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MOESM1 of A reconstruction problem for a class of phylogenetic networks with lateral gene transfers

Gabriel Cardona, Joan Pons, Francesc Rossellรณ
2016 Figshare  
This implies, by the compatibility of clusters in phylogenetic trees, that either B ⊆Ā orĀ ⊆ B and hence that ∅ = B ∩ A k−1 , which is false.  ...  Since B U k , h is a proper descendant of u k . Assume that the path u k h contains some intermediate nodeū, with C T (ū) = B Ā with ∅ =Ā A k .  ... 
doi:10.6084/m9.figshare.c.3609314_d1 fatcat:246jcrsdhndm5cd7q2bqb2tx3i

A reconstruction problem for a class of phylogenetic networks with lateral gene transfers

Gabriel Cardona, Joan Carles Pons, Francesc Rosselló
2015 Algorithms for Molecular Biology  
In this paper we consider LGT networks, a general model of phylogenetic networks with lateral gene transfers which consist, roughly, of a principal rooted tree with its leaves labelled on a set of taxa  ...  genes and the secondary lines of evolution through lateral gene transfers.  ...  Acknowledgements We thank the anonymous reviewers for many comments and suggestions that have substantially improved the quality and readability of the paper.  ... 
doi:10.1186/s13015-015-0059-z pmid:26691555 pmcid:PMC4683721 fatcat:753gdv5lfzgvlnd4prmo5oztku

Phylogenetic Network Construction Approaches [chapter]

Vladimir Makarenkov, Dmytro Kevorkov, Pierre Legendre
2006 Applied Mycology and Biotechnology  
However, the "molecular clock" assumption is usually inappropriate for distantly related sequences and the reconstruction of a correct phylogenetic tree becomes problematic under this hypothesis.  ...  Reticulate evolution includes horizontal gene transfer between taxa, hybridization events and homoplasy. Genetic recombination creates reticulate evolution within lineages.  ...  If a multiple copy of a gene appears in the species tree, the algorithm recognizes it as a possible lateral gene transfer.  ... 
doi:10.1016/s1874-5334(06)80006-7 fatcat:m5bu6onibfaozjmexhwibubh44

Phylogenetic networks: modeling, reconstructibility, and accuracy

B.M.E. Moret, L. Nakhleh, T. Warnow, C.R. Linder, A. Tholse, A. Padolina, J. Sun, R. Timme
2004 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
Phylogenetic networks model the evolutionary history of sets of organisms when events such as hybrid speciation and horizontal gene transfer occur.  ...  Previously, we proposed the first such measure, which applied only to a restricted class of networks.  ...  ACKNOWLEDGMENTS The authors want to thank the anonymous referees for many detailed and helpful comments, as well as for their insistence on clarity: Their reviews led to substantial improvements in the  ... 
doi:10.1109/tcbb.2004.10 pmid:17048405 fatcat:bc55zexwozgatlqv5kggizpklm

Reconstructing patterns of reticulate evolution in plants

C Randal Linder, Loren H Rieseberg
2004 American Journal of Botany  
This situation should change rapidly with the development of multiple nuclear markers for phylogenetic reconstruction and new methods for reconstructing reticulate evolution.  ...  Current models and methods that allow hybrid speciation to be detected and reconstructed are discussed, with a focus on how lineage sorting and meiotic and sexual recombination affect network reconstruction  ...  Towards identifying lateral gene transfer events. Proceedings  ... 
pmid:18677414 pmcid:PMC2493047 fatcat:a7j5r7sj4fephlrtd3bpzv5gjq

Efficient parsimony-based methods for phylogenetic network reconstruction

G. Jin, L. Nakhleh, S. Snir, T. Tuller
2007 Bioinformatics  
Further, we devise efficient heuristics for parsimony-based reconstruction of phylogenetic networks.  ...  Results: In the present work we prove that the problem of scoring the parsimony of a phylogenetic network is NP-hard and provide an improved fixed parameter tractable algorithm for it.  ...  INTRODUCTION Phylogenetic networks are a special class of directed acyclic graphs that models evolutionary histories when trees are inappropriate, such as in the cases of horizontal gene transfer (HGT)  ... 
doi:10.1093/bioinformatics/btl313 pmid:17237079 fatcat:qvghmrfjmrhx5k6cnfhhp7qp7y

Within-species lateral genetic transfer and the evolution of transcriptional regulation in Escherichia coli and Shigella

Elizabeth Skippington, Mark A Ragan
2011 BMC Genomics  
Neighbour regulators show no evidence of co-transfer with their nearby target genes.  ...  Here we apply phylogenetic and network-based methods to investigate the relationship between units of lateral transfer and recombination within the Escherichia coli -Shigella clade and the topological  ...  Phylogenetic analyses were performed using high-performance computing resources of the National Computational Infrastructure (NCI) National Facility at the Australian National University.  ... 
doi:10.1186/1471-2164-12-532 pmid:22035052 pmcid:PMC3212841 fatcat:wmyasyquwzbv5fy6wey7ykbxty

Evolutionary Phylogenetic Networks: Models and Issues [chapter]

Luay Nakhleh
2010 Problem Solving Handbook in Computational Biology and Bioinformatics  
Several excellent surveys of the different flavors of phylogenetic networks and methods for their reconstruction have been written recently.  ...  Nonetheless, the term 'phylogenetic network' has been generically used to refer to a class of models whose core shared property is tree generalization.  ...  The illustration in Fig. 18 and its accompanying discussion are the result of a discussion with Laura S. Kubatko and James Degnan.  ... 
doi:10.1007/978-0-387-09760-2_7 fatcat:a7ugipi3fvdypgllt556bdkcqq

Algorithms and Complexity in Phylogenetics (Dagstuhl Seminar 19443)

Magnus Bordewich, Britta Dorn, Simone Linz, Rolf Niedermeier, Michael Wagner
2020 Dagstuhl Reports  
Phylogenetics is the study of ancestral relationships between species. Its central goal is the reconstruction and analysis of phylogenetic trees and networks.  ...  It contains an executive summary, abstracts of talks, short summaries of working groups, and a list of open problems that were posed during the seminar.  ...  Non-treelike (reticulate) processes in evolution include lateral gene transfer and hybridisation.  ... 
doi:10.4230/dagrep.9.10.134 dblp:journals/dagstuhl-reports/BordewichDLN19 fatcat:nypkd3nzjvg5jdsd3cidktwyei

Modelling phylogenetic relationships using reticulated networks

Vladimir Makarenkov, Pierre Legendre, Yves Desdevises
2004 Zoologica Scripta  
For instance, reticulate models can adequately describe such complicated mechanisms as lateral gene transfer in bacteria or species hybridization.  ...  In this paper, we present the main features of a new distance-based method for modelling phylogenetic relationships among species by means of reticulated networks (RNs).  ...  Acknowledgements The authors are grateful to Philippe Casgrain for his contribution to programming T-Rex, which makes the new method of reticulation analysis available to the scientific community.  ... 
doi:10.1111/j.1463-6409.2004.00141.x fatcat:7g73bhkwx5c5bcpqxkibsl5yk4

Horizontal gene transfer in evolution: facts and challenges

L. Boto
2009 Proceedings of the Royal Society of London. Biological Sciences  
Even several authors propose that horizontal gene transfer may be used as a tool in phylogenetic reconstruction, providing with sinapomorphies that facilitate the reconstruction of problematic relationships  ...  In relation to phylogenetic incongruence the problem is that it is difficult to differentiate in a a phylogenetic tree between horizontal gene transfer and gene loss (Ragan 2001; Ragan 2002; Lawrence  ... 
doi:10.1098/rspb.2009.1679 pmid:19864285 pmcid:PMC2842723 fatcat:jj3lhfanlrb5bkxdr5aprk4htm

Who is Who in Phylogenetic Networks: Articles, Authors and Programs [article]

Tushar Agarwal, Philippe Gambette, David Morrison
2016 arXiv   pre-print
, lateral gene transfer, etc.  ...  "Who is Who in Phylogenetic Networks" comprises more than 600 publications and 500 authors interlinked with a rich set of more than 200 keywords related to phylogenetic networks.  ...  This reflects the recent development of efficient methods to reconstruct reconciliation scenarios taking into account not only lateral gene transfer but also duplication and loss, as well as the introduction  ... 
arXiv:1610.01674v1 fatcat:h2nzslpm4va3lem7okcs225une

The comparison of tree-sibling time consistent phylogenetic networks is graph isomorphism-complete [article]

Gabriel Cardona, Merce Llabres, Francesc Rossello, Gabriel Valiente
2009 arXiv   pre-print
In a previous work, we gave a metric on the class of semibinary tree-sibling time consistent phylogenetic networks that is computable in polynomial time; in particular, the problem of deciding if two networks  ...  More precisely, we proof that the isomorphism problem for generic tree-sibling time consistent phylogenetic networks is polynomially equivalent to the graph isomorphism problem.  ...  Acknowledgements The authors would like to thank Antoni Lozano for his comments on an early version of this manuscript.  ... 
arXiv:0902.4640v1 fatcat:wpuuzvcxbfdgjeazr6ywz7t2vy

Reconstructing patterns of reticulate evolution in plants

C. Randal Linder, Loren H. Rieseberg
2004 American Journal of Botany  
This situation should change rapidly with the development of multiple nuclear markers for phylogenetic reconstruction and new methods for reconstructing reticulate evolution.  ...  Current models and methods that allow hybrid speciation to be detected and reconstructed are discussed, with a focus on how lineage sorting and meiotic and sexual recombination affect network reconstruction  ...  Hallett and Lagergren (2001) used a set of simplifying assumptions to create DAGs that were more biologically realistic than splits graphs and created a method for inferring lateral gene transfer events  ... 
doi:10.3732/ajb.91.10.1700 pmid:21652318 fatcat:7btn4gmtrfdxxi4nqt5mqkteoy

Molecular Evolution Perspectives on Intraspecific Lateral DNA Transfer of Topoisomerase and Gyrase Loci in Streptococcus pneumoniae, with Implications for Fluoroquinolone Resistance Development and Spread

M. J. Stanhope, S. L. Walsh, J. A. Becker, M. J. Italia, K. A. Ingraham, M. N. Gwynn, T. Mathie, J. A. Poupard, L. A. Miller, J. R. Brown, H. Amrine-Madsen
2005 Antimicrobial Agents and Chemotherapy  
with an intraspecific lateral transfer hypothesis.  ...  Also evident were examples of interspecific transfer, with two isolates possessing a parE-parC gene region arising from viridans group streptococci.  ...  ACKNOWLEDGMENT We thank the GSK US-based sequencing facility, under the management of Ganesh Sathe, for all their efforts on this project.  ... 
doi:10.1128/aac.49.10.4315-4326.2005 pmid:16189113 pmcid:PMC1251522 fatcat:ayjibqtn4jdrtndr2vylekn4du
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