
Steven Kelk,
Leo van Iersel,
Celine Scornavacca and
Mathias Weller. Phylogenetic incongruence through the lens of Monadic Second Order logic. In JGAA, Vol. 20(2):189215, 2016. Keywords: agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, MSOL, phylogenetic network, phylogeny, reconstruction. Note: http://jgaa.info/accepted/2016/KelkIerselScornavaccaWeller2016.20.2.pdf.



Andreas Gunawan,
Bhaskar DasGupta and
Louxin Zhang. Locating a Tree in a ReticulationVisible Network in Cubic Time. In RECOMB2016, Vol. 9649:266 of LNBI, Springer, 2016. Keywords: cluster containment, explicit network, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulationvisible network, tree containment. Note: http://arxiv.org/abs/1507.02119.



Philippe Gambette,
Andreas Gunawan,
Anthony Labarre,
Stéphane Vialette and
Louxin Zhang. Solving the Tree Containment Problem for Genetically Stable Networks in Quadratic Time. In IWOCA15, Vol. 9538:197208 of LNCS, springer, 2016. Keywords: explicit network, from network, from rooted trees, genetically stable network, phylogenetic network, phylogeny, polynomial, tree containment. Note: https://halupecupem.archivesouvertes.fr/hal01226035 .















Sha Zhu and
James H. Degnan. Displayed Trees Do Not Determine Distinguishability Under the Network Multispecies Coalescent. In SB, 2016. Keywords: branch length, coalescent, explicit network, from network, likelihood, phylogenetic network, phylogeny, Program Hybridcoal, Program HybridLambda, Program PhyloNet, software, uniqueness. Note: to appear, presentation available at https://www.youtube.com/watch?v=JLYGTfEZG7g.



Philippe Gambette,
Andreas Gunawan,
Anthony Labarre,
Stéphane Vialette and
Louxin Zhang. Locating a Tree in A Phylogenetic Network in Quadratic Time. In RECOMB15, Vol. 9029:96107 of LNCS, Springer, 2015. Keywords: evaluation, explicit network, from network, from rooted trees, genetically stable network, nearlystable network, phylogenetic network, phylogeny, polynomial, tree containment. Note: https://hal.archivesouvertes.fr/hal01116231/en.





Quan Nguyen and
Teemu Roos. Likelihoodbased inference of phylogenetic networks from sequence data by PhyloDAG. In ALCOB2015, Vol. 9199:126140 of LNCS, springer, 2015. Keywords: BIC, explicit network, from sequences, likelihood, phylogenetic network, phylogeny, Program PhyloDAG, reconstruction, software. Note: http://www.cs.helsinki.fi/u/ttonteri/pub/alcob2015.pdf.





Jittat Fakcharoenphol,
Tanee Kumpijit and
Attakorn Putwattana. A Faster Algorithm for the Tree Containment Problem for Binary Nearly Stable Phylogenetic Networks. In Proceedings of the The 12th International Joint Conference on Computer Science and Software Engineering (JCSSE'15), Pages 337342, IEEE, 2015. Keywords: dynamic programming, explicit network, from network, from rooted trees, nearlystable network, phylogenetic network, phylogeny, polynomial, tree containment.



Misagh Kordi and
Mukul S. Bansal. On the Complexity of DuplicationTransferLoss Reconciliation with NonBinary Gene Trees. In ISBRA15, Vol. 9096:187198 of LNCS, springer, 2015. Keywords: duplication, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, phylogenetic network, phylogeny, reconstruction. Note: http://compbio.engr.uconn.edu/papers/Kordi_ISBRA2015.pdf.



Yun Yu and
Luay Nakhleh. A DistanceBased Method for Inferring Phylogenetic Networks in the Presence of Incomplete Lineage Sorting. In ISBRA15, Vol. 9096:378389 of LNCS, springer, 2015. Keywords: bootstrap, explicit network, from distances, heuristic, incomplete lineage sorting, phylogenetic network, phylogeny, reconstruction. Note: http://bioinfo.cs.rice.edu/sites/bioinfo.cs.rice.edu/files/YuNakhlehISBRA15.pdf.





Yun Yu and
Luay Nakhleh. A maximum pseudolikelihood approach for phylogenetic networks. In RECOMBCG15, Vol. 16(Suppl 10)(S10):110 of BMC Genomics, BioMed Central, 2015. Keywords: explicit network, from rooted trees, hybridization, incomplete lineage sorting, likelihood, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, tripartition distance. Note: http://dx.doi.org/10.1186/1471216416S10S10.



Gergely J. Szöllösi,
Adrián Arellano Davín,
Eric Tannier,
Vincent Daubin and
Bastien Boussau. Genomescale phylogenetic analysis finds extensive gene transfer among fungi. In Philosophical Transactions of the Royal Society of London B: Biological Sciences, Vol. 370(1678):111, 2015. Keywords: duplication, from sequences, lateral gene transfer, loss, phylogenetic network, phylogeny, Program ALE, reconstruction. Note: http://dx.doi.org/10.1098/rstb.2014.0335.





Gabriel Cardona,
Joan Carles Pons and
Francesc Rosselló. A reconstruction problem for a class of phylogenetic networks with lateral gene transfers. In ALMOB, Vol. 10(28):115, 2015. Keywords: explicit network, from rooted trees, lateral gene transfer, phylogenetic network, phylogeny, Program LGTnetwork, reconstruction, software, treebased network. Note: http://dx.doi.org/10.1186/s130150150059z.



Leo van Iersel and
Steven Kelk. Kernelizations for the hybridization number problem on multiple nonbinary trees. In WG14, Vol. 8747:299311 of LNCS, springer, 2014. Keywords: explicit network, from rooted trees, kernelization, minimum number, phylogenetic network, phylogeny, Program Treeduce, reconstruction. Note: http://arxiv.org/abs/1311.4045.



Ran LibeskindHadas,
YiChieh Wu,
Mukul S. Bansal and
Manolis Kellis. Paretooptimal phylogenetic tree reconciliation. In ISMB14, Vol. 30:i87i95 of BIO, 2014. Keywords: duplication, lateral gene transfer, loss, phylogenetic network, phylogeny, polynomial, Program Xscape, reconstruction. Note: http://dx.doi.org/10.1093/bioinformatics/btu289.
Toggle abstract
"Motivation: Phylogenetic tree reconciliation is a widely used method for reconstructing the evolutionary histories of gene families and species, hosts and parasites and other dependent pairs of entities. Reconciliation is typically performed using maximum parsimony, in which each evolutionary event type is assigned a cost and the objective is to find a reconciliation of minimum total cost. It is generally understood that reconciliations are sensitive to event costs, but little is understood about the relationship between event costs and solutions. Moreover, choosing appropriate event costs is a notoriously difficult problem. Results: We address this problem by giving an efficient algorithm for computing Paretooptimal sets of reconciliations, thus providing the first systematic method for understanding the relationship between event costs and reconciliations. This, in turn, results in new techniques for computing event support values and, for cophylogenetic analyses, performing robust statistical tests. We provide new software tools and demonstrate their use on a number of datasets from evolutionary genomic and cophylogenetic studies. © 2014 The Author. Published by Oxford University Press. All rights reserved."





JohannMattis List,
Shijulal NelsonSathi,
Hans Geisler and
William Martin. Networks of lexical borrowing and lateral gene transfer in language and genome evolution. In BioEssays, Vol. 36(2):141150, 2014. Keywords: explicit network, minimal lateral network, phylogenetic network, Program lingpy. Note: http://dx.doi.org/10.1002/bies.201300096.
Toggle abstract
"Like biological species, languages change over time. As noted by Darwin, there are many parallels between language evolution and biological evolution. Insights into these parallels have also undergone change in the past 150 years. Just like genes, words change over time, and language evolution can be likened to genome evolution accordingly, but what kind of evolution? There are fundamental differences between eukaryotic and prokaryotic evolution. In the former, natural variation entails the gradual accumulation of minor mutations in alleles. In the latter, lateral gene transfer is an integral mechanism of natural variation. The study of language evolution using biological methods has attracted much interest of late, most approaches focusing on language tree construction. These approaches may underestimate the important role that borrowing plays in language evolution. Network approaches that were originally designed to study lateral gene transfer may provide more realistic insights into the complexities of language evolution. Editor's suggested further reading in BioEssays Linguistic evidence supports date for Homeric epics. © 2014 The Authors. BioEssays Published by WILEY Periodicals, Inc."



Yufeng Wu. An Algorithm for Constructing Parsimonious Hybridization Networks with Multiple Phylogenetic Trees. In RECOMB13, Vol. 7821:291303 of LNCS, springer, 2013. Keywords: explicit network, exponential algorithm, from rooted trees, phylogenetic network, phylogeny, Program PIRN, reconstruction. Note: http://www.engr.uconn.edu/~ywu/Papers/ExactNetRecomb2013.pdf.
Toggle abstract
"Phylogenetic network is a model for reticulate evolution. Hybridization network is one type of phylogenetic network for a set of discordant gene trees, and "displays" each gene tree. A central computational problem on hybridization networks is: given a set of gene trees, reconstruct the minimum (i.e. most parsimonious) hybridization network that displays each given gene tree. This problem is known to be NPhard, and existing approaches for this problem are either heuristics or make simplifying assumptions (e.g. work with only two input trees or assume some topological properties). In this paper, we develop an exact algorithm (called PIRNC ) for inferring the minimum hybridization networks from multiple gene trees. The PIRNC algorithm does not rely on structural assumptions. To the best of our knowledge, PIRN C is the first exact algorithm for this formulation. When the number of reticulation events is relatively small (say four or fewer), PIRNC runs reasonably efficient even for moderately large datasets. For building more complex networks, we also develop a heuristic version of PIRNC called PIRNCH. Simulation shows that PIRNCH usually produces networks with fewer reticulation events than those by an existing method. © 2013 SpringerVerlag."



Mukul S. Bansal,
Eric J. Alm and
Manolis Kellis. Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss. In RECOMB13, Vol. 7821:113 of LNCS, springer, 2013. Keywords: duplication, from rooted trees, from species tree, loss, phylogenetic network, phylogeny, polynomial, Program RANGERDTL, reconstruction. Note: http://people.csail.mit.edu/mukul/Bansal_RECOMB2013.pdf.
Toggle abstract
"Phylogenetic tree reconciliation is a powerful approach for inferring evolutionary events like gene duplication, horizontal gene transfer, and gene loss, which are fundamental to our understanding of molecular evolution. While DuplicationLoss (DL) reconciliation leads to a unique maximumparsimony solution, DuplicationTransferLoss (DTL) reconciliation yields a multitude of optimal solutions, making it difficult the infer the true evolutionary history of the gene family. Here, we present an effective, efficient, and scalable method for dealing with this fundamental problem in DTL reconciliation. Our approach works by sampling the space of optimal reconciliations uniformly at random and aggregating the results. We present an algorithm to efficiently sample the space of optimal reconciliations uniformly at random in O(mn 2) time, where m and n denote the number of genes and species, respectively. We use these samples to understand how different optimal reconciliations vary in their node mapping and event assignments, and to investigate the impact of varying event costs. © 2013 SpringerVerlag."



Hoa Vu,
Francis Chin,
WingKai Hon,
Henry Leung,
Kunihiko Sadakane,
WingKin Sung and
SiuMing Yiu. Reconstructing kReticulated Phylogenetic Network from a Set of Gene Trees. In ISBRA13, Vol. 7875:112124 of LNCS, springer, 2013. Keywords: from rooted trees, kreticulated, phylogenetic network, phylogeny, polynomial, Program ARTNET, Program CMPT, reconstruction. Note: http://grid.cs.gsu.edu/~xguo9/publications/2013_Cloud%20computing%20for%20de%20novo%20metagenomic%20sequence%20assembly.pdf#page=123.
Toggle abstract
"The time complexity of existing algorithms for reconstructing a levelx phylogenetic network increases exponentially in x. In this paper, we propose a new classification of phylogenetic networks called kreticulated network. A kreticulated network can model all levelk networks and some levelx networks with x > k. We design algorithms for reconstructing kreticulated network (k = 1 or 2) with minimum number of hybrid nodes from a set of m binary trees, each with n leaves in O(mn 2) time. The implication is that some levelx networks with x > k can now be reconstructed in a faster way. We implemented our algorithm (ARTNET) and compared it with CMPT. We show that ARTNET outperforms CMPT in terms of running time and accuracy. We also consider the case when there does not exist a 2reticulated network for the input trees. We present an algorithm computing a maximum subset of the species set so that a new set of subtrees can be combined into a 2reticulated network. © 2013 SpringerVerlag."



Mukul S. Bansal,
Guy Banay,
Timothy J. Harlow,
J. Peter Gogarten and
Ron Shamir. Systematic inference of highways of horizontal gene transfer in prokaryotes. In BIO, Vol. 29(5):571579, 2013. Keywords: duplication, explicit network, from species tree, from unrooted trees, lateral gene transfer, phylogenetic network, phylogeny, Program HiDe, Program RANGERDTL, reconstruction. Note: http://people.csail.mit.edu/mukul/Bansal_Highways_Bioinformatics_2013.pdf.









Hyun Jung Park and
Luay Nakhleh. MURPAR: A fast heuristic for inferring parsimonious phylogenetic networks from multiple gene trees. In ISBRA12, Vol. 7292:213224 of LNCS, springer, 2012. Keywords: explicit network, heuristic, phylogenetic network, phylogeny, reconstruction, software.
Toggle abstract
"Phylogenetic networks provide a graphical representation of evolutionary histories that involve nontreelike evolutionary events, such as horizontal gene transfer (HGT). One approach for inferring phylogenetic networks is based on reconciling gene trees, assuming all incongruence among the gene trees is due to HGT. Several mathematical results and algorithms, both exact and heuristic, have been introduced to construct and analyze phylogenetic networks. Here, we address the computational problem of inferring phylogenetic networks with minimum reticulations from a collection of gene trees. As this problem is known to be NPhard even for a pair of gene trees, the problem at hand is very hard. In this paper, we present an efficient heuristic, MURPAR, for inferring a phylogenetic network from a collection of gene trees by using pairwise reconciliations of trees in the collection. Given the development of efficient and accurate methods for pairwise gene tree reconciliations, MURPAR inherits this efficiency and accuracy. Further, the method includes a formulation for combining pairwise reconciliations that is naturally amenable to an efficient integer linear programming (ILP) solution. We show that MURPAR produces more accurate results than other methods and is at least as fast, when run on synthetic and biological data. We believe that our method is especially important for rapidly obtaining estimates of genomescale evolutionary histories that can be further refined by more detailed and computeintensive methods. © 2012 SpringerVerlag."



Pawel Górecki and
Jerzy Tiuryn. Inferring evolutionary scenarios in the duplication, loss and horizontal gene transfer model. In Logic and Program Semantics, Vol. 7230:83105 of LNCS, springer, 2012. Keywords: duplication, explicit network, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction. Note: http://dx.doi.org/10.1007/9783642294853_7.
Toggle abstract
"An Htree is a formal model of evolutionary scenario. It can be used to represent any processes with gene duplication and loss, horizontal gene transfer (HGT) and speciation events. The model of Htrees, introduced in [26], is an extension of the duplicationloss model (DLmodel). Similarly to its ancestor, it has a number of interesting mathematical and biological properties. It is, however, more computationally complex than the DLmodel. In this paper, we primarily address the problem of inferring Htrees that are compatible with a given gene tree and a given phylogeny of species with HGTs. These results create a mathematical and computational foundation for a more general and practical problem of inferring HGTs from given gene and species trees with HGTs. We also demonstrate how our model can be used to support HGT hypotheses based on empirical data sets. © 2012 SpringerVerlag Berlin Heidelberg."



Mukul S. Bansal,
Eric J. Alm and
Manolis Kellis. Efficient Algorithms for the Reconciliation Problem with Gene Duplication, Horizontal Transfer, and Loss. In ISMB12, Vol. 28(12):i283i291 of BIO, 2012. Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program Angst, Program Mowgli, Program RANGERDTL, reconstruction. Note: http://dx.doi.org/10.1093/bioinformatics/bts225.
Toggle abstract
"Motivation: Gene family evolution is driven by evolutionary events such as speciation, gene duplication, horizontal gene transfer and gene loss, and inferring these events in the evolutionary history of a given gene family is a fundamental problem in comparative and evolutionary genomics with numerous important applications. Solving this problem requires the use of a reconciliation framework, where the input consists of a gene family phylogeny and the corresponding species phylogeny, and the goal is to reconcile the two by postulating speciation, gene duplication, horizontal gene transfer and gene loss events. This reconciliation problem is referred to as duplicationtransferloss (DTL) reconciliation and has been extensively studied in the literature. Yet, even the fastest existing algorithms for DTL reconciliation are too slow for reconciling large gene families and for use in more sophisticated applications such as gene tree or species tree reconstruction.Results: We present two new algorithms for the DTL reconciliation problem that are dramatically faster than existing algorithms, both asymptotically and in practice. We also extend the standard DTL reconciliation model by considering distancedependent transfer costs, which allow for more accurate reconciliation and give an efficient algorithm for DTL reconciliation under this extended model. We implemented our new algorithms and demonstrated up to 100 000fold speedup over existing methods, using both simulated and biological datasets. This dramatic improvement makes it possible to use DTL reconciliation for performing rigorous evolutionary analyses of large gene families and enables its use in advanced reconciliationbased gene and species tree reconstruction methods. © The Author(s) 2012. Published by Oxford University Press."



AnChiang Chu,
Jesper Jansson,
Richard Lemence,
Alban Mancheron and
KunMao Chao. Asymptotic Limits of a New Type of Maximization Recurrence with an Application to Bioinformatics. In TAMC12, Vol. 7287:177188 of LNCS, springer, 2012. Keywords: from triplets, galled network, level k phylogenetic network, phylogenetic network. Note: preliminary version.
Toggle abstract
"We study the asymptotic behavior of a new type of maximization recurrence, defined as follows. Let k be a positive integer and p k(x) a polynomial of degree k satisfying p k(0) = 0. Define A 0 = 0 and for n ≥ 1, let A n = max 0≤i<n{A i+n kp k(i/n)}. We prove that lim n→∞A n/n n = sup{pk(x)/1x k : 0≤x<1}. We also consider two closely related maximization recurrences S n and S′ n, defined as S 0 = S′ 0 = 0, and for n ≥ 1, S n = max 0≤i<n{S i + i(ni)(ni1)/2} and S′ n = max 0≤i<n{S′ i + ( 3 ni) + 2i( 2 ni) + (ni)( 2 i)}. We prove that lim n→∞ S′n/3( 3 n) = 2(√31)/3 ≈ 0.488033..., resolving an open problem from Bioinformatics about rooted triplets consistency in phylogenetic networks. © 2012 SpringerVerlag."



Jesper Jansson and
Andrzej Lingas. Computing the rooted triplet distance between galled trees by counting triangles. In CPM12, Vol. 7354:385398 of LNCS, springer, 2012. Keywords: distance between networks, explicit network, from network, galled tree, phylogenetic network, phylogeny, polynomial, triplet distance. Note: http://www.df.lth.se/~jj/Publications/d_rt_for_Galled_Trees5_CPM_2012.pdf.
Toggle abstract
"We consider a generalization of the rooted triplet distance between two phylogenetic trees to two phylogenetic networks. We show that if each of the two given phylogenetic networks is a socalled galled tree with n leaves then the rooted triplet distance can be computed in o(n 2.688) time. Our upper bound is obtained by reducing the problem of computing the rooted triplet distance to that of counting monochromatic and almost monochromatic triangles in an undirected, edgecolored graph. To count different types of colored triangles in a graph efficiently, we extend an existing technique based on matrix multiplication and obtain several new related results that may be of independent interest. © 2012 SpringerVerlag."



Leo van Iersel,
Steven Kelk,
Nela Lekic and
Celine Scornavacca. A practical approximation algorithm for solving massive instances of hybridization number. In WABI12, Vol. 7534(430440) of LNCS, springer, 2012. Keywords: agreement forest, approximation, explicit network, from rooted trees, hybridization, phylogenetic network, phylogeny, Program CycleKiller, Program Dendroscope, Program HybridNET, reconstruction, software. Note: http://arxiv.org/abs/1205.3417.
Toggle abstract
"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. In practice, exact solvers struggle to solve instances with reticulation number larger than 40. For such instances, one has to resort to heuristics and approximation algorithms. Here we present the algorithm CycleKiller which is the first approximation algorithm that can produce solutions verifiably close to optimality for instances with hundreds or even thousands of reticulations. Theoretically, the algorithm is an exponentialtime 2approximation (or 4approximation in its fastest mode). However, using simulations we demonstrate that in practice the algorithm runs quickly for large and difficult instances, producing solutions within one percent of optimality. An implementation of this algorithm, which extends the theoretical work of [14], has been made publicly available. © 2012 SpringerVerlag."



Hyun Jung Park and
Luay Nakhleh. Inference of reticulate evolutionary histories by maximum likelihood:
The performance of information criteria. In RECOMBCG'12, Vol. 13(suppl 19):S12 of BMCB, 2012. Keywords: AIC, BIC, explicit network, heuristic, likelihood, phylogenetic network, phylogeny, reconstruction, statistical model. Note: http://www.biomedcentral.com/14712105/13/S19/S12.



Maureen Stolzer,
Han Lai,
Minli Xu,
Deepa Sathaye,
Benjamin Vernot and
Dannie Durand. Inferring Duplications, Losses, Transfers, and Incomplete Lineage Sorting with NonBinary Species Trees. In ECCB12, Vol. 28(18):i409i415 of BIO, 2012. Keywords: duplication, explicit network, from rooted trees, lateral gene transfer, loss, phylogenetic network, phylogeny, Program Notung, reconstruction. Note: http://dx.doi.org/10.1093/bioinformatics/bts386.
Toggle abstract
"Motivation: Gene duplication (D), transfer (T), loss (L) and incomplete lineage sorting (I) are crucial to the evolution of gene families and the emergence of novel functions.The history of these events can be inferred via comparison of gene and species trees, a process called reconciliation, yet current reconciliation algorithms model only a subset of these evolutionary processes. Results: We present an algorithm to reconcile a binary gene tree with a nonbinary species tree under a DTLI parsimony criterion. This is the first reconciliation algorithm to capture all four evolutionary processes driving tree incongruence and the first to reconcile nonbinary species trees with a transfer model. Our algorithm infers all optimal solutions and reports complete, temporally feasible event histories, giving the gene and species lineages in which each event occurred. It is fixedparameter tractable, with polytime complexity when the maximum species outdegree is fixed. Application of our algorithms to prokaryotic and eukaryotic data show that use of an incomplete event model has substantial impact on the events inferred and resulting biological conclusions. © The Author(s) 2012. Published by Oxford University Press."



ThiHau Nguyen,
JeanPhilippe Doyon,
Stéphanie Pointet,
AnneMuriel Chifolleau Arigon,
Vincent Ranwez and
Vincent Berry. Accounting for Gene Tree Uncertainties Improves Gene Trees and Reconciliation Inference. In WABI12, Vol. 7534:123134 of LNCS, springer, 2012. Keywords: duplication, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program Mowgli, reconstruction. Note: http://hal.archivesouvertes.fr/hal00718347/en/.
Toggle abstract
"We propose a reconciliation heuristic accounting for gene duplications, losses and horizontal transfers that specifically takes into account the uncertainties in the gene tree. Rearrangements are tried for gene tree edges that are weakly supported, and are accepted whenever they improve the reconciliation cost. We prove useful properties on the dynamic programming matrix used to compute reconciliations, which allows to speedup the tree space exploration when rearrangements are generated by Nearest Neighbor Interchanges (NNI) edit operations. Experimental results on simulated and real data confirm that running times are greatly reduced when considering the abovementioned optimization in comparison to the naïve rearrangement procedure. Results also show that gene trees modified by such NNI rearrangements are closer to the correct (simulated) trees and lead to more correct event predictions on average. The program is available at http://www.atgcmontpellier.fr/ Mowgli/. © 2012 SpringerVerlag."



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.
Toggle abstract
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.



Cayla McBee. Generalizing Fourier Calculus on Evolutionary Trees to Splits Networks. In ISPAN'12, Pages 149155, 2012. Keywords: abstract network, from sequences, phylogenetic network, phylogeny, split network, statistical model.
Toggle abstract
"Biologists have been interested in Phylogenetics, the study of evolutionary relatedness among various groups of organisms, for more than 140 years. In spite of this, it has only been in the last 40 years that advances in technology and the availability of DNA sequences have led to statistical, computational and algorithmic work on determining evolutionary relatedness between organisms. One method of determining historical relationships between organisms is to assume a group based evolutionary model and use a discrete Fourier transform. The 1993 paper 'Fourier Calculus on Evolutionary Trees' by L.A. Szekely, M.A. Steel and P.L. Erdos outlines this process. The transform presented in Szekely et al provides an invertible relationship between phylogenetic trees and expected frequencies of nucleotide patterns in nucleotide sequences. This implies that given a set of nucleotide sequences from various organisms it is possible to construct a phylogenetic tree that represents the historical relationships of those organisms. Some scenarios are poorly described by phylogenetic trees and there are biological and statistical reasons for using networks to model phylogenetic relationships. Given this motivation I have generalized Szekely et al's result to apply to a specific type of phylogenetic network known as a splits network. © 2012 IEEE."



Fenglou Mao,
David Williams,
Olga Zhaxybayeva,
Maria S. Poptsova,
Pascal Lapierre,
J. Peter Gogarten and
Ying Xu. Quartet decomposition server: a platform for analyzing phylogenetic trees. In BMCB, Vol. 13:123, 2012. Keywords: abstract network, from quartets, phylogenetic network, phylogeny, Program Quartet Decomposition, reconstruction, software, split network.
Toggle abstract
"Background: The frequent exchange of genetic material among prokaryotes means that extracting a majority or plurality phylogenetic signal from many gene families, and the identification of gene families that are in significant conflict with the plurality signal is a frequent task in comparative genomics, and especially in phylogenomic analyses. Decomposition of gene trees into embedded quartets (unrooted trees each with four taxa) is a convenient and statistically powerful technique to address this challenging problem. This approach was shown to be useful in several studies of completely sequenced microbial genomes.Results: We present here a web server that takes a collection of gene phylogenies, decomposes them into quartets, generates a Quartet Spectrum, and draws a split network. Users are also provided with various data download options for further analyses. Each gene phylogeny is to be represented by an assessment of phylogenetic information content, such as sets of trees reconstructed from bootstrap replicates or sampled from a posterior distribution. The Quartet Decomposition server is accessible at http://quartets.uga.edu.Conclusions: The Quartet Decomposition server presented here provides a convenient means to perform Quartet Decomposition analyses and will empower users to find statistically supported phylogenetic conflicts. © 2012 Mao et al.; licensee BioMed Central Ltd."



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.
Toggle abstract
"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."



JeanPhilippe Doyon,
Celine Scornavacca,
Konstantin Yu Gorbunov,
Gergely J. Szöllösi,
Vincent Ranwez and
Vincent Berry. An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications, and transfers. In Proceedings of the Eighth RECOMB Comparative Genomics Satellite Workshop (RECOMBCG'10), Vol. 6398:93108 of LNCS, springer, 2011. Keywords: branch length, duplication, dynamic programming, explicit network, from multilabeled tree, from species tree, from unrooted trees, lateral gene transfer, loss, phylogenetic network, phylogeny, polynomial, Program Mowgli, reconstruction. Note: http://www.lirmm.fr/~vberry/Publis/MPRDoyonEtAl.pdf, software available at http://www.atgcmontpellier.fr/MPR/.
Toggle abstract
"Tree reconciliation methods aim at estimating the evolutionary events that cause discrepancy between gene trees and species trees. We provide a discrete computational model that considers duplications, transfers and losses of genes. The model yields a fast and exact algorithm to infer time consistent and most parsimonious reconciliations. Then we study the conditions under which parsimony is able to accurately infer such events. Overall, it performs well even under realistic rates, transfers being in general less accurately recovered than duplications. An implementation is freely available at http://www.atgc montpellier.fr/MPR. © 2010 SpringerVerlag."



Mukul S. Bansal,
J. Peter Gogarten and
Ron Shamir. Detecting Highways of Horizontal Gene Transfer. In Proceedings of the Eighth RECOMB Comparative Genomics Satellite Workshop (RECOMBCG'10), Vol. 6398:109120 of LNCS, springer, 2011. Keywords: explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, polynomial, reconstruction. Note: http://www.cs.iastate.edu/~bansal/Highways_RCG10.pdf.
Toggle abstract
"In a horizontal gene transfer (HGT) event a gene is transferred between two species that do not share 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, our method requires O(n 4) time, 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. © 2010 SpringerVerlag."



Yun Yu,
Cuong Than,
James H. Degnan and
Luay Nakhleh. Coalescent Histories on Phylogenetic Networks and Detection of Hybridization Despite Incomplete Lineage Sorting. In Systematic Biology, Vol. 60(2):138149, 2011. Keywords: coalescent, hybridization, lineage sorting, reconstruction, statistical model. Note: http://www.cs.rice.edu/~nakhleh/Papers/YuEtAlSB11.pdf.
Toggle abstract
"Analyses of the increasingly available genomic data continue to reveal the extent of hybridization and its role in the evolutionary diversification of various groups of species. We show, through extensive coalescentbased simulations of multilocus data sets on phylogenetic networks, how divergence times before and after hybridization events can result in incomplete lineage sorting with gene tree incongruence signatures identical to those exhibited by hybridization. Evolutionary analysis of such data under the assumption of a species tree model can miss all hybridization events, whereas analysis under the assumption of a species network model would grossly overestimate hybridization events. These issues necessitate a paradigm shift in evolutionary analysis under these scenarios, from a model that assumes a priori a single source of gene tree incongruence to one that integrates multiple sources in a unifying framework. We propose a framework of coalescence within the branches of a phylogenetic network and show how this framework can be used to detect hybridization despite incomplete lineage sorting. We apply the model to simulated data and show that the signature of hybridization can be revealed as long as the interval between the divergence times of the species involved in hybridization is not too small. We reanalyze a data set of 106 loci from 7 ingroup Saccharomyces species for which a species tree with no hybridization has been reported in the literature. Our analysis supports the hypothesis that hybridization occurred during the evolution of this group, explaining a large amount of the incongruence in the data. Our findings show that an integrative approach to gene tree incongruence and its reconciliation is needed. Our framework will help in systematically analyzing genomic data for the occurrence of hybridization and elucidating its evolutionary role. [Coalescent history; incomplete lineage sorting; hybridization; phylogenetic network.]. © 2011 The Author(s)."



Celine Scornavacca,
Franziska Zickmann and
Daniel H. Huson. Tanglegrams for Rooted Phylogenetic Trees and Networks. In ISMB11, Vol. 27(13):i248i256 of BIO, 2011. Keywords: from network, heuristic, phylogenetic network, phylogeny, Program Dendroscope, tanglegram, visualization. Note: http://dx.doi.org/10.1093/bioinformatics/btr210.
Toggle abstract
"Motivation: In systematic biology, one is often faced with the task of comparing different phylogenetic trees, in particular in multigene analysis or cospeciation studies. One approach is to use a tanglegram in which two rooted phylogenetic trees are drawn opposite each other, using auxiliary lines to connect matching taxa. There is an increasing interest in using rooted phylogenetic networks to represent evolutionary history, so as to explicitly represent reticulate events, such as horizontal gene transfer, hybridization or reassortment. Thus, the question arises how to define and compute a tanglegram for such networks. Results: In this article, we present the first formal definition of a tanglegram for rooted phylogenetic networks and present a heuristic approach for computing one, called the NNtanglegram method. We compare the performance of our method with existing tree tanglegram algorithms and also show a typical application to real biological datasets. For maximum usability, the algorithm does not require that the trees or networks are bifurcating or bicombining, or that they are on identical taxon sets. © The Author(s) 2011. Published by Oxford University Press."



Changiz Eslahchi and
Reza Hassanzadeh. New Algorithm for Constructing Supernetworks from Partial Trees. In MCCMB11, Pages 106107, 2011. Keywords: abstract network, from unrooted trees, heuristic, phylogenetic network, phylogeny, Program SNSA, reconstruction, simulated annealing, split network. Note: http://mccmb.belozersky.msu.ru/2011/mccmb11.pdf#page=106.



Louxin Zhang,
Yen Kaow Ng,
Taoyang Wu and
Yu Zheng. Network model and efficient method for detecting relative duplications or horizontal gene transfers. In ICCABS11, Pages 214219, 2011. Keywords: dynamic programming, explicit network, from network, from rooted trees, from species tree, phylogenetic network, phylogeny, polynomial, reconstruction.
Toggle abstract
"Background: Horizontal gene transfer and gene duplication are two significant forces behind genome evolution. As more and more wellsupported examples of HGTs are being revealed, there is a growing awareness that HGT is more widespread than previously thought, occurring often not only within bacteria, but also between species remotely related such as bacteria and plants or plants and animals. Although a substantial number of genomic sequences are known, HGT inference remains challenging. Parsimonybased inferences of HGT events are typically NPhard under the framework of gene tree and species tree comparison; it is even more timeconsuming if the maximum likelihood approach is used. The fact that gene tree and species tree incongruence can be further confounded by gene duplication and gene loss events motivates us to incorporate considerations for these events into our inference of HGT events. Similarly, it will be beneficial if known HGT events are considered in the inference of gene duplications and gene losses. © 2011 IEEE."



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.
Toggle abstract
"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."



Leo van Iersel,
Steven Kelk,
Regula Rupp and
Daniel H. Huson. Phylogenetic Networks Do not Need to Be Complex: Using Fewer Reticulations to Represent Conflicting Clusters. In ISMB10, Vol. 26(12):i124i131 of BIO, 2010. Keywords: from clusters, level k phylogenetic network, Program Dendroscope, Program HybridInterleave, Program HybridNumber, reconstruction. Note: http://dx.doi.org/10.1093/bioinformatics/btq202, with proofs: http://arxiv.org/abs/0910.3082.
Toggle abstract
"Phylogenetic trees are widely used to display estimates of how groups of species are evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees are obtained for several datasets (e.g. for different genes), then their clusters are often contradicting. Consequently, the set of all clusters of such a dataset cannot be combined into a single phylogenetic tree. Phylogenetic networks are a generalization of phylogenetic trees that can be used to display more complex evolutionary histories, including reticulate events, such as hybridizations, recombinations and horizontal gene transfers. Here, we present the new CASS algorithm that can combine any set of clusters into a phylogenetic network. We show that the networks constructed by CASS are usually simpler than networks constructed by other available methods. Moreover, we show that CASS is guaranteed to produce a network with at most two reticulations per biconnected component, whenever such a network exists. We have implemented CASS and integrated it into the freely available Dendroscope software. Contact: l.j.j.v.iersel@gmail.com. Supplementary information: Supplementary data are available at Bioinformatics online. © The Author(s) 2010. Published by Oxford University Press."



Tetsuo Asano,
Jesper Jansson,
Kunihiko Sadakane,
Ryuhei Uehara and
Gabriel Valiente. Faster Computation of the RobinsonFoulds Distance between Phylogenetic Networks. In CPM10, Vol. 6129:190201 of LNCS, springer, 2010. Keywords: distance between networks, explicit network, level k phylogenetic network, phylogenetic network, polynomial, spread. Note: http://hdl.handle.net/10119/9859, slides available at http://cs.nyu.edu/parida/CPM2010/MainPage_files/18.pdf.
Toggle abstract
"The RobinsonFoulds distance, which is the most widely used metric for comparing phylogenetic trees, has recently been generalized to phylogenetic networks. Given two networks N1,N2 with n leaves, m nodes, and e edges, the RobinsonFoulds distance measures the number of clusters of descendant leaves that are not shared by N1 and N2. The fastest known algorithm for computing the RobinsonFoulds distance between those networks runs in O(m(m + e)) time. In this paper, we improve the time complexity to O(n(m+ e)/ log n) for general networks and O(nm/log n) for general networks with bounded degree, and to optimal O(m + e) time for planar phylogenetic networks and boundedlevel phylogenetic networks.We also introduce the natural concept of the minimum spread of a phylogenetic network and show how the running time of our new algorithm depends on this parameter. As an example, we prove that the minimum spread of a levelk phylogenetic network is at most k + 1, which implies that for two levelk phylogenetic networks, our algorithm runs in O((k + 1)(m + e)) time. © SpringerVerlag Berlin Heidelberg 2010."



Yufeng Wu. Close Lower and Upper Bounds for the Minimum Reticulate Network of Multiple Phylogenetic Trees. In ISMB10, Vol. 26(12):i140i148 of BIO, 2010. Keywords: explicit network, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program PIRN, software. Note: http://dx.doi.org/10.1093/bioinformatics/btq198.
Toggle abstract
"Motivation: Reticulate network is a model for displaying and quantifying the effects of complex reticulate processes on the evolutionary history of species undergoing reticulate evolution. A central computational problem on reticulate networks is: given a set of phylogenetic trees (each for some region of the genomes), reconstruct the most parsimonious reticulate network (called the minimum reticulate network) that combines the topological information contained in the given trees. This problem is wellknown to be NPhard. Thus, existing approaches for this problem either work with only two input trees or make simplifying topological assumptions. Results: We present novel results on the minimum reticulate network problem. Unlike existing approaches, we address the fully general problem: there is no restriction on the number of trees that are input, and there is no restriction on the form of the allowed reticulate network. We present lower and upper bounds on the minimum number of reticulation events in the minimum reticulate network (and infer an approximately parsimonious reticulate network). A program called PIRN implements these methods, which also outputs a graphical representation of the inferred network. Empirical results on simulated and biological data show that our methods are practical for a wide range of data. More importantly, the lower and upper bounds match for many datasets (especially when the number of trees is small or reticulation level is low), and this allows us to solve the minimum reticulate network problem exactly for these datasets. Availability: A software tool, PIRN, is available for download from the web page: http://www.engr.uconn.edu/ywu. Contact: ywu@engr.uconn.edu. Supplementary information: Supplementary data is available at Bioinformatics online. © The Author(s) 2010. Published by Oxford University Press."



Yufeng Wu and
Jiayin Wang. Fast Computation of the Exact Hybridization Number of Two Phylogenetic Trees. In ISBRA10, Vol. 6053:203214 of LNCS, springer, 2010. Keywords: agreement forest, explicit network, from rooted trees, hybridization, integer linear programming, minimum number, phylogenetic network, phylogeny, Program HybridNumber, Program SPRDist, SPR distance. Note: http://www.engr.uconn.edu/~ywu/Papers/ISBRA10WuWang.pdf.
Toggle abstract
"Hybridization is a reticulate evolutionary process. An established problem on hybridization is computing the minimum number of hybridization events, called the hybridization number, needed in the evolutionary history of two phylogenetic trees. This problem is known to be NPhard. In this paper, we present a new practical method to compute the exact hybridization number. Our approach is based on an integer linear programming formulation. Simulation results on biological and simulated datasets show that our method (as implemented in program SPRDist) is more efficient and robust than an existing method. © 2010 SpringerVerlag Berlin Heidelberg."



David A. Morrison. Phylogenetic networks in systematic biology (and elsewhere) In
R.M. Mohan editor, Research Advances in Systematic Biology, Global Research Network, Trivandrum, India, 2010. Keywords: abstract network, explicit network, phylogenetic network, phylogeny, reconstruction, survey.



Chris Whidden,
Robert G. Beiko and
Norbert Zeh. Fast FPT Algorithms for Computing Rooted Agreement Forests: Theory and Experiments. In Proceedings of the ninth International Symposium on Experimental Algorithms (SEA'10), Vol. 6049:141153 of LNCS, springer, 2010. Keywords: agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, SPR distance. Note: https://www.cs.dal.ca/sites/default/files/technical_reports/CS201003.pdf.
Toggle abstract
"We improve on earlier FPT algorithms for computing a rooted maximum agreement forest (MAF) or a maximum acyclic agreement forest (MAAF) of a pair of phylogenetic trees. Their sizes give the subtreepruneandregraft (SPR) distance and the hybridization number of the trees, respectively. We introduce new branching rules that reduce the running time of the algorithms from O(3 kn) and O(3 kn log n) to O(2.42 kn) and O(2.42 kn log n), respectively. In practice, the speed up may be much more than predicted by the worstcase analysis.We confirm this intuition experimentally by computing MAFs for simulated trees and trees inferred from protein sequence data. We show that our algorithm is orders of magnitude faster and can handle much larger trees and SPR distances than the best previous methods, treeSAT and sprdist. © SpringerVerlag Berlin Heidelberg 2010."





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.



Luay Nakhleh,
Derek Ruths and
Hideki Innan. Gene Trees, Species Trees, and Species Networks. In
R. Guerra,
D. B. Allison and
D. Goldstein editors, Metaanalysis and Combining Information in Genetics and Genomics, 2009. Keywords: coalescent, explicit network, from rooted trees, from species tree, phylogenetic network, phylogeny, reconstruction. Note: http://www.cs.rice.edu/~nakhleh/Papers/GuerraGoldsteinBookChapter.pdf.



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



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



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.



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.
Toggle abstract
"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."





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



Leo van Iersel,
Judith Keijsper,
Steven Kelk,
Leen Stougie,
Ferry Hagen and
Teun Boekhout. Constructing level2 phylogenetic networks from triplets. In RECOMB08, Vol. 4955:450462 of LNCS, springer, 2008. Keywords: explicit network, from triplets, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, polynomial, Program Level2, reconstruction. Note: http://homepages.cwi.nl/~iersel/level2full.pdf. An appendix with proofs can be found here http://arxiv.org/abs/0707.2890.
Toggle abstract
"Jansson and Sung showed that, given a dense set of input triplets T (representing hypotheses about the local evolutionary relationships of triplets of taxa), it is possible to determine in polynomial time whether there exists a level1 network consistent with T, and if so, to construct such a network [24]. Here, we extend this work by showing that this problem is even polynomial time solvable for the construction of level2 networks. This shows that, assuming density, it is tractable to construct plausible evolutionary histories from input triplets even when such histories are heavily nontreelike. This further strengthens the case for the use of tripletbased methods in the construction of phylogenetic networks. We also implemented the algorithm and applied it to yeast data. © 2009 IEEE."



Leo van Iersel and
Steven Kelk. Constructing the Simplest Possible Phylogenetic Network from Triplets. In ISAAC08, Vol. 5369:472483 of LNCS, springer, 2008. Keywords: explicit network, from triplets, galled tree, level k phylogenetic network, minimum number, phylogenetic network, phylogeny, polynomial, Program Marlon, Program Simplistic. Note: http://arxiv.org/abs/0805.1859.





Cuong Than and
Luay Nakhleh. SPRbased Tree Reconciliation: Nonbinary Trees and Multiple Solutions. In APBC08, Pages 251260, 2008. Keywords: evaluation, from rooted trees, lateral gene transfer, phylogenetic network, phylogeny, Program LatTrans, Program PhyloNet, reconstruction, SPR distance. Note: http://www.cs.rice.edu/~nakhleh/Papers/apbc08.pdf.



Daniel H. Huson and
Regula Rupp. Summarizing Multiple Gene Trees Using Cluster Networks. In WABI08, Vol. 5251:296305 of LNCS, springer, 2008. Keywords: abstract network, from clusters, from rooted trees, phylogenetic network, phylogeny, polynomial, Program Dendroscope. Note: http://dx.doi.org/10.1007/9783540873617_25, slides from the MIEP Conference available at http://www.lirmm.fr/MIEP08/slides/11_13_rupp.pdf.
Toggle abstract
"The result of a multiple gene tree analysis is usually a number of different tree topologies that are each supported by a significant proportion of the genes. We introduce the concept of a cluster network that can be used to combine such trees into a single rooted network, which can be drawn either as a cladogram or phylogram. In contrast to split networks, which can grow exponentially in the size of the input, cluster networks grow only quadratically. A cluster network is easily computed using a modification of the treepopping algorithm, which we call networkpopping. The approach has been implemented as part of the Dendroscope treedrawing program and its application is illustrated using data and results from three recent studies on large numbers of gene trees. © 2008 SpringerVerlag Berlin Heidelberg."



Lichen Bao and
Sergey Bereg. Clustered SplitsNetworks. In COCOA08, Vol. 5165:469478 of LNCS, springer, 2008. Keywords: abstract network, from distances, NeighborNet, realization, reconstruction. Note: http://dx.doi.org/10.1007/9783540850977_44, slides available at http://www.utdallas.edu/~besp/cocoa08talk.pdf.
Toggle abstract
"We address the problem of constructing phylogenetic networks using two criteria: the number of cycles and the fit value of the network. Traditionally the fit value is the main objective for evaluating phylogenetic networks. However, a small number of cycles in a network is desired and pointed out in several publications. We propose a new phylogenetic network called CSnetwork and a method for constructing it. The method is based on the wellknown splitstree method. A CSnetwork contains a face which is kcycle, k ≥ 3 (not as splitstree). We discuss difficulties of using nonparallelogram faces in splitstree networks. Our method involves clustering and optimization of weights of the network edges. The algorithm for constructing the underlying graph (except the optimization step) has a polynomial time. Experimental results show a good performance of our algorithm. © SpringerVerlag Berlin Heidelberg 2008."





Sagi Snir and
Tamir Tuller. Novel Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. In WABI08, Vol. 5251:354368 of LNCS, springer, 2008. Keywords: explicit network, from sequences, HMM, lateral gene transfer, likelihood, phylogenetic network, phylogeny, statistical model. Note: http://dx.doi.org/10.1007/9783540873617_30.
Toggle abstract
"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 for analyzing and modeling phylogenetic networks, the NETHMM. 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 data set. 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 two different biological inputs. © 2008 SpringerVerlag Berlin Heidelberg."



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.
Toggle abstract
"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."



Gabriel Cardona,
Mercè Llabrés,
Francesc Rosselló and
Gabriel Valiente. Phylogenetic Networks: Justification, Models, Distances and Algorithms. In VI Jornadas de Matemática Discreta y Algorítmica (JMDA'08), 2008. Keywords: distance between networks, mu distance, phylogenetic network, phylogeny, polynomial, survey, time consistent network, tree child network, tripartition distance, triplet distance. Note: http://bioinfo.uib.es/media/uploaded/jmda2008_submission_611.pdf.



Ernst Althaus and
Rouven Naujoks. Reconstructing Phylogenetic Networks with One Recombination. In Proceedings of the seventh International Workshop on Experimental Algorithms (WEA'08), Vol. 5038:275288 of LNCS, springer, 2008. Keywords: enumeration, explicit network, exponential algorithm, from sequences, generation, parsimony, phylogenetic network, phylogeny, reconstruction, unicyclic network. Note: http://dx.doi.org/10.1007/9783540685524_21.
Toggle abstract
"In this paper we propose a new method for reconstructing phylogenetic networks under the assumption that recombination events have occurred rarely. For a fixed number of recombinations, we give a generalization of the maximum parsimony criterion. Furthermore, we describe an exact algorithm for one recombination event and show that in this case our method is not only able to identify the recombined sequence but also to reliably reconstruct the complete evolutionary history. © 2008 SpringerVerlag Berlin Heidelberg."



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.
Toggle abstract
"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."



Miguel Arenas and
David Posada. Recodon: Coalescent simulation of coding DNA sequences with recombination, migration and demography. In BMCB, Vol. 8(458), 2008. Keywords: coalescent, generation, Program Recodon, software. Note: http://dx.doi.org/10.1186/147121058458.
Toggle abstract
"Background: Coalescent simulations have proven very useful in many population genetics studies. In order to arrive to meaningful conclusions, it is important that these simulations resemble the process of molecular evolution as much as possible. To date, no single coalescent program is able to simulate codon sequences sampled from populations with recombination, migration and growth. Results: We introduce a new coalescent program, called Recodon, which is able to simulate samples of coding DNA sequences under complex scenarios in which several evolutionary forces can interact simultaneously (namely, recombination, migration and demography). The basic codon model implemented is an extension to the general timereversible model of nucleotide substitution with a proportion of invariable sites and amongsite rate variation. In addition, the program implements nonreversible processes and mixtures of different codon models. Conclusion: Recodon is a flexible tool for the simulation of coding DNA sequences under realistic evolutionary models. These simulations can be used to build parameter distributions for testing evolutionary hypotheses using experimental data. Recodon is written in C, can run in parallel, and is freely available from http://darwin.uvigo.es/. © 2007 Arenas and Posada; licensee BioMed Central Ltd."



Cuong Than,
Guohua Jin and
Luay Nakhleh. Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer. In Proceedings of the Sixth RECOMB Comparative Genomics Satellite Workshop (RECOMBCG'08), Vol. 5267:113127 of LNCS, springer, 2008. Keywords: bootstrap, explicit network, from rooted trees, from sequences, lateral gene transfer, phylogenetic network, phylogeny, Program Nepal, Program PhyloNet, reconstruction. Note: http://www.cs.rice.edu/~nakhleh/Papers/recombcg08.pdf, slides available at http://igm.univmlv.fr/RCG08/RCG08slides/Cuong_Than_RCG08.pdf.



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.
Toggle abstract
"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."



Daniel H. Huson. Split networks and Reticulate Networks. In
Olivier Gascuel and
Mike Steel editors, Reconstructing Evolution, New Mathematical and Computational Advances, Pages 247276, Oxford University Press, 2007. Keywords: abstract network, consensus, from rooted trees, from sequences, from splits, from unrooted trees, galled tree, hybridization, phylogenetic network, phylogeny, Program Beagle, Program Spectronet, Program SplitsTree, Program SPNet, recombination, reconstruction, split network, survey. Note: similar to http://wwwab.informatik.unituebingen.de/research/phylonets/GCB2006.pdf.



Daniel H. Huson and
Tobias Kloepper. Beyond Galled Trees  Decomposition and Computation of Galled Networks. In RECOMB07, Vol. 4453:211225 of LNCS, springer, 2007. Keywords: FPT, from splits, from trees, galled network, phylogenetic network, phylogeny, Program SplitsTree, reconstruction. Note: http://dx.doi.org/10.1007/9783540716815_15, errata..





Guohua Jin,
Luay Nakhleh,
Sagi Snir and
Tamir Tuller. A New Lineartime Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance. In ISBRA07, Vol. 4463:6172 of LNCS, springer, 2007. Keywords: approximation, heuristic, parsimony, phylogenetic network, phylogeny, Program Nepal. Note: http://www.cs.rice.edu/~nakhleh/Papers/isbra07.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.
Toggle abstract
"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."



Hadas Birin,
Zohar GalOr,
Isaac Elias and
Tamir Tuller. Inferring Models of Rearrangements, Recombinations, and Horizontal Transfers by the Minimum Evolution Criterion. In WABI07, Vol. 4645:111123 of LNCS, springer, 2007. Keywords: explicit network, from sequences, phylogenetic network, phylogeny, reconstruction. Note: http://safrabio.cs.tau.ac.il/download/Papers/Birin_et_al.pdf.







Cuong Than,
Derek Ruths,
Hideki Innan and
Luay Nakhleh. Identifiability Issues in PhylogenyBased Detection of Horizontal Gene Transfer. In Proceedings of the Fourth RECOMB Comparative Genomics Satellite Workshop (RECOMBCG'06), Vol. 4205:215229 of LNCS, springer, 2006. 1 comment 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/recombcg06final.pdf.





Guillaume Bourque and
Louxin Zhang. Models and Methods in Comparative Genomics. In
ChauWen Tseng editor, Advances in Computers, Special Volume: Computational Biology, Vol. 68, Elsevier, 2006. Keywords: from distances, from rooted trees, from sequences, galled tree, phylogenetic network, phylogeny, survey. Note: http://www.math.nus.edu.sg/~matzlx/papers/CompGen_ZLX.pdf.



Sergey Bereg and
Yuanyi Zhang. Phylogenetic Networks Based on the Molecular Clock Hypothesis. In BIBE05, Pages 320323, 2005. Note: http://dx.doi.org/10.1109/BIBE.2005.46.
Toggle abstract
A classical result in phylogenetic trees is that a binary phylogenetic tree adhering to the molecular clock hypothesis exists if and only if the matrix of distances between taxa is ultrametric. The ultrametric condition is very restrictive. In this paper we study phylogenetic networks that can be constructed assuming the molecular clock hypothesis. We characterize distance matrices that admit such networks for 3 and 4 taxa. We design an efficient algorithm for a special class of phylogenetic networks that can detect the existence of a network and constructs it. © 2005 IEEE.





Elena Dubrova. Phylogenetic networks with edgedisjoint recombination cycles. In Proceedings of SPIE Bioengineered and Bioinspired Systems II (SPIEBBS II), Vol. 5839:381388, 2005. Keywords: galled tree, phylogenetic network, polynomial, site consistency. Note: http://dx.doi.org/10.1117/12.607910.
Toggle abstract
"Phylogenetic analysis is a branch of biology that establishes the evolutionary relationships between living organisms. The goal of phylogenetic analysis is to determine the order and approximate timing of speciation events in the evolution of a given set of species. Phylogenetic networks allow to represent evolutionary histories that include events like recombination and hybridization. In this paper, we introduce a class of phylogenetic networks called extended galledtrees in which recombination cycles share no edge. We show that the site consistency problem, which is NPhard in general, can be solved in polynomial time for this class of phylogenetic networks."





Trinh N. D. Huynh,
Jesper Jansson,
Nguyen Bao Nguyen and
WingKin Sung. Constructing a Smallest Refining Galled Phylogenetic Network. In RECOMB05, Vol. 3500:265280 of LNCS, springer, 2005. Keywords: from rooted trees, galled tree, NP complete, phylogenetic network, phylogeny, polynomial, Program SPNet, reconstruction. Note: http://www.df.lth.se/~jj/Publications/refining_gn3_RECOMB2005.pdf.



Daniel H. Huson,
Tobias Kloepper,
Peter J. Lockhart and
Mike Steel. Reconstruction of Reticulate Networks from Gene Trees. In RECOMB05, Vol. 3500:233249 of LNCS, springer, 2005. Keywords: from rooted trees, from splits, phylogenetic network, phylogeny, reconstruction, split, split network, visualization. Note: http://dx.doi.org/10.1007/11415770_18.



Daniel H. Huson and
Tobias Kloepper. Computing recombination networks from binary sequences. In ECCB05, Vol. 21(suppl. 2):ii159ii165 of BIO, 2005. Keywords: from sequences, phylogenetic network, phylogeny, recombination. Note: http://dx.doi.org/10.1093/bioinformatics/bti1126.
Toggle abstract
"Motivation:Phylogenetic networks are becoming an important tool in molecular evolution, as the evolutionary role of reticulate events, such as hybridization, horizontal gene transfer and recombination, is becoming more evident, and as the available data is dramatically increasing in quantity and quality. Results: This paper addresses the problem of computing a most parsimonious recombination network for an alignment of binary sequences that are assumed to have arisen under the 'infinite sites' model of evolution with recombinations. Using the concept of a splits network as the underlying datastructure, this paper shows how a recent method designed for the computation of hybridization networks can be extended to also compute recombination networks. A robust implementation of the approach is provided and is illustrated using a number of real biological datasets. © The Author 2005. Published by Oxford University Press. All rights reserved."





Jesper Jansson,
Nguyen Bao Nguyen and
WingKin Sung. Algorithms for Combining Rooted Triplets into a Galled Phylogenetic Network. In SODA05, Pages 349358, 2005. 1 comment Keywords: approximation, explicit network, from triplets, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction. Note: http://portal.acm.org/citation.cfm?id=1070481.



Rune Lyngsø,
Yun S. Song and
Jotun Hein. Minimum Recombination Histories by Branch and Bound. In WABI05, Vol. 3692:239250 of LNCS, springer, 2005. Keywords: ARG, branch and bound, from sequences, minimum number, Program Beagle, recombination, reconstruction, software. Note: http://www.cs.ucdavis.edu/~yssong/Pub/WABI05239.pdf.



Luay Nakhleh and
LiSan Wang. Phylogenetic Networks, Trees, and Clusters. In IWBRA05, Vol. 3515:919926 of LNCS, springer, 2005. Keywords: cluster containment, evaluation, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, tree child network, tree containment. Note: http://www.cs.rice.edu/~nakhleh/Papers/NakhlehWang.pdf.



Luay Nakhleh and
LiSan Wang. Phylogenetic Networks: Properties and Relationship to Trees and Clusters. In TCSB2, Vol. 3680:8299 of LNCS, springer, 2005. Keywords: cluster containment, evaluation, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, tree child network, tree containment. Note: http://www.cs.rice.edu/~nakhleh/Papers/LNCS_TCSB05.pdf.









Yun S. Song,
Yufeng Wu and
Dan Gusfield. Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution. In ISMB05, Vol. 21:i413i422 of BIO, 2005. Keywords: minimum number, Program HapBound, Program SHRUB, recombination. Note: http://dx.doi.org/10.1093/bioinformatics/bti1033.
Toggle abstract
"Motivation: We are interested in studying the evolution of DNA single nucleotide polymorphism sequences which have undergone (meiotic) recombination. For a given set of sequences, computing the minimum number of recombinations needed to explain the sequences (with one mutation per site) is a standard question of interest, but it has been shown to be NPhard, and previous algorithms that compute it exactly work either only on very small datasets or on problems with special structure. Results: In this paper, we present efficient, practical methods for computing both upper and lower bounds on the minimum number of needed recombinations, and for constructing evolutionary histories that explain the input sequences. We study in detail the efficiency and accuracy of these algorithms on both simulated and real data sets. The algorithms produce very close upper and lower bounds, which match exactly in a surprisingly wide range of data. Thus, with the use of new, very effective lower bounding methods and an efficient algorithm for computing upper bounds, this approach allows the efficient, exact computation of the minimum number of needed recombinations, with high frequency in a large range of data. When upper and lower bounds match, evolutionary histories found by our algorithm correspond to the most parsimonious histories. © The Author 2005. Published by Oxford University Press. All rights reserved."



Bhaskar DasGupta,
Sergio Ferrarini,
Uthra Gopalakrishnan and
Nisha Raj Paryani. Inapproximability results for the lateral gene transfer problem. In Proceedings of the Ninth Italian Conference on Theoretical Computer Science (ICTCS'05), Pages 182195, springer, 2005. 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/ictcsfinal.pdf.





Charles Choy,
Jesper Jansson,
Kunihiko Sadakane and
WingKin Sung. Computing the maximum agreement of phylogenetic networks. In Proceedings of Computing: the Tenth Australasian Theory Symposium (CATS'04), Vol. 91:134147 of Electronic Notes in Theoretical Computer Science, 2004. Keywords: dynamic programming, FPT, level k phylogenetic network, MASN, NP complete, phylogenetic network, phylogeny. Note: http://www.df.lth.se/~jj/Publications/masn6_CATS2004.pdf.
Toggle abstract
"We introduce the maximum agreement phylogenetic subnetwork problem (MASN) of finding a 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 contains at most f nodes having indegree 2 in N. Our algorithm can be extended to yield a polynomialtime algorithm for two levelf phylogenetic networks N 1,N2 for any f which is upperbounded by a constant; more precisely, its running time is O(V(N1)·V(N 2)·4f), where V(Ni) denotes the set of nodes of Ni. © 2004 Published by Elsevier B.V."



Jesper Jansson and
WingKin Sung. Inferring a level1 phylogenetic network from a dense set of rooted triplets. In COCOON04, Vol. 3106:462471 of LNCS, springer, 2004. 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/ipnrt6_COCOON2004.pdf.



Luay Nakhleh,
Tandy Warnow and
C. Randal Linder. Reconstructing reticulate evolution in species  theory and practice. In RECOMB04, Pages 337346, 2004. Keywords: from rooted trees, galled tree, phylogenetic network, phylogeny, polynomial, Program SPNet, reconstruction, software. Note: http://www.cs.rice.edu/~nakhleh/Papers/144nakhleh.pdf.



Mike Hallett,
Jens Lagergren and
Ali Tofigh. Simultaneous Identification of Duplications and Lateral Transfers. In RECOMB04, Pages 347356, 2004. Keywords: duplication, explicit network, FPT, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction. Note: http://www.nada.kth.se/~jensl/p164hallett.pdf.



Pawel Górecki. Reconciliation problems for duplication, loss and horizontal gene transfer. In RECOMB04, Pages 316325, 2004. Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction. Note: http://ai.stanford.edu/~serafim/CS374_2004/Papers/Gorecki_Reconciliation.pdf.









Luay Nakhleh,
Jerry Sun,
Tandy Warnow,
C. Randal Linder,
Bernard M. E. Moret and
Anna Tholse. Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods. In PSB03, 2003. Keywords: distance between networks, evaluation, phylogenetic network, phylogeny, polynomial, tripartition distance. Note: http://www.cs.rice.edu/~nakhleh/Papers/psb03.pdf.







Pawel Górecki. Single step reconciliation algorithm for duplication, loss and horizontal gene transfer model. In ECCB03, 2003. Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction. Note: http://www.inra.fr/eccb2003/posters/pdf/short/S_gorecki.ps.



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.









Lusheng Wang,
Kaizhong Zhang and
Louxin Zhang. Perfect phylogenetic networks with recombination. In SAC01, Pages 4650, 2001. Keywords: from sequences, galled tree, NP complete, perfect, phylogenetic network, phylogeny, polynomial, recombination, reconstruction. Note: http://dx.doi.org/10.1145/372202.372271.









Vincent Berry and
David Bryant. Faster reliable phylogenetic analysis. In RECOMB99, Pages 5968, 1999. Keywords: abstract network, from quartets, phylogenetic network, phylogeny, polynomial, Program SplitsTree, reconstruction, split network, weakly compatible. Note: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.95.9151.



Bin Ma,
Lusheng Wang and
Ming Li. Fixed topology alignment with recombination. In CPM98, Vol. 1448:174188 of LNCS, springer, 1998. Keywords: approximation, explicit network, from network, from sequences, galled tree, inapproximability, phylogenetic network, phylogeny, recombination. Note: http://dx.doi.org/10.1007/BFb0030789.



HansJürgen Bandelt. Phylogenetic Networks. In Verhandlungen des Naturwissenschaftlichen Vereins Hamburg, Vol. 34:5171, 1994.







HansJürgen Bandelt and
Andreas W. M. Dress. A relational approach to split decomposition. In
H.H. Bock,
W. Lenski and
M. M. Richter editors, Information Systems and Data Analysis, Proceedings of the 17th Annual Conference of the Gesellschaft Für Klassifikation (GFKL93), Vol. 42:123131 of Studies in Classification, Data Analysis, and Knowledge Organization, springer, 1994. Keywords: characterization, from quartets, phylogenetic network, weakly compatible.



HansJürgen Bandelt and
Andreas W. M. Dress. A canonical decomposition theory for metrics on a finite set. In Advances in Mathematics, Vol. 92(1):47105, 1992. Keywords: abstract network, circular split system, from distances, split, split decomposition, split network, weak hierarchy, weakly compatible.
Toggle abstract
"We consider specific additive decompositions d = d1 + ... + dn of metrics, defined on a finite set X (where a metric may give distance zero to pairs of distinct points). The simplest building stones are the slit metrics, associated to splits (i.e., bipartitions) of the given set X. While an additive decomposition of a Hamming metric into split metrics is in no way unique, we achieve uniqueness by restricting ourselves to coherent decompositions, that is, decompositions d = d1 + ... + dn such that for every map f:X → R with f(x) + f(y) ≥ d(x, y) for all x, y ε{lunate} X there exist maps f1, ..., fn: X → R with f = f1 + ... + fn and fi(x) + fi(y) ≥ di(x, y) for all i = 1,..., n and all x, y ε{lunate} X. These coherent decompositions are closely related to a geometric decomposition of the injective hull of the given metric. A metric with a coherent decomposition into a (weighted) sum of split metrics will be called totally splitdecomposable. Tree metrics (and more generally, the sum of two tree metrics) are particular instances of totally splitdecomposable metrics. Our main result confirms that every metric admits a coherent decomposition into a totally splitdecomposable metric and a splitprime residue, where all the split summands and hence the decomposition can be determined in polynomial time, and that a family of splits can occur this way if and only if it does not induce on any fourpoint subset all three splits with block size two. © 1992."



Richard R. Hudson. Properties of the neutral allele model with intragenic recombination. In TPP, Vol. 23:183201, 1983. Keywords: coalescent. Note: http://dx.doi.org/10.1016/00405809(83)900138, see also http://www.brics.dk/~compbio/coalescent/hudson_animator.html.
Toggle abstract
"An infinitesite neutral allele model with crossingover possible at any of an infinite number of sites is studied. A formula for the variance of the number of segregating sites in a sample of gametes is obtained. An approximate expression for the expected homozygosity is also derived. Simulation results are presented to indicate the accuracy of the approximations. The results concerning the number of segregating sites and the expected homozygosity indicate that a twolocus model and the infinitesite model behave similarly for 4Nu ≤ 2 and r ≤ 5u, where N is the population size, u is the neutral mutation rate, and r is the recombination rate. Simulations of a twolocus model and a fourlocus model were also carried out to determine the effect of intragenic recombination on the homozygosity test ofWatterson (Genetics 85, 789814; 88, 405417) and on the number of unique alleles in a sample. The results indicate that for 4Nu ≤ 2 and r ≤ 10u, the effect of recombination is quite small. © 1983."




