




Andrew R. Francis,
Katharina Huber,
Vincent Moulton and
Taoyang Wu. Bounds for phylogenetic network space metrics. In JOMB, Vol. 76(5):12291248, 2018. Keywords: bound, distance between networks, from network, NNI distance, phylogenetic network, phylogeny, SPR distance, TBR distance. Note: https://arxiv.org/abs/1702.05609.



Andrew R. Francis,
Katharina Huber and
Vincent Moulton. Treebased unrooted phylogenetic networks. In BMB, Vol. 80(2):404416, 2018. Keywords: characterization, explicit network, NP complete, phylogenetic network, phylogeny, tree containment, treebased network, Unrooted treebased network. Note: https://arxiv.org/abs/1704.02062.



Sarah Bastkowski,
Daniel Mapleson,
Andreas Spillner,
Taoyang Wu,
Monika Balvociute and
Vincent Moulton. SPECTRE: a Suite of PhylogEnetiC Tools for Reticulate Evolution. In BIO, Vol. 34(6):10571058, 2018. Keywords: abstract network, NeighborNet, phylogenetic network, phylogeny, Program FlatNJ, Program QNet, Program SplitsTree, reconstruction, software, split network. Note: https://doi.org/10.1101/169177.



Katharina Huber,
Vincent Moulton,
Charles Semple and
Taoyang Wu. Quarnet inference rules for level1 networks. In BMB, Vol. 80:21372153, 2018. Keywords: explicit network, from quarnets, from subnetworks, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction. Note: https://arxiv.org/abs/1711.06720.







Magnus Bordewich,
Katharina Huber,
Vincent Moulton and
Charles Semple. Recovering normal networks from shortest intertaxa distance information. In JOMB, Vol. 77(3):571594, 2018. Keywords: explicit network, from distances, normal network, phylogenetic network, phylogeny, polynomial, reconstruction, uniqueness. Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BHMS18.pdf.






Katharina Huber,
Leo van Iersel,
Vincent Moulton,
Celine Scornavacca and
Taoyang Wu. Reconstructing phylogenetic level1 networks from nondense binet and trinet sets. In ALG, Vol. 77(1):173200, 2017. Keywords: explicit network, FPT, from binets, from subnetworks, from trinets, NP complete, phylogenetic network, phylogeny, polynomial, reconstruction. Note: http://arxiv.org/abs/1411.6804.





Leo van Iersel,
Vincent Moulton,
Eveline De Swart and
Taoyang Wu. Binets: fundamental building blocks for phylogenetic networks. In BMB, Vol. 79(5):11351154, 2017. Keywords: approximation, explicit network, from binets, from subnetworks, galled tree, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, reconstruction. Note: http://dx.doi.org/10.1007/s1153801702754.








Katharina Huber,
Vincent Moulton,
Mike Steel and
Taoyang Wu. Folding and unfolding phylogenetic trees and networks. In JOMB, Vol. 73(6):17611780, 2016. Keywords: compressed network, explicit network, FUstable network, NP complete, phylogenetic network, phylogeny, tree containment, tree sibling network. Note: http://arxiv.org/abs/1506.04438.







James Oldman,
Taoyang Wu,
Leo van Iersel and
Vincent Moulton. TriLoNet: Piecing together small networks to reconstruct reticulate evolutionary histories. In MBE, Vol. 33(8):21512162, 2016. Keywords: explicit network, from subnetworks, from trinets, galled tree, phylogenetic network, phylogeny, Program LEV1ATHAN, Program TriLoNet, reconstruction.






Katharina Huber,
Leo van Iersel,
Vincent Moulton and
Taoyang Wu. How much information is needed to infer reticulate evolutionary histories? In Systematic Biology, Vol. 64(1):102111, 2015. Keywords: explicit network, from network, from rooted trees, from subnetworks, from trinets, identifiability, phylogenetic network, phylogeny, reconstruction, uniqueness. Note: http://dx.doi.org/10.1093/sysbio/syu076.








Leo van Iersel and
Vincent Moulton. Trinets encode treechild and level2 phylogenetic networks. In JOMB, Vol. 68(7):17071729, 2014. Keywords: explicit network, from subnetworks, from trinets, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction. Note: http://arxiv.org/abs/1210.0362.
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"Phylogenetic networks generalize evolutionary trees, and are commonly used to represent evolutionary histories of species that undergo reticulate evolutionary processes such as hybridization, recombination and lateral gene transfer. Recently, there has been great interest in trying to develop methods to construct rooted phylogenetic networks from triplets, that is rooted trees on three species. However, although triplets determine or encode rooted phylogenetic trees, they do not in general encode rooted phylogenetic networks, which is a potential issue for any such method. Motivated by this fact, Huber and Moulton recently introduced trinets as a natural extension of rooted triplets to networks. In particular, they showed that level1 phylogenetic networks are encoded by their trinets, and also conjectured that all "recoverable" rooted phylogenetic networks are encoded by their trinets. Here we prove that recoverable binary level2 networks and binary treechild networks are also encoded by their trinets. To do this we prove two decomposition theorems based on trinets which hold for all recoverable binary rooted phylogenetic networks. Our results provide some additional evidence in support of the conjecture that trinets encode all recoverable rooted phylogenetic networks, and could also lead to new approaches to construct phylogenetic networks from trinets. © 2013 SpringerVerlag Berlin Heidelberg."



Sarah Bastkowski,
Andreas Spillner and
Vincent Moulton. Fishing for minimum evolution trees with NeighborNets. In IPL, Vol. 114(12):318, 2014. Keywords: circular split system, from distances, NeighborNet, phylogeny, polynomial.
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"In evolutionary biology, biologists commonly use a phylogenetic tree to represent the evolutionary history of some set of species. A common approach taken to construct such a tree is to search through the space of all possible phylogenetic trees on the set so as to find one that optimizes some score function, such as the minimum evolution criterion. However, this is hampered by the fact that the space of phylogenetic trees is extremely large in general. Interestingly, an alternative approach, which has received somewhat less attention in the literature, is to instead search for trees within some set of bipartitions or splits of the set of species in question. Here we consider the problem of searching through a set of splits that is circular. Such sets can, for example, be generated by the NeighborNet algorithm for constructing phylogenetic networks. More specifically, we present an O(n4) time algorithm for finding an optimal minimum evolution tree in a circular set of splits on a set of species of size n. In addition, using simulations, we compare the performance of this algorithm when applied to NeighborNet output with that of FastME, a leading method for searching for minimum evolution trees in tree space. We find that, even though a circular set of splits represents just a tiny fraction of the total number of possible splits of a set, the trees obtained from circular sets compare quite favorably with those obtained with FastME, suggesting that the approach could warrant further investigation. © 2013 Elsevier B.V."



Monika Balvociute,
Andreas Spillner and
Vincent Moulton. FlatNJ: A Novel NetworkBased Approach to Visualize Evolutionary and Biogeographical Relationships. In Systematic Biology, Vol. 63(3):383396, 2014. Keywords: abstract network, flat, phylogenetic network, phylogeny, Program FlatNJ, Program SplitsTree, split network. Note: http://dx.doi.org/10.1093/sysbio/syu001.
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"Split networks are a type of phylogenetic network that allow visualization of conflict in evolutionary data. We present a new method for constructing such networks called FlatNetJoining (FlatNJ). A key feature of FlatNJ is that it produces networks that can be drawn in the plane in which labels may appear inside of the network. For complex data sets that involve, for example, nonneutral molecular markers, this can allow additional detail to be visualized as compared to previous methods such as split decomposition and NeighborNet. We illustrate the application of FlatNJ by applying it to whole HIV genome sequences, where recombination has taken place, fluorescent proteins in corals, where ancestral sequences are present, and mitochondrial DNA sequences from gall wasps, where biogeographical relationships are of interest. We find that the networks generated by FlatNJ can facilitate the study of genetic variation in the underlying molecular sequence data and, in particular, may help to investigate processes such as intralocus recombination. FlatNJ has been implemented in Java and is freely available at www.uea.ac.uk/computing/software/ flatnj. [flat split system; NeighborNet; Phylogenetic network; QNet; split; split network.] © The Author(s) 2014."






Katharina Huber and
Vincent Moulton. Encoding and Constructing 1Nested Phylogenetic Networks with Trinets. In ALG, Vol. 66(3):714738, 2013. Keywords: explicit network, from subnetworks, 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."



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."








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."



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."



Katharina Huber,
Vincent Moulton,
Andreas Spillner,
Sabine Storandt and
Radoslaw Suchecki. Computing a consensus of multilabeled trees. In ALENEX12, Pages 8492, 2012. Keywords: duplication, explicit network, exponential algorithm, phylogenetic network, phylogeny. Note: http://siam.omnibooksonline.com/2012ALENEX/data/papers/020.pdf.
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In this paper we consider two challenging problems that arise in the context of computing a consensus of a collection of multilabeled trees, namely (1) selecting a compatible collection of clusters on a multiset from an ordered list of such clusters and (2) optimally refining high degree vertices in a multilabeled tree. Forming such a consensus is part of an approach to reconstruct the evolutionary history of a set of species for which events such as genome duplication and hybridization have occurred in the past. We present exact algorithms for solving (1) and (2) that have an exponential runtime in the worst case. To give some impression of their performance in practice, we apply them to simulated input and to a real biological data set highlighting the impact of several structural properties of the input on the performance.






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."






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



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



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."



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."








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."



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.
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"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."



Stefan Grünewald,
Andreas Spillner,
Kristoffer Forslund and
Vincent Moulton. Constructing Phylogenetic Supernetworks from Quartets. In WABI08, Vol. 5251:284295 of LNCS, springer, 2008. Keywords: abstract network, from quartets, from unrooted trees, phylogenetic network, phylogeny, Program QNet, Program SplitsTree, reconstruction, split network. Note: http://dx.doi.org/10.1007/9783540873617_24.
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"In phylogenetics it is common practice to summarize collections of partial phylogenetic trees in the form of supertrees. Recently it has been proposed to construct phylogenetic supernetworks as an alternative to supertrees as these allow the representation of conflicting information in the trees, information that may not be representable in a single tree. Here we introduce SuperQ, a new method for constructing such supernetworks. It works by breaking the input trees into quartet trees, and stitching together the resulting set to form a network. The stitching process is performed using an adaptation of the QNet method for phylogenetic network reconstruction. In addition to presenting the new method, we illustrate the applicability of SuperQ to three data sets and discuss future directions for testing and development. © 2008 SpringerVerlag Berlin Heidelberg."



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."






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.
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"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."



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.
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"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."



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."



David Bryant,
Vincent Moulton and
Andreas Spillner. Consistency of the NeighborNet Algorithm. In AMB, Vol. 2(8), 2007. Keywords: abstract network, consistency, from distances, NeighborNet. Note: http://dx.doi.org/10.1186/1748718828.
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"Background: NeighborNet is a novel method for phylogenetic analysis that is currently being widely used in areas such as virology, bacteriology, and plant evolution. Given an input distance matrix, NeighborNet produces a phylogenetic network, a generalization of an evolutionary or phylogenetic tree which allows the graphical representation of conflicting phylogenetic signals. Results: In general, any network construction method should not depict more conflict than is found in the data, and, when the data is fitted well by a tree, the method should return a network that is close to this tree. In this paper we provide a formal proof that NeighborNet satisfies both of these requirements so that, in particular, NeighborNet is statistically consistent on circular distances. © 2007 Bryant et al; licensee BioMed Central Ltd."








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."








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."



Barbara R. Holland,
Frédéric Delsuc and
Vincent Moulton. Visualizing Conflicting Evolutionary Hypotheses in Large Collections of Trees: Using Consensus Networks to Study the Origins of Placentals and Hexapods. In Systematic Biology, Vol. 54(1):6676, 2005. Keywords: consensus. Note: http://halsde.archivesouvertes.fr/halsde00193050/fr/.
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"Many phylogenetic methods produce large collections of trees as opposed to a single tree, which allows the exploration of support for various evolutionary hypotheses. However, to be useful, the information contained in large collections of trees should be summarized; frequently this is achieved by constructing a consensus tree. Consensus trees display only those signals that are present in a large proportion of the trees. However, by their very nature consensus trees require that any conflicts between the trees are necessarily disregarded. We present a method that extends the notion of consensus trees to allow the visualization of conflicting hypotheses in a consensus network. We demonstrate the utility of this method in highlighting differences amongst maximum likelihood bootstrap values and Bayesian posterior probabilities in the placental mammal phylogeny, and also in comparing the phylogenetic signal contained in amino acid versus nucleotide characters for hexapod monophyly. Copyright © Society of Systematic Biologists."





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.






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.
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"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."



Katharina Huber,
Vincent Moulton and
Charles Semple. Replacing cliques by stars in quasimedian graphs. In DAM, Vol. 143(13), 2004. Note: http://dx.doi.org/10.1016/j.dam.2004.03.002.
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"For a multiset Σ of splits (bipartitions) of a finite set X, we introduce the multisplit graph G(Σ). This graph is a natural extension of the Buneman graph, Indeed, it is shown that several results pertaining to the Buneman graph extend to the multisplit graph. In addition, in case Σ is derived from a set ℛ of partitions of X by taking parts together with their complements, we show that the extremal instances where ℛ is either strongly compatible or strongly incompatible are equivalent to G(Σ) being either a tree or a Cartesian product of star trees, respectively. © 2004 Elsevier B.V. All rights reserved."



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.










David Bryant and
Vincent Moulton. NeighborNet: An Agglomerative Method for the Construction of Planar Phylogenetic Networks. In WABI02, Vol. 2452:375391 of LNCS, springer, 2002. Keywords: abstract network, circular split system, from distances, NeighborNet, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network. Note: http://dx.doi.org/10.1007/3540457844_28.






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."














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.



