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Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence

Wandrille Duchemin, Vincent Daubin, Eric Tannier
2015 BMC Genomics  
© 2015 Duchemin et al.; This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted  ... 
doi:10.1186/1471-2164-16-s10-s9 pmid:26450112 pmcid:PMC4603589 fatcat:5lloeyznfbalnow2nxrqwhelqy

HyLiTE: accurate and flexible analysis of gene expression in hybrid and allopolyploid species

Wandrille Duchemin, Pierre-Yves Dupont, Matthew A Campbell, Austen RD Ganley, Murray P Cox
2015 BMC Bioinformatics  
Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand Full list of author information is available at the end of the article © 2015 Duchemin  ... 
doi:10.1186/s12859-014-0433-8 pmid:25592117 pmcid:PMC4300824 fatcat:kxvrjuwb4jdftlt5kson4zfpoa

Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes

Yoann Anselmetti, Wandrille Duchemin, Eric Tannier, Cedric Chauve, Sèverine Bérard
2018 BMC Genomics  
Genomes rearrangements carry valuable information for phylogenetic inference or the elucidation of molecular mechanisms of adaptation. However, the detection of genome rearrangements is often hampered by current deficiencies in data and methods: Genomes obtained from short sequence reads have generally very fragmented assemblies, and comparing multiple gene orders generally leads to computationally intractable algorithmic questions. Results: We present a computational method, ADSEQ, which, by
more » ... mbining ancestral gene order reconstruction, comparative scaffolding and de novo scaffolding methods, overcomes these two caveats. ADSEQ provides simultaneously improved assemblies and ancestral genomes, with statistical supports on all local features. Compared to previous comparative methods, it runs in polynomial time, it samples solutions in a probabilistic space, and it can handle a significantly larger gene complement from the considered extant genomes, with complex histories including gene duplications and losses. We use ADSEQ to provide improved assemblies and a genome history made of duplications, losses, gene translocations, rearrangements, of 18 complete Anopheles genomes, including several important malaria vectors. We also provide additional support for a differentiated mode of evolution of the sex chromosome and of the autosomes in these mosquito genomes. Conclusions: We demonstrate the method's ability to improve extant assemblies accurately through a procedure simulating realistic assembly fragmentation. We study a debated issue regarding the phylogeny of the Gambiae complex group of Anopheles genomes in the light of the evolution of chromosomal rearrangements, suggesting that the phylogenetic signal they carry can differ from the phylogenetic signal carried by gene sequences, more prone to introgression.
doi:10.1186/s12864-018-4466-7 pmid:29764366 pmcid:PMC5954271 fatcat:e375ybpt5zdedb7r657ymibeti

Episodes of gene flow and selection during the evolutionary history of domesticated barley

Peter Civáň, Konstantina Drosou, David Armisen-Gimenez, Wandrille Duchemin, Jérôme Salse, Terence A. Brown
2021 BMC Genomics  
Background Barley is one of the founder crops of Neolithic agriculture and is among the most-grown cereals today. The only trait that universally differentiates the cultivated and wild subspecies is 'non-brittleness' of the rachis (the stem of the inflorescence), which facilitates harvesting of the crop. Other phenotypic differences appear to result from facultative or regional selective pressures. The population structure resulting from these regional events has been interpreted as evidence
more » ... multiple domestications or a mosaic ancestry involving genetic interaction between multiple wild or proto-domesticated lineages. However, each of the three mutations that confer non-brittleness originated in the western Fertile Crescent, arguing against multiregional origins for the crop. Results We examined exome data for 310 wild, cultivated and hybrid/feral barley accessions and showed that cultivated barley is structured into six genetically-defined groups that display admixture, resulting at least in part from two or more significant passages of gene flow with distinct wild populations. The six groups are descended from a single founding population that emerged in the western Fertile Crescent. Only a few loci were universally targeted by selection, the identity of these suggesting that changes in seedling emergence and pathogen resistance could represent crucial domestication switches. Subsequent selection operated on a regional basis and strongly contributed to differentiation of the genetic groups. Conclusions Identification of genetically-defined groups provides clarity to our understanding of the population history of cultivated barley. Inference of population splits and mixtures together with analysis of selection sweeps indicate descent from a single founding population, which emerged in the western Fertile Crescent. This founding population underwent relatively little genetic selection, those changes that did occur affecting traits involved in seedling emergence and pathogen resistance, indicating that these phenotypes should be considered as 'domestication traits'. During its expansion out of the western Fertile Crescent, the crop underwent regional episodes of gene flow and selection, giving rise to a modern genetic signature that has been interpreted as evidence for multiple domestications, but which we show can be rationalized with a single origin.
doi:10.1186/s12864-021-07511-7 pmid:33794767 fatcat:jusqr4jwczgehfglkanvvns44u

Digital and Handcrafting Processes Applied to Sound-Studies of Archaeological Bone Flutes [chapter]

Etienne Safa, Jean-Baptiste Barreau, Ronan Gaugne, Wandrille Duchemin, Jean-Daniel Talma, Bruno Arnaldi, Georges Dumont, Valérie Gouranton
2016 Lecture Notes in Computer Science  
Bone flutes make use of a naturally hollow raw-material. As nature does not produce duplicates, each bone has its own inner cavity, and thus its own sound-potential. This morphological variation implies acoustical specificities, thus making it impossible to handcraft a true and exact sound-replica in another bone. This phenomenon has been observed in a handcrafting context and has led us to conduct two series of experiments (the first-one using handcrafting process, the second-one using 3D
more » ... ss) in order to investigate its exact influence on acoustics as well as on sound-interpretation based on replicas. The comparison of the results has shed light upon epistemological and methodological issues that have yet to be fully understood. This work contributes to assessing the application of digitization, 3D printing and handcrafting to flute-like sound instruments studied in the field of archaeomusicology.
doi:10.1007/978-3-319-48496-9_15 fatcat:vr7lnph6jfe3baschlmjr7lw5y

DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies

Wandrille Duchemin, Yoann Anselmetti, Murray Patterson, Yann Ponty, S�verine B�rard, Cedric Chauve, Celine Scornavacca, Vincent Daubin, Eric Tannier
2017 Genome Biology and Evolution  
Gene trees were constructed with RAxML (Stamatakis 2014) and corrected with ProfileNJ (Nouhati et al. 2016 ) (keeping all branches with a 100% Duchemin et al.  ... 
doi:10.1093/gbe/evx069 pmid:28402423 pmcid:PMC5441342 fatcat:qc3w4cowcvdaphrfshltrcwlly

RecPhyloXML: a format for reconciled gene trees

Wandrille Duchemin, Guillaume Gence, Anne-Muriel Arigon Chifolleau, Lars Arvestad, Mukul S Bansal, Vincent Berry, Bastien Boussau, François Chevenet, Nicolas Comte, Adrián A Davín, Christophe Dessimoz, David Dylus (+10 others)
2018 Bioinformatics  
All these scripts and APIs are available at https://github.com/WandrilleD/recPhyloXML.  ...  B.subtilis" geneName="gC"></leaf> </eventsRec> </clade> </clade> </clade> </phylogeny> </recGeneTree> </recPhylo> both as input and output options in the adjacency history computing software DeCoSTAR (Duchemin  ... 
doi:10.1093/bioinformatics/bty389 pmid:29762653 fatcat:4x5yhdsxvzex5fe3vvc3mml6gy

Multi-insecticide resistant malaria vectors in the field remain susceptible to malathion, despite the presence of Ace1 point mutations

Nadja C. Wipf, Wandrille Duchemin, France-Paraudie A. Kouadio, Behi K. Fodjo, Christabelle G. Sadia, Chouaïbou S. Mouhamadou, Laura Vavassori, Pascal Mäser, Konstantinos Mavridis, John Vontas, Pie Müller, Subba Reddy Palli
2022 PLoS Genetics  
Insecticide resistance in Anopheles mosquitoes is seriously threatening the success of insecticide-based malaria vector control. Surveillance of insecticide resistance in mosquito populations and identifying the underlying mechanisms enables optimisation of vector control strategies. Here, we investigated the molecular mechanisms of insecticide resistance in three Anopheles coluzzii field populations from southern Côte d'Ivoire, including Agboville, Dabou and Tiassalé. All three populations
more » ... resistant to bendiocarb, deltamethrin and DDT, but not or only very weakly resistant to malathion. The absence of malathion resistance is an unexpected result because we found the acetylcholinesterase mutation Ace1-G280S at high frequencies, which would typically confer cross-resistance to carbamates and organophosphates, including malathion. Notably, Tiassalé was the most susceptible population to malathion while being the most resistant one to the pyrethroid deltamethrin. The resistance ratio to deltamethrin between Tiassalé and the laboratory reference colony was 1,800 fold. By sequencing the transcriptome of individual mosquitoes, we found numerous cytochrome P450-dependent monooxygenases – including CYP6M2, CYP6P2, CYP6P3, CYP6P4 and CYP6P5 – overexpressed in all three field populations. This could be an indication for negative cross-resistance caused by overexpression of pyrethroid-detoxifying cytochrome P450s that may activate pro-insecticides, thereby increasing malathion susceptibility. In addition to the P450s, we found several overexpressed carboxylesterases, glutathione S-transferases and other candidates putatively involved in insecticide resistance.
doi:10.1371/journal.pgen.1009963 pmid:35143477 pmcid:PMC8830663 fatcat:svywbwmyuzckxfs26jgxrkg2wa

Crowdsourcing Cultural Heritage: From 3D Modeling to the Engagement of Young Generations [chapter]

Laura Inzerillo, Cettina Santagati
2016 Lecture Notes in Computer Science  
Duchemin, Jean-Daniel Talma, Bruno Arnaldi, Georges Dumont, and Valérie Gouranton Full Paper: Digital Applications for Materials' Preservation and Conservation in Cultural Heritage Evolution of Building  ...  Handcrafting Processes Applied to Sound-Studies of Archaeological Bone Flutes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184 Etienne Safa, Jean-Baptiste Barreau, Ronan Gaugne, Wandrille  ... 
doi:10.1007/978-3-319-48496-9_70 fatcat:c4iu3jo5src77iti372w7qvrxm

Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages

2019 Bioinformatics  
Acknowledgements We thank Vincent Daubin, Wandrille Duchemin, Nicolas Lartillot and Thibault Latrille for insightful discussions during the preparation of this manuscript.  ...  provides the user with a clear and detailed output of the complete evolutionary process simulated, including the reconciled gene trees with the species tree in the RecPhyloXML reconciliation standard (Duchemin  ... 
doi:10.1093/bioinformatics/btz710 pmid:31566657 pmcid:PMC7031779 fatcat:wfyywcllkreblankienj7tiama

Zombi: A simulator of species, genes and genomes that accounts for extinct lineages [article]

Adrian A. Davin, Theo Tricou, Eric Tannier, Damien M. de Vienne, Gergely J. Szollosi
2018 bioRxiv   pre-print
We thank Vincent Daubin, Wandrille Duchemin, Nicolas Lartillot and Thibault Latrille for insightful discussions during the preparation of this manuscript.  ...  Reconciled gene trees with the species tree can also be output in the RecPhyloXML reconciliation standard (Duchemin et al., 2018) .  ... 
doi:10.1101/339473 fatcat:culuee67efhbjfu622rtwnbvkm

morse: an R-package in support of Environmental Risk Assessment [article]

Sandrine Charles, Virgile Baudrot
2021 bioRxiv   pre-print
Duchemin, Benoît Goussen, Nils Kehrein, Guillaume Kon-Kam-King, Christelle 177 Lopes, Philippe Ruiz, Alexander Singer and Philippe Veber.  ...  project admin-173 istration, formal analysis, data curation, writing manuscript. 174 Acknowledgments 175 Authors fully thank all contributors to the morse package: Marie Laure Delignette-Muller, 176 Wandrille  ... 
doi:10.1101/2021.04.07.438826 fatcat:jn2sd5u6wnbkjof2g55i5wciru

morse: an R-package to analyse toxicity test data

Virgile Baudrot, Sandrine Charles
2021 Journal of Open Source Software  
Acknowledgments We fully thank all contributors to the morse package: Marie Laure Delignette-Muller, Wandrille Duchemin, Benoît Goussen, Nils Kehrein, Guillaume Kon-Kam-King, Christelle Lopes, Philippe  ... 
doi:10.21105/joss.03200 fatcat:lgwpoiedojekrjxv3gzs7j3ori

INCEPTION Standard for Heritage BIM Models [chapter]

Peter Bonsma, Iveta Bonsma, Anna Elisabetta Ziri, Silvia Parenti, Pedro Martín Lerones, José Luis Hernández, Federica Maietti, Marco Medici, Beatrice Turillazzi, Ernesto Iadanza
2016 Lecture Notes in Computer Science  
Duchemin, Jean-Daniel Talma, Bruno Arnaldi, Georges Dumont, and Valérie Gouranton Full Paper: Digital Applications for Materials' Preservation and Conservation in Cultural Heritage Evolution of Building  ...  Handcrafting Processes Applied to Sound-Studies of Archaeological Bone Flutes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184 Etienne Safa, Jean-Baptiste Barreau, Ronan Gaugne, Wandrille  ... 
doi:10.1007/978-3-319-48496-9_47 fatcat:76pglzfrxfdbxahuxxnnr6pzgm

Is Global Microbial Biodiversity Increasing, Decreasing, or Staying the Same?

David S. Thaler
2021 Frontiers in Ecology and Evolution  
ACKNOWLEDGMENTS Thanks to Jesse Ausubel, Fiona Doetsch, Wandrille Duchemin, Jackie Faherty, Geoffrey Fucile, Mark Stoeckle, and Iddo Wernick for discussion and encouragement.  ... 
doi:10.3389/fevo.2021.565649 fatcat:pax6tfgo25hhdg54v2vckgrfka
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