose evolutionary past is likely to include reticulation events such as horizontal gene transfer or hybridization. However, the reconstructed networks are rarely guaranteed to be temporal. If a reticulation network is temporal, then it satisfies the two biologically motivated timing constraints of instantaneously occurring reticulation events and successively occurring speciation events. On the other hand, if a reticulation network is not temporal, it is always possible to make it temporal by adding a number of additional unsampled or extinct taxa. In the first half of the paper, we show that deciding whether a given number of additional taxa is sufficient to transform a nontemporal reticulation network into a temporal one is an NPcomplete problem. As one is often given a set of gene trees instead of a network in the context of hybridization, this motivates the second half of the paper which provides an algorithm, called TemporalHybrid, for reconstructing a temporal hybridization network that simultaneously explains the ancestral history of two trees or indicates that no such network exists. We further derive two methods to decide whether or not a temporal hybridization network exists for two given trees and illustrate one of the methods on a grass data set. © 2009 The Author(s)."



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."



Tal Dagan,
Yael ArtzyRandrup and
William Martin. Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. In PNAS, Vol. 105:1003910044, 2008. Keywords: from sequences, from species tree, heuristic, lateral gene transfer, phylogenetic network, phylogeny, reconstruction. Note: http://dx.doi.org/10.1073/pnas.0800679105.
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"Lateral gene transfer is an important mechanism of natural variation among prokaryotes, but the significance of its quantitative contribution to genome evolution is debated. Here, we report networks that capture both vertical and lateral components of evolutionary history among 539,723 genes distributed across 181 sequenced prokaryotic genomes. Partitioning of these networks by an eigenspectrum analysis identifies community structure in prokaryotic genesharing networks, the modules of which do not correspond to a strictly hierarchical prokaryotic classification. Our results indicate that, on average, at least 81 ± 15% of the genes in each genome studied were involved in lateral gene transfer at some point in their history, even though they can be vertically inherited after acquisition, uncovering a substantial cumulative effect of lateral gene transfer on longer evolutionary time scales. © 2008 by The National Academy of Sciences of the USA."



Ali Tofigh,
Mike Hallett and
Jens Lagergren. Simultaneous Identification of Duplications and Lateral Gene Transfers. In TCBB, Vol. 8(2):517535, 2011. Keywords: duplication, explicit network, FPT, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, phylogenetic network, phylogeny, reconstruction. Note: http://dx.doi.org/10.1109/TCBB.2010.14.
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"The incongruency between a gene tree and a corresponding species tree can be attributed to evolutionary events such as gene duplication and gene loss. This paper describes a combinatorial model where socalled DTLscenarios are used to explain the differences between a gene tree and a corresponding species tree taking into account gene duplications, gene losses, and lateral gene transfers (also known as horizontal gene transfers). The reasonable biological constraint that a lateral gene transfer may only occur between contemporary species leads to the notion of acyclic DTLscenarios. Parsimony methods are introduced by defining appropriate optimization problems. We show that finding most parsimonious acyclic DTLscenarios is NPhard. However, by dropping the condition of acyclicity, the problem becomes tractable, and we provide a dynamic programming algorithm as well as a fixedparameter tractable algorithm for finding most parsimonious DTLscenarios. © 2011 IEEE."



HansJürgen Bandelt and
Arne Dür. Translating DNA data tables into quasimedian networks for parsimony analysis and error detection. In MPE, Vol. 42(1):256271, 2007. Keywords: abstract network, from sequences, parsimony, phylogenetic network, phylogeny, quasimedian network, reconstruction. Note: http://dx.doi.org/10.1016/j.ympev.2006.07.013.
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"Every DNA data table can be turned into a quasimedian network that faithfully represents the data. We show that for (weighted) condensed data tables the associated network harbors all most parsimonious reconstructions for any tree that connects the sampled haplotypes. Structural features of this network can be computed directly from the data table. The key principle repeatedly used is that the quasimedian network is uniquely determined by the subtables for pairs of characters. The translation of a table into a network enhances the understanding of the properties of the data in regard to homoplasy and potential artifacts. The total number of nodes of such a network measures the complexity of the data. In particular, networks that display the results of filter analyses by which hotspot mutations are removed help to detect data idiosyncrasies and thus pinpoint sequencing problems. A pertinent example drawn from human mtDNA illustrates these points. © 2006 Elsevier Inc. All rights reserved."



Leo van Iersel and
Steven Kelk. When two trees go to war. In JTB, Vol. 269(1):245255, 2011. Keywords: APX hard, explicit network, from clusters, from rooted trees, from sequences, from triplets, level k phylogenetic network, minimum number, NP complete, phylogenetic network, phylogeny, polynomial, reconstruction. Note: http://arxiv.org/abs/1004.5332.
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"Rooted phylogenetic networks are used to model nontreelike evolutionary histories. Such networks are often constructed by combining trees, clusters, triplets or characters into a single network that in some welldefined sense simultaneously represents them all. We review these four models and investigate how they are related. Motivated by the parsimony principle, one often aims to construct a network that contains as few reticulations (nontreelike evolutionary events) as possible. In general, the model chosen influences the minimum number of reticulation events required. However, when one obtains the input data from two binary (i.e. fully resolved) trees, we show that the minimum number of reticulations is independent of the model. The number of reticulations necessary to represent the trees, triplets, clusters (in the softwired sense) and characters (with unrestricted multiple crossover recombination) are all equal. Furthermore, we show that these results also hold when not the number of reticulations but the level of the constructed network is minimised. We use these unification results to settle several computational complexity questions that have been open in the field for some time. We also give explicit examples to show that already for data obtained from three binary trees the models begin to diverge. © 2010 Elsevier Ltd."



Robert G. Beiko. Gene sharing and genome evolution: networks in trees and trees in networks. In Biology and Philosophy, Vol. 25(4):659673, 2010. Keywords: abstract network, explicit network, from rooted trees, galled network, phylogenetic network, phylogeny, Program Dendroscope, Program SplitsTree, reconstruction, split network, survey. Note: http://dx.doi.org/10.1007/s1053901092173.
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"Frequent lateral genetic transfer undermines the existence of a unique "tree of life" that relates all organisms. Vertical inheritance is nonetheless of vital interest in the study of microbial evolution, and knowing the "tree of cells" can yield insights into ecological continuity, the rates of change of different cellular characters, and the evolutionary plasticity of genomes. Notwithstanding withinspecies recombination, the relationships most frequently recovered from genomic data at shallow to moderate taxonomic depths are likely to reflect cellular inheritance. At the same time, it is clear that several types of 'average signals' from whole genomes can be highly misleading, and the existence of a central tendency must not be taken as prima facie evidence of vertical descent. Phylogenetic networks offer an attractive solution, since they can be formulated in ways that mitigate the misleading aspects of hybrid evolutionary signals in genomes. But the connections in a network typically show genetic relatedness without distinguishing between vertical and lateral inheritance of genetic material. The solution may lie in a compromise between strict treethinking and network paradigms: build a phylogenetic network, but identify the set of connections in the network that are potentially due to vertical descent. Even if a single tree cannot be unambiguously identified, choosing a subnetwork of putative vertical connections can still lead to drastic reductions in the set of candidate vertical hypotheses. © 2010 Springer Science+Business Media B.V."



Hyun Jung Park,
Guohua Jin and
Luay Nakhleh. Bootstrapbased Support of HGT Inferred by Maximum Parsimony. In BMCEB, Vol. 10:131, 2010. Keywords: bootstrap, explicit network, from sequences, lateral gene transfer, parsimony, phylogenetic network, phylogeny, Program Nepal, reconstruction. Note: http://dx.doi.org/10.1186/1471214810131.
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"Background. Maximum parsimony is one of the most commonly used criteria for reconstructing phylogenetic trees. Recently, Nakhleh and coworkers extended this criterion to enable reconstruction of phylogenetic networks, and demonstrated its application to detecting reticulate evolutionary relationships. However, one of the major problems with this extension has been that it favors more complex evolutionary relationships over simpler ones, thus having the potential for overestimating the amount of reticulation in the data. An ad hoc solution to this problem that has been used entails inspecting the improvement in the parsimony length as more reticulation events are added to the model, and stopping when the improvement is below a certain threshold. Results. In this paper, we address this problem in a more systematic way, by proposing a nonparametric bootstrapbased measure of support of inferred reticulation events, and using it to determine the number of those events, as well as their placements. A number of samples is generated from the given sequence alignment, and reticulation events are inferred based on each sample. Finally, the support of each reticulation event is quantified based on the inferences made over all samples. Conclusions. We have implemented our method in the NEPAL software tool (available publicly at http://bioinfo.cs.rice.edu/), and studied its performance on both biological and simulated data sets. While our studies show very promising results, they also highlight issues that are inherently challenging when applying the maximum parsimony criterion to detect reticulate evolution. © 2010 Park et al; licensee BioMed Central Ltd."



Sophie Abby,
Eric Tannier,
Manolo Gouy and
Vincent Daubin. Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests. In BMCB, Vol. 11:324, 2010. Keywords: explicit network, from rooted trees, from species tree, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program EEEP, Program PhyloNet, Program Prunier, reconstruction, software. Note: http://www.biomedcentral.com/14712105/11/324.
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"Background: To understand the evolutionary role of Lateral Gene Transfer (LGT), accurate methods are needed to identify transferred genes and infer their timing of acquisition. Phylogenetic methods are particularly promising for this purpose, but the reconciliation of a gene tree with a reference (species) tree is computationally hard. In addition, the application of these methods to real data raises the problem of sorting out real and artifactual phylogenetic conflict.Results: We present Prunier, a new method for phylogenetic detection of LGT based on the search for a maximum statistical agreement forest (MSAF) between a gene tree and a reference tree. The program is flexible as it can use any definition of "agreement" among trees. We evaluate the performance of Prunier and two other programs (EEEP and RIATAHGT) for their ability to detect transferred genes in realistic simulations where gene trees are reconstructed from sequences. Prunier proposes a single scenario that compares to the other methods in terms of sensitivity, but shows higher specificity. We show that LGT scenarios carry a strong signal about the position of the root of the species tree and could be used to identify the direction of evolutionary time on the species tree. We use Prunier on a biological dataset of 23 universal proteins and discuss their suitability for inferring the tree of life.Conclusions: The ability of Prunier to take into account branch support in the process of reconciliation allows a gain in complexity, in comparison to EEEP, and in accuracy in comparison to RIATAHGT. Prunier's greedy algorithm proposes a single scenario of LGT for a gene family, but its quality always compares to the best solutions provided by the other algorithms. When the root position is uncertain in the species tree, Prunier is able to infer a scenario per root at a limited additional computational cost and can easily run on large datasets.Prunier is implemented in C++, using the Bio++ library and the phylogeny program Treefinder. It is available at: http://pbil.univlyon1.fr/software/prunier. © 2010 Abby et al; licensee BioMed Central Ltd."



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.



Tao Sang and
Yang Zhong. Testing Hybridization Hypotheses Based on Incongruent Gene Trees. In Systematic Biology, Vol. 49(3):422434, 2000. Keywords: bootstrap, from rooted trees, hybridization, lateral gene transfer, lineage sorting, phylogenetic network, phylogeny, reconstruction, statistical model. Note: http://dx.doi.org/10.1080/10635159950127321.



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."



Nicolas Galtier. A model of horizontal gene transfer and the bacterial phylogeny problem. In Systematic Biology, Vol. 56(4):633642, 2007. Keywords: explicit network, generation, lateral gene transfer, phylogenetic network, phylogeny, Program HGT_simul, software, statistical model. Note: http://dx.doi.org/10.1080/10635150701546231.
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"How much horizontal gene transfer (HGT) between species influences bacterial phylogenomics is a controversial issue. This debate, however, lacks any quantitative assessment of the impact of HGT on phylogenies and of the ability of treebuilding methods to cope with such events. I introduce a Markov model of genome evolution with HGT, accounting for the constraints on timean HGT event can only occur between concomitantly living species. This model is used to simulate multigene sequence data sets with or without HGT. The consequences of HGT on phylogenomic inference are analyzed and compared to other wellknown phylogenetic artefacts. It is found that supertree methods are quite robust to HGT, keeping high levels of performance even when gene trees are largely incongruent with each other. Gene tree incongruence per se is not indicative of HGT. HGT, however, removes the (otherwise observed) positive relationship between sequence length and gene tree congruence to the estimated species tree. Surprisingly, when applied to a bacterial and a eukaryotic multigene data set, this criterion rejects the HGT hypothesis for the former, but not the latter data set. Copyright © Society of Systematic Biologists."



Mihaela Baroni and
Mike Steel. Accumulation Phylogenies. In ACOM, Vol. 10(1):1930, 2006. Keywords: abstract network, from clusters, from distances, phylogenetic network, phylogeny, polynomial, reconstruction, regular network. Note: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.137.1960.
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"We investigate the computational complexity of a new combinatorial problem of inferring a smallest possible multilabeled phylogenetic tree (MUL tree) which is consistent with each of the rooted triplets in a given set. We prove that even the restricted case of determining if there exists a MUL tree consistent with the input and having just one leaf duplication is NPhard. Furthermore, we show that the general minimization problem is NPhard to approximate within a ratio of n 1ε for any constant 0<ε≤1, where n denotes the number of distinct leaf labels in the input set, although a simple polynomialtime approximation algorithm achieves the approximation ratio n. We also provide an exact algorithm for the problem running in O *(7 n ) time and O *(3 n ) space. © 2009 SpringerVerlag Berlin Heidelberg."



Mark T. Holder,
Jennifer A. Anderson and
Alisha K. Holloway. Difficulties in Detecting Hybridization. In Systematic Biology, Vol. 50(6):978982, 2001. Keywords: bootstrap, from rooted trees, hybridization, lateral gene transfer, lineage sorting, phylogenetic network, phylogeny, reconstruction, statistical model. Note: http://dx.doi.org/10.1080/106351501753462911.
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[No abstract available]



ZhiZhong Chen and
Lusheng Wang. HybridNET: a tool for constructing hybridization networks. In BIO, Vol. 26(22):29122913, 2010. Keywords: agreement forest, FPT, from rooted trees, hybridization, phylogenetic network, phylogeny, Program HybridNET, software. Note: http://rnc.r.dendai.ac.jp/~chen/papers/note2.pdf.
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"Motivations: When reticulation events occur, the evolutionary history of a set of existing species can be represented by a hybridization network instead of an evolutionary tree. When studying the evolutionary history of a set of existing species, one can obtain a phylogenetic tree of the set of species with high confidence by looking at a segment of sequences or a set of genes. When looking at another segment of sequences, a different phylogenetic tree can be obtained with high confidence too. This indicates that reticulation events may occur. Thus, we have the following problem: given two rooted phylogenetic trees on a set of species that correctly represent the treelike evolution of different parts of their genomes, what is the hybridization network with the smallest number of reticulation events to explain the evolution of the set of species under consideration? Results: We develop a program, named HybridNet, for constructing a hybridization network with the minimum number of reticulate vertices from two input trees. We first implement the O(3dn)time algorithm by Whidden et al. for computing a maximum (acyclic) agreement forest. Our program can output all the maximum (acyclic) agreement forests. We then augment the program so that it can construct an optimal hybridization network for each given maximum acyclic agreement forest. To our knowledge, this is the first time that optimal hybridization networks can be rapidly constructed. © The Author 2010. Published by Oxford University Press. All rights reserved."





Steven Kelk,
Celine Scornavacca and
Leo van Iersel. On the elusiveness of clusters. In TCBB, Vol. 9(2):517534, 2012. Keywords: explicit network, from clusters, from rooted trees, from triplets, level k phylogenetic network, phylogenetic network, phylogeny, Program Clustistic, reconstruction, software. Note: http://arxiv.org/abs/1103.1834.



Jeremy G. Sumner,
Barbara R. Holland and
Peter D. Jarvis. The algebra of the general Markov model on phylogenetic trees and networks. In BMB, Vol. 74(4):858880, 2012. Keywords: abstract network, phylogenetic network, phylogeny, split, split network, statistical model. Note: http://arxiv.org/abs/1012.5165.
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"It is known that the Kimura 3ST model of sequence evolution on phylogenetic trees can be extended quite naturally to arbitrary split systems. However, this extension relies heavily on mathematical peculiarities of the associated Hadamard transformation, and providing an analogous augmentation of the general Markov model has thus far been elusive. In this paper, we rectify this shortcoming by showing how to extend the general Markov model on trees to include incompatible edges; and even further to more general network models. This is achieved by exploring the algebra of the generators of the continuoustime Markov chain together with the "splitting" operator that generates the branching process on phylogenetic trees. For simplicity, we proceed by discussing the two state case and then show that our results are easily extended to more states with little complication. Intriguingly, upon restriction of the two state general Markov model to the parameter space of the binary symmetric model, our extension is indistinguishable from the Hadamard approach only on trees; as soon as any incompatible splits are introduced the two approaches give rise to differing probability distributions with disparate structure. Through exploration of a simple example, we give an argument that our extension to more general networks has desirable properties that the previous approaches do not share. In particular, our construction allows for convergent evolution of previously divergent lineages; a property that is of significant interest for biological applications. © 2011 Society for Mathematical Biology."





Marc Thuillard and
Vincent Moulton. Identifying and reconstructing lateral transfers from distance matrices by combining the Minimum Contradiction Method and NeighborNet. In JBCB, Vol. 9(4):453470, 2011. Keywords: from distances, lateral gene transfer, minimum contradiction, NeighborNet, phylogenetic network, phylogeny, reconstruction. Note: http://dx.doi.org/10.1142/S0219720011005409, slides available at http://www.newton.ac.uk/programmes/PLG/seminars/062015501.html.
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"Identifying lateral gene transfers is an important problem in evolutionary biology. Under a simple model of evolution, the expected values of an evolutionary distance matrix describing a phylogenetic tree fulfill the socalled Kalmanson inequalities. The Minimum Contradiction method for identifying lateral gene transfers exploits the fact that lateral transfers may generate large deviations from the Kalmanson inequalities. Here a new approach is presented to deal with such cases that combines the NeighborNet algorithm for computing phylogenetic networks with the Minimum Contradiction method. A subset of taxa, prescribed using NeighborNet, is obtained by measuring how closely the Kalmanson inequalities are fulfilled by each taxon. A criterion is then used to identify the taxa, possibly involved in a lateral transfer between nonconsecutive taxa. We illustrate the utility of the new approach by applying it to a distance matrix for Archaea, Bacteria, and Eukaryota. © 2011 Imperial College Press."



Gergely J. Szöllösi and
Vincent Daubin. Modeling Gene Family Evolution and Reconciling Phylogenetic Discord. In Evolutionary Genomics, Statistical and Computational Methods, Volume 2, Methods in Molecular Biology, Vol. 856:2951, Chapter 2, springer, 2011. Keywords: duplication, from multilabeled tree, lateral gene transfer, likelihood, phylogeny, reconstruction, statistical model. Note: ArXiv version entitled The pattern and process of gene family evolution.
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"Largescale databases are available that contain homologous gene families constructed from hundreds of complete genome sequences from across the three domains of life. Here, we discuss the approaches of increasing complexity aimed at extracting information on the pattern and process of gene family evolution from such datasets. In particular, we consider the models that invoke processes of gene birth (duplication and transfer) and death (loss) to explain the evolution of gene families. First, we review birthanddeath models of family size evolution and their implications in light of the universal features of family size distribution observed across different species and the three domains of life. Subsequently, we proceed to recent developments on models capable of more completely considering information in the sequences of homologous gene families through the probabilistic reconciliation of the phylogenetic histories of individual genes with the phylogenetic history of the genomes in which they have resided. To illustrate the methods and results presented, we use data from the HOGENOM database, demonstrating that the distribution of homologous gene family sizes in the genomes of the eukaryota, archaea, and bacteria exhibits remarkably similar shapes. We show that these distributions are best described by models of gene family size evolution, where for individual genes the death (loss) rate is larger than the birth (duplication and transfer) rate but new families are continually supplied to the genome by a process of origination. Finally, we use probabilistic reconciliation methods to take into consideration additional information from gene phylogenies, and find that, for prokaryotes, the majority of birth events are the result of transfer. © 2012 Springer Science+Business Media, LLC."



Lawrence A. David and
Eric J. Alm. Rapid evolutionary innovation during an Archaean genetic expansion. In Nature, Vol. 469:9396, 2011. Keywords: duplication, dynamic programming, from multilabeled tree, from rooted trees, from species tree, parsimony, phylogenetic network, phylogeny, Program Angst. Note: http://dx.doi.org/10.1038/nature09649, Program Angst described here.



Andreas Spillner,
Binh T. Nguyen and
Vincent Moulton. Constructing and Drawing Regular Planar Split Networks. In TCBB, Vol. 9(2):395407, 2012. Keywords: abstract network, from splits, phylogenetic network, phylogeny, reconstruction, visualization. Note: slides and presentation available at http://www.newton.ac.uk/programmes/PLG/seminars/062111501.html.
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"Split networks are commonly used to visualize collections of bipartitions, also called splits, of a finite set. Such collections arise, for example, in evolutionary studies. Split networks can be viewed as a generalization of phylogenetic trees and may be generated using the SplitsTree package. Recently, the NeighborNet method for generating split networks has become rather popular, in part because it is guaranteed to always generate a circular split system, which can always be displayed by a planar split network. Even so, labels must be placed on the "outside" of the network, which might be problematic in some applications. To help circumvent this problem, it can be helpful to consider socalled flat split systems, which can be displayed by planar split networks where labels are allowed on the inside of the network too. Here, we present a new algorithm that is guaranteed to compute a minimal planar split network displaying a flat split system in polynomial time, provided the split system is given in a certain format. We will also briefly discuss two heuristics that could be useful for analyzing phylogeographic data and that allow the computation of flat split systems in this format in polynomial time. © 2006 IEEE."



Paul Phipps and
Sergey Bereg. Optimizing Phylogenetic Networks for Circular Split Systems. In TCBB, Vol. 9(2):535547, 2012. Keywords: abstract network, from distances, from splits, phylogenetic network, phylogeny, Program PhippsNetwork, reconstruction, software.
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"We address the problem of realizing a given distance matrix by a planar phylogenetic network with a minimum number of faces. With the help of the popular software SplitsTree4, we start by approximating the distance matrix with a distance metric that is a linear combination of circular splits. The main results of this paper are the necessary and sufficient conditions for the existence of a network with a single face. We show how such a network can be constructed, and we present a heuristic for constructing a network with few faces using the first algorithm as the base case. Experimental results on biological data show that this heuristic algorithm can produce phylogenetic networks with far fewer faces than the ones computed by SplitsTree4, without affecting the approximation of the distance matrix. © 2012 IEEE."



Steven Kelk and
Celine Scornavacca. Constructing minimal phylogenetic networks from softwired clusters is fixed parameter tractable. In ALG, Vol. 68(4):886915, 2014. Keywords: explicit network, FPT, from clusters, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction. Note: http://arxiv.org/abs/1108.3653.
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"Here we show that, given a set of clusters C on a set of taxa X, where X=n, it is possible to determine in time f(k)×poly(n) whether there exists a level≤k network (i.e. a network where each biconnected component has reticulation number at most k) that represents all the clusters in C in the softwired sense, and if so to construct such a network. This extends a result from Kelk et al. (in IEEE/ACM Trans. Comput. Biol. Bioinform. 9:517534, 2012) which showed that the problem is polynomialtime solvable for fixed k. By defining "kreticulation generators" analogous to "levelk generators", we then extend this fixed parameter tractability result to the problem where k refers not to the level but to the reticulation number of the whole network. © 2012 Springer Science+Business Media New York."



Andreas Spillner and
Vincent Moulton. Optimal algorithms for computing edge weights in planar splitnetworks. In Journal of Applied Mathematics and Computing, Vol. 39(12):113, 2012. Keywords: abstract network, from distances, phylogenetic network, phylogeny, reconstruction, split, split network. Note: http://dx.doi.org/10.1007/s121900110506z.
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"In phylogenetics, biologists commonly compute split networks when trying to better understand evolutionary data. These graphtheoretical structures represent collections of weighted bipartitions or splits of a finite set, and provide a means to display conflicting evolutionary signals. The weights associated to the splits are used to scale the edges in the network and are often computed using some distance matrix associated with the data. In this paper we present optimal polynomial time algorithms for three basic problems that arise in this context when computing split weights for planar splitnetworks. These generalize algorithms that have been developed for special classes of split networks (namely, trees and outerlabeled planar networks). As part of our analysis, we also derive a Crofton formula for full flat split systems, structures that naturally arise when constructing planar splitnetworks. © 2011 Korean Society for Computational and Applied Mathematics."





Marta Melé,
Asif Javed,
Marc Pybus,
Francesc Calafell,
Laxmi Parida,
Jaume Bertranpetit and
Genographic Consortium. A New Method to Reconstruct Recombination Events at a Genomic Scale. In PLoS Computational Biology, Vol. 6(11):e1001010, 2010. Keywords: explicit network, from sequences, phylogenetic network, phylogeny. Note: http://dx.doi.org/10.1371/journal.pcbi.1001010.
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"Recombination is one of the main forces shaping genome diversity, but the information it generates is often overlooked. A recombination event creates a junction between two parental sequences that may be transmitted to the subsequent generations. Just like mutations, these junctions carry evidence of the shared past of the sequences. We present the IRiS algorithm, which detects past recombination events from extant sequences and specifies the place of each recombination and which are the recombinants sequences. We have validated and calibrated IRiS for the human genome using coalescent simulations replicating standard human demographic history and a variable recombination rate model, and we have finetuned IRiS parameters to simultaneously optimize for false discovery rate, sensitivity, and accuracy in placing the recombination events in the sequence. Newer recombinations overwrite traces of past ones and our results indicate more recent recombinations are detected by IRiS with greater sensitivity. IRiS analysis of the MS32 region, previously studied using sperm typing, showed good concordance with estimated recombination rates. We also applied IRiS to haplotypes for 18 Xchromosome regions in HapMap Phase 3 populations. Recombination events detected for each individual were recoded as binary allelic states and combined into recotypes. Principal component analysis and multidimensional scaling based on recotypes reproduced the relationships between the eleven HapMap Phase III populations that can be expected from known human population history, thus further validating IRiS. We believe that our new method will contribute to the study of the distribution of recombination events across the genomes and, for the first time, it will allow the use of recombination as genetic marker to study human genetic variation. © 2010 Mele ́ et al."



Sagi Snir and
Edward Trifonov. A Novel Technique for Detecting Putative Horizontal Gene Transfer in the Sequence Space. In JCB, Vol. 17(11):15351548, 2010. Keywords: from sequences, phylogenetic network, phylogeny, reconstruction. Note: http://research.haifa.ac.il/~ssagi/published%20papers/JCBHGT.pdf.
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"Horizontal transfer (HT) is the event of a DNA sequence being transferred between species not by inheritance. This phenomenon violates the treelike evolution of the species under study turning the trees into networks. At the sequence level, HT offers basic characteristics that enable not only clear identification and distinguishing from other sequence similarity cases but also the possibility of dating the events. We developed a novel, selfcontained technique to identify relatively recent horizontal transfer elements (HTEs) in the sequences. Appropriate formalism allows one to obtain confidence values for the events detected. The technique does not rely on such problematic prerequisites as reliable phylogeny and/or statistically justified pairwise sequence alignment. In conjunction with the unique properties of HT, it gives rise to a twolevel sequence similarity algorithm that, to the best of our knowledge, has not been explored. From evolutionary perspective, the novelty of the work is in the combination of small scale and large scale mutational events. The technique is employed on both simulated and real biological data. The simulation results show high capability of discriminating between HT and conserved regions. On the biological data, the method detected documented HTEs along with their exact locations in the recipient genomes. Supplementary Material is available online at www.libertonline.com/cmb. Copyright 2010, Mary Ann Liebert, Inc."



Mukul S. Bansal,
Guy Banay,
J. Peter Gogarten and
Ron Shamir. Detecting Highways of Horizontal Gene Transfer. In JCB, Vol. 18(9):10871114, 2011. Keywords: explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, polynomial, reconstruction. Note: http://people.csail.mit.edu/mukul/HighwayFull_preprint.pdf.
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"In a horizontal gene transfer (HGT) event, a gene is transferred between two species that do not have an ancestordescendant relationship. Typically, no more than a few genes are horizontally transferred between any two species. However, several studies identified pairs of species between which many different genes were horizontally transferred. Such a pair is said to be linked by a highway of gene sharing. We present a method for inferring such highways. Our method is based on the fact that the evolutionary histories of horizontally transferred genes disagree with the corresponding species phylogeny. Specifically, given a set of gene trees and a trusted rooted species tree, each gene tree is first decomposed into its constituent quartet trees and the quartets that are inconsistent with the species tree are identified. Our method finds a pair of species such that a highway between them explains the largest (normalized) fraction of inconsistent quartets. For a problem on n species and m input quartet trees, we give an efficient O(m+n 2)time algorithm for detecting highways, which is optimal with respect to the quartets input size. An application of our method to a dataset of 1128 genes from 11 cyanobacterial species, as well as to simulated datasets, illustrates the efficacy of our method. © 2011, Mary Ann Liebert, Inc."



Celine Scornavacca,
Simone Linz and
Benjamin Albrecht. A first step towards computing all hybridization networks for two rooted binary phylogenetic trees. In JCB, Vol. 19:12271242, 2012. Keywords: agreement forest, explicit network, FPT, from rooted trees, phylogenetic network, phylogeny, Program Dendroscope, Program Hybroscale, reconstruction. Note: http://arxiv.org/abs/1109.3268.
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"Recently, considerable effort has been put into developing fast algorithms to reconstruct a rooted phylogenetic network that explains two rooted phylogenetic trees and has a minimum number of hybridization vertices. With the standard app1235roach to tackle this problem being combinatorial, the reconstructed network is rarely unique. From a biological point of view, it is therefore of importance to not only compute one network, but all possible networks. In this article, we make a first step toward approaching this goal by presenting the first algorithmcalled allMAAFsthat calculates all maximumacyclicagreement forests for two rooted binary phylogenetic trees on the same set of taxa. © Copyright 2012, Mary Ann Liebert, Inc. 2012."



Katharina Huber and
Vincent Moulton. Encoding and Constructing 1Nested Phylogenetic Networks with Trinets. In ALG, Vol. 66(3):714738, 2013. Keywords: explicit network, from trinets, phylogenetic network, phylogeny, reconstruction, uniqueness. Note: http://arxiv.org/abs/1110.0728.
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"Phylogenetic networks are a generalization of phylogenetic trees that are used in biology to represent reticulate or nontreelike evolution. Recently, several algorithms have been developed which aim to construct phylogenetic networks from biological data using triplets, i.e. binary phylogenetic trees on 3element subsets of a given set of species. However, a fundamental problem with this approach is that the triplets displayed by a phylogenetic network do not necessarily uniquely determine or encode the network. Here we propose an alternative approach to encoding and constructing phylogenetic networks, which uses phylogenetic networks on 3element subsets of a set, or trinets, rather than triplets. More specifically, we show that for a special, wellstudied type of phylogenetic network called a 1nested network, the trinets displayed by a 1nested network always encode the network. We also present an efficient algorithm for deciding whether a dense set of trinets (i.e. one that contains a trinet on every 3element subset of a set) can be displayed by a 1nested network or not and, if so, constructs that network. In addition, we discuss some potential new directions that this new approach opens up for constructing and comparing phylogenetic networks. © 2012 Springer Science+Business Media, LLC."



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."



Simon Joly. JML: Testing hybridization from species trees. In Molecular Ecology Ressources, Vol. 12(1):179184, 2012. Keywords: from species tree, hybridization, lineage sorting, phylogenetic network, phylogeny, Program JML, statistical model. Note: http://www.plantevolution.org/pdf/JMLpaper_accepted.pdf.
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"I introduce the software jml that tests for the presence of hybridization in multispecies sequence data sets by posterior predictive checking following Joly, McLenachan and Lockhart (2009, American Naturalist e54). Although their method could potentially be applied on any data set, the lack of appropriate software made its application difficult. The software jml thus fills a need for an easy application of the method but also includes improvements such as the possibility to incorporate uncertainty in the species tree topology. The jml software uses a posterior distribution of species trees, population sizes and branch lengths to simulate replicate sequence data sets using the coalescent with no migration. A test quantity, defined as the minimum pairwise sequence distance between sequences of two species, is then evaluated on the simulated data sets and compared to the one estimated from the original data. Because the test quantity is a good predictor of hybridization events, departure from the bifurcating species tree model could be interpreted as evidence of hybridization. Software performance in terms of computing time is evaluated for several parameters. I also show an application example of the software for detecting hybridization among native diploid North American roses. © 2011 Blackwell Publishing Ltd."



ZhiZhong Chen and
Lusheng Wang. Algorithms for Reticulate Networks of Multiple Phylogenetic Trees. In TCBB, Vol. 9(2):372384, 2012. Keywords: explicit network, from rooted trees, minimum number, phylogenetic network, phylogeny, Program CMPT, Program MaafB, reconstruction, software. Note: http://rnc.r.dendai.ac.jp/~chen/papers/rMaaf.pdf.
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"A reticulate network N of multiple phylogenetic trees may have nodes with two or more parents (called reticulation nodes). There are two ways to define the reticulation number of N. One way is to define it as the number of reticulation nodes in N in this case, a reticulate network with the smallest reticulation number is called an optimal typeI reticulate network of the trees. The better way is to define it as the total number of parents of reticulation nodes in N minus the number of reticulation nodes in N ; in this case, a reticulate network with the smallest reticulation number is called an optimal typeII reticulate network of the trees. In this paper, we first present a fast fixedparameter algorithm for constructing one or all optimal typeI reticulate networks of multiple phylogenetic trees. We then use the algorithm together with other ideas to obtain an algorithm for estimating a lower bound on the reticulation number of an optimal typeII reticulate network of the input trees. To our knowledge, these are the first fixedparameter algorithms for the problems. We have implemented the algorithms in ANSI C, obtaining programs CMPT and MaafB. Our experimental data show that CMPT can construct optimal typeI reticulate networks rapidly and MaafB can compute better lower bounds for optimal typeII reticulate networks within shorter time than the previously best program PIRN designed by Wu. © 2006 IEEE."



Stephen J. Willson. Treeaverage distances on certain phylogenetic networks have their weights uniquely determined. In ALMOB, Vol. 7(13), 2012. Keywords: from distances, from network, normal network, phylogenetic network, phylogeny, reconstruction, tree child network. Note: hhttp://www.public.iastate.edu/~swillson/TreeAverageDis10All.pdf.
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"A phylogenetic network N has vertices corresponding to species and arcs corresponding to direct genetic inheritance from the species at the tail to the species at the head. Measurements of DNA are often made on species in the leaf set, and one seeks to infer properties of the network, possibly including the graph itself. In the case of phylogenetic trees, distances between extant species are frequently used to infer the phylogenetic trees by methods such as neighborjoining.This paper proposes a treeaverage distance for networks more general than trees. The notion requires a weight on each arc measuring the genetic change along the arc. For each displayed tree the distance between two leaves is the sum of the weights along the path joining them. At a hybrid vertex, each character is inherited from one of its parents. We will assume that for each hybrid there is a probability that the inheritance of a character is from a specified parent. Assume that the inheritance events at different hybrids are independent. Then for each displayed tree there will be a probability that the inheritance of a given character follows the tree; this probability may be interpreted as the probability of the tree. The treeaverage distance between the leaves is defined to be the expected value of their distance in the displayed trees.For a class of rooted networks that includes rooted trees, it is shown that the weights and the probabilities at each hybrid vertex can be calculated given the network and the treeaverage distances between the leaves. Hence these weights and probabilities are uniquely determined. The hypotheses on the networks include that hybrid vertices have indegree exactly 2 and that vertices that are not leaves have a treechild. © 2012 Willson; licensee BioMed Central Ltd."



JeanPhilippe Doyon,
Vincent Ranwez,
Vincent Daubin and
Vincent Berry. Models, algorithms and programs for phylogeny reconciliation. In Briefings in Bioinformatics, Vol. 12(5):392400, 2011. Keywords: explicit network, lateral gene transfer, phylogenetic network, phylogeny, reconstruction, survey.
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"Gene sequences contain a goldmine of phylogenetic information. But unfortunately for taxonomists this information does not only tell the story of the species from which it was collected. Genes have their own complex histories which record speciation events, of course, but also many other events. Among them, gene duplications, transfers and losses are especially important to identify. These events are crucial to account for when reconstructing the history of species, and they play a fundamental role in the evolution of genomes, the diversification of organisms and the emergence of new cellular functions.We review reconciliations between gene and species trees, which are rigorous approaches for identifying duplications, transfers and losses that mark the evolution of a gene family. Existing reconciliation models and algorithms are reviewed and difficulties in modeling gene transfers are discussed. We also compare different reconciliation programs along with their advantages and disadvantages. © The Author 2011. Published by Oxford University Press."



Alix Boc and
Vladimir Makarenkov. Towards an accurate identification of mosaic genes and partial horizontal gene transfers. In NAR, Vol. 39(21):e144, 2011. Keywords: explicit network, from sequences, lateral gene transfer, phylogenetic network, phylogeny, Program T REX, reconstruction. Note: http://dx.doi.org/10.1093/nar/gkr735.
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"Many bacteria and viruses adapt to varying environmental conditions through the acquisition of mosaic genes. A mosaic gene is composed of alternating sequence polymorphisms either belonging to the host original allele or derived from the integrated donor DNA. Often, the integrated sequence contains a selectable genetic marker (e.g. marker allowing for antibiotic resistance). An effective identification of mosaic genes and detection of corresponding partial horizontal gene transfers (HGTs) are among the most important challenges posed by evolutionary biology. We developed a method for detecting partial HGT events and related intragenic recombination giving rise to the formation of mosaic genes. A bootstrap procedure incorporated in our method is used to assess the support of each predicted partial gene transfer. The proposed method can be also applied to confirm or discard complete (i.e. traditional) horizontal gene transfers detected by any HGT inferring method. While working on a fullgenome scale, the new method can be used to assess the level of mosaicism in the considered genomes as well as the rates of complete and partial HGT underlying their evolution. © 2011 The Author(s)."



Changiz Eslahchi,
Reza Hassanzadeh,
Ehsan Mottaghi,
Mahnaz Habibi,
Hamid Pezeshk and
Mehdi Sadeghi. Constructing circular phylogenetic networks from weighted quartets using simulated annealing. In MBIO, Vol. 235(2):123127, 2012. Keywords: abstract network, from quartets, heuristic, phylogenetic network, phylogeny, Program SAQNet, Program SplitsTree, reconstruction, simulated annealing, software, split network. Note: http://dx.doi.org/10.1016/j.mbs.2011.11.003.
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"In this paper, we present a heuristic algorithm based on the simulated annealing, SAQNet, as a method for constructing phylogenetic networks from weighted quartets. Similar to QNet algorithm, SAQNet constructs a collection of circular weighted splits of the taxa set. This collection is represented by a split network. In order to show that SAQNet performs better than QNet, we apply these algorithm to both the simulated and actual data sets containing salmonella, Bees, Primates and Rubber data sets. Then we draw phylogenetic networks corresponding to outputs of these algorithms using SplitsTree4 and compare the results. We find that SAQNet produces a better circular ordering and phylogenetic networks than QNet in most cases. SAQNet has been implemented in Matlab and is available for download at http://bioinf.cs.ipm.ac.ir/softwares/saq.net. © 2011 Elsevier Inc."



Benjamin Albrecht,
Celine Scornavacca,
Alberto Cenci and
Daniel H. Huson. Fast computation of minimum hybridization networks. In BIO, Vol. 28(2):191197, 2012. Keywords: explicit network, from rooted trees, minimum number, phylogenetic network, phylogeny, Program Dendroscope, Program Hybroscale, reconstruction. Note: http://dx.doi.org/10.1093/bioinformatics/btr618.
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"Motivation: Hybridization events in evolution may lead to incongruent gene trees. One approach to determining possible interspecific hybridization events is to compute a hybridization network that attempts to reconcile incongruent gene trees using a minimum number of hybridization events. Results: We describe how to compute a representative set of minimum hybridization networks for two given bifurcating input trees, using a parallel algorithm and provide a userfriendly implementation. A simulation study suggests that our program performs significantly better than existing software on biologically relevant data. Finally, we demonstrate the application of such methods in the context of the evolution of the Aegilops/Triticum genera. Availability and implementation: The algorithm is implemented in the program Dendroscope 3, which is freely available from www.dendroscope.org and runs on all three major operating systems. © The Author 2011. Published by Oxford University Press. All rights reserved."





Steven Kelk,
Leo van Iersel,
Nela Lekic,
Simone Linz,
Celine Scornavacca and
Leen Stougie. Cycle killer... qu'estce que c'est? On the comparative approximability of hybridization number and directed feedback vertex set. In SIDMA, Vol. 26(4):16351656, 2012. Keywords: agreement forest, approximation, explicit network, from rooted trees, minimum number, phylogenetic network, phylogeny, Program CycleKiller, reconstruction. Note: http://arxiv.org/abs/1112.5359, about the title.
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"We show that the problem of computing the hybridization number of two rooted binary phylogenetic trees on the same set of taxa X has a constant factor polynomialtime approximation if and only if the problem of computing a minimumsize feedback vertex set in a directed graph (DFVS) has a constant factor polynomialtime approximation. The latter problem, which asks for a minimum number of vertices to be removed from a directed graph to transform it into a directed acyclic graph, is one of the problems in Karp's seminal 1972 list of 21 NPcomplete problems. Despite considerable attention from the combinatorial optimization community, it remains to this day unknown whether a constant factor polynomialtime approximation exists for DFVS. Our result thus places the (in)approximability of hybridization number in a much broader complexity context, and as a consequence we obtain that it inherits inapproximability results from the problem Vertex Cover. On the positive side, we use results from the DFVS literature to give an O(log r log log r) approximation for the hybridization number where r is the correct value. Copyright © by SIAM."



Rosalba Radice. A Bayesian Approach to Modelling Reticulation Events with Application to the Ribosomal Protein Gene rps11 of Flowering Plants. In Australian & New Zealand Journal of Statistics, Vol. 54(4):401426, 2012. Keywords: bayesian, phylogenetic network, phylogeny, reconstruction, statistical model.
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"Traditional phylogenetic inference assumes that the history of a set of taxa can be explained by a tree. This assumption is often violated as some biological entities can exchange genetic material giving rise to nontreelike events often called reticulations. Failure to consider these events might result in incorrectly inferred phylogenies. Phylogenetic networks provide a flexible tool which allows researchers to model the evolutionary history of a set of organisms in the presence of reticulation events. In recent years, a number of methods addressing phylogenetic network parameter estimation have been introduced. Some of them are based on the idea that a phylogenetic network can be defined as a directed acyclic graph. Based on this definition, we propose a Bayesian approach to the estimation of phylogenetic network parameters which allows for different phylogenies to be inferred at different parts of a multiple DNA alignment. The algorithm is tested on simulated data and applied to the ribosomal protein gene rps11 data from five flowering plants, where reticulation events are suspected to be present. The proposed approach can be applied to a wide variety of problems which aim at exploring the possibility of reticulation events in the history of a set of taxa. © 2012 Australian Statistical Publishing Association Inc. Published by Wiley Publishing Asia Pty Ltd."



Philippe Gambette,
Vincent Berry and
Christophe Paul. Quartets and Unrooted Phylogenetic Networks. In JBCB, Vol. 10(4):1250004, 2012. Keywords: abstract network, circular split system, explicit network, from quartets, level k phylogenetic network, phylogenetic network, phylogeny, polynomial, reconstruction, split, split network. Note: http://hal.archivesouvertes.fr/hal00678046/en/.
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"Phylogenetic networks were introduced to describe evolution in the presence of exchanges of genetic material between coexisting species or individuals. Split networks in particular were introduced as a special kind of abstract network to visualize conflicts between phylogenetic trees which may correspond to such exchanges. More recently, methods were designed to reconstruct explicit phylogenetic networks (whose vertices can be interpreted as biological events) from triplet data. In this article, we link abstract and explicit networks through their combinatorial properties, by introducing the unrooted analog of levelk networks. In particular, we give an equivalence theorem between circular split systems and unrooted level1 networks. We also show how to adapt to quartets some existing results on triplets, in order to reconstruct unrooted levelk phylogenetic networks. These results give an interesting perspective on the combinatorics of phylogenetic networks and also raise algorithmic and combinatorial questions. © 2012 Imperial College Press."



Yun Yu,
James H. Degnan and
Luay Nakhleh. The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection. In PLoS Genetics, Vol. 8(4):e1002660, 2012. Keywords: AIC, BIC, explicit network, hybridization, phylogenetic network, phylogeny, statistical model. Note: http://dx.doi.org/10.1371/journal.pgen.1002660.
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"Gene tree topologies have proven a powerful data source for various tasks, including species tree inference and species delimitation. Consequently, methods for computing probabilities of gene trees within species trees have been developed and widely used in probabilistic inference frameworks. All these methods assume an underlying multispecies coalescent model. However, when reticulate evolutionary events such as hybridization occur, these methods are inadequate, as they do not account for such events. Methods that account for both hybridization and deep coalescence in computing the probability of a gene tree topology currently exist for very limited cases. However, no such methods exist for general cases, owing primarily to the fact that it is currently unknown how to compute the probability of a gene tree topology within the branches of a phylogenetic network. Here we present a novel method for computing the probability of gene tree topologies on phylogenetic networks and demonstrate its application to the inference of hybridization in the presence of incomplete lineage sorting. We reanalyze a Saccharomyces species data set for which multiple analyses had converged on a species tree candidate. Using our method, though, we show that an evolutionary hypothesis involving hybridization in this group has better support than one of strict divergence. A similar reanalysis on a group of three Drosophila species shows that the data is consistent with hybridization. Further, using extensive simulation studies, we demonstrate the power of gene tree topologies at obtaining accurate estimates of branch lengths and hybridization probabilities of a given phylogenetic network. Finally, we discuss identifiability issues with detecting hybridization, particularly in cases that involve extinction or incomplete sampling of taxa. © 2012 Yu et al."



Reza Hassanzadeh,
Changiz Eslahchi and
WingKin Sung. Constructing phylogenetic supernetworks based on simulated annealing. In MPE, Vol. 63(3):738744, 2012. Keywords: abstract network, from unrooted trees, heuristic, phylogenetic network, phylogeny, Program SNSA, reconstruction, simulated annealing, software, split network. Note: http://dx.doi.org/10.1016/j.ympev.2012.02.009.
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Different partial phylogenetic trees can be derived from different sources of evidence and different methods. One important problem is to summarize these partial phylogenetic trees using a supernetwork. We propose a novel simulated annealing based method called SNSA which uses an optimization function to produce a simple network that still retains a great deal of phylogenetic information. We report the performance of this new method on real and simulated datasets. © 2012 Elsevier Inc.



Leo van Iersel and
Simone Linz. A quadratic kernel for computing the hybridization number of multiple trees. In IPL, Vol. 113:318323, 2013. Keywords: explicit network, FPT, from rooted trees, kernelization, minimum number, phylogenetic network, phylogeny, Program Clustistic, Program MaafB, Program PIRN, reconstruction. Note: http://arxiv.org/abs/1203.4067, poster.
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"It has recently been shown that the NPhard problem of calculating the minimum number of hybridization events that is needed to explain a set of rooted binary phylogenetic trees by means of a hybridization network is fixedparameter tractable if an instance of the problem consists of precisely two such trees. In this paper, we show that this problem remains fixedparameter tractable for an arbitrarily large set of rooted binary phylogenetic trees. In particular, we present a quadratic kernel. © 2013 Elsevier B.V."



Hadi Poormohammadi,
Changiz Eslahchi and
Ruzbeh Tusserkani. TripNet: A Method for Constructing Rooted Phylogenetic Networks from Rooted Triplets. In PLoS ONE, Vol. 9(9):e106531, 2014. Keywords: explicit network, from triplets, heuristic, level k phylogenetic network, phylogenetic network, phylogeny, Program TripNet, reconstruction, software. Note: http://arxiv.org/abs/1201.3722.
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"The problem of constructing an optimal rooted phylogenetic network from an arbitrary set of rooted triplets is an NPhard problem. In this paper, we present a heuristic algorithm called TripNet, which tries to construct a rooted phylogenetic network with the minimum number of reticulation nodes from an arbitrary set of rooted triplets. Despite of current methods that work for dense set of rooted triplets, a key innovation is the applicability of TripNet to nondense set of rooted triplets. We prove some theorems to clarify the performance of the algorithm. To demonstrate the efficiency of TripNet, we compared TripNet with SIMPLISTIC. It is the only available software which has the ability to return some rooted phylogenetic network consistent with a given dense set of rooted triplets. But the results show that for complex networks with high levels, the SIMPLISTIC running time increased abruptly. However in all cases TripNet outputs an appropriate rooted phylogenetic network in an acceptable time. Also we tetsed TripNet on the Yeast data. The results show that Both TripNet and optimal networks have the same clustering and TripNet produced a level3 network which contains only one more reticulation node than the optimal network."



Chris Whidden,
Robert G. Beiko and
Norbert Zeh. FixedParameter Algorithms for Maximum Agreement Forests. In SICOMP, Vol. 42(4):14311466, 2013. Keywords: agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, SPR distance. Note: http://arxiv.org/abs/1108.2664, slides.
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"We present new and improved fixedparameter algorithms for computing maximum agreement forests of pairs of rooted binary phylogenetic trees. The size of such a forest for two trees corresponds to their subtree pruneandregraft distance and, if the agreement forest is acyclic, to their hybridization number. These distance measures are essential tools for understanding reticulate evolution. Our algorithm for computing maximum acyclic agreement forests is the first depthbounded search algorithm for this problem. Our algorithms substantially outperform the best previous algorithms for these problems. © 2013 Society for Industrial and Applied Mathematics."



Stefan Grünewald,
Andreas Spillner,
Sarah Bastkowski,
Anja Bögershausen and
Vincent Moulton. SuperQ: Computing Supernetworks from Quartets. In TCBB, Vol. 10(1):151160, 2013. Keywords: abstract network, circular split system, from quartets, heuristic, phylogenetic network, phylogeny, Program QNet, Program SplitsTree, Program SuperQ, software, split network.
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"Supertrees are a commonly used tool in phylogenetics to summarize collections of partial phylogenetic trees. As a generalization of supertrees, phylogenetic supernetworks allow, in addition, the visual representation of conflict between the trees that is not possible to observe with a single tree. Here, we introduce SuperQ, a new method for constructing such supernetworks (SuperQ is freely available at >www.uea.ac.uk/computing/superq.). It works by first breaking the input trees into quartet trees, and then stitching these together to form a special kind of phylogenetic network, called a split network. This stitching process is performed using an adaptation of the QNet method for split network reconstruction employing a novel approach to use the branch lengths from the input trees to estimate the branch lengths in the resulting network. Compared with previous supernetwork methods, SuperQ has the advantage of producing a planar network. We compare the performance of SuperQ to the Zclosure and Qimputation supernetwork methods, and also present an analysis of some published data sets as an illustration of its applicability. © 20042012 IEEE."



Lavanya Kannan and
Ward C Wheeler. Maximum Parsimony on Phylogenetic Networks. In ALMOB, Vol. 7:9, 2012. Keywords: dynamic programming, explicit network, from sequences, heuristic, parsimony, phylogenetic network, phylogeny. Note: http://dx.doi.org/10.1186/1748718879.
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"Background: Phylogenetic networks are generalizations of phylogenetic trees, that are used to model evolutionary events in various contexts. Several different methods and criteria have been introduced for reconstructing phylogenetic trees. Maximum Parsimony is a characterbased approach that infers a phylogenetic tree by minimizing the total number of evolutionary steps required to explain a given set of data assigned on the leaves. Exact solutions for optimizing parsimony scores on phylogenetic trees have been introduced in the past.Results: In this paper, we define the parsimony score on networks as the sum of the substitution costs along all the edges of the network; and show that certain wellknown algorithms that calculate the optimum parsimony score on trees, such as Sankoff and Fitch algorithms extend naturally for networks, barring conflicting assignments at the reticulate vertices. We provide heuristics for finding the optimum parsimony scores on networks. Our algorithms can be applied for any cost matrix that may contain unequal substitution costs of transforming between different characters along different edges of the network. We analyzed this for experimental data on 10 leaves or fewer with at most 2 reticulations and found that for almost all networks, the bounds returned by the heuristics matched with the exhaustively determined optimum parsimony scores.Conclusion: The parsimony score we define here does not directly reflect the cost of the best tree in the network that displays the evolution of the character. However, when searching for the most parsimonious network that describes a collection of characters, it becomes necessary to add additional cost considerations to prefer simpler structures, such as trees over networks. The parsimony score on a network that we describe here takes into account the substitution costs along the additional edges incident on each reticulate vertex, in addition to the substitution costs along the other edges which are common to all the branching patterns introduced by the reticulate vertices. Thus the score contains an inbuilt cost for the number of reticulate vertices in the network, and would provide a criterion that is comparable among all networks. Although the problem of finding the parsimony score on the network is believed to be computationally hard to solve, heuristics such as the ones described here would be beneficial in our efforts to find a most parsimonious network. © 2012 Kannan and Wheeler; licensee BioMed Central Ltd."



Alix Boc,
Alpha B. Diallo and
Vladimir Makarenkov. TREX: a web server for inferring, validating and visualizing phylogenetic trees and networks. In NAR, Vol. 40(W1):W573W579, 2012. Keywords: from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, Program T REX, reconstruction, reticulogram, software. Note: http://dx.doi.org/10.1093/nar/gks485.
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"TREX (Tree and reticulogram REConstruction) is a web server dedicated to the reconstruction of phylogenetic trees, reticulation networks and to the inference of horizontal gene transfer (HGT) events. TREX includes several popular bioinformatics applications such as MUSCLE, MAFFT, Neighbor Joining, NINJA, BioNJ, PhyML, RAxML, random phylogenetic tree generator and some wellknown sequencetodistance transformation models. It also comprises fast and effective methods for inferring phylogenetic trees from complete and incomplete distance matrices as well as for reconstructing reticulograms and HGT networks, including the detection and validation of complete and partial gene transfers, inference of consensus HGT scenarios and interactive HGT identification, developed by the authors. The included methods allows for validating and visualizing phylogenetic trees and networks which can be built from distance or sequence data. The web server is available at: www.trex.uqam.ca. © 2012 The Author(s)."



Daniel H. Huson and
Celine Scornavacca. Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks. In Systematic Biology, Vol. 61(6):10611067, 2012. Keywords: from rooted trees, from triplets, phylogenetic network, phylogeny, Program Dendroscope, reconstruction, software, visualization.
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"Dendroscope 3 is a new program for working with rooted phylogenetic trees and networks. It provides a number of methods for drawing and comparing rooted phylogenetic networks, and for computing them from rooted trees. The program can be used interactively or in commandline mode. The program is written in Java, use of the software is free, and installers for all 3 major operating systems can be downloaded from www.dendroscope.org. [Phylogenetic trees; phylogenetic networks; software.] © 2012 The Author(s)."



ZhiZhong Chen,
Lusheng Wang and
Satoshi Yamanaka. A fast tool for minimum hybridization networks. In BMCB, Vol. 13:155, 2012. Keywords: agreement forest, explicit network, from rooted trees, phylogenetic network, phylogeny, Program FastHN, reconstruction, software. Note: http://dx.doi.org/10.1186/1471210513155.
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"Background: Due to hybridization events in evolution, studying two different genes of a set of species may yield two related but different phylogenetic trees for the set of species. In this case, we want to combine the two phylogenetic trees into a hybridization network with the fewest hybridization events. This leads to three computational problems, namely, the problem of computing the minimum size of a hybridization network, the problem of constructing one minimum hybridization network, and the problem of enumerating a representative set of minimum hybridization networks. The previously best software tools for these problems (namely, Chen and Wang's HybridNet and Albrecht et al.'s Dendroscope 3) run very slowly for large instances that cannot be reduced to relatively small instances. Indeed, when the minimum size of a hybridization network of two given trees is larger than 23 and the problem for the trees cannot be reduced to relatively smaller independent subproblems, then HybridNet almost always takes longer than 1 day and Dendroscope 3 often fails to complete. Thus, a faster software tool for the problems is in need.Results: We develop a software tool in ANSI C, named FastHN, for the following problems: Computing the minimum size of a hybridization network, constructing one minimum hybridization network, and enumerating a representative set of minimum hybridization networks. We obtain FastHN by refining HybridNet with three ideas. The first idea is to preprocess the input trees so that the trees become smaller or the problem becomes to solve two or more relatively smaller independent subproblems. The second idea is to use a fast algorithm for computing the rSPR distance of two given phylognetic trees to cut more branches of the search tree in the exhaustivesearch stage of the algorithm. The third idea is that during the exhaustivesearch stage of the algorithm, we find two sibling leaves in one of the two forests (obtained from the given trees by cutting some edges) such that they are as far as possible in the other forest. As the result, FastHN always runs much faster than HybridNet. Unlike Dendroscope 3, FastHN is a singlethreaded program. Despite this disadvantage, our experimental data shows that FastHN runs substantially faster than the multithreaded Dendroscope 3 on a PC with multiple cores. Indeed, FastHN can finish within 16 minutes (on average on a Windows7 (x64) desktop PC with i72600 CPU) even if the minimum size of a hybridization network of two given trees is about 25, the trees each have 100 leaves, and the problem for the input trees cannot be reduced to two or more independent subproblems via cluster reductions. It is also worth mentioning that like HybridNet, FastHN does not use much memory (indeed, the amount of memory is at most quadratic in the input size). In contrast, Dendroscope 3 uses a huge amount of memory. Executables of FastHN for Windows XP (x86), Windows 7 (x64), Linux, and Mac OS are available (see the Results and discussion section for details).Conclusions: For both biological datasets and simulated datasets, our experimental results show that FastHN runs substantially faster than HybridNet and Dendroscope 3. The superiority of FastHN in speed over the previous tools becomes more significant as the hybridization number becomes larger. In addition, FastHN uses much less memory than Dendroscope 3 and uses the same amount of memory as HybridNet. © 2012 Chen et al.; licensee BioMed Central Ltd."



Michel Habib and
ThuHien To. Constructing a Minimum Phylogenetic Network from a Dense Triplet Set. In JBCB, Vol. 10(5):1250013, 2012. Keywords: explicit network, from triplets, level k phylogenetic network, phylogenetic network, phylogeny, polynomial, reconstruction. Note: http://arxiv.org/abs/1103.2266.
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"For a given set L of species and a set T of triplets on L, we seek to construct a phylogenetic network which is consistent with T i.e. which represents all triplets of T. The level of a network is defined as the maximum number of hybrid vertices in its biconnected components. When T is dense, there exist polynomial time algorithms to construct level0,1 and 2 networks (Aho et al., 1981; Jansson, Nguyen and Sung, 2006; Jansson and Sung, 2006; Iersel et al., 2009). For higher levels, partial answers were obtained in the paper by Iersel and Kelk (2008), with a polynomial time algorithm for simple networks. In this paper, we detail the first complete answer for the general case, solving a problem proposed in Jansson and Sung (2006) and Iersel et al. (2009). For any k fixed, it is possible to construct a levelk network having the minimum number of hybrid vertices and consistent with T, if there is any, in time O(T k+1 n⌊4k/3⌋+1). © 2012 Imperial College Press."



Ruogu Sheng and
Sergey Bereg. Approximating Metrics with Planar BoundaryLabeled Phylogenetic Networks. In JBCB, Vol. 10(6):1250017, 2012. Keywords: abstract network, from distances, phylogenetic network, phylogeny, reconstruction.
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"Phylogenetic networks are useful for visualizing evolutionary relationships between species with reticulate events such as hybridizations and horizontal gene transfers. In this paper, we consider the problem of constructing undirected phylogenetic networks that (1) are planar graphs and (2) admit embeddings in the plane where the vertices labeling all taxa are on the boundary of the network. We develop a new algorithm for constructing phylogenetic networks satisfying these constraints. First, we show that only approximate networks can be constructed for some distance matrices with at least five taxa. Then we prove that any fivepoint metric can be represented approximately by a planar boundarylabeled network with guaranteed fit value of 94.79. We extend the networks constructed in the proof to design an algorithm for computing planar boundarylabeled networks for any number of taxa. © 2012 Imperial College Press."



Teresa Piovesan and
Steven Kelk. A simple fixed parameter tractable algorithm for computing the hybridization number of two (not necessarily binary) trees. In TCBB, Vol. 10(1):1825, 2013. Keywords: FPT, from rooted trees, phylogenetic network, phylogeny, Program TerminusEst, reconstruction. Note: http://arxiv.org/abs/1207.6090.
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"Here, we present a new fixed parameter tractable algorithm to compute the hybridization number (r) of two rooted, not necessarily binary phylogenetic trees on taxon set (X) in time ((6r r) · poly(n)), where (n= X). The novelty of this approach is its use of terminals, which are maximal elements of a natural partial order on (X), and several insights from the softwired clusters literature. This yields a surprisingly simple and practical boundedsearch algorithm and offers an alternative perspective on the underlying combinatorial structure of the hybridization number problem. © 20042012 IEEE."





 
