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Article (Journal)
publications sorted by year
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Gabriel Cardona and
Louxin Zhang. Counting and Enumerating Tree-Child Networks and Their Subclasses. In JCSS, Vol. 114:84-104, 2020.
Keywords: counting, enumeration, explicit network, galled network, galled tree, normal network, phylogenetic network, phylogeny, tree-child network.
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Leo van Iersel,
Remie Janssen,
Mark Jones,
Yukihiro Murakami and
Norbert Zeh. Polynomial-Time Algorithms for Phylogenetic Inference Problems Involving Duplication and Reticulation. In TCBB, Vol. 17(1):14-26, 2020.
Keywords: hybridization, minimum number, parental hybridization, phylogenetic network, phylogeny, reconstruction, weakly displaying.
Note: http://pure.tudelft.nl/ws/portalfiles/portal/71270795/08798653.pdf.
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Hadi Poormohammadi,
Mohsen Sardari Zarchi and
Hossein Ghaneai. NCHB: A method for constructing rooted phylogenetic networks from rooted triplets based on height function and binarization. In JTB, Vol. 489(110144), 2020.
Keywords: explicit network, from triplets, heuristic, phylogenetic network, phylogeny, Program Simplistic, Program TripNet, reconstruction.
Note: https://doi.org/10.1016/j.jtbi.2019.110144.
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Joan Carles Pons,
Charles Semple and
Mike Steel. Tree-based networks: characterisations, metrics, and support trees. In JOMB, Vol. 78(4):899-918, 2019.
Keywords: characterization, explicit network, from network, phylogenetic network, phylogeny, time consistent network, tree-based network.
Note: https://arxiv.org/abs/1710.07836.
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Janosch Döcker,
Leo van Iersel,
Steven Kelk and
Simone Linz. Deciding the existence of a cherry-picking sequence is hard on two trees. In DAM, Vol. 260:131-143, 2019.
Keywords: cherry-picking, explicit network, hybridization, minimum number, NP complete, phylogenetic network, phylogeny, reconstruction, temporal-hybridization number, time consistent network, tree-child network.
Note: https://arxiv.org/abs/1712.02965.
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Andreas Gunawan,
Hongwei Yan and
Louxin Zhang. Compression of Phylogenetic Networks and Algorithm for the Tree Containment Problem. In JCB, Vol. 25(3), 2019.
Keywords: explicit network, phylogenetic network, phylogeny, polynomial, quasi-reticulation-visible network, reticulation-visible network, tree containment, tree-child network.
Note: https://arxiv.org/abs/1806.07625.
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Yukihiro Murakami,
Leo van Iersel,
Remie Janssen,
Mark Jones and
Vincent Moulton. Reconstructing Tree-Child Networks from Reticulate-Edge-Deleted Subnetworks. In BMB, Vol. 81:3823-3863, 2019.
Keywords: from subnetworks, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction, tree-child network, uniqueness, valid network.
Note: https://doi.org/10.1007/s11538-019-00641-w.
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Juan Wang and
Maozu Guo. A review of metrics measuring dissimilarity for rooted phylogenetic networks. In Briefings in Bioinformatics, Vol. 20(6):1972-1980, 2019.
Keywords: distance between networks, explicit network, from network, mu distance, phylogenetic network, phylogeny, survey, tree sibling network, tree-child network.
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Gabriel Cardona,
Joan Carles Pons and
Celine Scornavacca. Generation of Binary Tree-Child phylogenetic networks. In PLoS Computational Biology, Vol. 15(10):e1007440.1-29, 2019.
Keywords: enumeration, explicit network, generation, phylogenetic network, phylogeny, Program PhyloNetwork, Program TCGenerators, software, tree-child network.
Note: https://doi.org/10.1371/journal.pcbi.1007440.
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Leo van Iersel,
Steven Kelk,
Giorgios Stamoulis,
Leen Stougie and
Olivier Boes. On unrooted and root-uncertain variants of several well-known phylogenetic network problems. In ALG, Vol. 80(11):2993-3022, 2018.
Keywords: explicit network, FPT, from network, from unrooted trees, NP complete, phylogenetic network, phylogeny, reconstruction, tree containment.
Note: https://hal.inria.fr/hal-01599716.
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Andrew R. Francis,
Katharina Huber,
Vincent Moulton and
Taoyang Wu. Bounds for phylogenetic network space metrics. In JOMB, Vol. 76(5):1229-1248, 2018.
Keywords: bound, distance between networks, from network, NNI distance, NNI moves, phylogenetic network, phylogeny, SPR distance, TBR distance.
Note: https://arxiv.org/abs/1702.05609.
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Andrew R. Francis,
Katharina Huber and
Vincent Moulton. Tree-based unrooted phylogenetic networks. In BMB, Vol. 80(2):404-416, 2018.
Keywords: characterization, explicit network, NP complete, phylogenetic network, phylogeny, tree containment, tree-based network, unrooted tree-based network.
Note: https://arxiv.org/abs/1704.02062.
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Magnus Bordewich,
Charles Semple and
Nihan Tokac. Constructing tree-child networks from distance matrices. In Algorithmica, Vol. 80(8):2240-2259, 2018.
Keywords: compressed network, explicit network, from distances, phylogenetic network, phylogeny, polynomial, reconstruction, tree-child network, uniqueness.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BSN17.pdf.
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Philippe Gambette,
Andreas Gunawan,
Anthony Labarre,
Stéphane Vialette and
Louxin Zhang. Solving the Tree Containment Problem in Linear Time for Nearly Stable Phylogenetic Networks. In DAM, Vol. 246:62-79, 2018.
Keywords: explicit network, from network, from rooted trees, nearly-stable network, phylogenetic network, phylogeny, polynomial, tree containment.
Note: https://hal-upec-upem.archives-ouvertes.fr/hal-01575001/en/.
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Remie Janssen,
Mark Jones,
Péter L. Erdös,
Leo van Iersel and
Celine Scornavacca. Exploring the tiers of rooted phylogenetic network space using tail moves. In BMB, Vol. 80(8):2177-2208, 2018.
Keywords: distance between networks, explicit network, from network, NNI moves, orientation, phylogenetic network, phylogeny, SPR distance.
Note: https://arxiv.org/abs/1708.07656.
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Sarah Bastkowski,
Daniel Mapleson,
Andreas Spillner,
Taoyang Wu,
Monika Balvociute and
Vincent Moulton. SPECTRE: a Suite of PhylogEnetiC Tools for Reticulate Evolution. In BIO, Vol. 34(6):1057-1058, 2018.
Keywords: abstract network, NeighborNet, phylogenetic network, phylogeny, Program FlatNJ, Program QNet, Program SplitsTree, reconstruction, software, split network.
Note: https://doi.org/10.1101/169177.
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Paul Bastide,
Claudia Solís-Lemus,
Ricardo Kriebel,
Kenneth William Sparks and
Cécile Ané. Phylogenetic Comparative Methods on Phylogenetic Networks with Reticulations. In SB, Vol. 67(5):800-820, 2018.
Keywords: ancestral trait reconstruction, from network, likelihood, Program PhyloNetworks SNaQ, software, statistical model, statistical test.
Note: https://doi.org/10.1101/194050.
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Katharina Huber,
Vincent Moulton,
Charles Semple and
Taoyang Wu. Quarnet inference rules for level-1 networks. In BMB, Vol. 80:2137-2153, 2018.
Keywords: explicit network, from quarnets, from subnetworks, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction.
Note: https://arxiv.org/abs/1711.06720.
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Janosch Döcker and
Simone Linz. On the existence of a cherry-picking sequence. In TCS, Vol. 714:36-50, 2018.
Keywords: cherry-picking, explicit network, from rooted trees, NP complete, phylogenetic network, phylogeny, reconstruction, temporal-hybridization number, time consistent network, tree-child network.
Note: https://arxiv.org/abs/1712.04127.
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Leo van Iersel,
Mark Jones and
Celine Scornavacca. Improved maximum parsimony models for phylogenetic networks. In SB, Vol. 67(3):518-542, 2018.
Keywords: explicit network, FPT, from sequences, NP complete, parsimony, phylogenetic network, phylogeny, reconstruction, weakly displaying.
Note: https://leovaniersel.files.wordpress.com/2017/12/improved_parsimony_networks.pdf.
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Magnus Bordewich,
Katharina Huber,
Vincent Moulton and
Charles Semple. Recovering normal networks from shortest inter-taxa distance information. In JOMB, Vol. 77(3):571-594, 2018.
Keywords: explicit network, from distances, normal network, phylogenetic network, phylogeny, polynomial, reconstruction, uniqueness.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BHMS18.pdf.
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Chi Zhang,
Huw A. Ogilvie,
Alexei J. Drummond and
Tanja Stadler. Bayesian Inference of Species Networks from Multilocus Sequence Data. In MBE, Vol. 35(2):504-517, 2018.
Keywords: bayesian, explicit network, from sequences, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: https://dx.doi.org/10.1093/molbev/msx307.
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Dingqiao Wen,
Yun Yu,
Jiafan Zhu and
Luay Nakhleh. Inferring Phylogenetic Networks Using PhyloNet. In SB, Vol. 67(4):735-740, 2018.
Keywords: bayesian, likelihood, parsimony, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, software.
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Jiafan Zhu,
Dingqiao Wen,
Yun Yu,
Heidi M. Meudt and
Luay Nakhleh. Bayesian inference of phylogenetic networks from bi-allelic genetic markers. In PLoS Computational Biology, Vol. 14(1):e1005932.1-32, 2018.
Keywords: bayesian, explicit network, from multistate characters, phylogenetic network, phylogeny, Program PhyloNet.
Note: https://doi.org/10.1371/journal.pcbi.1005932.
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Katharina Huber,
Leo van Iersel,
Vincent Moulton,
Celine Scornavacca and
Taoyang Wu. Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets. In ALG, Vol. 77(1):173-200, 2017.
Keywords: explicit network, FPT, from binets, from subnetworks, from trinets, NP complete, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://arxiv.org/abs/1411.6804.
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Philippe Gambette,
Katharina Huber and
Guillaume Scholz. Uprooted Phylogenetic Networks. In BMB, Vol. 79(9):2022-2048, 2017.
Keywords: circular split system, explicit network, from splits, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction, split network, uniqueness.
Note: http://arxiv.org/abs/1511.08387.
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Julia Matsieva,
Steven Kelk,
Celine Scornavacca,
Chris Whidden and
Dan Gusfield. A Resolution of the Static Formulation Question for the Problem of Computing the History Bound. In TCBB, Vol. 14(2):404-417, 2017.
Keywords: ARG, explicit network, from sequences, minimum number, phylogenetic network, phylogeny.
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Sha Zhu and
James H. Degnan. Displayed Trees Do Not Determine Distinguishability Under the Network Multispecies Coalescent. In SB, Vol. 66(2):283-298, 2017.
Keywords: branch length, coalescent, explicit network, from network, likelihood, phylogenetic network, phylogeny, Program Hybrid-coal, Program Hybrid-Lambda, Program PhyloNet, software, uniqueness.
Note: presentation available at https://www.youtube.com/watch?v=JLYGTfEZG7g.
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Misagh Kordi and
Mukul S. Bansal. On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees. In TCBB, Vol. 14(3):587-599, 2017.
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_DTLreconciliationPreprint2015.pdf.
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Andreas Gunawan,
Bhaskar DasGupta and
Louxin Zhang. A decomposition theorem and two algorithms for reticulation-visible networks. In Information and Computation, Vol. 252:161-175, 2017.
Keywords: cluster containment, explicit network, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulation-visible network, tree containment.
Note: https://www.cs.uic.edu/~dasgupta/resume/publ/papers/Infor_Comput_IC4848_final.pdf.
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Magnus Bordewich,
Simone Linz and
Charles Semple. Lost in space? Generalising subtree prune and regraft to spaces of phylogenetic networks. In JTB, Vol. 423:1-12, 2017.
Keywords: distance between networks, explicit network, phylogenetic network, phylogeny, reticulation-visible network, SPR distance, tree-based network, tree-child network.
Note: https://simonelinz.files.wordpress.com/2017/04/bls171.pdf.
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Celine Scornavacca,
Joan Carles Pons and
Gabriel Cardona. Fast algorithm for the reconciliation of gene trees and LGT networks. In JTB, Vol. 418:129-137, 2017.
Keywords: duplication, explicit network, from network, from rooted trees, lateral gene transfer, LGT network, loss, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction.
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Leo van Iersel,
Vincent Moulton,
Eveline De Swart and
Taoyang Wu. Binets: fundamental building blocks for phylogenetic networks. In BMB, Vol. 79(5):1135-1154, 2017.
Keywords: approximation, explicit network, from binets, from subnetworks, galled tree, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1007/s11538-017-0275-4.
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Philippe Gambette,
Leo van Iersel,
Mark Jones,
Manuel Lafond,
Fabio Pardi and
Celine Scornavacca. Rearrangement Moves on Rooted Phylogenetic Networks. In PLoS Computational Biology, Vol. 13(8):e1005611.1-21, 2017.
Keywords: distance between networks, explicit network, from network, NNI distance, NNI moves, phylogenetic network, phylogeny, SPR distance.
Note: https://hal-upec-upem.archives-ouvertes.fr/hal-01572624/en/.
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Claudia Solís-Lemus,
Paul Bastide and
Cécile Ané. PhyloNetworks: A Package for Phylogenetic Networks. In MBE, Vol. 34(12):3292-3298, 2017.
Keywords: from sequences, from trees, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, reconstruction, software.
Note: https://doi.org/10.1093/molbev/msx235.
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Klaus Schliep,
Alastair J. Potts,
David A. Morrison and
Guido W. Grimm. Intertwining phylogenetic trees and networks. In Methods in Ecology and Evolution, Vol. 8(10):1212-1220, 2017.
Keywords: abstract network, from network, from unrooted trees, phylogenetic network, phylogeny, split network, visualization.
Note: http://dx.doi.org/10.1111/2041-210X.12760.
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Edwin Jacox,
Mathias Weller,
Eric Tannier and
Celine Scornavacca. Resolution and reconciliation of non-binary gene trees with transfers, duplications and losses. In BIO, Vol. 33(7):980-987, 2017.
Keywords: duplication, explicit network, FPT, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1093/bioinformatics/btw778.
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Leo van Iersel,
Steven Kelk,
Nela Lekic,
Chris Whidden and
Norbert Zeh. Hybridization Number on Three Rooted Binary Trees is EPT. In SIDMA, Vol. 30(3):1607-1631, 2016.
Keywords: agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1402.2136.
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Katharina Huber,
Vincent Moulton,
Mike Steel and
Taoyang Wu. Folding and unfolding phylogenetic trees and networks. In JOMB, Vol. 73(6):1761-1780, 2016.
Keywords: compressed network, explicit network, FU-stable network, NP complete, phylogenetic network, phylogeny, tree containment, tree sibling network.
Note: http://arxiv.org/abs/1506.04438.
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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):189-215, 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.
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Sajad Mirzaei and
Yufeng Wu. Fast Construction of Near Parsimonious Hybridization Networks for Multiple Phylogenetic Trees. In TCBB, Vol. 13(3):565-570, 2016.
Keywords: bound, explicit network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program PIRN, reconstruction, software.
Note: http://www.engr.uconn.edu/~ywu/Papers/PIRNs-preprint.pdf.
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Vincent Ranwez,
Celine Scornavacca,
Jean-Philippe Doyon and
Vincent Berry. Inferring gene duplications, transfers and losses can be done in a discrete framework. In JOMB, Vol. 72(7):1811-1844, 2016.
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction.
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François Chevenet,
Jean-Philippe Doyon,
Celine Scornavacca,
Edwin Jacox,
Emmanuelle Jousselin and
Vincent Berry. SylvX: a viewer for phylogenetic tree reconciliations. In BIO, Vol. 32(4):608-610, 2016.
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program SylvX, software, visualization.
Note: https://www.researchgate.net/profile/Emmanuelle_Jousselin/publication/283446016_SylvX_a_viewer_for_phylogenetic_tree_reconciliations/links/5642146108aec448fa621efa.pdf.
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Hussein A. Hejase and
Kevin J. Liu. A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation. Vol. 17(422):1-12, 2016.
Keywords: abstract network, evaluation, from sequences, phylogenetic network, phylogeny, Program PhyloNet, Program PhyloNetworks SNaQ, reconstruction, simulation, unicyclic network.
Note: http://dx.doi.org/10.1186/s12859-016-1277-1.
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Philippe Gambette,
Leo van Iersel,
Steven Kelk,
Fabio Pardi and
Celine Scornavacca. Do branch lengths help to locate a tree in a phylogenetic network? In BMB, Vol. 78(9):1773-1795, 2016.
Keywords: branch length, explicit network, FPT, from network, from rooted trees, NP complete, phylogenetic network, phylogeny, pseudo-polynomial, time consistent network, tree containment, tree sibling network.
Note: http://arxiv.org/abs/1607.06285.
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Maria Anaya,
Olga Anipchenko-Ulaj,
Aisha Ashfaq,
Joyce Chiu,
Mahedi Kaiser,
Max Shoji Ohsawa,
Megan Owen,
Ella Pavlechko,
Katherine St. John,
Shivam Suleria,
Keith Thompson and
Corrine Yap. On Determining if Tree-based Networks Contain Fixed Trees. In BMB, Vol. 78(5):961-969, 2016.
Keywords: explicit network, FPT, NP complete, phylogenetic network, phylogeny, tree-based network.
Note: http://arxiv.org/abs/1602.02739.
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James Oldman,
Taoyang Wu,
Leo van Iersel and
Vincent Moulton. TriLoNet: Piecing together small networks to reconstruct reticulate evolutionary histories. In MBE, Vol. 33(8):2151-2162, 2016.
Keywords: explicit network, from subnetworks, from trinets, galled tree, phylogenetic network, phylogeny, Program LEV1ATHAN, Program TriLoNet, reconstruction.
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Juan Wang. A Survey of Methods for Constructing Rooted Phylogenetic Networks. In PLoS ONE, Vol. 11(11):e0165834, 2016.
Keywords: evaluation, explicit network, from clusters, phylogenetic network, phylogeny, Program BIMLR, Program Dendroscope, Program LNetwork, reconstruction, survey.
Note: http://dx.doi.org/10.1371/journal.pone.0165834.
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Leo van Iersel,
Steven Kelk and
Celine Scornavacca. Kernelizations for the hybridization number problem on multiple nonbinary trees. In JCSS, Vol. 82(6):1075-1089, 2016.
Keywords: explicit network, from rooted trees, kernelization, minimum number, phylogenetic network, phylogeny, Program Treeduce, reconstruction.
Note: https://arxiv.org/abs/1311.4045v3.
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Edwin Jacox,
Cédric Chauve,
Gergely J. Szöllösi,
Yann Ponty and
Celine Scornavacca. EcceTERA: comprehensive gene tree-species tree reconciliation using parsimony. In BIO, Vol. 32(13):2056-2058, 2016.
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, parsimony, phylogenetic network, phylogeny, polynomial, Program ecceTERA.
Note: https://doi.org/10.1093/bioinformatics/btw105.
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Mareike Fischer,
Leo van Iersel,
Steven Kelk and
Celine Scornavacca. On Computing The Maximum Parsimony Score Of A Phylogenetic Network. In SIDMA, Vol. 29(1):559-585, 2015.
Keywords: APX hard, cluster containment, explicit network, FPT, from network, from sequences, integer linear programming, level k phylogenetic network, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, Program MPNet, reconstruction, software.
Note: http://arxiv.org/abs/1302.2430.
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Katharina Huber,
Leo van Iersel,
Vincent Moulton and
Taoyang Wu. How much information is needed to infer reticulate evolutionary histories? In Systematic Biology, Vol. 64(1):102-111, 2015.
Keywords: explicit network, from network, from rooted trees, from subnetworks, from trinets, identifiability, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: http://dx.doi.org/10.1093/sysbio/syu076.
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Benjamin Albrecht. Computing all hybridization networks for multiple binary phylogenetic input trees. In BMCB, Vol. 16(236):1-15, 2015.
Keywords: agreement forest, explicit network, exponential algorithm, FPT, from rooted trees, phylogenetic network, phylogeny, Program Hybroscale, Program PIRN, reconstruction.
Note: http://dx.doi.org/10.1186/s12859-015-0660-7.
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Sha Zhu,
James H. Degnan,
Sharyn J. Goldstein and
Bjarki Eldon. Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees. In BMCB, Vol. 16(292):1-7, 2015.
Keywords: explicit network, from network, phylogenetic network, phylogeny, Program Hybrid-Lambda, simulation, software.
Note: http://dx.doi.org/10.1186/s12859-015-0721-y.
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Gergely J. Szöllösi,
Adrián Arellano Davín,
Eric Tannier,
Vincent Daubin and
Bastien Boussau. Genome-scale phylogenetic analysis finds extensive gene transfer among fungi. In Philosophical Transactions of the Royal Society of London B: Biological Sciences, Vol. 370(1678):1-11, 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.
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Marc Thuillard and
Didier Fraix-Burnet. Phylogenetic Trees and Networks Reduce to Phylogenies on Binary States: Does It Furnish an Explanation to the Robustness of Phylogenetic Trees against Lateral Transfers? In Evolutionary Bioinformatics, Vol. 11:213-221, 2015. [Abstract]
Keywords: circular split system, explicit network, from multistate characters, outerplanar, perfect, phylogenetic network, phylogeny, planar, polynomial, reconstruction, split.
Note: http://dx.doi.org/10.4137%2FEBO.S28158.
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Jessica W. Leigh and
David Bryant. PopART: full-feature software for haplotype network construction. In Methods in Ecology and Evolution, Vol. 6(9):1110-1116, 2015.
Keywords: abstract network, from sequences, haplotype network, MedianJoining, phylogenetic network, phylogeny, population genetics, Program PopART, Program TCS, software.
Note: http://dx.doi.org/10.1111/2041-210X.12410.
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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):1-15, 2015.
Keywords: explicit network, from rooted trees, lateral gene transfer, phylogenetic network, phylogeny, Program LGTnetwork, reconstruction, software, tree-based network.
Note: http://dx.doi.org/10.1186/s13015-015-0059-z.
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Leo van Iersel,
Steven Kelk,
Nela Lekic and
Leen Stougie. Approximation algorithms for nonbinary agreement forests. In SIDMA, Vol. 28(1):49-66, 2014.
Keywords: agreement forest, approximation, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1210.3211.
Toggle abstract
"Given two rooted phylogenetic trees on the same set of taxa X, the Maximum Agreement Forest (maf) problem asks to find a forest that is, in a certain sense, common to both trees and has a minimum number of components. The Maximum Acyclic Agreement Forest (maaf) problem has the additional restriction that the components of the forest cannot have conflicting ancestral relations in the input trees. There has been considerable interest in the special cases of these problems in which the input trees are required to be binary. However, in practice, phylogenetic trees are rarely binary, due to uncertainty about the precise order of speciation events. Here, we show that the general, nonbinary version of maf has a polynomial-time 4-approximation and a fixedparameter tractable (exact) algorithm that runs in O(4opoly(n)) time, where n = |X| and k is the number of components of the agreement forest minus one. Moreover, we show that a c-approximation algorithm for nonbinary maf and a d-approximation algorithm for the classical problem Directed Feedback Vertex Set (dfvs) can be combined to yield a d(c+3)-approximation for nonbinary maaf. The algorithms for maf have been implemented and made publicly available. © 2014 Society for Industrial and Applied Mathematics."
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Gabriel Cardona,
Mercè Llabrés,
Francesc Rosselló and
Gabriel Valiente. The comparison of tree-sibling time consistent phylogenetic networks is graph-isomorphism complete. In The Scientific World Journal, Vol. 2014(254279):1-6, 2014.
Keywords: abstract network, distance between networks, from network, isomorphism, phylogenetic network, tree sibling network.
Note: http://arxiv.org/abs/0902.4640.
Toggle abstract
"Several polynomial time computable metrics on the class of semibinary tree-sibling time consistent phylogenetic networks are available in the literature; in particular, the problem of deciding if two networks of this kind are isomorphic is in P. In this paper, we show that if we remove the semibinarity condition, then the problem becomes much harder. More precisely, we prove that the isomorphism problem for generic tree-sibling time consistent phylogenetic networks is polynomially equivalent to the graph isomorphism problem. Since the latter is believed not to belong to P, the chances are that it is impossible to define a metric on the class of all tree-sibling time consistent phylogenetic networks that can be computed in polynomial time. © 2014 Gabriel Cardona et al."
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Steven Kelk and
Celine Scornavacca. Constructing minimal phylogenetic networks from softwired clusters is fixed parameter tractable. In ALG, Vol. 68(4):886-915, 2014.
Keywords: explicit network, FPT, from clusters, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1108.3653.
Toggle abstract
"Here we show that, given a set of clusters C on a set of taxa X, where |X|=n, it is possible to determine in time f(k)×poly(n) whether there exists a level-≤k network (i.e. a network where each biconnected component has reticulation number at most k) that represents all the clusters in C in the softwired sense, and if so to construct such a network. This extends a result from Kelk et al. (in IEEE/ACM Trans. Comput. Biol. Bioinform. 9:517-534, 2012) which showed that the problem is polynomial-time solvable for fixed k. By defining "k-reticulation generators" analogous to "level-k generators", we then extend this fixed parameter tractability result to the problem where k refers not to the level but to the reticulation number of the whole network. © 2012 Springer Science+Business Media New York."
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Hadi Poormohammadi,
Changiz Eslahchi and
Ruzbeh Tusserkani. TripNet: A Method for Constructing Rooted Phylogenetic Networks from Rooted Triplets. In PLoS ONE, Vol. 9(9):e106531, 2014.
Keywords: explicit network, from triplets, heuristic, level k phylogenetic network, phylogenetic network, phylogeny, Program TripNet, reconstruction, software.
Note: http://arxiv.org/abs/1201.3722.
Toggle abstract
"The problem of constructing an optimal rooted phylogenetic network from an arbitrary set of rooted triplets is an NP-hard problem. In this paper, we present a heuristic algorithm called TripNet, which tries to construct a rooted phylogenetic network with the minimum number of reticulation nodes from an arbitrary set of rooted triplets. Despite of current methods that work for dense set of rooted triplets, a key innovation is the applicability of TripNet to non-dense set of rooted triplets. We prove some theorems to clarify the performance of the algorithm. To demonstrate the efficiency of TripNet, we compared TripNet with SIMPLISTIC. It is the only available software which has the ability to return some rooted phylogenetic network consistent with a given dense set of rooted triplets. But the results show that for complex networks with high levels, the SIMPLISTIC running time increased abruptly. However in all cases TripNet outputs an appropriate rooted phylogenetic network in an acceptable time. Also we tetsed TripNet on the Yeast data. The results show that Both TripNet and optimal networks have the same clustering and TripNet produced a level-3 network which contains only one more reticulation node than the optimal network."
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Leo van Iersel and
Vincent Moulton. Trinets encode tree-child and level-2 phylogenetic networks. In JOMB, Vol. 68(7):1707-1729, 2014.
Keywords: explicit network, from subnetworks, from trinets, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1210.0362.
Toggle abstract
"Phylogenetic networks generalize evolutionary trees, and are commonly used to represent evolutionary histories of species that undergo reticulate evolutionary processes such as hybridization, recombination and lateral gene transfer. Recently, there has been great interest in trying to develop methods to construct rooted phylogenetic networks from triplets, that is rooted trees on three species. However, although triplets determine or encode rooted phylogenetic trees, they do not in general encode rooted phylogenetic networks, which is a potential issue for any such method. Motivated by this fact, Huber and Moulton recently introduced trinets as a natural extension of rooted triplets to networks. In particular, they showed that level-1 phylogenetic networks are encoded by their trinets, and also conjectured that all "recoverable" rooted phylogenetic networks are encoded by their trinets. Here we prove that recoverable binary level-2 networks and binary tree-child networks are also encoded by their trinets. To do this we prove two decomposition theorems based on trinets which hold for all recoverable binary rooted phylogenetic networks. Our results provide some additional evidence in support of the conjecture that trinets encode all recoverable rooted phylogenetic networks, and could also lead to new approaches to construct phylogenetic networks from trinets. © 2013 Springer-Verlag Berlin Heidelberg."
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Anthony Labarre and
Sicco Verwer. Merging partially labelled trees: hardness and a declarative programming solution. In TCBB, Vol. 11(2):389-397, 2014.
Keywords: abstract network, from unrooted trees, heuristic, NP complete, phylogenetic network, phylogeny, reconstruction.
Note: https://hal-upec-upem.archives-ouvertes.fr/hal-00855669.
Toggle abstract
"Intraspecific studies often make use of haplotype networks instead of gene genealogies to represent the evolution of a set of genes. Cassens et al. proposed one such network reconstruction method, based on the global maximum parsimony principle, which was later recast by the first author of the present work as the problem of finding a minimum common supergraph of a set of t partially labelled trees. Although algorithms have been proposed for solving that problem on two graphs, the complexity of the general problem on trees remains unknown. In this paper, we show that the corresponding decision problem is NP-complete for t=3. We then propose a declarative programming approach to solving the problem to optimality in practice, as well as a heuristic approach, both based on the idpsystem, and assess the performance of both methods on randomly generated data. © 2004-2012 IEEE."
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Jesper Jansson and
Andrzej Lingas. Computing the rooted triplet distance between galled trees by counting triangles. In Journal of Discrete Algorithms, Vol. 25:66-78, 2014.
Keywords: distance between networks, explicit network, from network, galled network, phylogenetic network, phylogeny, polynomial, triplet distance.
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 so-called galled tree with n leaves then the rooted triplet distance can be computed in o(n2.687) time. Our upper bound is obtained by reducing the problem of computing the rooted triplet distance between two galled trees to that of counting monochromatic and almost-monochromatic triangles in an undirected, edge-colored 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 algorithmic results that may be of independent interest: (i) the number of triangles in a connected, undirected, uncolored graph with m edges can be computed in o(m1.408) time; (ii) if G is a connected, undirected, edge-colored graph with n vertices and C is a subset of the set of edge colors then the number of monochromatic triangles of G with colors in C can be computed in o(n2.687) time; and (iii) if G is a connected, undirected, edge-colored graph with n vertices and R is a binary relation on the colors that is computable in O(1) time then the number of R-chromatic triangles in G can be computed in o(n2.687) time. © 2013 Elsevier B.V. All rights reserved."
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Ward C Wheeler. Phyletic groups on networks. In Cladistics, Vol. 30(4):447-451, 2014.
Keywords: explicit network, from network, phylogenetic network, phylogeny.
Note: http://dx.doi.org/10.1111/cla.12062.
Toggle abstract
"Three additional phyletic group types, "periphyletic," "epiphyletic", and "anaphyletic" (in addition to Hennigian mono-, para-, and polyphyletic) are defined in terms of trees and phylogenetic networks (trees with directed reticulate edges) via a generalization of the algorithmic definitions of Farris. These designations concern groups defined as monophyletic on trees, but with additional gains or losses of members from network edges. These distinctions should be useful in discussion of systems with non-vertical inheritance such as recombination between viruses, horizontal exchange between bacteria, hybridization in plants and animals, as well as human linguistic evolution. Examples are illustrated with Indo-European language groups. © The Willi Hennig Society 2013."
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Sarah Bastkowski,
Andreas Spillner and
Vincent Moulton. Fishing for minimum evolution trees with Neighbor-Nets. In IPL, Vol. 114(1-2):3-18, 2014.
Keywords: circular split system, from distances, NeighborNet, phylogeny, polynomial.
Toggle abstract
"In evolutionary biology, biologists commonly use a phylogenetic tree to represent the evolutionary history of some set of species. A common approach taken to construct such a tree is to search through the space of all possible phylogenetic trees on the set so as to find one that optimizes some score function, such as the minimum evolution criterion. However, this is hampered by the fact that the space of phylogenetic trees is extremely large in general. Interestingly, an alternative approach, which has received somewhat less attention in the literature, is to instead search for trees within some set of bipartitions or splits of the set of species in question. Here we consider the problem of searching through a set of splits that is circular. Such sets can, for example, be generated by the NeighborNet algorithm for constructing phylogenetic networks. More specifically, we present an O(n4) time algorithm for finding an optimal minimum evolution tree in a circular set of splits on a set of species of size n. In addition, using simulations, we compare the performance of this algorithm when applied to NeighborNet output with that of FastME, a leading method for searching for minimum evolution trees in tree space. We find that, even though a circular set of splits represents just a tiny fraction of the total number of possible splits of a set, the trees obtained from circular sets compare quite favorably with those obtained with FastME, suggesting that the approach could warrant further investigation. © 2013 Elsevier B.V."
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Lavanya Kannan and
Ward C Wheeler. Exactly Computing the Parsimony Scores on Phylogenetic Networks Using Dynamic Programming. In JCB, Vol. 21(4):303-319, 2014.
Keywords: explicit network, exponential algorithm, from network, from sequences, parsimony, phylogenetic network, phylogeny, reconstruction.
Toggle abstract
"Scoring a given phylogenetic network is the first step that is required in searching for the best evolutionary framework for a given dataset. Using the principle of maximum parsimony, we can score phylogenetic networks based on the minimum number of state changes across a subset of edges of the network for each character that are required for a given set of characters to realize the input states at the leaves of the networks. Two such subsets of edges of networks are interesting in light of studying evolutionary histories of datasets: (i) the set of all edges of the network, and (ii) the set of all edges of a spanning tree that minimizes the score. The problems of finding the parsimony scores under these two criteria define slightly different mathematical problems that are both NP-hard. In this article, we show that both problems, with scores generalized to adding substitution costs between states on the endpoints of the edges, can be solved exactly using dynamic programming. We show that our algorithms require O(mpk) storage at each vertex (per character), where k is the number of states the character can take, p is the number of reticulate vertices in the network, m = k for the problem with edge set (i), and m = 2 for the problem with edge set (ii). This establishes an O(nmpk2) algorithm for both the problems (n is the number of leaves in the network), which are extensions of Sankoff's algorithm for finding the parsimony scores for phylogenetic trees. We will discuss improvements in the complexities and show that for phylogenetic networks whose underlying undirected graphs have disjoint cycles, the storage at each vertex can be reduced to O(mk), thus making the algorithm polynomial for this class of networks. We will present some properties of the two approaches and guidance on choosing between the criteria, as well as traverse through the network space using either of the definitions. We show that our methodology provides an effective means to study a wide variety of datasets. © Copyright 2014, Mary Ann Liebert, Inc. 2014."
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Jialiang Yang,
Stefan Grünewald,
Yifei Xu and
Xiu-Feng Wan. Quartet-based methods to reconstruct phylogenetic networks. In BMC Systems Biology, Vol. 80(21), 2014.
Keywords: abstract network, from quartets, phylogenetic network, phylogeny, Program QuartetMethods, Program QuartetNet, Program SplitsTree, reconstruction.
Note: http://dx.doi.org/10.1186/1752-0509-8-21
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Toggle abstract
"Background: Phylogenetic networks are employed to visualize evolutionary relationships among a group of nucleotide sequences, genes or species when reticulate events like hybridization, recombination, reassortant and horizontal gene transfer are believed to be involved. In comparison to traditional distance-based methods, quartet-based methods consider more information in the reconstruction process and thus have the potential to be more accurate.Results: We introduce QuartetSuite, which includes a set of new quartet-based methods, namely QuartetS, QuartetA, and QuartetM, to reconstruct phylogenetic networks from nucleotide sequences. We tested their performances and compared them with other popular methods on two simulated nucleotide sequence data sets: one generated from a tree topology and the other from a complicated evolutionary history containing three reticulate events. We further validated these methods to two real data sets: a bacterial data set consisting of seven concatenated genes of 36 bacterial species and an influenza data set related to recently emerging H7N9 low pathogenic avian influenza viruses in China.Conclusion: QuartetS, QuartetA, and QuartetM have the potential to accurately reconstruct evolutionary scenarios from simple branching trees to complicated networks containing many reticulate events. These methods could provide insights into the understanding of complicated biological evolutionary processes such as bacterial taxonomy and reassortant of influenza viruses. © 2014 Yang et al.; licensee BioMed Central Ltd."
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Kevin J. Liu,
Jingxuan Dai,
Kathy Truong,
Ying Song,
Michael H. Kohn and
Luay Nakhleh. An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes. In PLoS ONE, Vol. 10(6):e1003649, 2014.
Keywords: explicit network, from network, phylogenetic network, phylogeny, Program PhyloNet-HMM.
Note: http://arxiv.org/abs/1310.7989.
Toggle abstract
"One outcome of interspecific hybridization and subsequent effects of evolutionary forces is introgression, which is the integration of genetic material from one species into the genome of an individual in another species. The evolution of several groups of eukaryotic species has involved hybridization, and cases of adaptation through introgression have been already established. In this work, we report on PhyloNet-HMM-a new comparative genomic framework for detecting introgression in genomes. PhyloNet-HMM combines phylogenetic networks with hidden Markov models (HMMs) to simultaneously capture the (potentially reticulate) evolutionary history of the genomes and dependencies within genomes. A novel aspect of our work is that it also accounts for incomplete lineage sorting and dependence across loci. Application of our model to variation data from chromosome 7 in the mouse (Mus musculus domesticus) genome detected a recently reported adaptive introgression event involving the rodent poison resistance gene Vkorc1, in addition to other newly detected introgressed genomic regions. Based on our analysis, it is estimated that about 9% of all sites within chromosome 7 are of introgressive origin (these cover about 13 Mbp of chromosome 7, and over 300 genes). Further, our model detected no introgression in a negative control data set. We also found that our model accurately detected introgression and other evolutionary processes from synthetic data sets simulated under the coalescent model with recombination, isolation, and migration. Our work provides a powerful framework for systematic analysis of introgression while simultaneously accounting for dependence across sites, point mutations, recombination, and ancestral polymorphism. © 2014 Liu et al."
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Leo van Iersel,
Steven Kelk,
Nela Lekic and
Celine Scornavacca. A practical approximation algorithm for solving massive instances of hybridization number for binary and nonbinary trees. In BMCB, Vol. 15(127):1-12, 2014.
Keywords: agreement forest, approximation, explicit network, from rooted trees, phylogenetic network, phylogeny, Program CycleKiller, Program TerminusEst, reconstruction.
Note: http://dx.doi.org/10.1186/1471-2105-15-127.
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Monika Balvociute,
Andreas Spillner and
Vincent Moulton. FlatNJ: A Novel Network-Based Approach to Visualize Evolutionary and Biogeographical Relationships. In Systematic Biology, Vol. 63(3):383-396, 2014.
Keywords: abstract network, flat, phylogenetic network, phylogeny, Program FlatNJ, Program SplitsTree, split network.
Note: http://dx.doi.org/10.1093/sysbio/syu001.
Toggle abstract
"Split networks are a type of phylogenetic network that allow visualization of conflict in evolutionary data. We present a new method for constructing such networks called FlatNetJoining (FlatNJ). A key feature of FlatNJ is that it produces networks that can be drawn in the plane in which labels may appear inside of the network. For complex data sets that involve, for example, non-neutral molecular markers, this can allow additional detail to be visualized as compared to previous methods such as split decomposition and NeighborNet. We illustrate the application of FlatNJ by applying it to whole HIV genome sequences, where recombination has taken place, fluorescent proteins in corals, where ancestral sequences are present, and mitochondrial DNA sequences from gall wasps, where biogeographical relationships are of interest. We find that the networks generated by FlatNJ can facilitate the study of genetic variation in the underlying molecular sequence data and, in particular, may help to investigate processes such as intra-locus recombination. FlatNJ has been implemented in Java and is freely available at www.uea.ac.uk/computing/software/ flatnj. [flat split system; NeighborNet; Phylogenetic network; QNet; split; split network.] © The Author(s) 2014."
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Johann-Mattis List,
Shijulal Nelson-Sathi,
Hans Geisler and
William Martin. Networks of lexical borrowing and lateral gene transfer in language and genome evolution. In BioEssays, Vol. 36(2):141-150, 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."
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Juan Wang. A new algorithm to construct phylogenetic networks from trees. In Genetics and Molecular Research, Vol. 13(1):1456-1464, 2014.
Keywords: explicit network, from clusters, heuristic, phylogenetic network, Program LNetwork, Program QuickCass, reconstruction.
Note: http://dx.doi.org/10.4238/2014.March.6.4.
Toggle abstract
"Developing appropriate methods for constructing phylogenetic networks from tree sets is an important problem, and much research is currently being undertaken in this area. BIMLR is an algorithm that constructs phylogenetic networks from tree sets. The algorithm can construct a much simpler network than other available methods. Here, we introduce an improved version of the BIMLR algorithm, QuickCass. QuickCass changes the selection strategy of the labels of leaves below the reticulate nodes, i.e., the nodes with an indegree of at least 2 in BIMLR. We show that QuickCass can construct simpler phylogenetic networks than BIMLR. Furthermore, we show that QuickCass is a polynomial-time algorithm when the output network that is constructed by QuickCass is binary. © FUNPEC-RP."
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Matthieu Willems,
Nadia Tahiri and
Vladimir Makarenkov. A new efficient algorithm for inferring explicit hybridization networks following the Neighbor-Joining principle. In JBCB, Vol. 12(5), 2014.
Keywords: explicit network, from distances, heuristic, phylogenetic network, phylogeny, reconstruction.
Toggle abstract
"Several algorithms and software have been developed for inferring phylogenetic trees. However, there exist some biological phenomena such as hybridization, recombination, or horizontal gene transfer which cannot be represented by a tree topology. We need to use phylogenetic networks to adequately represent these important evolutionary mechanisms. In this article, we present a new efficient heuristic algorithm for inferring hybridization networks from evolutionary distance matrices between species. The famous Neighbor-Joining concept and the least-squares criterion are used for building networks. At each step of the algorithm, before joining two given nodes, we check if a hybridization event could be related to one of them or to both of them. The proposed algorithm finds the exact tree solution when the considered distance matrix is a tree metric (i.e. it is representable by a unique phylogenetic tree). It also provides very good hybrids recovery rates for large trees (with 32 and 64 leaves in our simulations) for both distance and sequence types of data. The results yielded by the new algorithm for real and simulated datasets are illustrated and discussed in detail. © Imperial College Press."
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Paul Cordue,
Simone Linz and
Charles Semple. Phylogenetic Networks that Display a Tree Twice. In BMB, Vol. 76(10):2664-2679, 2014.
Keywords: from rooted trees, normal network, phylogenetic network, phylogeny, reconstruction, tree-child network.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/CLS14.pdf.
Toggle abstract
"In the last decade, the use of phylogenetic networks to analyze the evolution of species whose past is likely to include reticulation events, such as horizontal gene transfer or hybridization, has gained popularity among evolutionary biologists. Nevertheless, the evolution of a particular gene can generally be described without reticulation events and therefore be represented by a phylogenetic tree. While this is not in contrast to each other, it places emphasis on the necessity of algorithms that analyze and summarize the tree-like information that is contained in a phylogenetic network. We contribute to the toolbox of such algorithms by investigating the question of whether or not a phylogenetic network embeds a tree twice and give a quadratic-time algorithm to solve this problem for a class of networks that is more general than tree-child networks. © 2014, Society for Mathematical Biology."
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Joel Sjöstrand,
Ali Tofigh,
Vincent Daubin,
Lars Arvestad,
Bengt Sennblad and
Jens Lagergren. A Bayesian Method for Analyzing Lateral Gene Transfer. In Systematic Biology, Vol. 63(3):409-420, 2014.
Keywords: bayesian, duplication, from rooted trees, from sequences, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program JPrIME-DLTRS, reconstruction.
Note: http://dx.doi.org/10.1093/sysbio/syu007.
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Adrià Alcalà Mena,
Mercè Llabrés,
Francesc Rosselló and
Pau Rullan. Tree-Child Cluster Networks. In Fundamenta Informaticae, Vol. 134(1-2):1-15, 2014.
Keywords: explicit network, from clusters, phylogenetic network, phylogeny, Program PhyloNetwork, reconstruction, tree-child network.
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Katharina Huber and
Vincent Moulton. Encoding and Constructing 1-Nested Phylogenetic Networks with Trinets. In ALG, Vol. 66(3):714-738, 2013.
Keywords: explicit network, from subnetworks, from trinets, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: http://arxiv.org/abs/1110.0728.
Toggle abstract
"Phylogenetic networks are a generalization of phylogenetic trees that are used in biology to represent reticulate or non-treelike evolution. Recently, several algorithms have been developed which aim to construct phylogenetic networks from biological data using triplets, i.e. binary phylogenetic trees on 3-element subsets of a given set of species. However, a fundamental problem with this approach is that the triplets displayed by a phylogenetic network do not necessarily uniquely determine or encode the network. Here we propose an alternative approach to encoding and constructing phylogenetic networks, which uses phylogenetic networks on 3-element subsets of a set, or trinets, rather than triplets. More specifically, we show that for a special, well-studied type of phylogenetic network called a 1-nested network, the trinets displayed by a 1-nested network always encode the network. We also present an efficient algorithm for deciding whether a dense set of trinets (i.e. one that contains a trinet on every 3-element subset of a set) can be displayed by a 1-nested network or not and, if so, constructs that network. In addition, we discuss some potential new directions that this new approach opens up for constructing and comparing phylogenetic networks. © 2012 Springer Science+Business Media, LLC."
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Leo van Iersel and
Simone Linz. A quadratic kernel for computing the hybridization number of multiple trees. In IPL, Vol. 113:318-323, 2013.
Keywords: explicit network, FPT, from rooted trees, kernelization, minimum number, phylogenetic network, phylogeny, Program Clustistic, Program MaafB, Program PIRN, reconstruction.
Note: http://arxiv.org/abs/1203.4067, poster.
Toggle abstract
"It has recently been shown that the NP-hard problem of calculating the minimum number of hybridization events that is needed to explain a set of rooted binary phylogenetic trees by means of a hybridization network is fixed-parameter tractable if an instance of the problem consists of precisely two such trees. In this paper, we show that this problem remains fixed-parameter tractable for an arbitrarily large set of rooted binary phylogenetic trees. In particular, we present a quadratic kernel. © 2013 Elsevier B.V."
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Chris Whidden,
Robert G. Beiko and
Norbert Zeh. Fixed-Parameter Algorithms for Maximum Agreement Forests. In SICOMP, Vol. 42(4):1431-1466, 2013.
Keywords: agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, SPR distance.
Note: http://arxiv.org/abs/1108.2664, slides.
Toggle abstract
"We present new and improved fixed-parameter algorithms for computing maximum agreement forests of pairs of rooted binary phylogenetic trees. The size of such a forest for two trees corresponds to their subtree prune-and-regraft distance and, if the agreement forest is acyclic, to their hybridization number. These distance measures are essential tools for understanding reticulate evolution. Our algorithm for computing maximum acyclic agreement forests is the first depth-bounded search algorithm for this problem. Our algorithms substantially outperform the best previous algorithms for these problems. © 2013 Society for Industrial and Applied Mathematics."
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Stefan Grünewald,
Andreas Spillner,
Sarah Bastkowski,
Anja Bögershausen and
Vincent Moulton. SuperQ: Computing Supernetworks from Quartets. In TCBB, Vol. 10(1):151-160, 2013.
Keywords: abstract network, circular split system, from quartets, heuristic, phylogenetic network, phylogeny, Program QNet, Program SplitsTree, Program SuperQ, software, split network.
Toggle abstract
"Supertrees are a commonly used tool in phylogenetics to summarize collections of partial phylogenetic trees. As a generalization of supertrees, phylogenetic supernetworks allow, in addition, the visual representation of conflict between the trees that is not possible to observe with a single tree. Here, we introduce SuperQ, a new method for constructing such supernetworks (SuperQ is freely available at >www.uea.ac.uk/computing/superq.). It works by first breaking the input trees into quartet trees, and then stitching these together to form a special kind of phylogenetic network, called a split network. This stitching process is performed using an adaptation of the QNet method for split network reconstruction employing a novel approach to use the branch lengths from the input trees to estimate the branch lengths in the resulting network. Compared with previous supernetwork methods, SuperQ has the advantage of producing a planar network. We compare the performance of SuperQ to the Z-closure and Q-imputation supernetwork methods, and also present an analysis of some published data sets as an illustration of its applicability. © 2004-2012 IEEE."
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Teresa Piovesan and
Steven Kelk. A simple fixed parameter tractable algorithm for computing the hybridization number of two (not necessarily binary) trees. In TCBB, Vol. 10(1):18-25, 2013.
Keywords: FPT, from rooted trees, phylogenetic network, phylogeny, Program TerminusEst, reconstruction.
Note: http://arxiv.org/abs/1207.6090.
Toggle abstract
"Here, we present a new fixed parameter tractable algorithm to compute the hybridization number (r) of two rooted, not necessarily binary phylogenetic trees on taxon set (X) in time ((6r r) · poly(n)), where (n= |X|). The novelty of this approach is its use of terminals, which are maximal elements of a natural partial order on (X), and several insights from the softwired clusters literature. This yields a surprisingly simple and practical bounded-search algorithm and offers an alternative perspective on the underlying combinatorial structure of the hybridization number problem. © 2004-2012 IEEE."
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Stephen J. Willson. Reconstruction of certain phylogenetic networks from their tree-average distances. In BMB, Vol. 75(10):1840-1878, 2013.
Keywords: explicit network, from distances, galled tree, normal network, phylogenetic network, phylogeny, unicyclic network.
Note: http://www.public.iastate.edu/~swillson/Tree-AverageReconPaper9.pdf.
Toggle abstract
"Trees are commonly utilized to describe the evolutionary history of a collection of biological species, in which case the trees are called phylogenetic trees. Often these are reconstructed from data by making use of distances between extant species corresponding to the leaves of the tree. Because of increased recognition of the possibility of hybridization events, more attention is being given to the use of phylogenetic networks that are not necessarily trees. This paper describes the reconstruction of certain such networks from the tree-average distances between the leaves. For a certain class of phylogenetic networks, a polynomial-time method is presented to reconstruct the network from the tree-average distances. The method is proved to work if there is a single reticulation cycle. © 2013 Society for Mathematical Biology."
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Peter J. Humphries,
Simone Linz and
Charles Semple. On the complexity of computing the temporal hybridization number for two phylogenies. In DAM, Vol. 161:871-880, 2013.
Keywords: agreement forest, APX hard, characterization, from rooted trees, hybridization, NP complete, phylogenetic network, phylogeny, reconstruction, time consistent network.
Note: http://ab.inf.uni-tuebingen.de/people/linz/publications/TAFapx.pdf.
Toggle abstract
"Phylogenetic networks are now frequently used to explain the evolutionary history of a set of species for which a collection of gene trees, reconstructed from genetic material of different parts of the species' genomes, reveal inconsistencies. However, in the context of hybridization, the reconstructed networks are often not temporal. If a hybridization network is temporal, then it satisfies the time constraint of instantaneously occurring hybridization events; i.e. all species that are involved in such an event coexist in time. Furthermore, although a collection of phylogenetic trees can often be merged into a hybridization network that is temporal, many algorithms do not necessarily find such a network since their primary optimization objective is to minimize the number of hybridization events. In this paper, we present a characterization for when two rooted binary phylogenetic trees admit a temporal hybridization network. Furthermore, we show that the underlying optimization problem is APX-hard and, therefore, NP-hard. Thus, unless P=NP, it is unlikely that there are efficient algorithms for either computing an exact solution or approximating it within a ratio arbitrarily close to one. © 2012 Elsevier B.V. All rights reserved."
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Jialiang Yang,
Stefan Grünewald and
Xiu-Feng Wan. Quartet-Net: A Quartet Based Method to Reconstruct Phylogenetic Networks. In MBE, Vol. 30(5):1206-1217, 2013.
Keywords: from quartets, phylogenetic network, phylogeny, Program QuartetNet, reconstruction.
Toggle abstract
"Phylogenetic networks can model reticulate evolutionary events such as hybridization, recombination, and horizontal gene transfer. However, reconstructing such networks is not trivial. Popular character-based methods are computationally inefficient, whereas distance-based methods cannot guarantee reconstruction accuracy because pairwise genetic distances only reflect partial information about a reticulate phylogeny. To balance accuracy and computational efficiency, here we introduce a quartet-based method to construct a phylogenetic network from a multiple sequence alignment. Unlike distances that only reflect the relationship between a pair of taxa, quartets contain information on the relationships among four taxa; these quartets provide adequate capacity to infer a more accurate phylogenetic network. In applications to simulated and biological data sets, we demonstrate that this novel method is robust and effective in reconstructing reticulate evolutionary events and it has the potential to infer more accurate phylogenetic distances than other conventional phylogenetic network construction methods such as Neighbor-Joining, Neighbor-Net, and Split Decomposition. This method can be used in constructing phylogenetic networks from simple evolutionary events involving a few reticulate events to complex evolutionary histories involving a large number of reticulate events. A software called Quartet-Net is implemented and available at http://sysbio.cvm.msstate.edu/QuartetNet/. © 2013 The Author."
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Thi-Hau Nguyen,
Vincent Ranwez,
Stéphanie Pointet,
Anne-Muriel Chifolleau Arigon,
Jean-Philippe Doyon and
Vincent Berry. Reconciliation and local gene tree rearrangement can be of mutual profit. In ALMOB, Vol. 8(12), 2013.
Keywords: duplication, explicit network, from rooted trees, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program Mowgli, Program MowgliNNI, Program Prunier, reconstruction, software.
Toggle abstract
"Background: Reconciliation methods compare gene trees and species trees to recover evolutionary events such as duplications, transfers and losses explaining the history and composition of genomes. It is well-known that gene trees inferred from molecular sequences can be partly erroneous due to incorrect sequence alignments as well as phylogenetic reconstruction artifacts such as long branch attraction. In practice, this leads reconciliation methods to overestimate the number of evolutionary events. Several methods have been proposed to circumvent this problem, by collapsing the unsupported edges and then resolving the obtained multifurcating nodes, or by directly rearranging the binary gene trees. Yet these methods have been defined for models of evolution accounting only for duplications and losses, i.e. can not be applied to handle prokaryotic gene families.Results: We propose a reconciliation method accounting for gene duplications, losses and horizontal transfers, that specifically takes into account the uncertainties in gene trees by rearranging their weakly supported edges. Rearrangements are performed on edges having a low confidence value, 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 speed-up the tree space exploration when rearrangements are generated by Nearest Neighbor Interchanges (NNI) edit operations. Experiments on synthetic data show that gene trees modified by such NNI rearrangements are closer to the correct simulated trees and lead to better event predictions on average. Experiments on real data demonstrate that the proposed method leads to a decrease in the reconciliation cost and the number of inferred events. Finally on a dataset of 30 k gene families, this reconciliation method shows a ranking of prokaryotic phyla by transfer rates identical to that proposed by a different approach dedicated to transfer detection [BMCBIOINF 11:324, 2010, PNAS 109(13):4962-4967, 2012].Conclusions: Prokaryotic gene trees can now be reconciled with their species phylogeny while accounting for the uncertainty of the gene tree. More accurate and more precise reconciliations are obtained with respect to previous parsimony algorithms not accounting for such uncertainties [LNCS 6398:93-108, 2010, BIOINF 28(12): i283-i291, 2012].A software implementing the method is freely available at http://www.atgc-montpellier.fr/Mowgli/. © 2013 Nguyen et al.; licensee BioMed Central Ltd."
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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):571-579, 2013.
Keywords: duplication, explicit network, from species tree, from unrooted trees, lateral gene transfer, phylogenetic network, phylogeny, Program HiDe, Program RANGER-DTL, reconstruction.
Note: http://people.csail.mit.edu/mukul/Bansal_Highways_Bioinformatics_2013.pdf.
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Eric Bapteste,
Leo van Iersel,
Axel Janke,
Scott Kelchner,
Steven Kelk,
James O. McInerney,
David A. Morrison,
Luay Nakhleh,
Mike Steel,
Leen Stougie and
James B. Whitfield. Networks: expanding evolutionary thinking. In Trends in Genetics, Vol. 29(8):439-441, 2013.
Keywords: abstract network, explicit network, phylogenetic network, phylogeny, reconstruction.
Note: http://bioinf.nuim.ie/wp-content/uploads/2013/06/Bapteste-TiG-2013.pdf.
Toggle abstract
"Networks allow the investigation of evolutionary relationships that do not fit a tree model. They are becoming a leading tool for describing the evolutionary relationships between organisms, given the comparative complexities among genomes. © 2013 Elsevier Ltd."
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Yun Yu,
R. Matthew Barnett and
Luay Nakhleh. Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting. In Systematic Biology, Vol. 62(5):738-751, 2013.
Keywords: from network, from rooted trees, hybridization, lineage sorting, parsimony, phylogenetic network, phylogeny, Program PhyloNet, reconstruction.
Toggle abstract
"Hybridization plays an important evolutionary role in several groups of organisms. A phylogenetic approach to detect hybridization entails sequencing multiple loci across the genomes of a group of species of interest, reconstructing their gene trees, and taking their differences as indicators of hybridization. However, methods that follow this approach mostly ignore population effects, such as incomplete lineage sorting (ILS). Given that hybridization occurs between closely related organisms, ILS may very well be at play and, hence, must be accounted for in the analysis framework. To address this issue, we present a parsimony criterion for reconciling gene trees within the branches of a phylogenetic network, and a local search heuristic for inferring phylogenetic networks from collections of gene-tree topologies under this criterion. This framework enables phylogenetic analyses while accounting for both hybridization and ILS. Further, we propose two techniques for incorporating information about uncertainty in gene-tree estimates. Our simulation studies demonstrate the good performance of our framework in terms of identifying the location of hybridization events, as well as estimating the proportions of genes that underwent hybridization. Also, our framework shows good performance in terms of efficiency on handling large data sets in our experiments. Further, in analysing a yeast data set, we demonstrate issues that arise when analysing real data sets. Although a probabilistic approach was recently introduced for this problem, and although parsimonious reconciliations have accuracy issues under certain settings, our parsimony framework provides a much more computationally efficient technique for this type of analysis. Our framework now allows for genome-wide scans for hybridization, while also accounting for ILS. [Phylogenetic networks; hybridization; incomplete lineage sorting; coalescent; multi-labeled trees.] © 2013 The Author(s). All rights reserved."
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Juan Wang,
Maozu Guo,
Xiaoyan Liu,
Yang Liu,
Chunyu Wang,
Linlin Xing and
Kai Che. LNETWORK: An Efficient and Effective Method for Constructing Phylogenetic Networks. In BIO, Vol. 29(18):2269-2276, 2013.
Keywords: explicit network, from rooted trees, phylogenetic network, phylogeny, Program LNetwork, reconstruction, software.
Toggle abstract
"Motivation: The evolutionary history of species is traditionally represented with a rooted phylogenetic tree. Each tree comprises a set of clusters, i.e. subsets of the species that are descended from a common ancestor. When rooted phylogenetic trees are built from several different datasets (e.g. from different genes), the clusters are often conflicting. These conflicting clusters cannot be expressed as a simple phylogenetic tree; however, they can be expressed in a phylogenetic network. Phylogenetic networks are a generalization of phylogenetic trees that can account for processes such as hybridization, horizontal gene transfer and recombination, which are difficult to represent in standard tree-like models of evolutionary histories. There is currently a large body of research aimed at developing appropriate methods for constructing phylogenetic networks from cluster sets. The Cass algorithm can construct a much simpler network than other available methods, but is extremely slow for large datasets or for datasets that need lots of reticulate nodes. The networks constructed by Cass are also greatly dependent on the order of input data, i.e. it generally derives different phylogenetic networks for the same dataset when different input orders are used.Results: In this study, we introduce an improved Cass algorithm, Lnetwork, which can construct a phylogenetic network for a given set of clusters. We show that Lnetwork is significantly faster than Cass and effectively weakens the influence of input data order. Moreover, we show that Lnetwork can construct a much simpler network than most of the other available methods. © The Author 2013."
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Juan Wang,
Maozu Guo,
Linlin Xing,
Kai Che,
Xiaoyan Liu and
Chunyu Wang. BIMLR: A Method for Constructing Rooted Phylogenetic Networks from Rooted Phylogenetic Trees. In Gene, Vol. 527(1):344-351, 2013.
Keywords: explicit network, from clusters, from rooted trees, phylogenetic network, phylogeny, Program BIMLR, Program Dendroscope, reconstruction, software.
Toggle abstract
"Rooted phylogenetic trees constructed from different datasets (e.g. from different genes) are often conflicting with one another, i.e. they cannot be integrated into a single phylogenetic tree. Phylogenetic networks have become an important tool in molecular evolution, and rooted phylogenetic networks are able to represent conflicting rooted phylogenetic trees. Hence, the development of appropriate methods to compute rooted phylogenetic networks from rooted phylogenetic trees has attracted considerable research interest of late. The CASS algorithm proposed by van Iersel et al. is able to construct much simpler networks than other available methods, but it is extremely slow, and the networks it constructs are dependent on the order of the input data. Here, we introduce an improved CASS algorithm, BIMLR. We show that BIMLR is faster than CASS and less dependent on the input data order. Moreover, BIMLR is able to construct much simpler networks than almost all other methods. BIMLR is available at http://nclab.hit.edu.cn/wangjuan/BIMLR/. © 2013 Elsevier B.V."
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Zhi-Zhong Chen and
Lusheng Wang. An Ultrafast Tool for Minimum Reticulate Networks. In JCB, Vol. 20(1):38-41, 2013.
Keywords: agreement forest, explicit network, from rooted trees, phylogenetic network, phylogeny, Program ultra-Net, reconstruction.
Note: http://www.cs.cityu.edu.hk/~lwang/research/jcb2013.pdf.
Toggle abstract
"Due to hybridization events in evolution, studying different genes of a set of species may yield two or more related but different phylogenetic trees for the set of species. In this case, we want to combine the trees into a reticulate network with the fewest hybridization events. In this article, we develop a software tool (named UltraNet) for several fundamental problems related to the construction of minimum reticulate networks from two or more phylogenetic trees. Our experimental results show that UltraNet is much faster than all previous tools for these problems. © 2013 Mary Ann Liebert, Inc."
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Peter J. Humphries,
Simone Linz and
Charles Semple. Cherry picking: a characterization of the temporal hybridization number for a set of phylogenies. In BMB, Vol. 75(10):1879-1890, 2013.
Keywords: characterization, cherry-picking, from rooted trees, hybridization, NP complete, phylogenetic network, phylogeny, reconstruction, time consistent network.
Note: http://ab.inf.uni-tuebingen.de/people/linz/publications/CPSpaper.pdf.
Toggle abstract
"Recently, we have shown that calculating the minimum-temporal-hybridization number for a set P of rooted binary phylogenetic trees is NP-hard and have characterized this minimum number when P consists of exactly two trees. In this paper, we give the first characterization of the problem for P being arbitrarily large. The characterization is in terms of cherries and the existence of a particular type of sequence. Furthermore, in an online appendix to the paper, we show that this new characterization can be used to show that computing the minimum-temporal hybridization number for two trees is fixed-parameter tractable. © 2013 Society for Mathematical Biology."
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Alexey A. Morozov,
Yuri P. Galachyants and
Yelena V. Likhoshway. Inferring Phylogenetic Networks from Gene Order Data. In BMRI, Vol. 2013(503193):1-7, 2013.
Keywords: abstract network, from distances, from gene order, NeighborNet, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split decomposition, split network.
Toggle abstract
"Existing algorithms allow us to infer phylogenetic networks from sequences (DNA, protein or binary), sets of trees, and distance matrices, but there are no methods to build them using the gene order data as an input. Here we describe several methods to build split networks from the gene order data, perform simulation studies, and use our methods for analyzing and interpreting different real gene order datasets. All proposed methods are based on intermediate data, which can be generated from genome structures under study and used as an input for network construction algorithms. Three intermediates are used: set of jackknife trees, distance matrix, and binary encoding. According to simulations and case studies, the best intermediates are jackknife trees and distance matrix (when used with Neighbor-Net algorithm). Binary encoding can also be useful, but only when the methods mentioned above cannot be used. © 2013 Alexey Anatolievich Morozov et al."
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Celine Scornavacca,
Paprotny Wojciech,
Vincent Berry and
Vincent Ranwez. Representing a set of reconciliations in a compact way. In JBCB, Vol. 11(2):1250025, 2013.
Keywords: duplication, explicit network, from network, from rooted trees, from species tree, phylogeny, Program GraphDTL, Program TERA, visualization.
Note: http://hal-lirmm.ccsd.cnrs.fr/lirmm-00818801.
Toggle abstract
"Comparative genomic studies are often conducted by reconciliation analyses comparing gene and species trees. One of the issues with reconciliation approaches is that an exponential number of optimal scenarios is possible. The resulting complexity is masked by the fact that a majority of reconciliation software pick up a random optimal solution that is returned to the end-user. However, the alternative solutions should not be ignored since they tell different stories that parsimony considers as viable as the output solution. In this paper, we describe a polynomial space and time algorithm to build a minimum reconciliation graph-a graph that summarizes the set of all most parsimonious reconciliations. Amongst numerous applications, it is shown how this graph allows counting the number of non-equivalent most parsimonious reconciliations. © 2013 Imperial College Press."
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Luay Nakhleh. Computational approaches to species phylogeny inference and gene tree reconciliation. In Trends in Ecology and Evolution, Vol. 28(12):719-728, 2013.
Keywords: from rooted trees, from species tree, phylogenetic network, phylogeny, reconstruction, survey.
Note: http://bioinfo.cs.rice.edu/sites/bioinfo.cs.rice.edu/files/TREE-Nakhleh13.pdf.
Toggle abstract
"An intricate relation exists between gene trees and species phylogenies, due to evolutionary processes that act on the genes within and across the branches of the species phylogeny. From an analytical perspective, gene trees serve as character states for inferring accurate species phylogenies, and species phylogenies serve as a backdrop against which gene trees are contrasted for elucidating evolutionary processes and parameters. In a 1997 paper, Maddison discussed this relation, reviewed the signatures left by three major evolutionary processes on the gene trees, and surveyed parsimony and likelihood criteria for utilizing these signatures to elucidate computationally this relation. Here, I review progress that has been made in developing computational methods for analyses under these two criteria, and survey remaining challenges. © 2013 Elsevier Ltd."
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Thi-Hau Nguyen,
Vincent Ranwez,
Vincent Berry and
Celine Scornavacca. Support Measures to Estimate the Reliability of Evolutionary Events Predicted by Reconciliation Methods. In PLoS ONE, Vol. 8(10):e73667, 2013.
Keywords: duplication, from rooted trees, from species tree, phylogenetic network, phylogeny, polynomial, Program GraphDTL, reconstruction.
Note: http://dx.doi.org/10.1371/journal.pone.0073667.
Toggle abstract
"The genome content of extant species is derived from that of ancestral genomes, distorted by evolutionary events such as gene duplications, transfers and losses. Reconciliation methods aim at recovering such events and at localizing them in the species history, by comparing gene family trees to species trees. These methods play an important role in studying genome evolution as well as in inferring orthology relationships. A major issue with reconciliation methods is that the reliability of predicted evolutionary events may be questioned for various reasons: Firstly, there may be multiple equally optimal reconciliations for a given species tree-gene tree pair. Secondly, reconciliation methods can be misled by inaccurate gene or species trees. Thirdly, predicted events may fluctuate with method parameters such as the cost or rate of elementary events. For all of these reasons, confidence values for predicted evolutionary events are sorely needed. It was recently suggested that the frequency of each event in the set of all optimal reconciliations could be used as a support measure. We put this proposition to the test here and also consider a variant where the support measure is obtained by additionally accounting for suboptimal reconciliations. Experiments on simulated data show the relevance of event supports computed by both methods, while resorting to suboptimal sampling was shown to be more effective. Unfortunately, we also show that, unlike the majority-rule consensus tree for phylogenies, there is no guarantee that a single reconciliation can contain all events having above 50% support. In this paper, we detail how to rely on the reconciliation graph to efficiently identify the median reconciliation. Such median reconciliation can be found in polynomial time within the potentially exponential set of most parsimonious reconciliations. © 2013 Nguyen et al."
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Mukul S. Bansal,
Eric J. Alm and
Manolis Kellis. Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss. In JCB, Vol. 20(10):738-754, 2013.
Keywords: duplication, from rooted trees, from species tree, loss, phylogenetic network, phylogeny, Program RANGER-DTL, reconstruction.
Note: http://www.engr.uconn.edu/~mukul/Bansal_JCB2013.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 duplication-loss (DL) reconciliation leads to a unique maximum-parsimony solution, duplication-transfer-loss (DTL) reconciliation yields a multitude of optimal solutions, making it difficult to infer the true evolutionary history of the gene family. This problem is further exacerbated by the fact that different event cost assignments yield different sets of optimal reconciliations. Here, we present an effective, efficient, and scalable method for dealing with these fundamental problems in DTL reconciliation. Our approach works by sampling the space of optimal reconciliations uniformly at random and aggregating the results. We show that even gene trees with only a few dozen genes often have millions of optimal reconciliations and present an algorithm to efficiently sample the space of optimal reconciliations uniformly at random in O(mn 2) time per sample, 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 mappings and event assignments and to investigate the impact of varying event costs. We apply our method to a biological dataset of approximately 4700 gene trees from 100 taxa and observe that 93% of event assignments and 73% of mappings remain consistent across different multiple optima. Our analysis represents the first systematic investigation of the space of optimal DTL reconciliations and has many important implications for the study of gene family evolution. © 2013 Mary Ann Liebert, Inc."
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Alberto Apostolico,
Matteo Comin,
Andreas W. M. Dress and
Laxmi Parida. Ultrametric networks: a new tool for phylogenetic analysis. In Algorithms for Molecular Biology, Vol. 8(7):1-10, 2013.
Keywords: abstract network, from distances, phylogenetic network, phylogeny, Program Ultranet.
Note: http://dx.doi.org/10.1186/1748-7188-8-7.
Toggle abstract
"Background: The large majority of optimization problems related to the inference of distance-based trees used in phylogenetic analysis and classification is known to be intractable. One noted exception is found within the realm of ultrametric distances. The introduction of ultrametric trees in phylogeny was inspired by a model of evolution driven by the postulate of a molecular clock, now dismissed, whereby phylogeny could be represented by a weighted tree in which the sum of the weights of the edges separating any given leaf from the root is the same for all leaves. Both, molecular clocks and rooted ultrametric trees, fell out of fashion as credible representations of evolutionary change. At the same time, ultrametric dendrograms have shown good potential for purposes of classification in so far as they have proven to provide good approximations for additive trees. Most of these approximations are still intractable, but the problem of finding the nearest ultrametric distance matrix to a given distance matrix with respect to the L∞ distance has been long known to be solvable in polynomial time, the solution being incarnated in any minimum spanning tree for the weighted graph subtending to the matrix.Results: This paper expands this subdominant ultrametric perspective by studying ultrametric networks, consisting of the collection of all edges involved in some minimum spanning tree. It is shown that, for a graph with n vertices, the construction of such a network can be carried out by a simple algorithm in optimal time O(n2) which is faster by a factor of n than the direct adaptation of the classical O(n3) paradigm by Warshall for computing the transitive closure of a graph. This algorithm, called UltraNet, will be shown to be easily adapted to compute relaxed networks and to support the introduction of artificial points to reduce the maximum distance between vertices in a pair. Finally, a few experiments will be discussed to demonstrate the applicability of subdominant ultrametric networks.Availability: http://www.dei.unipd.it/~ciompin/main/Ultranet/Ultranet.html. © 2013 Apostolico et al.; licensee BioMed Central Ltd."
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Mehdi Layeghifard,
Pedro R. Peres-Neto and
Vladimir Makarenkov. Inferring explicit weighted consensus networks to represent alternative evolutionary histories. In BMCEB, Vol. 13(274):1-25, 2013.
Keywords: explicit network, from rooted trees, from species tree, phylogenetic network, phylogeny, Program ConsensusNetwork, reconstruction.
Note: http://dx.doi.org/10.1186/1471-2148-13-274.
Toggle abstract
"Background: The advent of molecular biology techniques and constant increase in availability of genetic material have triggered the development of many phylogenetic tree inference methods. However, several reticulate evolution processes, such as horizontal gene transfer and hybridization, have been shown to blur the species evolutionary history by causing discordance among phylogenies inferred from different genes. Methods. To tackle this problem, we hereby describe a new method for inferring and representing alternative (reticulate) evolutionary histories of species as an explicit weighted consensus network which can be constructed from a collection of gene trees with or without prior knowledge of the species phylogeny. Results: We provide a way of building a weighted phylogenetic network for each of the following reticulation mechanisms: diploid hybridization, intragenic recombination and complete or partial horizontal gene transfer. We successfully tested our method on some synthetic and real datasets to infer the above-mentioned evolutionary events which may have influenced the evolution of many species. Conclusions: Our weighted consensus network inference method allows one to infer, visualize and validate statistically major conflicting signals induced by the mechanisms of reticulate evolution. The results provided by the new method can be used to represent the inferred conflicting signals by means of explicit and easy-to-interpret phylogenetic networks. © 2013 Layeghifard et al.; licensee BioMed Central Ltd."
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Gergely J. Szöllösi,
Eric Tannier,
Nicolas Lartillot and
Vincent Daubin. Lateral Gene Transfer from the Dead. In Systematic Biology, Vol. 62(3):386-397, 2013.
Keywords: duplication, lateral gene transfer, likelihood, loss, phylogeny, Program TERA, reconstruction.
Note: http://dx.doi.org/10.1093/sysbio/syt003.
Toggle abstract
"In phylogenetic studies, the evolution of molecular sequences is assumed to have taken place along the phylogeny traced by the ancestors of extant species. In the presence of lateral gene transfer, however, this may not be the case, because the species lineage from which a gene was transferred may have gone extinct or not have been sampled. Because it is not feasible to specify or reconstruct the complete phylogeny of all species, we must describe the evolution of genes outside the represented phylogeny by modeling the speciation dynamics that gave rise to the complete phylogeny. We demonstrate that if the number of sampled species is small compared with the total number of existing species, the overwhelming majority of gene transfers involve speciation to and evolution along extinct or unsampled lineages. We show that the evolution of genes along extinct or unsampled lineages can to good approximation be treated as those of independently evolving lineages described by a few global parameters. Using this result, we derive an algorithm to calculate the probability of a gene tree and recover the maximum-likelihood reconciliation given the phylogeny of the sampled species. Examining 473 near-universal gene families from 36 cyanobacteria, we find that nearly a third of transfer events (28%) appear to have topological signatures of evolution along extinct species, but only approximately 6% of transfers trace their ancestry to before the common ancestor of the sampled cyanobacteria. © 2013 The Author(s)."
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Gergely J. Szöllösi,
Wojciech Rosikiewicz,
Bastien Boussau,
Eric Tannier and
Vincent Daubin. Efficient Exploration of the Space of Reconciled Gene Trees. In Systematic Biology, Vol. 62(6):901-912, 2013.
Keywords: duplication, explicit network, lateral gene transfer, likelihood, loss, phylogeny, Program ALE, reconstruction.
Note: http://arxiv.org/abs/1306.2167.
Toggle abstract
"Gene trees record the combination of gene-level events, such as duplication, transfer and loss (DTL), and species-level events, such as speciation and extinction. Gene tree-species tree reconciliation methods model these processes by drawing gene trees into the species tree using a series of gene and species-level events. The reconstruction of gene trees based on sequence alone almost always involves choosing between statistically equivalent or weakly distinguishable relationships that could be much better resolved based on a putative species tree. To exploit this potential for accurate reconstruction of gene trees, the space of reconciled gene trees must be explored according to a joint model of sequence evolution and gene tree-species tree reconciliation. Here we present amalgamated likelihood estimation (ALE), a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgamated as a combination of clades observed in a sample of gene trees. We implement the ALE approach in the context of a reconciliation model (Szöllo{double acute}si et al. 2013), which allows for the DTL of genes. We use ALE to efficiently approximate the sum of the joint likelihood over amalgamations and to find the reconciled gene tree that maximizes the joint likelihood among all such trees. We demonstrate using simulations that gene trees reconstructed using the joint likelihood are substantially more accurate than those reconstructed using sequence alone. Using realistic gene tree topologies, branch lengths, and alignment sizes, we demonstrate that ALE produces more accurate gene trees even if the model of sequence evolution is greatly simplified. Finally, examining 1099 gene families from 36 cyanobacterial genomes we find that joint likelihood-based inference results in a striking reduction in apparent phylogenetic discord, with respectively. 24%, 59%, and 46% reductions in the mean numbers of duplications, transfers, and losses per gene family. The open source implementation of ALE is available from https://github.com/ssolo/ALE.git. © The Author(s) 2013."
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Philippe Gambette and
Katharina Huber. On Encodings of Phylogenetic Networks of Bounded Level. In JOMB, Vol. 65(1):157-180, 2012.
Keywords: characterization, explicit network, from clusters, from rooted trees, from triplets, galled tree, identifiability, level k phylogenetic network, phylogenetic network, uniqueness, weak hierarchy.
Note: http://hal.archives-ouvertes.fr/hal-00609130/en/.
Toggle abstract
"Phylogenetic networks have now joined phylogenetic trees in the center of phylogenetics research. Like phylogenetic trees, such networks canonically induce collections of phylogenetic trees, clusters, and triplets, respectively. Thus it is not surprising that many network approaches aim to reconstruct a phylogenetic network from such collections. Related to the well-studied perfect phylogeny problem, the following question is of fundamental importance in this context: When does one of the above collections encode (i. e. uniquely describe) the network that induces it? For the large class of level-1 (phylogenetic) networks we characterize those level-1 networks for which an encoding in terms of one (or equivalently all) of the above collections exists. In addition, we show that three known distance measures for comparing phylogenetic networks are in fact metrics on the resulting subclass and give the diameter for two of them. Finally, we investigate the related concept of indistinguishability and also show that many properties enjoyed by level-1 networks are not satisfied by networks of higher level. © 2011 Springer-Verlag."
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Stephen J. Willson. CSD Homomorphisms Between Phylogenetic Networks. In TCBB, Vol. 9(4), 2012.
Keywords: explicit network, from network, from quartets, phylogenetic network.
Note: http://www.public.iastate.edu/~swillson/Relationships11IEEE.pdf, preliminary version entitled Relationships Among Phylogenetic Networks.
Toggle abstract
"Since Darwin, species trees have been used as a simplified description of the relationships which summarize the complicated network N of reality. Recent evidence of hybridization and lateral gene transfer, however, suggest that there are situations where trees are inadequate. Consequently it is important to determine properties that characterize networks closely related to N and possibly more complicated than trees but lacking the full complexity of N. A connected surjective digraph map (CSD) is a map f from one network N to another network M such that every arc is either collapsed to a single vertex or is taken to an arc, such that f is surjective, and such that the inverse image of a vertex is always connected. CSD maps are shown to behave well under composition. It is proved that if there is a CSD map from N to M, then there is a way to lift an undirected version of M into N, often with added resolution. A CSD map from N to M puts strong constraints on N. In general, it may be useful to study classes of networks such that, for any N, there exists a CSD map from N to some standard member of that class. © 2012 IEEE."
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Steven Kelk,
Celine Scornavacca and
Leo van Iersel. On the elusiveness of clusters. In TCBB, Vol. 9(2):517-534, 2012.
Keywords: explicit network, from clusters, from rooted trees, from triplets, level k phylogenetic network, phylogenetic network, phylogeny, Program Clustistic, reconstruction, software.
Note: http://arxiv.org/abs/1103.1834.
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Jeremy G. Sumner,
Barbara R. Holland and
Peter D. Jarvis. The algebra of the general Markov model on phylogenetic trees and networks. In BMB, Vol. 74(4):858-880, 2012.
Keywords: abstract network, phylogenetic network, phylogeny, split, split network, statistical model.
Note: http://arxiv.org/abs/1012.5165.
Toggle abstract
"It is known that the Kimura 3ST model of sequence evolution on phylogenetic trees can be extended quite naturally to arbitrary split systems. However, this extension relies heavily on mathematical peculiarities of the associated Hadamard transformation, and providing an analogous augmentation of the general Markov model has thus far been elusive. In this paper, we rectify this shortcoming by showing how to extend the general Markov model on trees to include incompatible edges; and even further to more general network models. This is achieved by exploring the algebra of the generators of the continuous-time Markov chain together with the "splitting" operator that generates the branching process on phylogenetic trees. For simplicity, we proceed by discussing the two state case and then show that our results are easily extended to more states with little complication. Intriguingly, upon restriction of the two state general Markov model to the parameter space of the binary symmetric model, our extension is indistinguishable from the Hadamard approach only on trees; as soon as any incompatible splits are introduced the two approaches give rise to differing probability distributions with disparate structure. Through exploration of a simple example, we give an argument that our extension to more general networks has desirable properties that the previous approaches do not share. In particular, our construction allows for convergent evolution of previously divergent lineages; a property that is of significant interest for biological applications. © 2011 Society for Mathematical Biology."
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Andreas Spillner,
Binh T. Nguyen and
Vincent Moulton. Constructing and Drawing Regular Planar Split Networks. In TCBB, Vol. 9(2):395-407, 2012.
Keywords: abstract network, from splits, phylogenetic network, phylogeny, reconstruction, visualization.
Note: slides and presentation available at http://www.newton.ac.uk/programmes/PLG/seminars/062111501.html.
Toggle abstract
"Split networks are commonly used to visualize collections of bipartitions, also called splits, of a finite set. Such collections arise, for example, in evolutionary studies. Split networks can be viewed as a generalization of phylogenetic trees and may be generated using the SplitsTree package. Recently, the NeighborNet method for generating split networks has become rather popular, in part because it is guaranteed to always generate a circular split system, which can always be displayed by a planar split network. Even so, labels must be placed on the "outside" of the network, which might be problematic in some applications. To help circumvent this problem, it can be helpful to consider so-called flat split systems, which can be displayed by planar split networks where labels are allowed on the inside of the network too. Here, we present a new algorithm that is guaranteed to compute a minimal planar split network displaying a flat split system in polynomial time, provided the split system is given in a certain format. We will also briefly discuss two heuristics that could be useful for analyzing phylogeographic data and that allow the computation of flat split systems in this format in polynomial time. © 2006 IEEE."
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Paul Phipps and
Sergey Bereg. Optimizing Phylogenetic Networks for Circular Split Systems. In TCBB, Vol. 9(2):535-547, 2012.
Keywords: abstract network, from distances, from splits, phylogenetic network, phylogeny, Program PhippsNetwork, reconstruction, software.
Toggle abstract
"We address the problem of realizing a given distance matrix by a planar phylogenetic network with a minimum number of faces. With the help of the popular software SplitsTree4, we start by approximating the distance matrix with a distance metric that is a linear combination of circular splits. The main results of this paper are the necessary and sufficient conditions for the existence of a network with a single face. We show how such a network can be constructed, and we present a heuristic for constructing a network with few faces using the first algorithm as the base case. Experimental results on biological data show that this heuristic algorithm can produce phylogenetic networks with far fewer faces than the ones computed by SplitsTree4, without affecting the approximation of the distance matrix. © 2012 IEEE."
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Andreas Spillner and
Vincent Moulton. Optimal algorithms for computing edge weights in planar split-networks. In Journal of Applied Mathematics and Computing, Vol. 39(1-2):1-13, 2012.
Keywords: abstract network, from distances, phylogenetic network, phylogeny, reconstruction, split, split network.
Note: http://dx.doi.org/10.1007/s12190-011-0506-z.
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"In phylogenetics, biologists commonly compute split networks when trying to better understand evolutionary data. These graph-theoretical structures represent collections of weighted bipartitions or splits of a finite set, and provide a means to display conflicting evolutionary signals. The weights associated to the splits are used to scale the edges in the network and are often computed using some distance matrix associated with the data. In this paper we present optimal polynomial time algorithms for three basic problems that arise in this context when computing split weights for planar split-networks. These generalize algorithms that have been developed for special classes of split networks (namely, trees and outer-labeled planar networks). As part of our analysis, we also derive a Crofton formula for full flat split systems, structures that naturally arise when constructing planar split-networks. © 2011 Korean Society for Computational and Applied Mathematics."
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Magnus Bordewich and
Charles Semple. Budgeted Nature Reserve Selection with diversity feature loss and arbitrary split systems. In JOMB, Vol. 64(1):69-85, 2012.
Keywords: abstract network, approximation, diversity, phylogenetic network, polynomial, split network.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BS11.pdf.
Toggle abstract
"Arising in the context of biodiversity conservation, the Budgeted Nature Reserve Selection (BNRS) problem is to select, subject to budgetary constraints, a set of regions to conserve so that the phylogenetic diversity (PD) of the set of species contained within those regions is maximized. Here PD is measured across either a single rooted tree or a single unrooted tree. Nevertheless, in both settings, this problem is NP-hard. However, it was recently shown that, for each setting, there is a polynomial-time (1-1/e)-approximation algorithm for it and that this algorithm is tight. In the first part of the paper, we consider two extensions of BNRS. In the rooted setting we additionally allow for the disappearance of features, for varying survival probabilities across species, and for PD to be measured across multiple trees. In the unrooted setting, we extend to arbitrary split systems. We show that, despite these additional allowances, there remains a polynomial-time (1-1/e)-approximation algorithm for each extension. In the second part of the paper, we resolve a complexity problem on computing PD across an arbitrary split system left open by Spillner et al. © 2011 Springer-Verlag."
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Celine Scornavacca,
Simone Linz and
Benjamin Albrecht. A fi rst step towards computing all hybridization networks for two rooted binary phylogenetic trees. In JCB, Vol. 19:1227-1242, 2012.
Keywords: agreement forest, explicit network, FPT, from rooted trees, phylogenetic network, phylogeny, Program Dendroscope, Program Hybroscale, reconstruction.
Note: http://arxiv.org/abs/1109.3268.
Toggle abstract
"Recently, considerable effort has been put into developing fast algorithms to reconstruct a rooted phylogenetic network that explains two rooted phylogenetic trees and has a minimum number of hybridization vertices. With the standard app1235roach to tackle this problem being combinatorial, the reconstructed network is rarely unique. From a biological point of view, it is therefore of importance to not only compute one network, but all possible networks. In this article, we make a first step toward approaching this goal by presenting the first algorithm-called allMAAFs-that calculates all maximum-acyclic-agreement forests for two rooted binary phylogenetic trees on the same set of taxa. © Copyright 2012, Mary Ann Liebert, Inc. 2012."
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Simon Joly. JML: Testing hybridization from species trees. In Molecular Ecology Ressources, Vol. 12(1):179-184, 2012.
Keywords: from species tree, hybridization, lineage sorting, phylogenetic network, phylogeny, Program JML, statistical model.
Note: http://www.plantevolution.org/pdf/JMLpaper_accepted.pdf.
Toggle abstract
"I introduce the software jml that tests for the presence of hybridization in multispecies sequence data sets by posterior predictive checking following Joly, McLenachan and Lockhart (2009, American Naturalist e54). Although their method could potentially be applied on any data set, the lack of appropriate software made its application difficult. The software jml thus fills a need for an easy application of the method but also includes improvements such as the possibility to incorporate uncertainty in the species tree topology. The jml software uses a posterior distribution of species trees, population sizes and branch lengths to simulate replicate sequence data sets using the coalescent with no migration. A test quantity, defined as the minimum pairwise sequence distance between sequences of two species, is then evaluated on the simulated data sets and compared to the one estimated from the original data. Because the test quantity is a good predictor of hybridization events, departure from the bifurcating species tree model could be interpreted as evidence of hybridization. Software performance in terms of computing time is evaluated for several parameters. I also show an application example of the software for detecting hybridization among native diploid North American roses. © 2011 Blackwell Publishing Ltd."
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Zhi-Zhong Chen and
Lusheng Wang. Algorithms for Reticulate Networks of Multiple Phylogenetic Trees. In TCBB, Vol. 9(2):372-384, 2012.
Keywords: explicit network, from rooted trees, minimum number, phylogenetic network, phylogeny, Program CMPT, Program MaafB, reconstruction, software.
Note: http://rnc.r.dendai.ac.jp/~chen/papers/rMaaf.pdf.
Toggle abstract
"A reticulate network N of multiple phylogenetic trees may have nodes with two or more parents (called reticulation nodes). There are two ways to define the reticulation number of N. One way is to define it as the number of reticulation nodes in N in this case, a reticulate network with the smallest reticulation number is called an optimal type-I reticulate network of the trees. The better way is to define it as the total number of parents of reticulation nodes in N minus the number of reticulation nodes in N ; in this case, a reticulate network with the smallest reticulation number is called an optimal type-II reticulate network of the trees. In this paper, we first present a fast fixed-parameter algorithm for constructing one or all optimal type-I reticulate networks of multiple phylogenetic trees. We then use the algorithm together with other ideas to obtain an algorithm for estimating a lower bound on the reticulation number of an optimal type-II reticulate network of the input trees. To our knowledge, these are the first fixed-parameter algorithms for the problems. We have implemented the algorithms in ANSI C, obtaining programs CMPT and MaafB. Our experimental data show that CMPT can construct optimal type-I reticulate networks rapidly and MaafB can compute better lower bounds for optimal type-II reticulate networks within shorter time than the previously best program PIRN designed by Wu. © 2006 IEEE."
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Stephen J. Willson. Tree-average distances on certain phylogenetic networks have their weights uniquely determined. In ALMOB, Vol. 7(13), 2012.
Keywords: from distances, from network, normal network, phylogenetic network, phylogeny, reconstruction, tree-child network.
Note: hhttp://www.public.iastate.edu/~swillson/Tree-AverageDis10All.pdf.
Toggle abstract
"A phylogenetic network N has vertices corresponding to species and arcs corresponding to direct genetic inheritance from the species at the tail to the species at the head. Measurements of DNA are often made on species in the leaf set, and one seeks to infer properties of the network, possibly including the graph itself. In the case of phylogenetic trees, distances between extant species are frequently used to infer the phylogenetic trees by methods such as neighbor-joining.This paper proposes a tree-average distance for networks more general than trees. The notion requires a weight on each arc measuring the genetic change along the arc. For each displayed tree the distance between two leaves is the sum of the weights along the path joining them. At a hybrid vertex, each character is inherited from one of its parents. We will assume that for each hybrid there is a probability that the inheritance of a character is from a specified parent. Assume that the inheritance events at different hybrids are independent. Then for each displayed tree there will be a probability that the inheritance of a given character follows the tree; this probability may be interpreted as the probability of the tree. The tree-average distance between the leaves is defined to be the expected value of their distance in the displayed trees.For a class of rooted networks that includes rooted trees, it is shown that the weights and the probabilities at each hybrid vertex can be calculated given the network and the tree-average distances between the leaves. Hence these weights and probabilities are uniquely determined. The hypotheses on the networks include that hybrid vertices have indegree exactly 2 and that vertices that are not leaves have a tree-child. © 2012 Willson; licensee BioMed Central Ltd."
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Changiz Eslahchi,
Reza Hassanzadeh,
Ehsan Mottaghi,
Mahnaz Habibi,
Hamid Pezeshk and
Mehdi Sadeghi. Constructing circular phylogenetic networks from weighted quartets using simulated annealing. In MBIO, Vol. 235(2):123-127, 2012.
Keywords: abstract network, from quartets, heuristic, phylogenetic network, phylogeny, Program SAQ-Net, Program SplitsTree, reconstruction, simulated annealing, software, split network.
Note: http://dx.doi.org/10.1016/j.mbs.2011.11.003.
Toggle abstract
"In this paper, we present a heuristic algorithm based on the simulated annealing, SAQ-Net, as a method for constructing phylogenetic networks from weighted quartets. Similar to QNet algorithm, SAQ-Net constructs a collection of circular weighted splits of the taxa set. This collection is represented by a split network. In order to show that SAQ-Net performs better than QNet, we apply these algorithm to both the simulated and actual data sets containing salmonella, Bees, Primates and Rubber data sets. Then we draw phylogenetic networks corresponding to outputs of these algorithms using SplitsTree4 and compare the results. We find that SAQ-Net produces a better circular ordering and phylogenetic networks than QNet in most cases. SAQ-Net has been implemented in Matlab and is available for download at http://bioinf.cs.ipm.ac.ir/softwares/saq.net. © 2011 Elsevier Inc."
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Benjamin Albrecht,
Celine Scornavacca,
Alberto Cenci and
Daniel H. Huson. Fast computation of minimum hybridization networks. In BIO, Vol. 28(2):191-197, 2012.
Keywords: explicit network, from rooted trees, minimum number, phylogenetic network, phylogeny, Program Dendroscope, Program Hybroscale, reconstruction.
Note: http://dx.doi.org/10.1093/bioinformatics/btr618.
Toggle abstract
"Motivation: Hybridization events in evolution may lead to incongruent gene trees. One approach to determining possible interspecific hybridization events is to compute a hybridization network that attempts to reconcile incongruent gene trees using a minimum number of hybridization events. Results: We describe how to compute a representative set of minimum hybridization networks for two given bifurcating input trees, using a parallel algorithm and provide a user-friendly implementation. A simulation study suggests that our program performs significantly better than existing software on biologically relevant data. Finally, we demonstrate the application of such methods in the context of the evolution of the Aegilops/Triticum genera. Availability and implementation: The algorithm is implemented in the program Dendroscope 3, which is freely available from www.dendroscope.org and runs on all three major operating systems. © The Author 2011. Published by Oxford University Press. All rights reserved."
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Steven Kelk,
Leo van Iersel,
Nela Lekic,
Simone Linz,
Celine Scornavacca and
Leen Stougie. Cycle killer... qu'est-ce que c'est? On the comparative approximability of hybridization number and directed feedback vertex set. In SIDMA, Vol. 26(4):1635-1656, 2012.
Keywords: agreement forest, approximation, explicit network, from rooted trees, minimum number, phylogenetic network, phylogeny, Program CycleKiller, reconstruction.
Note: http://arxiv.org/abs/1112.5359, about the title.
Toggle abstract
"We show that the problem of computing the hybridization number of two rooted binary phylogenetic trees on the same set of taxa X has a constant factor polynomial-time approximation if and only if the problem of computing a minimum-size feedback vertex set in a directed graph (DFVS) has a constant factor polynomial-time approximation. The latter problem, which asks for a minimum number of vertices to be removed from a directed graph to transform it into a directed acyclic graph, is one of the problems in Karp's seminal 1972 list of 21 NP-complete problems. Despite considerable attention from the combinatorial optimization community, it remains to this day unknown whether a constant factor polynomial-time approximation exists for DFVS. Our result thus places the (in)approximability of hybridization number in a much broader complexity context, and as a consequence we obtain that it inherits inapproximability results from the problem Vertex Cover. On the positive side, we use results from the DFVS literature to give an O(log r log log r) approximation for the hybridization number where r is the correct value. Copyright © by SIAM."
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Rosalba Radice. A Bayesian Approach to Modelling Reticulation Events with Application to the Ribosomal Protein Gene rps11 of Flowering Plants. In Australian & New Zealand Journal of Statistics, Vol. 54(4):401-426, 2012.
Keywords: bayesian, phylogenetic network, phylogeny, reconstruction, statistical model.
Toggle abstract
"Traditional phylogenetic inference assumes that the history of a set of taxa can be explained by a tree. This assumption is often violated as some biological entities can exchange genetic material giving rise to non-treelike events often called reticulations. Failure to consider these events might result in incorrectly inferred phylogenies. Phylogenetic networks provide a flexible tool which allows researchers to model the evolutionary history of a set of organisms in the presence of reticulation events. In recent years, a number of methods addressing phylogenetic network parameter estimation have been introduced. Some of them are based on the idea that a phylogenetic network can be defined as a directed acyclic graph. Based on this definition, we propose a Bayesian approach to the estimation of phylogenetic network parameters which allows for different phylogenies to be inferred at different parts of a multiple DNA alignment. The algorithm is tested on simulated data and applied to the ribosomal protein gene rps11 data from five flowering plants, where reticulation events are suspected to be present. The proposed approach can be applied to a wide variety of problems which aim at exploring the possibility of reticulation events in the history of a set of taxa. © 2012 Australian Statistical Publishing Association Inc. Published by Wiley Publishing Asia Pty Ltd."
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Philippe Gambette,
Vincent Berry and
Christophe Paul. Quartets and Unrooted Phylogenetic Networks. In JBCB, Vol. 10(4):1250004, 2012.
Keywords: abstract network, circular split system, explicit network, from quartets, level k phylogenetic network, orientation, phylogenetic network, phylogeny, polynomial, reconstruction, split, split network.
Note: http://hal.archives-ouvertes.fr/hal-00678046/en/.
Toggle abstract
"Phylogenetic networks were introduced to describe evolution in the presence of exchanges of genetic material between coexisting species or individuals. Split networks in particular were introduced as a special kind of abstract network to visualize conflicts between phylogenetic trees which may correspond to such exchanges. More recently, methods were designed to reconstruct explicit phylogenetic networks (whose vertices can be interpreted as biological events) from triplet data. In this article, we link abstract and explicit networks through their combinatorial properties, by introducing the unrooted analog of level-k networks. In particular, we give an equivalence theorem between circular split systems and unrooted level-1 networks. We also show how to adapt to quartets some existing results on triplets, in order to reconstruct unrooted level-k phylogenetic networks. These results give an interesting perspective on the combinatorics of phylogenetic networks and also raise algorithmic and combinatorial questions. © 2012 Imperial College Press."
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Yun Yu,
James H. Degnan and
Luay Nakhleh. The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection. In PLoS Genetics, Vol. 8(4):e1002660, 2012.
Keywords: AIC, BIC, explicit network, hybridization, phylogenetic network, phylogeny, statistical model.
Note: http://dx.doi.org/10.1371/journal.pgen.1002660.
Toggle abstract
"Gene tree topologies have proven a powerful data source for various tasks, including species tree inference and species delimitation. Consequently, methods for computing probabilities of gene trees within species trees have been developed and widely used in probabilistic inference frameworks. All these methods assume an underlying multispecies coalescent model. However, when reticulate evolutionary events such as hybridization occur, these methods are inadequate, as they do not account for such events. Methods that account for both hybridization and deep coalescence in computing the probability of a gene tree topology currently exist for very limited cases. However, no such methods exist for general cases, owing primarily to the fact that it is currently unknown how to compute the probability of a gene tree topology within the branches of a phylogenetic network. Here we present a novel method for computing the probability of gene tree topologies on phylogenetic networks and demonstrate its application to the inference of hybridization in the presence of incomplete lineage sorting. We reanalyze a Saccharomyces species data set for which multiple analyses had converged on a species tree candidate. Using our method, though, we show that an evolutionary hypothesis involving hybridization in this group has better support than one of strict divergence. A similar reanalysis on a group of three Drosophila species shows that the data is consistent with hybridization. Further, using extensive simulation studies, we demonstrate the power of gene tree topologies at obtaining accurate estimates of branch lengths and hybridization probabilities of a given phylogenetic network. Finally, we discuss identifiability issues with detecting hybridization, particularly in cases that involve extinction or incomplete sampling of taxa. © 2012 Yu et al."
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Bonnie Kirkpatrick,
Yakir Reshef,
Hilary Finucane,
Haitao Jiang,
Binhai Zhu and
Richard M. Karp. Comparing Pedigree Graphs. In JCB, Vol. 19(9):998-1014, 2012.
Keywords: distance between networks, from network, pedigree.
Note: http://arxiv.org/abs/1009.0909, preliminary version as poster at WABI 2010.
Toggle abstract
"Pedigree graphs, or family trees, are typically constructed by an expensive process of examining genealogical records to determine which pairs of individuals are parent and child. New methods to automate this process take as input genetic data from a set of extant individuals and reconstruct ancestral individuals. There is a great need to evaluate the quality of these methods by comparing the estimated pedigree to the true pedigree. In this article, we consider two main pedigree comparison problems. The first is the pedigree isomorphism problem, for which we present a linear-time algorithm for leaf-labeled pedigrees. The second is the pedigree edit distance problem, for which we present (1) several algorithms that are fast and exact in various special cases, and (2) a general, randomized heuristic algorithm. In the negative direction, we first prove that the pedigree isomorphism problem is as hard as the general graph isomorphism problem, and that the sub-pedigree isomorphism problem is NP-hard. We then show that the pedigree edit distance problem is APX-hard in general and NP-hard on leaf-labeled pedigrees. We use simulated pedigrees to compare our edit-distance algorithms to each other as well as to a branch-and-bound algorithm that always finds an optimal solution. © 2012, Mary Ann Liebert, Inc."
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Reza Hassanzadeh,
Changiz Eslahchi and
Wing-Kin Sung. Constructing phylogenetic supernetworks based on simulated annealing. In MPE, Vol. 63(3):738-744, 2012.
Keywords: abstract network, from unrooted trees, heuristic, phylogenetic network, phylogeny, Program SNSA, reconstruction, simulated annealing, software, split network.
Note: http://dx.doi.org/10.1016/j.ympev.2012.02.009.
Toggle abstract
Different partial phylogenetic trees can be derived from different sources of evidence and different methods. One important problem is to summarize these partial phylogenetic trees using a supernetwork. We propose a novel simulated annealing based method called SNSA which uses an optimization function to produce a simple network that still retains a great deal of phylogenetic information. We report the performance of this new method on real and simulated datasets. © 2012 Elsevier Inc.
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Tetsuo Asano,
Jesper Jansson,
Kunihiko Sadakane,
Ryuhei Uehara and
Gabriel Valiente. Faster computation of the Robinson–Foulds distance between phylogenetic networks. In Information Sciences, Vol. 197:77-90, 2012.
Keywords: distance between networks, explicit network, level k phylogenetic network, phylogenetic network, polynomial, spread.
Toggle abstract
"The Robinson-Foulds distance, a widely used metric for comparing phylogenetic trees, has recently been generalized to phylogenetic networks. Given two phylogenetic networks N 1, N 2 with n leaf labels and at most m nodes and e edges each, the Robinson-Foulds distance measures the number of clusters of descendant leaves not shared by N 1 and N 2. The fastest known algorithm for computing the Robinson-Foulds distance between N 1 and N 2 runs in O(me) time. In this paper, we improve the time complexity to O(ne/log n) for general phylogenetic networks and O(nm/log n) for general phylogenetic networks with bounded degree (assuming the word RAM model with a word length of ⌈logn⌉ bits), and to optimal O(m) time for leaf-outerplanar networks as well as optimal O(n) time for level-1 phylogenetic networks (that is, galled-trees). 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 level-k network is at most k + 1, which implies that for one level-1 and one level-k phylogenetic network, our algorithm runs in O((k + 1)e) time. © 2012 Elsevier Inc. All rights reserved."
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Lavanya Kannan and
Ward C Wheeler. Maximum Parsimony on Phylogenetic Networks. In ALMOB, Vol. 7:9, 2012.
Keywords: dynamic programming, explicit network, from sequences, heuristic, parsimony, phylogenetic network, phylogeny.
Note: http://dx.doi.org/10.1186/1748-7188-7-9.
Toggle abstract
"Background: Phylogenetic networks are generalizations of phylogenetic trees, that are used to model evolutionary events in various contexts. Several different methods and criteria have been introduced for reconstructing phylogenetic trees. Maximum Parsimony is a character-based approach that infers a phylogenetic tree by minimizing the total number of evolutionary steps required to explain a given set of data assigned on the leaves. Exact solutions for optimizing parsimony scores on phylogenetic trees have been introduced in the past.Results: In this paper, we define the parsimony score on networks as the sum of the substitution costs along all the edges of the network; and show that certain well-known algorithms that calculate the optimum parsimony score on trees, such as Sankoff and Fitch algorithms extend naturally for networks, barring conflicting assignments at the reticulate vertices. We provide heuristics for finding the optimum parsimony scores on networks. Our algorithms can be applied for any cost matrix that may contain unequal substitution costs of transforming between different characters along different edges of the network. We analyzed this for experimental data on 10 leaves or fewer with at most 2 reticulations and found that for almost all networks, the bounds returned by the heuristics matched with the exhaustively determined optimum parsimony scores.Conclusion: The parsimony score we define here does not directly reflect the cost of the best tree in the network that displays the evolution of the character. However, when searching for the most parsimonious network that describes a collection of characters, it becomes necessary to add additional cost considerations to prefer simpler structures, such as trees over networks. The parsimony score on a network that we describe here takes into account the substitution costs along the additional edges incident on each reticulate vertex, in addition to the substitution costs along the other edges which are common to all the branching patterns introduced by the reticulate vertices. Thus the score contains an in-built cost for the number of reticulate vertices in the network, and would provide a criterion that is comparable among all networks. Although the problem of finding the parsimony score on the network is believed to be computationally hard to solve, heuristics such as the ones described here would be beneficial in our efforts to find a most parsimonious network. © 2012 Kannan and Wheeler; licensee BioMed Central Ltd."
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Alix Boc,
Alpha B. Diallo and
Vladimir Makarenkov. T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks. In NAR, Vol. 40(W1):W573-W579, 2012.
Keywords: from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, Program T REX, reconstruction, reticulogram, software.
Note: http://dx.doi.org/10.1093/nar/gks485.
Toggle abstract
"T-REX (Tree and reticulogram REConstruction) is a web server dedicated to the reconstruction of phylogenetic trees, reticulation networks and to the inference of horizontal gene transfer (HGT) events. T-REX includes several popular bioinformatics applications such as MUSCLE, MAFFT, Neighbor Joining, NINJA, BioNJ, PhyML, RAxML, random phylogenetic tree generator and some well-known sequence-to-distance transformation models. It also comprises fast and effective methods for inferring phylogenetic trees from complete and incomplete distance matrices as well as for reconstructing reticulograms and HGT networks, including the detection and validation of complete and partial gene transfers, inference of consensus HGT scenarios and interactive HGT identification, developed by the authors. The included methods allows for validating and visualizing phylogenetic trees and networks which can be built from distance or sequence data. The web server is available at: www.trex.uqam.ca. © 2012 The Author(s)."
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Daniel H. Huson and
Celine Scornavacca. Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks. In Systematic Biology, Vol. 61(6):1061-1067, 2012.
Keywords: from rooted trees, from triplets, phylogenetic network, phylogeny, Program Dendroscope, reconstruction, software, visualization.
Toggle abstract
"Dendroscope 3 is a new program for working with rooted phylogenetic trees and networks. It provides a number of methods for drawing and comparing rooted phylogenetic networks, and for computing them from rooted trees. The program can be used interactively or in command-line mode. The program is written in Java, use of the software is free, and installers for all 3 major operating systems can be downloaded from www.dendroscope.org. [Phylogenetic trees; phylogenetic networks; software.] © 2012 The Author(s)."
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Zhi-Zhong Chen,
Lusheng Wang and
Satoshi Yamanaka. A fast tool for minimum hybridization networks. In BMCB, Vol. 13:155, 2012.
Keywords: agreement forest, explicit network, from rooted trees, phylogenetic network, phylogeny, Program FastHN, reconstruction, software.
Note: http://dx.doi.org/10.1186/1471-2105-13-155.
Toggle abstract
"Background: Due to hybridization events in evolution, studying two different genes of a set of species may yield two related but different phylogenetic trees for the set of species. In this case, we want to combine the two phylogenetic trees into a hybridization network with the fewest hybridization events. This leads to three computational problems, namely, the problem of computing the minimum size of a hybridization network, the problem of constructing one minimum hybridization network, and the problem of enumerating a representative set of minimum hybridization networks. The previously best software tools for these problems (namely, Chen and Wang's HybridNet and Albrecht et al.'s Dendroscope 3) run very slowly for large instances that cannot be reduced to relatively small instances. Indeed, when the minimum size of a hybridization network of two given trees is larger than 23 and the problem for the trees cannot be reduced to relatively smaller independent subproblems, then HybridNet almost always takes longer than 1 day and Dendroscope 3 often fails to complete. Thus, a faster software tool for the problems is in need.Results: We develop a software tool in ANSI C, named FastHN, for the following problems: Computing the minimum size of a hybridization network, constructing one minimum hybridization network, and enumerating a representative set of minimum hybridization networks. We obtain FastHN by refining HybridNet with three ideas. The first idea is to preprocess the input trees so that the trees become smaller or the problem becomes to solve two or more relatively smaller independent subproblems. The second idea is to use a fast algorithm for computing the rSPR distance of two given phylognetic trees to cut more branches of the search tree in the exhaustive-search stage of the algorithm. |
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