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Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach [article]

Cedric Chauve, Yann Ponty, Joao Paulo Peirera Zanetti
2015 bioRxiv   pre-print
., computes parsimonious evolutionary scenarios for gene adjacencies, from pairs of reconciled gene trees.  ...  Results: We apply our algorithms to a dataset of mammalian gene trees and adjacencies, and observe a significant reduction of the number of syntenic conflicts observed in the resulting ancestral gene adjacencies  ...  A reconciled gene tree is also a binary tree that describes the evolution of a set of genes, called a gene family, through the evolutionary mechanisms of speciation, gene duplication and gene loss, within  ... 
doi:10.1101/026310 fatcat:vhc5v2bzqjhy3jzvjrhsqrenjy

Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach

Cedric Chauve, Yann Ponty, João Zanetti
2015 BMC Bioinformatics  
., computes parsimonious evolutionary scenarios for gene adjacencies, from pairs of reconciled gene trees.  ...  Results: We apply our algorithms to a dataset of mammalian gene trees and adjacencies, and observe a significant reduction of the number of syntenic conflicts observed in the resulting ancestral gene adjacencies  ...  They introduced the notion of adjacency forest, that models the evolution of gene adjacencies within a phylogeny, motivated by the reconstruction of the architecture of ancestral genomes, and described  ... 
doi:10.1186/1471-2105-16-s19-s6 pmid:26696141 pmcid:PMC4686788 fatcat:tivavlil7jbbzpaxxoclnqwvwa

Evolution of Genes Neighborhood within Reconciled Phylogenies: An Ensemble Approach [chapter]

Cedric Chauve, Yann Ponty, João Paulo Pereira Zanetti
2014 Lecture Notes in Computer Science  
., computes parsimonious evolutionary scenarios for gene adjacencies, from pairs of reconciled gene trees.  ...  Results: We apply our algorithms to a dataset of mammalian gene trees and adjacencies, and observe a significant reduction of the number of syntenic conflicts observed in the resulting ancestral gene adjacencies  ...  They introduced the notion of adjacency forest, that models the evolution of gene adjacencies within a phylogeny, motivated by the reconstruction of the architecture of ancestral genomes, and described  ... 
doi:10.1007/978-3-319-12418-6_7 fatcat:vhb2c3zcqbhylcsv6jb476nwem

Evolution of gene neighborhoods within reconciled phylogenies

Sèverine Bérard, Coralie Gallien, Bastien Boussau, Gergely J. Szöllősi, Vincent Daubin, Eric Tannier
2012 Computer applications in the biosciences : CABIOS  
Results: We define an 'adjacency phylogenetic tree' that describes the evolution of an adjacency, a neighborhood relation between two genes, by speciation, duplication or loss of one or both genes, and  ...  We describe an algorithm that, given a species tree and a set of gene trees where the leaves are connected by adjacencies, computes an adjacency forest that minimizes the number of gains and breakages  ...  neighborhoods based on a model of evolution allowing gene duplications.  ... 
doi:10.1093/bioinformatics/bts374 pmid:22962456 pmcid:PMC3436801 fatcat:xcqjzszkp5cshbdgvsv5cu7mza

Assessing the robustness of parsimonious predictions for gene neighborhoods from reconciled phylogenies [article]

Ashok Rajaraman, Cedric Chauve, Yann Ponty (INRIA Saclay Ile de France, LIX)
2015 arXiv   pre-print
The availability of a large number of assembled genomes opens the way to study the evolution of syntenic character within a phylogenetic context.  ...  The DeCo algorithm, recently introduced by Bérard et al. allows the computation of parsimonious evolutionary scenarios for gene adjacencies, from pairs of reconciled gene trees.  ...  the convex hull computations within DeClone.  ... 
arXiv:1503.05292v2 fatcat:ympjtt44rnbdxhennuqbjekcma

Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies

Magali Semeria, Eric Tannier, Laurent Guéguen
2015 BMC Bioinformatics  
It uses reconciled phylogenies, which integrate sequence and gene content evolution.  ...  Probabilistic models of gene order evolution usually have to assume constant gene content or adopt a presence/absence coding of gene neighborhoods which is blind to complex events modifying gene content  ...  This work was performed using the computing facilities of the Computing Center LBBE/PRABI. This article has been published as part of BMC Bioinformatics Volume 16 Supplement 14, 2015  ... 
doi:10.1186/1471-2105-16-s14-s5 pmid:26452018 pmcid:PMC4603630 fatcat:czhsgbbkwnc55aywrumwp5wila

Assessing the Robustness of Parsimonious Predictions for Gene Neighborhoods from Reconciled Phylogenies: Supplementary Material [chapter]

Ashok Rajaraman, Cedric Chauve, Yann Ponty
2015 Lecture Notes in Computer Science  
The availability of many assembled genomes opens the way to study the evolution of syntenic character within a phylogenetic context.  ...  ., computes parsimonious evolutionary scenarios for gene adjacencies, from pairs of reconciled gene trees.  ...  the convex hull computations within DeClone.  ... 
doi:10.1007/978-3-319-19048-8_22 fatcat:qn2uhpyswvagdkrazir2fd4vhe

Homology and phylogeny and their automated inference

Georg Fuellen
2008 Die Naturwissenschaften  
For example, an integrative analysis of data from the genome sequencing projects for various species traces the evolution of the genomes and identifies conserved and innovative parts.  ...  Biological data is comparable if a common origin exists (homology), as is the case for members of a gene family originating via duplication of an ancestral gene.  ...  The EnsEMBL pipeline can also be thought of as a combinative approach, see Curwen et al, 2004 .  ... 
doi:10.1007/s00114-008-0348-1 pmid:18288471 fatcat:epi54zhudffl7ms3avrht2qgri

Structural Divergence in Vertebrate Phylogeny of a Duplicated Prototype Galectin

Ramray Bhat, Mahul Chakraborty, I.S. Mian, Stuart A. Newman
2014 Genome Biology and Evolution  
This inference is consistent with our finding of a lower proportion of conserved residues in sauropsid Gal-1Bs, and evidence for positive selection of sauropsid gal-1b, but not gal-1a genes.  ...  We investigated the origin of the Gal-1A/Gal-1B divergence to gain insight into when their developmental functions originated and how they could have contributed to vertebrate phenotypic evolution.  ...  Acknowledgments The authors thank Lawrence Kelley, Mirko Petrovic, and Marta Linde-Medina for help with the bioinformatic analyses and two anonymous referees for their constructive criticism of a previous  ... 
doi:10.1093/gbe/evu215 pmid:25260584 pmcid:PMC4224342 fatcat:244wd2rkxvcqjfcrydalttxdba

OrthoParaMap: distinguishing orthologs from paralogs by integrating comparative genome data and gene phylogenies

Steven B Cannon, Nevin D Young
2003 BMC Bioinformatics  
This kind of comparison can also help to describe how gene families have evolved within a single genome that has undergone polyploidy or other large-scale duplications, as in the case of Arabidopsis thaliana  ...  In eukaryotic genomes, most genes are members of gene families. When comparing genes from two species, therefore, most genes in one species will be homologous to multiple genes in the second.  ...  Special thanks to Andy Baumgarten, Georgiana May, and Alexander Kozik for conversations and advice along the way, to Kevin Roberg-Perez for suggesting use of the MAGE gene family in the mouse -human comparison  ... 
doi:10.1186/1471-2105-4-35 pmid:12952558 pmcid:PMC200972 fatcat:aesvcdqrbjehfkztxqqsiwqp4u

Synteny-guided resolution of gene trees clarifies the functional impact of whole genome duplications

Elise Parey, Alexandra Louis, Cédric Cabau, Yann Guiguen, Hugues Roest Crollius, Camille Berthelot, Koichiro Tamura
2020 Molecular biology and evolution  
We find that almost one in four teleost gene phylogenies in the Ensembl database (3,394) are inconsistent with their syntenic contexts.  ...  Here we present SCORPiOs, a novel method to reconstruct gene phylogenies in the context of a known WGD event.  ...  Acknowledgments We thank Pierre Vincens for the coordination of computing resources and all members of the GenoFish consortium for fruitful discussions. This work is funded by ANR GenoFish (Grant No.  ... 
doi:10.1093/molbev/msaa149 pmid:32556216 fatcat:lfyiprkzdnbsxgouylkgnlxic4

Efficient Gene Tree Correction Guided by Genome Evolution

Emmanuel Noutahi, Magali Semeria, Manuel Lafond, Jonathan Seguin, Bastien Boussau, Laurent Guéguen, Nadia El-Mabrouk, Eric Tannier, Marc Robinson-Rechavi
2016 PLoS ONE  
Motivations Gene trees inferred solely from multiple alignments of homologous sequences often contain weakly supported and uncertain branches.  ...  Information for their full resolution may lie in the dependency between gene families and their genomic context.  ...  We would Efficient Gene Tree Correction Guided by Genome Evolution need better exploration schemes with integrated models to really trust gene trees on a whole genome database within a deep phylogeny.  ... 
doi:10.1371/journal.pone.0159559 pmid:27513924 pmcid:PMC4981423 fatcat:otdbekpe7ve2veau5jhhqtarsy

The quest for orthologs: finding the corresponding gene across genomes

Arnold Kuzniar, Roeland C.H.J. van Ham, Sándor Pongor, Jack A.M. Leunissen
2008 Trends in Genetics  
(networks) using reliable species phylogeny and available genomic data from more than two species, and an insight into the processes of molecular evolution.  ...  An orthologous group consists only of genes that have 'best' matches within the group and no 'best' matches of any gene are outside that group.  ... 
doi:10.1016/j.tig.2008.08.009 pmid:18819722 fatcat:4w6qrixl7naw7aoqko73vruavq

Error Detection and Correction of Gene Trees [chapter]

Manuel Lafond, Krister M. Swenson, Nadia El-Mabrouk
2013 Models and Algorithms for Genome Evolution  
Reconstructing the phylogeny of a gene family and reconciling the obtained gene tree with the species tree reveals the history of duplications, losses and other events that have shaped the gene family,  ...  Analysing Ensembl gene trees of the fish genomes Stickleback, Medaka, Tetraodon, and Zebrafish reveals a significant number of erroneous gene trees.  ...  As exploring the space of all topologies is time and space prohibitive, gene tree correction methods explore the neighborhood of an input gene tree G, according to a tree-distance measure, such as the  ... 
doi:10.1007/978-1-4471-5298-9_12 fatcat:coes2t3vdrhd3hjk5lgaczjkna

Genome-scale coestimation of species and gene trees

B. Boussau, G. J. Szollosi, L. Duret, M. Gouy, E. Tannier, V. Daubin
2012 Genome Research  
historic record of gene duplications and losses throughout genome evolution.  ...  Comparisons of gene trees and species trees are key to understanding major processes of genome evolution such as gene duplication and loss.  ...  L(T i |A i ) is the likelihood of a phylogeny given an alignment, and can be computed using any probabilistic model of sequence evolution (Felsenstein 2003) .  ... 
doi:10.1101/gr.141978.112 pmid:23132911 pmcid:PMC3561873 fatcat:laidehu2tzabvahk54rcp57v4a
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