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Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence
2015
BMC Genomics
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© 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
2015
BMC Bioinformatics
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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
2018
BMC Genomics
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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
doi:10.1186/s12864-018-4466-7
pmid:29764366
pmcid:PMC5954271
fatcat:e375ybpt5zdedb7r657ymibeti
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... 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.
Episodes of gene flow and selection during the evolutionary history of domesticated barley
2021
BMC Genomics
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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
doi:10.1186/s12864-021-07511-7
pmid:33794767
fatcat:jusqr4jwczgehfglkanvvns44u
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... 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.
Digital and Handcrafting Processes Applied to Sound-Studies of Archaeological Bone Flutes
[chapter]
2016
Lecture Notes in Computer Science
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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
doi:10.1007/978-3-319-48496-9_15
fatcat:vr7lnph6jfe3baschlmjr7lw5y
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... 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.
DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies
2017
Genome Biology and Evolution
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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
2018
Bioinformatics
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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
2022
PLoS Genetics
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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
doi:10.1371/journal.pgen.1009963
pmid:35143477
pmcid:PMC8830663
fatcat:svywbwmyuzckxfs26jgxrkg2wa
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... 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.
Crowdsourcing Cultural Heritage: From 3D Modeling to the Engagement of Young Generations
[chapter]
2016
Lecture Notes in Computer Science
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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
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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]
2018
bioRxiv
pre-print
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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]
2021
bioRxiv
pre-print
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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
2021
Journal of Open Source Software
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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]
2016
Lecture Notes in Computer Science
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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?
2021
Frontiers in Ecology and Evolution
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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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