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Improved gene tree error correction in the presence of horizontal gene transfer

Mukul S. Bansal, Yi-Chieh Wu, Eric J. Alm, Manolis Kellis
2015 Computer applications in the biosciences : CABIOS  
Results: In this study, we introduce a new and highly effective method for gene tree error correction in the presence of horizontal gene transfer.  ...  As a result, the accurate inference of gene trees affected by horizontal gene transfer remains a largely unaddressed problem.  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btu806 pmid:25481006 pmcid:PMC4393519 fatcat:ur3e6f7vdnf6ldnmi3dnspg6ji

Causes, consequences and solutions of phylogenetic incongruence

A. Som
2014 Briefings in Bioinformatics  
Phylogenetic analysis is used to recover the evolutionary history of species, genes or proteins.  ...  Despite immense progress in recent years, phylogenetic reconstruction involves many challenges that create uncertainty with respect to the true evolutionary relationships of the species or genes analyzed  ...  Sudhir Kumar of Arizona State University and Dr. Dan Graur of University of Houston for useful discussions. I also thank the anonymous reviewers for their constructive comments.  ... 
doi:10.1093/bib/bbu015 pmid:24872401 fatcat:gzuppndvmbdhpgqnumqh5bibom

The impact of HGT on phylogenomic reconstruction methods

P. Lapierre, E. Lasek-Nesselquist, J. P. Gogarten
2012 Briefings in Bioinformatics  
In the face of very high or very low substitution rates without horizontal gene transfers, supermatrix approaches outperform supertrees as individual gene trees remain unresolved and additional sequences  ...  Our results show that overall, supermatrix approaches are preferable when a low amount of gene transfer is suspected to be present in the dataset, while supertrees have greater reliability in the presence  ...  FUNDING This work was supported by the National Science Foundation Assembling the Tree of Life Program (DEB 0 830 024).  ... 
doi:10.1093/bib/bbs050 pmid:22908214 fatcat:ha757hfernedhktdupjr4ijyge

Comparing Two Bayesian Methods for Gene Tree/Species Tree Reconstruction: Simulations with Incomplete Lineage Sorting and Horizontal Gene Transfer

Yujin Chung, Cécile Ané
2011 Systematic Biology  
DNA alignments were simulated under the influence of incomplete lineage sorting (ILS) and of horizontal gene transfer (HGT).  ...  BUCKy and BEST performed similarly in most other cases, including in the presence of strong ILS and of HGT events that were evenly placed across the tree.  ...  We would like to thank Ron DeBry and Laura Kubatko for their valuable comments and suggestions, which improved the quality of the manuscript.  ... 
doi:10.1093/sysbio/syr003 pmid:21368324 fatcat:o3caaknzqjadhh6du6k352tcua

The Consistent Phylogenetic Signal in Genome Trees Revealed by Reducing the Impact of Noise

Bas E. Dutilh, Martijn A. Huynen, William J. Bruno, Berend Snel
2004 Journal of Molecular Evolution  
Horizontal gene transfer or parallel gene loss does not cause systematic biases in the gene content tree.  ...  Yet it has been argued that shared gene content is unreliable for phylogenetic reconstruction because of convergence in gene content due to horizontal gene transfer and parallel gene loss.  ...  This work was supported in part by European Union Contract QLTR-2000-01676 and by a grant from The Netherlands Organization for Scientific Research (NWO).  ... 
doi:10.1007/s00239-003-2575-6 pmid:15170256 fatcat:i6mmsja7gngvnh2i6ksklht4x4

Phylogenomics with paralogs

Marc Hellmuth, Nicolas Wieseke, Marcus Lechner, Hans-Peter Lenhof, Martin Middendorf, Peter F. Stadler
2015 Proceedings of the National Academy of Sciences of the United States of America  
While the resolution is very poor for individual gene families, we show that genome-wide data sets are sufficient to generate fully resolved phylogenetic trees, even in the presence of horizontal gene  ...  Starting from tree-free estimates of orthology, cograph editing can sufficiently reduce the noise in order to find correct event-annotated gene trees.  ...  Andersen for helpful comments on the cograph-editing problem and the Integer Linear Program formulation. This work was funded by the German Research Foundation (Project MI439/14-1).  ... 
doi:10.1073/pnas.1412770112 pmid:25646426 pmcid:PMC4343152 fatcat:kkplhuhxezhljdivpmp43puwsu

TRACTION: Fast Non-Parametric Improvement of Estimated Gene Trees

Sarah Christensen, Erin K. Molloy, Pranjal Vachaspati, Tandy Warnow, Michael Wagner
2019 Workshop on Algorithms in Bioinformatics  
Here, we study the problem of gene tree correction where gene tree heterogeneity is instead due to incomplete lineage sorting (ILS, a common problem in eukaryotic phylogenetics) and horizontal gene transfer  ...  Gene tree correction aims to improve the accuracy of a gene tree by using computational techniques along with a reference tree (and in some cases available sequence data).  ...  Acknowledgements We thank Mike Steel for encouragement and the members of the Warnow lab for valuable feedback.  ... 
doi:10.4230/lipics.wabi.2019.4 dblp:conf/wabi/ChristensenMVW19 fatcat:y5dd2xv3v5b7fedd6ypbkbcvmu

A Rooted Net of Life

David Williams, Gregory P Fournier, Pascal Lapierre, Kristen S Swithers, Anna G Green, Cheryl P Andam, J Peter Gogarten
2011 Biology Direct  
Extant sampled ribosomes form the leaves of the tree scaffold.  ...  Given sufficient evidence, edges may then be differentiated as those representing vertical lines of inheritance within lineages and those representing horizontal genetic transfers or endosymbioses between  ...  Figure 2 2 Comparison of supermatrix and supertree approaches for recovering the correct tree following horizontal genetic transfer.  ... 
doi:10.1186/1745-6150-6-45 pmid:21936906 pmcid:PMC3189188 fatcat:64f6e7sjnzb3dca3s7grpcwlqy

Fast and accurate methods for phylogenomic analyses

Jimmy Yang, Tandy Warnow
2011 BMC Bioinformatics  
We also observe that methods that explicitly consider errors in the estimated gene trees produce more accurate trees than methods that assume the estimated gene trees are correct.  ...  However, true gene trees can differ from the true species tree (and hence from one another) due to biological processes such as horizontal gene transfer, incomplete lineage sorting, and gene duplication  ...  This article has been published as part of BMC Bioinformatics Authors' contributions TW conceived and designed the study; JY implemented the analysis tools, produced the data, and created the figures and  ... 
doi:10.1186/1471-2105-12-s9-s4 pmid:22152123 pmcid:PMC3283310 fatcat:rmt6g6bhyncobgakt2gcht6zzy

RecPD: A Recombination-aware measure of phylogenetic diversity

Cedoljub Bundalovic-Torma, Darrell Desveaux, David S. Guttman, Luis Pedro Coelho
2022 PLoS Computational Biology  
RecPD utilizes ancestral-state reconstruction to map the presence / absence of features onto ancestral nodes in a species tree, and then identifies potential recombination events in the evolutionary history  ...  Consequently, these approaches cannot accurately assess diversity for features that have undergone recombination or horizontal transfer.  ...  Acknowledgments We would like to thank all members of the Guttman and Desveaux labs for their insight input to this project.  ... 
doi:10.1371/journal.pcbi.1009899 pmid:35192600 pmcid:PMC8896707 fatcat:pnwe6sgtbja3bgk7uy3j5ygzdq

A TREE OBSCURED BY VINES: HORIZONTAL GENE TRANSFER AND THE MEDIAN TREE METHOD OF ESTIMATING SPECIES PHYLOGENY

JUNHYONG KIM, BENJAMIN A. SALISBURY
2000 Biocomputing 2001  
Acknowledgments This work was supported in part by NSF grant DEB-9806570 to JK. Two anonymous reviewers provided useful comments.  ...  D k will differ from D 0 in some of the elements if horizontal transfer event occurred in the kth gene.  ...  Gene trees were created by applying a constant rate, h, of horizontal transfer to a copy of the species tree. In the first stage, "donor" vertices were added to the tree.  ... 
doi:10.1142/9789814447362_0055 fatcat:bs3ph76hqfa5xm73wh5eko2rni

Systematic inference of highways of horizontal gene transfer in prokaryotes

Mukul S. Bansal, Guy Banay, Timothy J. Harlow, J. Peter Gogarten, Ron Shamir
2013 Computer applications in the biosciences : CABIOS  
Motivation: Horizontal gene transfer (HGT) plays a crucial role in the evolution of prokaryotic species. Typically, no more than a few genes are horizontally transferred between any two species.  ...  However, several studies identified pairs of species (or linages) between which many different genes were horizontally transferred. Such a pair is said to be linked by a highway of gene sharing.  ...  The presence of highways in a dataset can be inferred from the distribution of the reported horizontal edge scores.  ... 
doi:10.1093/bioinformatics/btt021 pmid:23335015 fatcat:qcbu73lycjcqtkazastdlqnqti

A Likelihood Ratio Test to Detect Conflicting Phylogenetic Signal

John P. Huelsenbeck, J. J. Bull, David Cannatella
1996 Systematic Biology  
the histories of the genes analyzed.  ...  It is generally unknown whether these different estimates of history result from random variation in the processes of nucleotide substitution or from fundamentally different evolutionary mechanisms underlying  ...  For example, horizontal gene transfer and recombination in bacteria cause different portions of the genome to have different histories (Dykhuizen and Green, 1991; Maynard Smith et al., 1991; Medigue et  ... 
doi:10.1093/sysbio/45.1.92 fatcat:nnvs4ik2rrhpnfil46bcyet66i

A Likelihood Ratio Test to Detect Conflicting Phylogenetic Signal

John P. Huelsenbeck, J. J. Bull
1996 Systematic Biology  
the histories of the genes analyzed.  ...  It is generally unknown whether these different estimates of history result from random variation in the processes of nucleotide substitution or from fundamentally different evolutionary mechanisms underlying  ...  For example, horizontal gene transfer and recombination in bacteria cause different portions of the genome to have different histories (Dykhuizen and Green, 1991; Maynard Smith et al., 1991; Medigue et  ... 
doi:10.2307/2413514 fatcat:jmtftfcs2bc6hncrmmrj77ofsm

On Inferring Additive and Replacing Horizontal Gene Transfers Through Phylogenetic Reconciliation [article]

Misagh Kordi, Soumya Kundu, Mukul S. Bansal
2020 bioRxiv   pre-print
It is well known that horizontal gene transfer can be either 'additive' or 'replacing' depending on whether the transferred gene adds itself as a new gene in the recipient genome or replaces an existing  ...  Horizontal gene transfer is one of the most important mechanisms for microbial evolution and adaptation.  ...  Acknowledgements: The authors thank Abhijit Mondal for pointing out an error in an initial implementation of the heuristic.  ... 
doi:10.1101/2020.03.27.010785 fatcat:xpvtnhed2jdw7osnpobeufoiom
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