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From Gene Trees to Species Trees through a Supertree Approach [chapter]

Celine Scornavacca, Vincent Berry, Vincent Ranwez
2009 Lecture Notes in Computer Science  
Inferring a species tree from a set of multi-labeled gene trees (MUL trees) is a wellknown problem in computational biology.  ...  Gene trees are leaf-labeled trees inferred from molecular sequences. Due to duplication events arising in genome evolution, gene trees usually have multiple copies of some labels, i.e. species.  ...  For this reason, species trees are usually estimated from a large number of gene trees. Inferring a species tree from gene trees is mostly done in a two-step approach.  ... 
doi:10.1007/978-3-642-00982-2_60 fatcat:hiam42c3lngrbjsrktq3h6e7ty

Supertree Construction: Opportunities and Challenges [article]

Tandy Warnow
2018 arXiv   pre-print
The traditional use of supertree methods is the assembly of a large species tree from previously computed smaller species trees; however, supertree methods are also used to address large-scale tree estimation  ...  Supertree construction is the process by which a set of phylogenetic trees, each on a subset of the overall set X of species, is combined into a tree on the full set S.  ...  Acknowledgements The author also wishes to thank Pranjal Vachaspati for a careful and thoughtful comments on the manuscript.  ... 
arXiv:1805.03530v1 fatcat:sl6btuirxzcqpk62t66buxavge

Bacterial molecular phylogeny using supertree approach

V Daubin, M Gouy, G Perrière
2001 Genome Informatics Series  
Here, we use a new method based on supertree construction, which permits to cumulate in one supertree the information and statistical support of hundreds of trees from orthologous gene families and to  ...  This approach gives a robust supertree, which demonstrates that a phylogeny of prokaryotic species is conceivable and challenges the hypothesis of a thermophilic origin of bacteria and present-day life  ...  Hence, we have excluded from analysis all gene trees where a species was represented more than once.  ... 
pmid:11791234 fatcat:n5rja2w3lfafvjtjgg6n56guea

The impact of HGT on phylogenomic reconstruction methods

P. Lapierre, E. Lasek-Nesselquist, J. P. Gogarten
2012 Briefings in Bioinformatics  
Supertrees build consensus trees from the topological information contained within individual gene trees.  ...  Methods developed to reconstruct organismal history from multiple genes can be divided into supermatrix and supertree approaches.  ...  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

The evolution of supertrees

Olaf R.P. Bininda-Emonds
2004 Trends in Ecology & Evolution  
Financial support was provided through the research program Bioinformatics for the Functional Analysis of Mammalian Genomes (BFAM), a project funded by the BMBF (Germany).  ...  Nieselt-Struwe and Mike Steel for the invitation to attend.  ...  [32, 33] ), and a supertree approach seems well suited to identify the shared components among the gene trees that should reflect the overall species tree.  ... 
doi:10.1016/j.tree.2004.03.015 pmid:16701277 fatcat:peqsqf5evbhjjh4ai3yurqdu7e

The evolution of supertrees

O BININDAEMONDS
2004 Trends in Ecology & Evolution  
Financial support was provided through the research program Bioinformatics for the Functional Analysis of Mammalian Genomes (BFAM), a project funded by the BMBF (Germany).  ...  Nieselt-Struwe and Mike Steel for the invitation to attend.  ...  [32, 33] ), and a supertree approach seems well suited to identify the shared components among the gene trees that should reflect the overall species tree.  ... 
doi:10.1016/s0169-5347(04)00070-9 fatcat:x3xtx7gscjhidn2bldhdblvr4u

A comprehensive phylogeny of extant horses, rhinos and tapirs (Perissodactyla) through data combination

Samantha A. Price, Olaf R. P. Bininda-Emonds
2009 Zoosystematics and Evolution  
Funding was provided through a Heisenberg Scholarship of the German Science Foundation (DFG; BI 825/2-1) (OBE) and a NESCent (NSF #EF-0423641) postdoctoral fellowship (SAP).  ...  We standardized d s by dividing it through its maximum value for a rooted tree of 2n-4, and subtracted this value from 1 to yield a similarity measure comparable to the CFI.  ...  The supertree approach also generates different topologies depending on whether bootstrap support is used to weight the gene trees obtained from the molecular data set.  ... 
doi:10.1002/zoos.200900005 fatcat:3sdha2op4faanaihz7mwn62lce

Supertrees Based on the Subtree Prune-and-Regraft Distance

Christopher Whidden, Norbert Zeh, Robert G. Beiko
2014 Systematic Biology  
Supertree methods reconcile a set of phylogenetic trees into a single structure that is often interpreted as a branching history of species.  ...  We successfully constructed an SPR supertree from a phylogenomic dataset of 40,631 gene trees that covered 244 genomes representing several major bacterial phyla.  ...  ACKNOWLEDGMENTS We thank Joel Navarrete for his help in evaluating variants of our supertree approach.  ... 
doi:10.1093/sysbio/syu023 pmid:24695589 pmcid:PMC4055872 fatcat:althli3qp5ft3pkrd4725xdlja

From Phylogenetics to Phylogenomics: The Evolutionary Relationships of Insect Endosymbiotic γ-Proteobacteria as a Test Case

Iñaki Comas, Andrés Moya, Fernando González-Candelas, Ron DeBry
2007 Systematic Biology  
A reference phylogeny reflecting the monophyletic origin of insect endosymbionts was further confirmed with different approaches, which led us to consider it as the presumed species tree.  ...  Most discrepancies between this tree and those obtained from individual genes or by concatenation of different genes were due to the grouping of Xanthomonadales with /3-Proteobacteria and not to uncertainties  ...  IC is recipient of a predoctoral fellowship from the Spanish Ministerio de Educacion y Ciencia.  ... 
doi:10.1080/10635150601109759 pmid:17366133 fatcat:6tvkeoucyvanvlbvpkjkkkkdyi

An Application of Supertree Methods to Mammalian Mitogenomic Sequences

Véronique Campbell, François-Joseph Lapointe
2010 Evolutionary Bioinformatics  
In this study, congruence of trees estimated by consensus and supertree approaches were compared to model trees obtained from a combined analysis of complete mitochondrial sequences of 102 species representing  ...  In the second, datasets are analyzed separately and the phylogenetic trees are then combined in a supertree.  ...  This study was supported by a FESP (Faculté des Études Supérieures de l'Université de Montréal) scholarship to VC and by NSERC grant OGP0155251 to FJL.  ... 
doi:10.4137/ebo.s4527 pmid:20535231 pmcid:PMC2880846 fatcat:2bbbjiqzojeuzofb34dnr7wrae

Efficient Quartet Representations of Trees and Applications to Supertree and Summary Methods [article]

Ruth Davidson, MaLyn Lawhorn, Joseph Rusinko, Noah Weber
2016 arXiv   pre-print
Quartet trees displayed by larger phylogenetic trees have long been used as inputs for species tree and supertree reconstruction.  ...  We show mathematically that the set of quartets obtained from a tree via an EQS contains all of the combinatorial information of the tree itself.  ...  ACKNOWLEDGMENT The authors wish to thank Laura Brunner for her assistance in running the supertree reconstruction analysis at the University of Wisconsin-Stevens Point.  ... 
arXiv:1512.05302v3 fatcat:xc5hlsbo2be53gydxdjhthgbf4

A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction

Leonardo De Oliveira Martins, Diego Mallo, David Posada
2014 Systematic Biology  
We conducted extensive simulations to evaluate the performance of our approach in comparison with other species tree approaches able to deal with more than one leaf from the same species.  ...  We do this by extending the idea of Maximum Likelihood (ML) supertrees to a hierarchical Bayesian model where several sources of gene tree/species tree disagreement can be accounted for in a modular manner  ...  We would also like to thank the editors and the three anonymous reviewers for their excellent advices.  ... 
doi:10.1093/sysbio/syu082 pmid:25281847 pmcid:PMC4851173 fatcat:posipbhcx5gshntsepnkup3tya

A Phylogenomic Approach to Bacterial Phylogeny: Evidence of a Core of Genes Sharing a Common History

V. Daubin
2002 Genome Research  
This article must therefore be hereby marked "advertisement" in accordance with 18 USC section 1734 solely to indicate this fact.  ...  Thus, all gene trees where a species was represented more than once were excluded from analysis.  ...  Each tree obtained for a set of species from a single orthologous gene family was coded into a binary matrix of informative sites.  ... 
doi:10.1101/gr.187002 pmid:12097345 pmcid:PMC186629 fatcat:idav72wx3fb4ziyd3nrbwk26lm

Assessment of phylogenomic and orthology approaches for phylogenetic inference

B. E. Dutilh, V. van Noort, R. T. J. M. van der Heijden, T. Boekhout, B. Snel, M. A. Huynen
2007 Computer applications in the biosciences : CABIOS  
Phylogenomic trees based on gene content show, relative to the other methods, a bias in the tree topology that parallels convergence in lifestyle among the species compared, indicating convergence in gene  ...  There are, however, fundamental differences between the ways in which phylogenomic approaches like gene content, superalignment, superdistance and supertree integrate the phylogenetic information from  ...  ACKNOWLEDGEMENTS Funding to pay the Open Access publication charges was provided by the Kluyver Centre for Genomics of Industrial Fermentation, which is supported by the Netherlands Genomics Initiative  ... 
doi:10.1093/bioinformatics/btm015 pmid:17237036 fatcat:dfbi5fhy6ndyxp4p3cmsq5lpay

Multilocus inference of species trees and DNA barcoding

Diego Mallo, David Posada
2016 Philosophical Transactions of the Royal Society of London. Biological Sciences  
One contribution of 16 to a theme issue 'From DNA barcodes to biomes'.  ...  D.P. also wants to acknowledge Paul Hebert and Mehrdad Hajibabaei for the invitation to the International Barcode of Life Conference that was held in Guelph, Canada, in 2015.  ...  We thank the editors for the invitation to this special issue and two anonymous reviewers for their very helpful comments.  ... 
doi:10.1098/rstb.2015.0335 pmid:27481787 pmcid:PMC4971187 fatcat:fovihzzjfrbepn4eys3rvlfuvm
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