Author: "Guillaume Achaz" / Topic: 03 medical and health sciences - Searchworks@Jio Institute Digital Library Search Results

Your search keyword '"Guillaume Achaz"' showing total 34 results

Start Over Author "Guillaume Achaz" Topic 03 medical and health sciences

34 results on '"Guillaume Achaz"'

1. An appeal for an objective, open, and transparent scientific debate about the origin of SARS-CoV-2

Author: Richard H. Ebright, Etienne Decroly, Milton Leitenberg, Serge Morand, Didier Casane, François Graner, José Halloy, Rossana Segreto, Bruno Canard, Fabien Colombo, Colin D. Butler, Jean-Michel Claverie, Jacques van Helden, Nikolai Petrovsky, Guillaume Achaz, Virginie Courtier, Theories and Approaches of Genomic Complexity (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Australian National University (ANU), Muséum national d'Histoire naturelle (MNHN), Architecture et fonction des macromolécules biologiques (AFMB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Recherche IRD 072, Laboratoire Evolution, Génomes, Comportement, Ecologie, Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), Université Bordeaux Montaigne, Institut Jacques Monod (IJM (UMR_7592)), Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Rutgers University [Newark], Rutgers University System (Rutgers), Matière et Systèmes Complexes (MSC (UMR_7057)), University of Maryland [College Park], University of Maryland System, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Flinders University [Adelaide, Australia], University of Innsbruck, Laboratoire Interdisciplinaire des Energies de Demain (LIED (UMR_8236)), Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Evolution, génomes, comportement et écologie (EGCE), Institut de Recherche pour le Développement (IRD)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Université Bordeaux Montaigne (UBM), Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Matière et Systèmes Complexes (MSC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Leopold Franzens Universität Innsbruck - University of Innsbruck, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), and Spinelli, Lionel
Subjects: 0303 health sciences, 2019-20 coronavirus outbreak, Coronavirus disease 2019 (COVID-19), SARS-CoV-2, business.industry, [SDV]Life Sciences [q-bio], Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Appeal, COVID-19, General Medicine, Public relations, Biology, 16. Peace & justice, [SDV] Life Sciences [q-bio], 03 medical and health sciences, 0302 clinical medicine, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Correspondence, Humans, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Scientific debate, business, ComputingMilieux_MISCELLANEOUS, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract: International audience
Published: 2021
Full Text: View/download PDF

2. Simulation of bacterial populations with SLiM

Author: Guillaume Achaz, Flora Jay, Benjamin C. Haller, Jean Cury, Laboratoire de Recherche en Informatique (LRI), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Cornell University [New York], Éco-Anthropologie (EAE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), TAckling the Underspecified (TAU), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Interdisciplinaire des Sciences du Numérique (LISN), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), BioInformatique (BioInfo), Laboratoire Interdisciplinaire des Sciences du Numérique (LISN), Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Science des Données (SDD), Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Éco-Anthropologie (EA), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Jay, Flora, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-École normale supérieure - Paris (ENS Paris), and Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Computer science, Population genetics, Genomic data, Distributed computing, [SDV.GEN] Life Sciences [q-bio]/Genetics, computer.software_genre, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Documentation, Protocol (object-oriented programming), [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, SLiM, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], 030304 developmental biology, Flexibility (engineering), 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, SIMPLE (military communications protocol), Bacteria, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Scripting language, Key (cryptography), Simulator, [INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], computer, Simulation
Abstract: Simulation of genomic data is a key tool in population genetics, yet, to date, there is no forward-in-time simulator of bacterial populations that is both computationally efficient and adaptable to a wide range of scenarios. Here we demonstrate how to simulate bacterial populations with SLiM, a forward-in-time simulator built for eukaryotes. SLiM has gained many users in recent years, due to its speed and power, and has extensive documentation showcasing various scenarios that it can simulate. This paper focuses on a simple demographic scenario, to explore unique aspects of modeling bacteria in SLiM’s scripting language. In addition, we illustrate the flexibility of SLiM by simulating the growth of bacteria on a Petri dish with antibiotic. To foster the development of bacterial simulations based upon this recipe, we explain the inner workings of its code. We also validate the simulator, by extensively testing the results of simulations against existing simulators, and against theoretical expectations for some summary statistics. This protocol, with the flexibility and power of SLiM, will enable the community to simulate bacterial populations efficiently under a wide range of evolutionary scenarios.
Published: 2021
Full Text: View/download PDF

3. The rapid divergence of the Antarctic crinoid species Promachocrinus kerguelensis

Author: Yacine Ben Chehida, Guillaume Achaz, Cyril Gallut, Marc Eléaume, Groningen Institute for Evolutionary Life Sciences [Groningen] (GELIFES), University of Groningen [Groningen], Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), and Fontaine lab
Subjects: 0106 biological sciences, Species complex, Lineage (evolution), Speciation, [SDV]Life Sciences [q-bio], Biodiversity, Allopatric speciation, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Genetic drift, Species delimitation, 14. Life underwater, Endemism, Southern Ocean, Promachocrinus kergulensis, 030304 developmental biology, 0303 health sciences, Ecology, Florometra mawsoni, Marine invertebrates, Crinoid, biology.organism_classification, Crinoids, "apparent" drift, Cryptic species, Recent divergence, [SDE]Environmental Sciences
Abstract: Climatic oscillations in Antarctica caused a succession of expansion and reduction of the ice sheets covering the continental shelf of the Southern Ocean. For marine invertebrates, these successions are suspected to have driven allopatric speciation, endemism and the prevalence of cryptic species, leading to the so-called Antarctic ‘biodiversity pump’ hypothesis. Here we took advantage of the recent sampling effort influenced by the International Polar Year (2007-8) to test for the validity of this hypothesis for 1,797 samples of two recognized crinoid species:Promachocrinus kerguelensisandFlorometra mawsoni. Species delimitation analysis identified seven phylogroups. As previously suggested,Promachocrinus kerguelensisforms a complex of six cryptic species. Conversely, despite the morphological differences, our results show thatFlorometra mawsoniis a lineage nested withinPromachocrinus kerguelensis. It suggests thatFlorometra mawsoniandPromachocrinus kerguelensisbelong to the same complex of species. Furthermore, this study indicates that over time and space the different sectors of the Southern Ocean show a remarkable rapid turn-over in term of phylogroups composition and also of genetic variants within phylogroups. We argue that strong “apparent” genetic drift causes this rapid genetic turn-over. Finally, we dated the last common ancestor of all phylogroups at less than 1,000 years, raising doubts on the relevance of the Antarctic “biodiversity pump” for this complex of species. This work is a first step towards a better understanding of how life is diversifying in the Southern Ocean.
Published: 2020

4. The quiescent X, the replicative Y and the Autosomes

Author: Serge Gangloff, Benoit Arcangioli, Guillaume Achaz, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Dynamique du Génome - Dynamics of the genome, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), This work was supported by the grants ANR-13-BSV8-0018 and ANR-12-BSV7-0012 Demochips from the Agence Nationale de la Recherche (France) to BA and GA, respectively., ANR-13-BSV8-0018,quiescenceDNA,stabilité génétique en quiescence(2013), ANR-12-BSV7-0012,demochips,Inférence de l'histoire démographique à partie des grands jeux de données de polymorphisme A.D.N.(2012), Gangloff, Serge, Blanc 2013 - stabilité génétique en quiescence - - quiescenceDNA2013 - ANR-13-BSV8-0018 - Blanc 2013 - VALID, BLANC - Inférence de l'histoire démographique à partie des grands jeux de données de polymorphisme A.D.N. - - demochips2012 - ANR-12-BSV7-0012 - BLANC - VALID, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), This work was supported by the grants ANR-13-BSV8-0018 and ANR-12-BSV7-0012 Demochips from the Agence Nationale de la Recherche(France) to BA and GA, respectively., Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Génétique des génomes - Genetics of Genomes (UMR 3525), Département de Génomes et Génétique - Department of Genomes and Genetics, and Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité)
Subjects: Genetics, 0303 health sciences, Mutation, Autosome, Lineage (genetic), [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], [SDV]Life Sciences [q-bio], food and beverages, Biology, medicine.disease_cause, [SDV] Life Sciences [q-bio], 03 medical and health sciences, 0302 clinical medicine, Anisogamy, medicine, Human genome, 1000 Genomes Project, Indel, 030217 neurology & neurosurgery, X chromosome, 030304 developmental biology
Abstract: From the analysis of the mutation spectrum in the 2,504 sequenced human genomes from the 1000 genomes project (phase 3), we show that sexual chromosomes (X and Y) exhibit a different proportion of indel mutations than autosomes (A), ranking them X>A>Y. We further show that X chromosomes exhibit a higher ratio of deletion/insertion when compared to autosomes. This simple pattern shows that the recent report that non-dividing quiescent yeast cells accumulate relatively more indels (and particularly deletions) than replicating ones also applies to metazoan cells, including humans. Indeed, the X chromosomes display more indels than the autosomes, having spent more time in quiescent oocytes, whereas the Y chromosomes are solely present in the replicating spermatocytes. From the proportion of indels, we have inferred that de novo mutations arising in the maternal lineage are twice more likely to be indels than mutations from the paternal lineage. Our observation, consistent with a recent trio analysis of the spectrum of mutations inherited from the maternal lineage, is likely a major component in our understanding of the origin of anisogamy.
Published: 2020
Full Text: View/download PDF

5. The genomic view of diversification

Author: Julie Marin, Amaury Lambert, Guillaume Achaz, Anton Crombach, Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Éco-Anthropologie (EA), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Artificial Evolution and Computational Biology (BEAGLE), Laboratoire d'InfoRmatique en Image et Systèmes d'information (LIRIS), Université Lumière - Lyon 2 (UL2)-École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Lumière - Lyon 2 (UL2)-École Centrale de Lyon (ECL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Probabilités, Statistique et Modélisation (LPSM (UMR_8001)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Éco-Anthropologie (EAE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'InfoRmatique en Image et Systèmes d'information (LIRIS), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-École Centrale de Lyon (ECL), Université de Lyon-Université Lumière - Lyon 2 (UL2)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-École Centrale de Lyon (ECL), Université de Lyon-Université Lumière - Lyon 2 (UL2), Laboratoire de Probabilités, Statistiques et Modélisations (LPSM (UMR_8001)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), and Crombach, Anton
Subjects: 0301 basic medicine, 0106 biological sciences, Genetic Speciation, [SDV]Life Sciences [q-bio], introgression, Population genetics, Inference, Diversification (marketing strategy), Biology, phylogeny, 010603 evolutionary biology, 01 natural sciences, species tree, Gene flow, Coalescent theory, 03 medical and health sciences, Genetic drift, Genetic algorithm, Gene, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, coalescent theory, 0303 health sciences, Genome, Hierarchy (mathematics), Models, Genetic, Gene tree, population genetics, Reproductive isolation, [SDV] Life Sciences [q-bio], Tree (data structure), multispecies coalescent, 030104 developmental biology, gene tree, speciation, Evolutionary biology, gene‐based diversification model, gene flow
Abstract: Evolutionary relationships between species are traditionally represented in the form of a tree, called the species tree. The reconstruction of the species tree from molecular data is hindered by frequent conflicts between gene genealogies. A standard way of dealing with this issue is to pos-tulate the existence of a unique species tree where disagreements between gene trees are explained by incomplete lineage sorting (ILS) due to random coalescences of gene lineages inside the edges of the species tree. This paradigm, known as the multi-species coalescent (MSC), is constantly violated by the ubiquitous presence of gene flow revealed by empirical studies, leading to topological incon-gruences of gene trees that cannot be explained by ILS alone. Here we argue that this paradigm should be revised in favor of a vision acknowledging the importance of gene flow and where gene histories shape the species tree rather than the opposite. We propose a new, plastic framework for modeling the joint evolution of gene and species lineages relaxing the hierarchy between the species tree and gene trees. As an illustration, we implement this framework in a mathematical model called the genomic diversification (GD) model based on coalescent theory, with four parameters tuning repli-cation, genetic differentiation, gene flow and reproductive isolation. We use it to evaluate the amount of gene flow in two empirical data-sets. We find that in these data-sets, gene tree distributions are better explained by the best fitting GD model than by the best fitting MSC model. This work should pave the way for approaches of diversification using the richer signal contained in genomic evolution-ary histories rather than in the mere species tree.
Published: 2020
Full Text: View/download PDF

6. Clinical and genetic study of Tunisian families with genetic generalized epilepsy: contribution of CACNA1H and MAST4 genes

Author: Saloua Mrabet, Caroline Nava, Imen Kacem, Eric LeGuern, Mouna Ben Djebara, Riadh Gouider, Eric Noé, A. Gargouri-Berrechid, Guillaume Achaz, Zied Landoulsi, Stéphanie Baulac, and Fatma Laatar
Subjects: Adult, Male, 0301 basic medicine, Proband, Multifactorial Inheritance, Candidate gene, Tunisia, Adolescent, Genetic Linkage, Pedigree chart, Protein Serine-Threonine Kinases, Quantitative trait locus, Cohort Studies, Calcium Channels, T-Type, Consanguinity, Young Adult, 03 medical and health sciences, Cellular and Molecular Neuroscience, 0302 clinical medicine, Childhood absence epilepsy, Genetics, CACNA1H, medicine, Humans, Family, Genetic Predisposition to Disease, Age of Onset, Child, Genetic Association Studies, Genetics (clinical), biology, Oligogenic Inheritance, medicine.disease, Pedigree, 030104 developmental biology, biology.protein, Epilepsy, Generalized, Female, Juvenile myoclonic epilepsy, Microtubule-Associated Proteins, 030217 neurology & neurosurgery
Abstract: Genetic generalized epilepsies (GGE) (childhood absence epilepsy (CAE), juvenile myoclonic epilepsy (JME) and epilepsy with generalized tonic-clonic seizures (GTCS)) are mainly determined by genetic factors. Since few mutations were identified in rare families with autosomal dominant GGE, a polygenic inheritance was suspected in most patients. Recent studies on large American or European cohorts of sporadic cases showed that susceptibility genes were numerous although their variants were rare, making their identification difficult. Here, we reported clinical and genetic characteristics of 30 Tunisian GGE families, including 71 GGE patients. The phenotype was close to that in sporadic cases. Nineteen pedigrees had a homogeneous type of GGE (JME-CAE-CGTS), and 11 combined these epileptic syndromes. Rare non-synonymous variants were selected in probands using a targeted panel of 30 candidate genes and their segregation was determined in families. Molecular studies incriminated different genes, mainly CACNA1H and MAST4. The segregation of at least two variants in different genes in some pedigrees was compatible with the hypothesis of an oligogenic inheritance, which was in accordance with the relatively low frequency of consanguineous probands. Since at least 2 susceptibility genes were likely shared by different populations, genetic factors involved in the majority of Tunisian GGE families remain to be discovered. Their identification should be easier in families with a homogeneous type of GGE, in which an intra-familial genetic homogeneity could be suspected.
Published: 2018
Full Text: View/download PDF

7. No HIV-1 molecular evolution on long-term antiretroviral therapy initiated during primary HIV-1 infection

Author: Aude Jary, Lambert Assoumou, Vincent Calvez, Cathia Soulié, Nathalie Désiré, Guillaume Achaz, Romain Palich, Roland Tubiana, Anne Simon, Christine Katlama, Sophie Brouillet, Thuy Van Nguyen, Basma Abdi, Marc-Antoine Valantin, Sophie Sayon, Anne-Geneviève Marcelin, Marc Wirden, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Service de Virologie [CHU Pitié-Salpêtrière], CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Service de Maladies Infectieuses et Tropicales [CHU Pitié-Salpêtrière], Service de médecine interne [CHU Pitié-Salpétrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Gestionnaire, Hal Sorbonne Université, Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de virologie [CHU Pitié-Salpêtrière], and Service des maladies infectieuses et tropicales [CHU Pitié-Salpêtrière]
Subjects: 0301 basic medicine, Anti-HIV Agents, [SDV]Life Sciences [q-bio], Immunology, Population, HIV Infections, medicine.disease_cause, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, Molecular evolution, medicine, Humans, Immunology and Allergy, 030212 general & internal medicine, education, Sida, Phylogeny, Retrospective Studies, Mutation, education.field_of_study, Phylogenetic tree, biology, business.industry, Viral Load, biology.organism_classification, Antiretroviral therapy, Virology, 3. Good health, [SDV] Life Sciences [q-bio], 030104 developmental biology, Infectious Diseases, Viral evolution, HIV-1, business, Viral load
Abstract: International audience; Objective: Most studies about HIV-1 molecular evolution have shown the lack of viral evolution on effective antiretroviral therapy (ART), although controversial results have been documented. We therefore aimed to look for evidence of HIV-1 evolution in patients who initiated ART at the time of primary HIV-1 infection (PHI).Design: We included retrospectively 20 patients diagnosed at PHI, treated at the time of acute infection and with subsequent effective long-term suppressive ART (HIV viral load
Published: 2020
Full Text: View/download PDF

8. ASAP: assemble species by automatic partitioning

Author: Nicolas Puillandre, Guillaume Achaz, Sophie Brouillet, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)
Subjects: 0106 biological sciences, 0301 basic medicine, Scoring system, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Barcode, computer.software_genre, 010603 evolutionary biology, 01 natural sciences, DNA barcoding, law.invention, Coalescent theory, 03 medical and health sciences, Species Specificity, law, Genetics, Cluster Analysis, DNA Barcoding, Taxonomic, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, Phylogeny, Single locus, Phylogenetic reconstruction, Hierarchical clustering, 030104 developmental biology, Pairwise comparison, Data mining, computer, Monte Carlo Method, Sequence Alignment, Algorithms, Software, Biotechnology
Abstract: Here, we describe Assemble Species by Automatic Partitioning (ASAP), a new method to build species partitions from single locus sequence alignments (i.e., barcode data sets). ASAP is efficient enough to split data sets as large 104 sequences into putative species in several minutes. Although grounded in evolutionary theory, ASAP is the implementation of a hierarchical clustering algorithm that only uses pairwise genetic distances, avoiding the computational burden of phylogenetic reconstruction. Importantly, ASAP proposes species partitions ranked by a new scoring system that uses no biological prior insight of intraspecific diversity. ASAP is a stand-alone program that can be used either through a graphical web-interface or that can be downloaded and compiled for local usage. We have assessed its power along with three others programs (ABGD, PTP and GMYC) on 10 real COI barcode data sets representing various degrees of challenge (from small and easy cases to large and complicated data sets). We also used Monte-Carlo simulations of a multispecies coalescent framework to assess the strengths and weaknesses of ASAP and the other programs. Through these analyses, we demonstrate that ASAP has the potential to become a major tool for taxonomists as it proposes rapidly in a full graphical exploratory interface relevant species hypothesis as a first step of the integrative taxonomy process.
Published: 2019
Full Text: View/download PDF

9. Correction: The landscape of epilepsy-related GATOR1 variants

Author: Johannes R. Lemke, Thomas Dorn, Laura Hernandez-Hernandez, Giuseppe d'Orsi, Eveline Hagebeuk, Annapurna Poduri, Douglas R. NordliJr, Hélène Catenoix, Melanie Jennesson, Veronique Darmency, Kevin Rostasy, Thomas Becher, Laura Licchetta, Peter Uldall, Lysa Boissé Lomax, Bianca Berghuis, Ilona Krey, Gaetan Lesca, Anne de Saint Martin, Boudewijn Gunning, Anne Fabienne Lepine, Renske Oegema, Brigitte Ricard-Mousnier, Sarah Ferrand-Sorbets, Arnaud Biraben, Charles Deckers, An Sofie Schoonjans, Martin Zenker, Simona Balestrini, Inga Talvik, Julitta de Bellescize, Christopher J. Yuskaitis, Georg Dorfmüller, Erik H. Niks, Guillaume Achaz, Laurence Faivre, Pasquale Striano, Shifteh Sattar, Karen Müller-Schlüter, Sanjay M. Sisodiya, Caroline Nava, Pia Zacher, Fabrice Bartolomei, Kristin Lindstrom, Sophie Julia, Eric LeGuern, Thomas Cloppenborg, Rikke S. Møller, Antonio Gambardella, Mathilde Chipaux, Sara Baldassari, Pavel Krsek, Marie Line Jacquemont, Ilse Wegner, Christian Brandt, Barbora Benova, Valerio Conti, Gabrielle Rudolf, Floor E. Jansen, Edouard Hirsch, S. Krithika, Jamel Chelly, Katrien Stouffs, Daniëlle de Jong, Courtney Kiss, Tilman Polster, Eva H. Brilstra, Tommaso Pippucci, Markus Wolff, Cécile Marchal, Giovanni Crichiutti, Kees P.J. Braun, Paolo Tinuper, Stéphanie Baulac, Valentin Sander, Anne-Sophie Lebre, Nienke E. Verbeek, Anna Jansen, Francesca Bisulli, Fabienne Picard, Natasha E. Schoeler, Julien Thevenon, Marjan J. A. van Kempen, Guido Rubboli, Sarah Weckhuysen, Renzo Guerrini, Eleni Panagiotakaki, Meral Balci, Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Hôpital Universitaire de Genève, Department of Genetics [Utrecht, the Netherlands], University Medical Center [Utrecht], Children's Hospital A. Meyer, Department of Clinical and Experimental Epilepsy, University College of London [London] (UCL), Molecular Cell Biology, Leiden University Medical Center (LUMC), Danish Epilepsy Centre, Denmark and Aarhus University, Aarhus, Centre Hospitalier Universitaire de La Réunion (CHU La Réunion), Service de Génétique Cytogénétique et Embryologie [CHU Pitié-Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Neurogénétique Moléculaire et Cellulaire, Institut Naltional de la Santé et de la Recherche Médicale, Epidémiologie et analyses en santé publique : risques, maladies chroniques et handicaps (LEASP), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Regional Epilepsy Center, Reggio Calabria, Centre de génétique - Centre de référence des maladies rares, anomalies du développement et syndromes malformatifs (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), FHU TRANSLAD (CHU de Dijon), Département de Sociologie [université de Bourgogne], UFR de sciences humaines [Université de Bourgogne], Université de Bourgogne (UB)-Université de Bourgogne (UB), Service de Neurophysiologie Clinique (CHU Dijon), Laboratoire Traitement du Signal et de l'Image (LTSI), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de génétique [Reims], Centre Hospitalier Universitaire de Reims (CHU Reims), Universitair Ziekenhuis Brussel, Equipe GAD (LNC - U1231), Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Université Bourgogne Franche-Comté [COMUE] (UBFC), Département d'Epilepsie, Sommeil et Neurophysiologie Pédiatrique [HCL, Lyon], Hospices Civils de Lyon (HCL), Institute of Human Genetics, University Hospital Magdeburg, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), University of Southern Denmark (SDU), Institut du Cerveau = Paris Brain Institute (ICM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Hôpital Universitaire de Genève = University Hospitals of Geneva (HUG), Universiteit Leiden-Universiteit Leiden, Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)
Subjects: 0303 health sciences, business.industry, Published Erratum, MEDLINE, medicine.disease, computer.software_genre, Spelling, 03 medical and health sciences, Epilepsy, 0302 clinical medicine, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, medicine, Artificial intelligence, business, Psychology, computer, 030217 neurology & neurosurgery, Genetics (clinical), Natural language processing, 030304 developmental biology
Abstract: International audience; The original version of this article contained an error in the spelling of the author Erik H. Niks, which was incorrectly given as Erik Niks. This has now been corrected in both the PDF and HTML versions of the article.
Published: 2019
Full Text: View/download PDF

10. Is reproductive strategy a key factor in understanding the evolutionary history of Southern Ocean Asteroidea (Echinodermata)?

Author: Quentin Jossart, Marc Eleaume, Bruno Danis, Thomas Saucède, Chester J. Sands, Guillaume Achaz, Camille Moreau, Antonio Agüera, Laboratoire de Biologie Marine, Université libre de Bruxelles (ULB), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Marine Biology, Vrije Universiteit Brussel (VUB), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), British Antarctic Survey (BAS), Natural Environment Research Council (NERC), Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Fonds pour la formation à la Recherche dans l'Industrie et l'Agriculture' (FRIA)., Laffont, Rémi, Biogéosciences [UMR 6282] [Dijon] (BGS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS Paris), and Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris)
Subjects: 0106 biological sciences, trans‐Antarctic seaway, invertebrate, Biology, 010603 evolutionary biology, 01 natural sciences, Santé publique, Environnement et pollution, 03 medical and health sciences, Asteroidea, lcsh:QH540-549.5, emergence, bipolarity, 14. Life underwater, Molecular clock, Ecology, Evolution, Behavior and Systematics, Original Research, 030304 developmental biology, Nature and Landscape Conservation, 0303 health sciences, Genetic diversity, trans-Antarctic seaway, Ecology, Phylogenetic tree, Ecologie, Cytochrome c oxidase subunit I, brooding, thermohaline expressway, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, Colonisation, Phylogeography, Genetic structure, Antarctica, lcsh:Ecology, Species richness, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Echinodermata
Abstract: Life traits such as reproductive strategy can be determining factors of species evolutionary history and explain the resulting diversity patterns. This can be investigated using phylogeographic analyses of genetic units. In this work, the genetic structure of five asteroid genera with contrasting reproductive strategies (brooding: Diplasterias, Notasterias and Lysasterias versus broadcasting: Psilaster and Bathybiaster) was investigated in the Southern Ocean. Over 1,400 mtDNA cytochrome C oxidase subunit I (COI) sequences were analysed using five species delineation methods (ABGD, ASAP, mPTP, sGMYC and mGMYC), two phylogenetic reconstructions (ML and BA), and molecular clock calibrations, in order to examine the weight of reproductive strategy in the observed differences among phylogeographic patterns. We hypothesised that brooding species would show higher levels of genetic diversity and species richness along with a clearer geographic structuring than broadcasting species. In contrast, genetic diversity and species richness were not found to be significantly different between brooders and broadcasters, but broadcasters are less spatially structured than brooders supporting our initial hypothesis and suggesting more complex evolutionary histories associated to this reproductive strategy. Broadcasters' phylogeography can be explained by different scenarios including deep-sea colonisation routes, bipolarity or cosmopolitanism, and sub-Antarctic emergence for the genus Bathybiaster; Antarctic- New Zealand faunal exchanges across the Polar Front for the genus Psilaster. Brooders' phylogeography could support the previously formulated hypothesis of a past trans-Antarctic seaway established between the Ross and the Weddell seas during the Plio-Pleistocene. Our results also show, for the first time, that the Weddell Sea is populated by a mixed asteroid fauna originating from both the East and West Antarctic., SCOPUS: ar.j, info:eu-repo/semantics/published
Published: 2019
Full Text: View/download PDF

11. Testing for population decline using maximal linkage disequilibrium blocks

Author: Elise Kerdoncuff, Amaury Lambert, Guillaume Achaz, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), and CCSD, Accord Elsevier
Subjects: 0301 basic medicine, 0106 biological sciences, Linkage disequilibrium, Range (biology), [SDV]Life Sciences [q-bio], Single-nucleotide polymorphism, Biology, 010603 evolutionary biology, 01 natural sciences, Polymorphism, Single Nucleotide, Linkage Disequilibrium, Coalescent theory, Population genomics, 03 medical and health sciences, Block (programming), Animals, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Population Density, 0303 health sciences, Population size, [SDV] Life Sciences [q-bio], Population decline, 030104 developmental biology, Evolutionary biology, Conservation status, Conservation biology
Abstract: Only 6% of known species have a conservation status. Methods that assess conservation statuses are often based on individual counts and are thus too laborious to be generalized to all species. Population genomics methods that infer past variations in population size are easy to use but limited to the relatively distant past. Here we propose a population genomics approach that tests for recent population decline and may be used to assess species conservation statuses. More specifically, we study Maximal Recombination Free (MRF) blocks, that are segments of a sequence alignment inherited from a common ancestor without recombination. MRF blocks are relatively longer in small than in large populations. We use the distribution of MRF block lengths rescaled by their mean to test for recent population decline. However, because MRF blocks are difficult to detect, we also consider Maximal Linkage Disequilibrium (MLD) blocks, which are runs of single nucleotide polymorphisms compatible with a single tree. We develop a new method capable of inferring a very recent decline (e.g. with a detection power of 50% for populations which size was halved toN, 0.05 ×Ngenerations ago) from rescaled MLD block lengths. Our framework could serve as a basis for quantitative tools to assess conservation status in a wide range of species.
Published: 2019
Full Text: View/download PDF

12. Is convergence an evidence for positive selection?

Author: Guillaume Achaz, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), and guillemaud, thomas
Subjects: 0106 biological sciences, 0303 health sciences, Positive selection, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], General Medicine, 010603 evolutionary biology, 01 natural sciences, 3. Good health, 03 medical and health sciences, Convergent evolution, [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Convergence (relationship), Mathematical economics, Selection (genetic algorithm), 030304 developmental biology, Mathematics
Abstract: International audience; A recommendation of the preprint: Frederic Bertels, Karin J Metzner, Roland R Regoes. Convergent evolution as an indicator for selection during acute HIV-1 infection (2018), bioRxiv, 168260, ver. 4 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/168260
Published: 2018
Full Text: View/download PDF

13. A Molecular Portrait of De Novo Genes in Yeasts

Author: Joshua J. Coon, Nikolaos Vakirlis, Dana A. Opulente, Chris Todd Hittinger, Gilles Fischer, Alexander S. Hebert, Guillaume Achaz, Ingrid Lafontaine, Biology of Genomes [LCQB] (LCQB-BiG), Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Systématique, adaptation, évolution (SAE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Department of Chemistry, and University of Wisconsin-Madison
Subjects: 0301 basic medicine, Computational biology, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Conserved sequence, Evolution, Molecular, Fungal Proteins, 03 medical and health sciences, Saccharomyces, 0302 clinical medicine, Intergenic region, Phylogenetics, Genetics, Selection, Genetic, Promoter Regions, Genetic, Molecular Biology, Gene, Ecology, Evolution, Behavior and Systematics, Discoveries, Conserved Sequence, ComputingMilieux_MISCELLANEOUS, Recombination, Genetic, Fungal protein, Base Sequence, Age Factors, Promoter, Phenotype, 030104 developmental biology, Homologous recombination, 030217 neurology & neurosurgery
Abstract: New genes, with novel protein functions, can evolve "from scratch" out of intergenic sequences. These de novo genes can integrate the cell's genetic network and drive important phenotypic innovations. Therefore, identifying de novo genes and understanding how the transition from noncoding to coding occurs are key problems in evolutionary biology. However, identifying de novo genes is a difficult task, hampered by the presence of remote homologs, fast evolving sequences and erroneously annotated protein coding genes. To overcome these limitations, we developed a procedure that handles the usual pitfalls in de novo gene identification and predicted the emergence of 703 de novo gene candidates in 15 yeast species from 2 genera whose phylogeny spans at least 100 million years of evolution. We validated 85 candidates by proteomic data, providing new translation evidence for 25 of them through mass spectrometry experiments. We also unambiguously identified the mutations that enabled the transition from noncoding to coding for 30 Saccharomyces de novo genes. We established that de novo gene origination is a widespread phenomenon in yeasts, only a few being ultimately maintained by selection. We also found that de novo genes preferentially emerge next to divergent promoters in GC-rich intergenic regions where the probability of finding a fortuitous and transcribed ORF is the highest. Finally, we found a more than 3-fold enrichment of de novo genes at recombination hot spots, which are GC-rich and nucleosome-free regions, suggesting that meiotic recombination contributes to de novo gene emergence in yeasts.
Published: 2018
Full Text: View/download PDF

14. Comparative Genomics of Tenacibaculum dicentrarchi and 'Tenacibaculum finnmarkense' Highlights Intricate Evolution of Fish-Pathogenic Species

Author: Ruben Avendaño-Herrera, Guillaume Achaz, Jean François Bernardet, Sébastien Bridel, Anne Berit Olsen, Hanne Nilsen, Eric Duchaud, Unité de recherche Virologie et Immunologie Moléculaires (VIM), Institut National de la Recherche Agronomique (INRA), FINALAB, Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Norwegian Veterinary Institute, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), Universidad Andrés Bello - UNAB (CHILE), Universidad de Concepción [Chile], Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), Norwegian Veterinary Institute [Oslo], Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Universidad Andrés Bello [Santiago] (UNAB), EU EMIDA ERA-NET project 'Control Flavobacteriaceae Infections in European Fish farms', Agence Nationale pour la Recherche [ANR-14-CE19-0020], National Infrastructure 'France Genomique' funded as part of the Investissement d'avenir program managed by Agence Nationale pour la Recherche [ANR-10-INBS-09], Comision Nacional de Investigacion Cientifica y Tecnologica (CONICYT, Chile) [FONDECYT 1150695, CONICYT/FONDAP/15110027], and Duchaud, Eric
Subjects: 0301 basic medicine, Tenacibaculum, tenacibaculosis, genomes, fish pathogens, virulence, evolution, Genome evolution, Evolution, Fish farming, [SDV]Life Sciences [q-bio], Zoology, Genomics, Biology, Genome, Fish Diseases, 03 medical and health sciences, Flavobacteriaceae Infections, Phylogenetics, Genetics, Animals, 14. Life underwater, Genomes, Sea bass, Fish pathogens, Phylogeny, Ecology, Evolution, Behavior and Systematics, Comparative genomics, Tenacibaculosis, Virulence, Fishes, Genome Report, 030104 developmental biology, Genome, Bacterial
Abstract: Data deposition: All genome sequencing data have been deposited at the European Nucleotide Archive under the accessions GCA_900239455, GCA_900239305, GCA_900239485, GCA_900239185, GCA_900239505, GCA_900239345, and GCA_900239495.; International audience; The genus Tenacibaculum encompasses several species pathogenic for marine fish. Tenacibaculum dicentrarchi and " Tenacibaculum finnmarkense " (Quotation marks denote species that have not been validly named.) were retrieved from skin lesions of farmed fish such as European sea bass or Atlantic salmon. They cause a condition referred to as tenacibaculosis and severe outbreaks and important fish losses have been reported in Spanish, Norwegian, and Chilean marine farms. We report here the draft genomes of the T. dicentrarchi and " T. finnmarkense " type strains. These genomes were compared with draft genomes from field isolates retrieved from Chile and Norway and with previously published Tenacibaculum genomes. We used Average Nucleotide Identity and core genome-based phylogeny as a proxy index for species boundary delineation. This work highlights evolution of closely related fish-pathogenic species and suggests that homologous recombination likely contributes to genome evolution.
Published: 2018
Full Text: View/download PDF

15. Evolutionary constraints in fitness landscapes

Author: Guillaume Achaz, Daniel M. Weinreich, Luca Ferretti, and Fumio Tajima
Subjects: 0106 biological sciences, 0301 basic medicine, Theoretical computer science, Fitness landscape, Small number, Genetic Fitness, Epistasis, Genetic, Biology, 010603 evolutionary biology, 01 natural sciences, Article, Constraint (information theory), Evolution, Molecular, 03 medical and health sciences, 030104 developmental biology, Similarity (psychology), Genetics, Epistasis, Predictability, Selection, Genetic, Genetics (clinical), Selection (genetic algorithm)
Abstract: In the last years, several genotypic fitness landscapes-combinations of a small number of mutations-have been experimentally resolved. To learn about the general properties of "real" fitness landscapes, it is key to characterize these experimental landscapes via simple measures of their structure, related to evolutionary features. Some of the most relevant measures are based on the selectively acessible paths and their properties. In this paper, we present some measures of evolutionary constraints based on (i) the similarity between accessible paths and (ii) the abundance and characteristics of "chains" of obligatory mutations, that are paths going through genotypes with a single fitter neighbor. These measures have a clear evolutionary interpretation. Furthermore, we show that chains are only weakly correlated to classical measures of epistasis. In fact, some of these measures of constraint are non-monotonic in the amount of epistatic interactions, but have instead a maximum for intermediate values. Finally, we show how these measures shed light on evolutionary constraints and predictability in experimentally resolved landscapes.
Published: 2018

16. The landscape of epilepsy-related GATOR1 variants

Author: Johannes R. Lemke, Pia Zacher, Thomas Dorn, Laura Hernandez-Hernandez, Natasha E. Schoeler, Stéphanie Baulac, Sara Baldassari, Anne de Saint Martin, Eleni Panagiotakaki, Anne Fabienne Lepine, Markus Wolff, Arnaud Biraben, Renske Oegema, Edouard Hirsch, Anna Jansen, Charles Deckers, Nienke E. Verbeek, Fabienne Picard, Georg Dorfmüller, Sarah Ferrand-Sorbets, Barbora Benova, Francesca Bisulli, Inga Talvik, Kristin Lindstrom, Tilman Polster, Douglas R. Nordli, Tommaso Pippucci, Eva H. Brilstra, Shifteh Sattar, Erik H. Niks, Marie Line Jacquemont, Kees P.J. Braun, Karen Müller-Schlüter, Sanjay M. Sisodiya, Sarah Weckhuysen, Lysa Boissé Lomax, Sophie Julia, Brigitte Ricard-Mousnier, Mathilde Chipaux, Laura Licchetta, Gaetan Lesca, Bianca Berghuis, S. Krithika, Jamel Chelly, Renzo Guerrini, Hélène Catenoix, Annapurna Poduri, Melanie Jennesson, Pasquale Striano, Rikke S. Møller, Antonio Gambardella, Guillaume Achaz, Peter Uldall, Fabrice Bartolomei, Giuseppe d'Orsi, Laurence Faivre, Floor E. Jansen, An Sofie Schoonjans, Kevin Rostasy, Thomas Becher, Pavel Krsek, Julien Thevenon, Marjan J. A. van Kempen, Guido Rubboli, Cécile Marchal, Meral Balci, Boudewijn Gunning, Ilona Krey, Julitta de Bellescize, Veronique Darmency, Christopher J. Yuskaitis, Daniëlle de Jong, Giovanni Crichiutti, Paolo Tinuper, Katrien Stouffs, Valentin Sander, Anne-Sophie Lebre, Thomas Cloppenborg, Valerio Conti, Gabrielle Rudolf, Courtney Kiss, Eveline Hagebeuk, Caroline Nava, Eric LeGuern, Ilse Wegner, Christian Brandt, Martin Zenker, Simona Balestrini, Picard, Fabienne, Baldassari S., Picard F., Verbeek N.E., van Kempen M., Brilstra E.H., Lesca G., Conti V., Guerrini R., Bisulli F., Licchetta L., Pippucci T., Tinuper P., Hirsch E., de Saint Martin A., Chelly J., Rudolf G., Chipaux M., Ferrand-Sorbets S., Dorfmuller G., Sisodiya S., Balestrini S., Schoeler N., Hernandez-Hernandez L., Krithika S., Oegema R., Hagebeuk E., Gunning B., Deckers C., Berghuis B., Wegner I., Niks E., Jansen F.E., Braun K., de Jong D., Rubboli G., Talvik I., Sander V., Uldall P., Jacquemont M.-L., Nava C., Leguern E., Julia S., Gambardella A., d'Orsi G., Crichiutti G., Faivre L., Darmency V., Benova B., Krsek P., Biraben A., Lebre A.-S., Jennesson M., Sattar S., Marchal C., Nordli D.R., Lindstrom K., Striano P., Lomax L.B., Kiss C., Bartolomei F., Lepine A.F., Schoonjans A.-S., Stouffs K., Jansen A., Panagiotakaki E., Ricard-Mousnier B., Thevenon J., de Bellescize J., Catenoix H., Dorn T., Zenker M., Muller-Schluter K., Brandt C., Krey I., Polster T., Wolff M., Balci M., Rostasy K., Achaz G., Zacher P., Becher T., Cloppenborg T., Yuskaitis C.J., Weckhuysen S., Poduri A., Lemke J.R., Moller R.S., Baulac S., Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Department of Genetics [Utrecht, the Netherlands], University Medical Center [Utrecht], Service de Génétique [HCL Groupement Hospitalier Est], Groupement Hospitalier Lyon-Est (GHE), Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Centre de recherche en neurosciences de Lyon - Lyon Neuroscience Research Center (CRNL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Children's Hospital A. Meyer, Service de Neurologie [Strasbourg], CHU Strasbourg-Hopital Civil, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Clinical and Experimental Epilepsy, University College of London [London] (UCL), Academic Center for Epileptology Kempenhaeghe & Maastricht UMC+ [Heeze], Danish Epilepsy Centre, Denmark and Aarhus University, Aarhus, Centre Hospitalier Universitaire de La Réunion (CHU La Réunion), Service de Génétique Cytogénétique et Embryologie [CHU Pitié-Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Service de génétique médicale [Toulouse], CHU Toulouse [Toulouse], Centre de génétique - Centre de référence des maladies rares, anomalies du développement et syndromes malformatifs (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), FHU TRANSLAD (CHU de Dijon), Université de Bourgogne (UB), Service de Neurophysiologie Clinique (CHU Dijon), CHU Pontchaillou [Rennes], Service de pédiatrie spécialisée et médecine infantile (neurologie, pneumologie, maladies héréditaires du métabolisme) [Hôpital de la Timone - APHM], Hôpital de la Timone [CHU - APHM] (TIMONE), Epilepsie, sommeil et explorations fonctionnelles neuropédiatriques, Hospices Civils de Lyon (HCL)-Hôpital Femme Mère Enfant, Equipe GAD (LNC - U1231), Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Université Bourgogne Franche-Comté [COMUE] (UBFC), Département d'Epilepsie, Sommeil et Neurophysiologie Pédiatrique [HCL, Lyon], Hospices Civils de Lyon (HCL), Institute of Human Genetics, University Hospital Magdeburg, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Groupement hospitalier Lyon-Est, Centre de recherche en neurosciences de Lyon (CRNL), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), and CHU Toulouse [Toulouse]-Hôpital Purpan [Toulouse]
Subjects: Male, 0301 basic medicine, Proband, DEPDC5, SUDEP, 030105 genetics & heredity, Bioinformatics, Loss of Function Mutation/genetics, Epilepsy, INDEL Mutation, Loss of Function Mutation, mTORC1 pathway, Genetics(clinical), Child, Genetics (clinical), Multiprotein Complexes/genetics, Brugada Syndrome, DNA Copy Number Variation, Brugada syndrome, INDEL Mutation/genetics, GTPase-Activating Proteins, NPRL3, Seizure, Phenotype, Pedigree, 3. Good health, Brugada Syndrome/genetics, Child, Preschool, Female, Human, Signal Transduction, DNA Copy Number Variations, Adolescent, Seizures/complications, Mechanistic Target of Rapamycin Complex 1/genetics, DNA Copy Number Variations/genetics, Mechanistic Target of Rapamycin Complex 1, Tumor Suppressor Proteins/genetics, Article, Focal cortical dysplasia, 03 medical and health sciences, Seizures, GTPase-Activating Proteins/genetics, medicine, Humans, Genetic Predisposition to Disease, Genetic focal epilepsy, Epilepsy/complications, Repressor Proteins/genetics, business.industry, GTPase-Activating Protein, Tumor Suppressor Proteins, Infant, Newborn, Correction, Infant, Repressor Protein, Cortical dysplasia, medicine.disease, ddc:616.8, Repressor Proteins, 030104 developmental biology, Frontal lobe seizures, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Multiprotein Complexes, Multiprotein Complexe, Signal Transduction/genetics, Human medicine, business
Abstract: Purpose:\ud \ud To define the phenotypic and mutational spectrum of epilepsies related to DEPDC5, NPRL2 and NPRL3 genes encoding the GATOR1 complex, a negative regulator of the mTORC1 pathway.\ud \ud Methods:\ud \ud We analyzed clinical and genetic data of 73 novel probands (familial and sporadic) with epilepsy-related variants in GATOR1-encoding genes and proposed new guidelines for clinical interpretation of GATOR1 variants.\ud \ud Results:\ud \ud The GATOR1 seizure phenotype consisted mostly in focal seizures (e.g., hypermotor or frontal lobe seizures in 50%), with a mean age at onset of 4.4 years, often sleep-related and drug-resistant (54%), and associated with focal cortical dysplasia (20%). Infantile spasms were reported in 10% of the probands. Sudden unexpected death in epilepsy (SUDEP) occurred in 10% of the families. Novel classification framework of all 140 epilepsy-related GATOR1 variants (including the variants of this study) revealed that 68% are loss-of-function pathogenic, 14% are likely pathogenic, 15% are variants of uncertain significance and 3% are likely benign.\ud \ud Conclusion:\ud \ud Our data emphasize the increasingly important role of GATOR1 genes in the pathogenesis of focal epilepsies (>180 probands to date). The GATOR1 phenotypic spectrum ranges from sporadic early-onset epilepsies with cognitive impairment comorbidities to familial focal epilepsies, and SUDEP.
Published: 2018
Full Text: View/download PDF

17. The neutral frequency spectrum of linked sites

Author: Emanuele Raineri, Thomas Wiehe, Guillaume Achaz, Alexander Klassmann, Luca Ferretti, Sebastian E. Ramos-Onsins, Agence Nationale de la Recherche (France), and German Research Foundation
Subjects: musculoskeletal diseases, 0301 basic medicine, 0106 biological sciences, Expected value, 010603 evolutionary biology, 01 natural sciences, Linkage Disequilibrium, Spectral line, Coalescent theory, Evolution, Molecular, 010104 statistics & probability, 03 medical and health sciences, fluids and secretions, Mutation Rate, Simple (abstract algebra), Quantitative Biology::Populations and Evolution, Statistical physics, Selection, Genetic, 0101 mathematics, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Physics, 0303 health sciences, Models, Genetic, Expression (mathematics), Genetics, Population, 030104 developmental biology, Mutation (genetic algorithm), Kolmogorov equations, Neutral theory of molecular evolution, Recombination
Abstract: bioRxiv, We introduce the conditional Site Frequency Spectrum (SFS) for a genomic region linked to a focal mutation of known frequency. An exact expression for its expected value is provided for the neutral model without recombination. Its relation with the expected SFS for two sites, 2-SFS, is discussed. These spectra derive from the coalescent approach of Fu (1995) for finite samples, which is reviewed. Remarkably simple expressions are obtained for the linked SFS of a large population, which are also solutions of the multi-allelic Kolmogorov equations. These formulae are the immediate extensions of the well known single site θ/f neutral SFS. Besides the general interest in these spectra, they relate to relevant biological cases, such as structural variants and introgressions. As an application, a recipe to adapt Tajima’s and other SFS-based neutrality tests to a non-recombining region containing a neutral marker is presented., GA and LF were supported by grant ANR-12-JSV7-0007 TempoMut from Agence Nationale de la Recherche. GA was also supported by grant ANR-12-BSV7-0012 Demochips, AK and TW by grants of the German Science Foundation (DFG-SFB680 and DFG-SPP 1590).
Published: 2018

18. Coalescent Processes with Skewed Offspring Distributions and Nonequilibrium Demography

Author: Guillaume Achaz, Marcel Hildebrandt, Sebastian Matuszewski, and Jeffrey D. Jensen
Subjects: 0301 basic medicine, education.field_of_study, Reproductive success, Ecology (disciplines), Population, Skew, Inference, Variation (game tree), Biology, Models, Theoretical, Investigations, Coalescent theory, 03 medical and health sciences, 030104 developmental biology, Exponential growth, Genetics, Quantitative Biology::Populations and Evolution, education, Algorithms, Demography
Abstract: Nonequilibrium demography impacts coalescent genealogies leaving detectable, well-studied signatures of variation. However, similar genomic footprints are also expected under models of large reproductive skew, posing a serious problem when trying to make inference. Furthermore, current approaches consider only one of the two processes at a time, neglecting any genomic signal that could arise from their simultaneous effects, preventing the possibility of jointly inferring parameters relating to both offspring distribution and population history. Here, we develop an extended Moran model with exponential population growth, and demonstrate that the underlying ancestral process converges to a time-inhomogeneous psi-coalescent. However, by applying a nonlinear change of time scale—analogous to the Kingman coalescent—we find that the ancestral process can be rescaled to its time-homogeneous analog, allowing the process to be simulated quickly and efficiently. Furthermore, we derive analytical expressions for the expected site-frequency spectrum under the time-inhomogeneous psi-coalescent, and develop an approximate-likelihood framework for the joint estimation of the coalescent and growth parameters. By means of extensive simulation, we demonstrate that both can be estimated accurately from whole-genome data. In addition, not accounting for demography can lead to serious biases in the inferred coalescent model, with broad implications for genomic studies ranging from ecology to conservation biology. Finally, we use our method to analyze sequence data from Japanese sardine populations, and find evidence of high variation in individual reproductive success, but few signs of a recent demographic expansion.
Published: 2017

19. Quiescence unveils a novel mutational force in fission yeast

Author: Samia Miled, Benoit Arcangioli, Adrien Villain, Serge Gangloff, Guillaume Achaz, and Claire Denis
Subjects: Genetics, 0303 health sciences, Natural selection, Cell division, DNA replication, Genomics, Biology, Phenotype, Genome, Yeast, 03 medical and health sciences, 0302 clinical medicine, Ploidy, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract: One Sentence SummaryThe quiescence-driven mutational landscape reveals a novel evolutionary force.AbstractDuring cell division, the spontaneous mutation rate is expressed as the probability of mutations per generation, whereas during quiescence it will be expressed per unit of time. In this study, we report that during quiescence, the unicellular haploid fission yeast accumulates mutations as a linear function of time. We determined that 3 days of quiescence generate a number of invalidating mutations equivalent to that of one round of DNA replication. The novel mutational landscape of quiescence is characterized by insertion/deletion accumulating as fast as single nucleotide variants, and elevated amounts of deletions. When we extended the study to 3 months of quiescence, we confirmed the replication-independent mutational spectrum at the whole-genome level of a clonally aged population and uncovered phenotypic variations that subject the cells to natural selection. Thus, our results support the idea that genomes continuously evolve under two alternating phases that will impact on their size and composition.
Published: 2017
Full Text: View/download PDF

20. Yeast de novo genes preferentially emerge from divergently transcribed, GC-rich intergenic regions

Author: Vakirlis N N, Alexander S. Hebert, Joshua J. Coon, Dana A. Opulente, Ingrid Lafontaine, Gilles Fischer, Guillaume Achaz, and Chris Todd Hittinger
Subjects: Genetics, 0303 health sciences, Promoter, Translation (biology), Biology, Genome, Yeast, 03 medical and health sciences, 0302 clinical medicine, Intergenic region, Phylogenetics, Homologous chromosome, Gene, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract: New genes, with novel protein functions, can evolve “from scratch” out of intergenic sequences. These de novo genes can integrate the cell’s genetic network and drive important phenotypic innovations. Therefore, identifying de novo genes and understanding how the transition from noncoding to coding occurs are key problems in evolutionary biology. However, identifying de novo genes is a difficult task, hampered by the presence of remote homologs, fast evolving sequences and erroneously annotated protein coding genes. To overcome these limitations, we developed a procedure that handles the usual pitfalls in de novo gene identification and predicted the emergence of 703 de novo genes in 15 yeast species from two genera whose phylogeny spans at least 100 million years of evolution. We established that de novo gene origination is a widespread phenomenon in yeasts, only a few being ultimately maintained by selection. We validated 82 candidates, by providing new translation evidence for 25 of them through mass spectrometry experiments. We also unambiguously identified the mutations that enabled the transition from non-coding to coding for 30 Saccharomyces de novo genes. We found that de novo genes preferentially emerge next to divergent promoters in GC-rich intergenic regions where the probability of finding a fortuitous and transcribed ORF is the highest. We found a more than 3-fold enrichment of de novo genes at recombination hot spots, which are GC-rich and nucleosome-free regions, suggesting that meiotic recombination would be a major driving force of de novo gene emergence in yeasts.
Published: 2017
Full Text: View/download PDF

21. Properties of selected mutations and genotypic landscapes under Fisher's geometric model

Author: François Blanquart, Guillaume Achaz, Thomas Bataillon, and Olivier Tenaillon
Subjects: 0106 biological sciences, Genetics, 0303 health sciences, Neutral network, Fitness landscape, Genetic Fitness, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, NK model, Evolutionary biology, Fisher's geometric model, Epistasis, Adaptation, General Agricultural and Biological Sciences, Ecology, Evolution, Behavior and Systematics, Selection (genetic algorithm), 030304 developmental biology
Abstract: The fitness landscape – the mapping between genotypes and fitness – determines properties of the process of adaptation. Several small genotypic fitness landscapes have recently been built by selecting a handful of beneficial mutations and measuring fitness of all combinations of these mutations. Here we generate several testable predictions for the properties of these small genotypic landscapes under Fisher’s geometric model of adaptation. When the ancestral strain is far from the fitness optimum, we analytically compute the fitness effect of selected mutations and their epistatic interactions. Epistasis may be negative or positive on average depending on the distance of the ancestral genotype to the optimum and whether mutations were independently selected, or co-selected in an adaptive walk. Simulations show that genotypic landscapes built from Fisher’s model are very close to an additive landscape when the ancestral strain is far from the optimum. However, when it is close to the optimum, a large diversity of landscape with substantial roughness and sign epistasis emerged. Strikingly, small genotypic landscapes built from several replicate adaptive walks on the same underlying landscape were highly variable, suggesting that several realizations of small genotypic landscapes are needed to gain information about the underlying architecture of the fitness landscape.
Published: 2014
Full Text: View/download PDF

22. Testing for independence between evolutionary processes

Author: Guillaume Achaz, Joël Pothier, Abdelkader Behdenna, Sophie S. Abby, Amaury Lambert, Adaptation aux milieux extrêmes, Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Atelier de BioInformatique (ABI), Université Pierre et Marie Curie - Paris 6 (UPMC), Génomique évolutive des Microbes / Microbial Evolutionary Genomics, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Systématique, adaptation, évolution (SAE), Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Probabilités et Modèles Aléatoires (LPMA), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Pierre et Marie Curie - Paris 6 (UPMC), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Biology, phylogeny, 03 medical and health sciences, 0302 clinical medicine, statistal test, Genetics, Computer Simulation, Ecology, Evolution, Behavior and Systematics, Independence (probability theory), Probability, Statistical hypothesis testing, Event (probability theory), Phylogenetic tree, Null model, Classification, Biological Evolution, [MATH.MATH-PR]Mathematics [math]/Probability [math.PR], Tree (data structure), 030104 developmental biology, Data Interpretation, Statistical, coevolution, Epistasis, Probability distribution, Algorithm, 030217 neurology & neurosurgery
Abstract: International audience; Evolutionary events co-occurring along phylogenetic trees usually point to complex adaptive phenomena, sometimes implicating epistasis. While a number of methods have been developed to account for co-occurrence of events on the same internal or external branch of an evolutionary tree, there is a need to account for the larger diversity of possible relative positions of events in a tree. Here we propose a method to quantify to what extent two or more evolutionary events are associated on a phylogenetic tree. The method is applicable to any discrete character, like substitutions within a coding sequence or gains/losses of a biological function. Our method uses a general approach to statistically test for significant associations between events along the tree, which encompasses both events inseparable on the same branch, and events genealogically ordered on different branches. It assumes that the phylogeny and themapping of branches is known without errors. We address this problem from the statistical viewpoint by a linear algebra representation of the localization of the evolutionary events on the tree.We compute the full probability distribution of the number of paired events occurring in the same branch or in different branches of the tree, under a null model of independence where each type of event occurs at a constant rate uniformly inthephylogenetic tree. The strengths andweaknesses of themethodare assessed via simulations;we then apply the method to explore the loss of cell motility in intracellular pathogens.
Published: 2016
Full Text: View/download PDF

23. MicNeSs: genotyping microsatellite loci from a collection of (NGS) reads

Author: Marie Suez, Sophie Brouillet, Paula Graça, Dominique Higuet, Guillaume Achaz, Abdelkader Behdenna, Evolution des Génomes Eucaryotes (EGE), Evolution Paris Seine, Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Cofiroute and the Parc Naturel Regional de la Haute Vallee de Chevreuse, Demochips from the Agence Nationale de la Recherche (France) [ANR-12-BSV7-0012], Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS)
Subjects: 0301 basic medicine, Genetics, Genotyping Techniques, Population genetics, Computational Biology, High-Throughput Nucleotide Sequencing, Locus (genetics), Computational biology, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, microsatellite loci, 03 medical and health sciences, 030104 developmental biology, genotyping, Genotype, Microsatellite, Pyrosequencing, Allele, next-generation sequencing (NGS), Genotyping, Ecology, Evolution, Behavior and Systematics, Biotechnology, Microsatellite Repeats
Abstract: International audience; Microsatellites are widely used in population genetics to uncover recent evolutionary events. They are typically genotyped using capillary sequencer, which capacity is usually limited to 9, at most 12 loci for each run, and which analysis is a tedious task that is performed by hand. With the rise of next-generation sequencing (NGS), a much larger number of loci and individuals are available from sequencing: for example, on a single run of a GS Junior, 28 loci from 96 individuals are sequenced with a 30X cover. We have developed an algorithm to automatically and efficiently genotype microsatellites from a collection of reads sorted by individual (e.g. specific PCR amplifications of a locus or a collection of reads that encompass a locus of interest). As the sequencing and the PCR amplification introduce artefactual insertions or deletions, the set of reads from a single microsatellite allele shows several length variants. The algorithm infers, without alignment, the true unknown allele(s) of each individual from the observed distributions of microsatellites length of all individuals. MicNeSs, a python implementation of the algorithm, can be used to genotype any microsatellite locus from any organism and has been tested on 454 pyrosequencing data of several loci from fruit flies (a model species) and red deers (a nonmodel species). Without any parallelization, it automatically genotypes 22 loci from 441 individuals in 11 hours on a standard computer. The comparison of MicNeSs inferences to the standard method shows an excellent agreement, with some differences illustrating the pros and cons of both methods.
Published: 2016
Full Text: View/download PDF

24. ABGD, Automatic Barcode Gap Discovery for primary species delimitation

Author: S. Brouillet, Nicolas Puillandre, Guillaume Achaz, and Amaury Lambert
Subjects: 0106 biological sciences, 0303 health sciences, biology, Ecology, Range (biology), Barcode, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, DNA barcoding, law.invention, 03 medical and health sciences, Phylogenetics, law, Evolutionary biology, Genetic algorithm, Genetics, Limit (mathematics), Hypothetical species, Divergence (statistics), Ecology, Evolution, Behavior and Systematics, 030304 developmental biology
Abstract: Within uncharacterized groups, DNA barcodes, short DNA sequences that are present in a wide range of species, can be used to assign organisms into species. We propose an automatic procedure that sorts the sequences into hypothetical species based on the barcode gap, which can be observed whenever the divergence among organisms belonging to the same species is smaller than divergence among organisms from different species. We use a range of prior intraspecific divergence to infer from the data a model-based one-sided confidence limit for intraspecific divergence. The method, called Automatic Barcode Gap Discovery (ABGD), then detects the barcode gap as the first significant gap beyond this limit and uses it to partition the data. Inference of the limit and gap detection are then recursively applied to previously obtained groups to get finer partitions until there is no further partitioning. Using six published data sets of metazoans, we show that ABGD is computationally efficient and performs well for standard prior maximum intraspecific divergences (a few per cent of divergence for the five data sets), except for one data set where less than three sequences per species were sampled. We further explore the theoretical limitations of ABGD through simulation of explicit speciation and population genetics scenarios. Our results emphasize in particular the sensitivity of the method to the presence of recent speciation events, via (unrealistically) high rates of speciation or large numbers of species. In conclusion, ABGD is fast, simple method to split a sequence alignment data set into candidate species that should be complemented with other evidence in an integrative taxonomic approach.
Published: 2011
Full Text: View/download PDF

25. The Impact of Selection, Gene Conversion, and Biased Sampling on the Assessment of Microbial Demography

Author: Marguerite Lapierre, Eduardo P. C. Rocha, Guillaume Achaz, Camille Blin, Amaury Lambert, Eduardo, Rocha, BLANC - Inférence de l'histoire démographique à partie des grands jeux de données de polymorphisme A.D.N. - - demochips2012 - ANR-12-BSV7-0012 - BLANC - VALID, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Génomique évolutive des Microbes / Microbial Evolutionary Genomics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC), Thales Services, THALES [France], This project was financed by the Centre National de la Recherche Scientifique (CNRS) and the Institut Pasteur. G.A. and M.L. acknowledge support from the grant ANR-12-BSV7-0012 Demochips from the Agence Nationale de la Recherche (France). M.L. is funded by the PhD program Interfaces for Life of the University Pierre and Marie Curie (Paris). C.B. is funded by the PhD program Complexité du Vivant of the University Pierre and Marie Curie (Paris)., ANR-12-BSV7-0012,demochips,Inférence de l'histoire démographique à partie des grands jeux de données de polymorphisme A.D.N.(2012), Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle (MNHN) - Université Pierre et Marie Curie - Paris 6 (UPMC) - École pratique des hautes études (EPHE) - Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS) - Institut National de la Santé et de la Recherche Médicale (INSERM) - Collège de France, Génomique évolutive des Microbes, Institut Pasteur [Paris] - Centre National de la Recherche Scientifique (CNRS), Laboratoire de Probabilités et Modèles Aléatoires (LPMA), Université Pierre et Marie Curie - Paris 6 (UPMC) - Université Paris Diderot - Paris 7 (UP7) - Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and THALES
Subjects: 0106 biological sciences, 0301 basic medicine, population size, population genomics, media_common.quotation_subject, Population, Biology, 010603 evolutionary biology, 01 natural sciences, Coalescent theory, Evolution, Molecular, 03 medical and health sciences, Negative selection, Statistics, Genetics, Escherichia coli, Selection, Genetic, education, bacteria, Molecular Biology, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Selection Bias, Discoveries, Ecology, Evolution, Behavior and Systematics, Selection (genetic algorithm), Sampling bias, media_common, Selection bias, education.field_of_study, Natural selection, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Models, Genetic, gene conversion, Genetic Variation, Sampling (statistics), natural selection, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Genetics, Population, 030104 developmental biology, 13. Climate action, [SDV.GEN.GPO] Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Metagenomics, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Genome, Bacterial
Abstract: International audience; Recent studies have linked demographic changes and epidemiological patterns in bacterial populations using coalescent-based approaches. We identified 26 studies using skyline plots and found that 21 inferred overall population expansion. This surprising result led us to analyze the impact of natural selection, recombination (gene conversion), and sampling biases on demographic inference using skyline plots and site frequency spectra (SFS). Forward simulations based on biologically relevant parameters from Escherichia coli populations showed that theoretical arguments on the detrimental impact of recombination and especially natural selection on the reconstructed genealogies cannot be ignored in practice. In fact, both processes systematically lead to spurious interpretations of population expansion in skyline plots (and in SFS for selection). Weak purifying selection, and especially positive selection, had important effects on skyline plots, showing patterns akin to those of population expansions. State-of-the-art techniques to remove recombination further amplified these biases. We simulated three common sampling biases in microbiological research: uniform, clustered, and mixed sampling. Alone, or together with recombination and selection, they further mislead demographic inferences producing almost any possible skyline shape or SFS. Interestingly, sampling sub-populations also affected skyline plots and SFS, because the coalescent rates of populations and their sub-populations had different distributions. This study suggests that extreme caution is needed to infer demographic changes solely based on reconstructed genealogies. We suggest that the development of novel sampling strategies and the joint analyzes of diverse population genetic methods are strictly necessary to estimate demographic changes in populations where selection, recombination, and biased sampling are present.
Published: 2016
Full Text: View/download PDF

26. Decomposing the site frequency spectrum: the impact of tree topology on neutrality tests

Author: Thomas Wiehe, Sebastian E. Ramos-Onsins, Guillaume Achaz, Luca Ferretti, Alice Ledda, National Institute for Health Research (UK), Agence Nationale de la Recherche (France), German Research Foundation, Ministerio de Ciencia e Innovación (España), Generalitat de Catalunya, and Ministerio de Economía y Competitividad (España)
Subjects: 0301 basic medicine, 0106 biological sciences, Population, Investigations, Biology, Expected value, 010603 evolutionary biology, 01 natural sciences, Measure (mathematics), Coalescent theory, 03 medical and health sciences, Mutation Rate, Genetics, Quantitative Biology::Populations and Evolution, Quantitative Biology - Genomics, Statistical physics, Selection, Genetic, Extreme value theory, education, Quantitative Biology - Populations and Evolution, Phylogeny, 030304 developmental biology, Mathematics, Genomics (q-bio.GN), 0303 health sciences, education.field_of_study, Models, Genetic, Populations and Evolution (q-bio.PE), Estimator, Function (mathematics), Tree (data structure), 030104 developmental biology, Sample size determination, FOS: Biological sciences, Neutral theory of molecular evolution
Abstract: bioRxiv preprint, We investigate the dependence of the site frequency spectrum on the topological structure of genealogical trees. We show that basic population genetic statistics, for instance, estimators of θ or neutrality tests such as Tajima’s D, can be decomposed into components of waiting times between coalescent events and of tree topology. Our results clarify the relative impact of the two components on these statistics. We provide a rigorous interpretation of positive or negative values of an important class of neutrality tests in terms of the underlying tree shape. In particular, we show that values of Tajima’s D and Fay and Wu’s H depend in a direct way on a peculiar measure of tree balance, which is mostly determined by the root balance of the tree. We present a new test for selection in the same class as Fay and Wu’s H and discuss its interpretation and power. Finally, we determine the trees corresponding to extreme expected values of these neutrality tests and present formulas for these extreme values as a function of sample size and number of segregating sites., A.L. is funded by the United Kingdom National Institute for Health Research, Health Protection Research Unit on Modelling Methodology (grant HPRU-2012-10080). L.F. and G.A. acknowledge support from the grant ANR-12-JSV7-0007 from Agence Nationale de Recherche (France). G.A. acknowledges support from the grant ANR-12-BSV7-0012-04 from Agence Nationale de Recherche (France). T.W. acknowledges support from DFG-SPP1590 by the German Science Foundation. S.E.R.O. is supported by grants CGL2009-09346 (MICINN, Spain), AGL2013-41834-R (MEC, Spain), by the CERCA Programme/Generalitat de Catalunya and acknowledges financial support from the Spanish Ministry of Economy and Competitiveness, through the Severo Ochoa Programme for Centres of Excellence in R&D 2016-2019 (SEV‐2015‐0533).
Published: 2015

27. Mutational pattern of a sample from a critical branching population

Author: Guillaume Achaz, Amaury Lambert, Cécile Delaporte, Probabilités, statistiques et biologie, Laboratoire de Probabilités et Modèles Aléatoires (LPMA), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Pierre et Marie Curie - Paris 6 (UPMC), Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Pierre et Marie Curie - Paris 6 (UPMC), Systématique, adaptation, évolution (SAE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, site frequency spectrum, Explicit formulae, Population, invariance principle, Poisson distribution, 01 natural sciences, poisson point measure, Combinatorics, 010104 statistics & probability, 03 medical and health sciences, symbols.namesake, Prior probability, Random tree, infinite-site model, Quantitative Biology::Populations and Evolution, Humans, 0101 mathematics, education, Phylogeny, Mathematics, education.field_of_study, Invariance principle, Models, Genetic, Applied Mathematics, Population size, 16. Peace & justice, Agricultural and Biological Sciences (miscellaneous), [MATH.MATH-PR]Mathematics [math]/Probability [math.PR], 030104 developmental biology, Genetics, Population, Convergence of random variables, Modeling and Simulation, Mutation, symbols, sampling coalescent point process, critical birth-death process
Abstract: International audience; We study a universal object for the genealogy of a sample in populations with mutations: the critical birth-death process with Poissonian mutations, conditioned on its population size at a fixed time horizon. We show how this process arises as the law of the genealogy of a sample in a large class of nearly critical branching populations with rare mutations at birth, namely populations converging, in a large population asymptotic, towards the continuum random tree. We extend this model to populations with random foundation times, with (potentially improper) prior distributions [Formula: see text], [Formula: see text], including the so-called uniform ([Formula: see text]) and log-uniform ([Formula: see text]) priors. We first investigate the mutational patterns arising from these models, by studying the site frequency spectrum of a sample with fixed size, i.e. the number of mutations carried by k individuals in the sample. Explicit formulae for the expected frequency spectrum of a sample are provided, in the cases of a fixed foundation time, and of a uniform and log-uniform prior on the foundation time. Second, we establish the convergence in distribution, for large sample sizes, of the (suitably renormalized) tree spanned by the sample with prior [Formula: see text] on the time of origin. We finally prove that the limiting genealogies with different priors can all be embedded in the same realization of a given Poisson point measure.
Published: 2014
Full Text: View/download PDF

28. Mutations of DEPDC5 cause autosomal dominant focal epilepsies

Author: Guillaume Achaz, Emeline Mundwiller, Fabienne Picard, Richard B. Miles, Pierre Thomas, Edouard Hirsch, Pierre Genton, Michel Baulac, Stéphanie Baulac, Saeko Ishida, Eric Noé, Eric LeGuern, Markus Wolff, Christian Marescaux, Gabrielle Rudolf, Evolution des Génomes Eucaryotes (EGE), Evolution Paris Seine, Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), French government, program Investissements d'Avenir [ANR-10-IAIHU-06], Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS)
Subjects: Adult, Exome/genetics, Male, Adolescent, Genotype, Guanine Nucleotide Exchange Factors/genetics, Mutation/genetics, Genetic Linkage, Nonsense mutation, Molecular Sequence Data, Autosomal dominant nocturnal frontal lobe epilepsy, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, Frameshift mutation, Cohort Studies, 03 medical and health sciences, Epilepsy, Young Adult, 0302 clinical medicine, Genetics, medicine, Missense mutation, Humans, Amino Acid Sequence, Child, Exome sequencing, 030304 developmental biology, 0303 health sciences, Sequence Homology, Amino Acid, Genome, Human, Genetic Predisposition to Disease/genetics, Computational Biology, Middle Aged, medicine.disease, NPRL3, DEPDC5, ddc:616.8, Epilepsies, Partial/diagnosis/genetics, Pedigree, Case-Control Studies, Brain/metabolism/pathology, Female, 030217 neurology & neurosurgery
Abstract: International audience; The main familial focal epilepsies are autosomal dominant nocturnal frontal lobe epilepsy, familial temporal lobe epilepsy and familial focal epilepsy with variable foci. A frameshift mutation in the DEPDC5 gene (encoding DEP domain-containing protein 5) was identified in a family with focal epilepsy with variable foci by linkage analysis and exome sequencing. Subsequent pyrosequencing of DEPDC5 in a cohort of 15 additional families with focal epilepsies identified 4 nonsense mutations and 1 missense mutation. Our findings provided evidence of frequent (37%) loss-of-function mutations in DEPDC5 associated with a broad spectrum of focal epilepsies. The implication of a DEP (Dishevelled, Egl-10 and Pleckstrin) domain-containing protein that may be involved in membrane trafficking and/or G protein signaling opens new avenues for research.
Published: 2013
Full Text: View/download PDF

29. Evolution of Coding Microsatellites in Primate Genomes

Author: Etienne Loire, Pierre Netter, Dominique Higuet, Guillaume Achaz, Evolution des Génomes Eucaryotes (EGE), Evolution Paris Seine, Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Groupement des Entreprises Francaises dans la lutte contre le Cancer (GEFLUC), CNRS through a Projets Exploratoires/Premier Soutien grant, Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS)
Subjects: Primates, Context (language use), [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, phylogeny, Genome, microsatellites, Evolution, Molecular, 03 medical and health sciences, Open Reading Frames, 0302 clinical medicine, INDEL Mutation, Phylogenetics, Genetics, Coding region, Animals, Humans, primate genomes, Frameshift Mutation, Gene, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, Phylogenetic tree, Genome, Human, Computational Biology, food and beverages, SSR, Human genome, 030217 neurology & neurosurgery, Microsatellite Repeats, Research Article
Abstract: International audience; Microsatellites (SSRs) are highly susceptible to expansions and contractions. When located in a coding sequence, the insertion or the deletion of a single unit for a mono-, di-, tetra-, or penta(nucleotide)-SSR creates a frameshift. As a consequence, one would expect to find only very few of these SSRs in coding sequences because of their strong deleterious potential. Unexpectedly, genomes contain many coding SSRs of all types. Here, we report on a study of their evolution in a phylogenetic context using the genomes of four primates: human, chimpanzee, orangutan, and macaque. In a set of 5,015 orthologous genes unambiguously aligned among the four species, we show that, except for tri- and hexa-SSRs, for which insertions and deletions are frequently observed, SSRs in coding regions evolve mainly by substitutions. We show that the rate of substitution in all types of coding SSRs is typically two times higher than in the rest of coding sequences. Additionally, we observe that although numerous coding SSRs are created and lost by substitutions in the lineages, their numbers remain constant. This last observation suggests that the coding SSRs have reached equilibrium. We hypothesize that this equilibrium involves a combination of mutation, drift, and selection. We thus estimated the fitness cost of mono-SSRs and show that it increases with the number of units. We finally show that the cost of coding mono-SSRs greatly varies from function to function, suggesting that the strength of the selection that acts against them can be correlated to gene functions.
Published: 2013
Full Text: View/download PDF

30. ViralORFeome: an integrated database to generate a versatile collection of viral ORFs

Author: Gregory Neveu, Laurent Jacotot, Patrice Andre, Vincent Navratil, Chantal Rabourdin-Combe, Marianne Lucas-Hourani, Anne Aublin-Gex, Frédéric Tangy, Laurène Meyniel, M. Le Breton, Yves Jacob, A. Guironnet-Paquet, Vincent Lotteau, Pierre-Olivier Vidalain, Michel Favre, Gilbert Deléage, A Chaboud, Johann Pellet, Christophe Combet, Lionel Tafforeau, Grégory Caignard, Sebastien Delmotte, Thibault Chantier, Patricia Cassonnet, Alexandre Deloire, Philippe Vaglio, Christian Gautier, Caroline Demeret, Guillaume Achaz, Immunité infection vaccination (I2V), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-IFR128-Institut National de la Santé et de la Recherche Médicale (INSERM), Génomique Virale et Vaccination, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Rétrovirus et Pathologie Comparée (RPC), Institut National de la Recherche Agronomique (INRA)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL), BioSciences Lyon-Gerland (BLG), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Modul-Bio, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Génétique, Papillomavirus et Cancer Humain, Institut Pasteur [Paris] (IP), Reproduction et développement des plantes (RDP), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Baobab, Département PEGASE [LBBE] (PEGASE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Institut de biologie et chimie des protéines [Lyon] (IBCP), The Institut National de la Santé et de la Recherche Médicale, the Institut National de la Recherche Agronomique, the Association de la Recherche contre le Cancer (3731XA0531F and 4867), the Ligue Nationale Contre le Cancer (RS07/75-75), the Agence Nationale de la Recherche (EPI-HPV-3D), the French Ministry of Industry, the Institut Pasteur, the Centre National de la Recherche Scientifique (Maladies Infectieuses Emergentes to P.O.V., G.C. and F.T.). Funding for open access charge: Institut Pasteur., We thank all members of PF1-Pasteur Genopole sequencing core facility, in particular C. Bouchier and C. Gouyette. We thank Drs Marie-Louise Michel, Charles M. Rice, Kaoru Takeuchi, T. Fabian Wild and Ali Amara for providing RNA or DNA templates used to build viral ORF clones. We also thank Eric Coissac for providing SQL codes, ANR-07-MIME-0009,EPI-HPV-3D,Vers la compréhension fonctionelle et structurale de l'interactome cellulaire des protéines précoces des Papilloma Virus Humains.(2007), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-École pratique des hautes études (EPHE)-Université Claude Bernard Lyon 1 (UCBL), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Institut Pasteur [Paris], Gau, Mireille, Microbiologie, immunologie et maladies émergentes - Vers la compréhension fonctionelle et structurale de l'interactome cellulaire des protéines précoces des Papilloma Virus Humains. - - EPI-HPV-3D2007 - ANR-07-MIME-0009 - MIME - VALID, and Institut National de la Recherche Agronomique (INRA)-École pratique des hautes études (EPHE)
Subjects: Genes, Viral, Cloning, Molecular, Computational Biology, Databases, Genetic, Nucleic Acid, Protein, Genes, Viral, Genetic Techniques, Genome, Information Storage and Retrieval, Internet, Open Reading Frames, Protein Structure, Tertiary, Software, User-Computer Interface, viruses, MESH: Protein Structure, Tertiary, Plasmid, Databases, Genetic, ORFS, Cloning, Molecular, ORFeome, Databases, Protein, MESH: Databases, Genetic, Genetics, 0303 health sciences, MESH: Genes, Viral, 030302 biochemistry & molecular biology, Microbiology and Parasitology, Articles, Microbiologie et Parasitologie, 3. Good health, MESH: Internet, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Proteome, MESH: Genome, Viral, Databases, Nucleic Acid, Biologie, MESH: Computational Biology, MESH: Databases, Protein, Computational Biology -- methods -- trends, Information Storage and Retrieval -- methods, Genome, Viral, Biology, MESH: Databases, Nucleic Acid, 03 medical and health sciences, MESH: Software, MESH: Cloning, Molecular, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Gene, 030304 developmental biology, MESH: User-Computer Interface, MESH: Information Storage and Retrieval, MESH: Open Reading Frames, Protein Structure, Tertiary, Open reading frame, MESH: Genetic Techniques
Abstract: Large collections of protein-encoding open reading frames (ORFs) established in a versatile recombination-based cloning system have been instrumental to study protein functions in high-throughput assays. Such 'ORFeome' resources have been developed for several organisms but in virology, plasmid collections covering a significant fraction of the virosphere are still needed. In this perspective, we present ViralORFeome 1.0 (http://www.viralorfeome.com), an open-access database and management system that provides an integrated set of bioinformatic tools to clone viral ORFs in the Gateway(R) system. ViralORFeome provides a convenient interface to navigate through virus genome sequences, to design ORF-specific cloning primers, to validate the sequence of generated constructs and to browse established collections of virus ORFs. Most importantly, ViralORFeome has been designed to manage all possible variants or mutants of a given ORF so that the cloning procedure can be applied to any emerging virus strain. A subset of plasmid constructs generated with ViralORFeome platform has been tested with success for heterologous protein expression in different expression systems at proteome scale. ViralORFeome should provide our community with a framework to establish a large collection of virus ORF clones, an instrumental resource to determine functions, activities and binding partners of viral proteins., Journal Article, Research Support, Non-U.S. Gov't, info:eu-repo/semantics/published
Published: 2010
Full Text: View/download PDF

31. Hypermutability of genes in Homo sapiens due to the hosting of long mono-SSR

Author: Pierre Netter, Françoise Praz, Guillaume Achaz, Dominique Higuet, Etienne Loire, Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche Saint-Antoine (UMRS893), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Systématique, adaptation, évolution (SAE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche Saint-Antoine (CR Saint-Antoine), and Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: Séquence nucléotidique, Evolution, Biology, Genome, 03 medical and health sciences, Exon, Negative selection, 0302 clinical medicine, Mutability, Genetics, Humans, Selection, Genetic, Microsatellites, Molecular Biology, Gene, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, Homo sapiens, Méthode statistique, Genome, Human, U10 - Informatique, mathématiques et statistiques, 000 - Autres thèmes, food and beverages, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Exons, L10 - Génétique et amélioration des animaux, SSR, génétique animale, 030220 oncology & carcinogenesis, Mutation, Microsatellite, DNA mismatch repair, Human genome, Microsatellite Repeats, Genre humain
Abstract: International audience; Simple Sequence Repeats (SSRs) are very common short repeats in eukaryotic genomes. Long SSRs are considered "hypermutable" sequences since they exhibit a high rate of expansion and contraction. Because they are potentially deleterious, long SSRs tend to be uncommon in coding sequences. However, several genes contain "long" SSRs in their exonic sequences. Here, we identify 1,291 human genes that host a mono-nucleotide SSR (mono-SSR) long enough to be prone to expansion or contraction, being called << hypermutable >> hereafter. On the basis of Gene Ontology annotations, we show that only a restricted number of functions are overrepresented among those hypermutable genes, including cell cycle and maintenance of DNA integrity. Using a probabilistic model, we show that genes involved in these functions are expected to host long SSRs because they tend to be long and/or are biased in nucleotide composition. Finally, we show that for almost all functions we observe fewer hypermutable sequences than expected under a neutral model. There are however interesting exceptions, for example, genes involved in protein and RNA transport, as well as meiosis and mismatch repair functions that have as many hypermutable genes as expected under neutrality. Conversely, there are functions (e.g. collagen related genes) where hypermutable genes are more often avoided than in other functions. Our results show that, even though several functions harbor unusually long SSR in their exons, long SSRs are deleterious sequences in almost all functions and are removed by purifying selection. The strength of this purifying selection however greatly varies from function to function. We discuss possible explanations for this intriguing result.
Published: 2009
Full Text: View/download PDF

32. Population structure of the fish-pathogenic bacterium Flavobacterium psychrophilum

Author: Guillaume Achaz, Stanislas Mondot, Jean-François Bernardet, Eric Duchaud, Pierre Nicolas, Catherine Bouchenot, Unité Mathématique Informatique et Génome (MIG), Institut National de la Recherche Agronomique (INRA), Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), Atelier de BioInformatique (ABI), Université Pierre et Marie Curie - Paris 6 (UPMC), Systématique, adaptation, évolution (SAE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), and Leballeur, Philippe
Subjects: BACTERIAL, Range (biology), [SDV]Life Sciences [q-bio], EPIDEMIOLOGY MOLECULAR, Flavobacterium psychrophilum, Applied Microbiology and Biotechnology, Genome, Bacterial cold water disease, Nucleotide diversity, Fish Diseases, FLAVOBACTERIUM PSYCHROPHILUM, Flavobacteriaceae Infections, [MATH]Mathematics [math], Pathogen, Phylogeny, ComputingMilieux_MISCELLANEOUS, Recombination, Genetic, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Genetics, Molecular Epidemiology, 0303 health sciences, Ecology, biology, ALLELE, Biotechnology, DNA, Bacterial, Genotype, Molecular Sequence Data, Flavobacterium, 03 medical and health sciences, Bacterial Proteins, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [INFO]Computer Science [cs], Evolutionary and Genomic Microbiology, 14. Life underwater, Alleles, 030304 developmental biology, Polymorphism, Genetic, 030306 microbiology, Sequence Analysis, DNA, ANIMAL, DNA, biology.organism_classification, BACTERIAL PROTEIN, CLUSTER ANALYSIS, Multilocus sequence typing, Food Science
Abstract: Flavobacterium psychrophilum is currently one of the main bacterial pathogens hampering the productivity of salmonid farming worldwide, and its control mainly relies on antibiotic treatments. To better understand the population structure of this bacterium and its mode of evolution, we have examined the nucleotide polymorphisms at 11 protein-coding loci of the core genome in a set of 50 isolates. These isolates were selected to represent the broadest possible diversity, originating from 10 different host fish species and four continents. The nucleotide diversity between pairs of sequences amounted to fewer than four differences per kilobase on average, corresponding to a particularly low level of diversity, possibly indicative of a small effective-population size. The recombination rate, however, seemed remarkably high, and as a consequence, most of the isolates harbored unique combinations of alleles (33 distinct sequence types were resolved). The analysis also showed the existence of several clonal complexes with worldwide geographic distribution but marked association with particular fish species. Such an association could reflect preferential routes of transmission and/or adaptive niche specialization. The analysis provided no clues that the initial range of the bacterium was originally limited to North America. Instead, the historical record of the expansion of the pathogen may reflect the spread of a few clonal complexes. As a resource for future epidemiological surveys, a multilocus sequence typing website based on seven highly informative loci is available.
Full Text: View/download PDF

33. Novel insights into RNAi off-target effects using C. elegans paralogs

Author: Niels Klitgord, Jean François Rual, and Guillaume Achaz
Subjects: Ribonuclease III, Small interfering RNA, lcsh:QH426-470, Base Pair Mismatch, lcsh:Biotechnology, Computational biology, Biology, Sensitivity and Specificity, 03 medical and health sciences, 0302 clinical medicine, RNA interference, lcsh:TP248.13-248.65, Genetics, Gene silencing, Animals, RNA, Small Interfering, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Gene, 030304 developmental biology, RNA, Double-Stranded, 0303 health sciences, Methodology Article, fungi, RNA, Computational Biology, biology.organism_classification, RNA silencing, lcsh:Genetics, Genetic Techniques, Models, Chemical, biology.protein, RNA Interference, 030217 neurology & neurosurgery, Biotechnology
Abstract: Background In the few years since its discovery, RNAi has turned into a very powerful tool for the study of gene function by allowing post-transcriptional gene silencing. The RNAi mechanism, which is based on the introduction of a double-stranded RNA (dsRNA) trigger whose sequence is similar to that of the targeted messenger RNA (mRNA), is subject to off-target cross-reaction. Results We use a novel strategy based on phenotypic analysis of paralogs and predict that, in Caenorhabditis elegans, off-target effects occur when an mRNA sequence shares more than 95% identity over 40 nucleotides with the dsRNA. Interestingly, our results suggest that the minimum length necessary of a high-similarity stretch between a dsRNA and its target in order to observe an efficient RNAi effect varies from 30 to 50 nucleotides rather than 22 nucleotides, which is the length of siRNAs in C. elegans. Conclusion Our predictive methods would improve the design of dsRNA and ultimately the use of RNAi as a therapeutic tool upon experimental verification.
Full Text: View/download PDF

34. Kin discrimination and outer membrane exchange in Myxococcus xanthus : A comparative analysis among natural isolates

Author: Sébastien Wielgoss, Yuen-Tsu Nicco Yu, Olaya Rendueles, Francesca Fiegna, Gregory J. Velicer, Department of Integrative Biology [Zurich], Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Génomique évolutive des Microbes / Microbial Evolutionary Genomics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), This work was supported by a EU Marie Curie PEOPLE Postdoctoral Fellowship for Career Development grant (FP7‐PEOPLE‐2012‐IEF‐331824) to S.W. and an EMBO Long‐Term Fellowship to O.R., We thank Guillaume Achaz and the three independent reviewers for helpful comments, European Project: 331824,EC:FP7:PEOPLE,FP7-PEOPLE-2012-IEF,MICROSOCIOGENOMYX(2013), and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Myxococcus xanthus, 030106 microbiology, Population, outer membrane exchange, Biology, Balancing selection, phylogeny, 03 medical and health sciences, Phylogenetics, Genetics, Allele, education, Ecology, Evolution, Behavior and Systematics, Alleles, education.field_of_study, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, behaviour, colony-merger incompatibility, Multicellular organism, 030104 developmental biology, Natural population growth, myxobacteria, sociobiogeography, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Bacterial outer membrane, Bacterial Outer Membrane Proteins
Abstract: Individual data sets for statistical analyses are provided at the Dryad Digital Repository: https://doi.org/10.5061/dryad.m5f7b44. Correspondence and request for materials should be addressed to G.J.V (gregory.velicer@env.ethz.ch) or S.W. (sebastien.wielgoss@env.ethz.ch).; International audience; Genetically similar cells of the soil bacterium Myxococcus xanthus cooperate at multiple social behaviours, including motility and multicellular development. Another social interaction in this species is outer membrane exchange (OME), a behaviour of unknown primary benefit in which cells displaying closely related variants of the outer membrane protein TraA transiently fuse and exchange membrane contents. Functionally incompatible TraA variants do not mediate OME, which led to the proposal that TraA incompatibilities determine patterns of intercellular cooperation in nature, but how this might occur remains unclear. Using natural isolates from a centimetre-scale patch of soil, we analyse patterns of TraA diversity and ask whether relatedness at TraA is causally related to patterns of kin discrimination in the form of both colony-merger incompatibilities (CMIs) and interstrain antagonisms. A large proportion of TraA functional diversity documented among global isolates is predicted to be contained within this cm-scale population. We find evidence of balancing selection on the highly variable PA14-portion of TraA and extensive transfer of traA alleles across genomic backgrounds. CMIs are shown to be common among strains identical at TraA, suggesting that CMIs are not generally caused by TraA dissimilarity. Finally, it has been proposed that interstrain antagonisms might be caused by OME-mediated toxin transfer. However, we predict that most strain pairs previously shown to exhibit strong antagonisms are incapable of OME due to TraA dissimilarity. Overall, our results suggest that most documented patterns of kin discrimination in a natural population of M. xanthus are not causally related to the TraA sequences of interactants.
Published: 2018
Full Text: View/download PDF

Catalog

Books, media, physical & digital resources

See catalog results

Searchworks

Select search scope, currently: Articles

Catalog

books, media & more in Jio Institute collections

Articles

journal articles & other e-resources

Refine your results

34 results on '"Guillaume Achaz"'

1. An appeal for an objective, open, and transparent scientific debate about the origin of SARS-CoV-2

2. Simulation of bacterial populations with SLiM

3. The rapid divergence of the Antarctic crinoid species Promachocrinus kerguelensis

4. The quiescent X, the replicative Y and the Autosomes

5. The genomic view of diversification

6. Clinical and genetic study of Tunisian families with genetic generalized epilepsy: contribution of CACNA1H and MAST4 genes

7. No HIV-1 molecular evolution on long-term antiretroviral therapy initiated during primary HIV-1 infection

8. ASAP: assemble species by automatic partitioning

9. Correction: The landscape of epilepsy-related GATOR1 variants

10. Is reproductive strategy a key factor in understanding the evolutionary history of Southern Ocean Asteroidea (Echinodermata)?

11. Testing for population decline using maximal linkage disequilibrium blocks

12. Is convergence an evidence for positive selection?

13. A Molecular Portrait of De Novo Genes in Yeasts

14. Comparative Genomics of Tenacibaculum dicentrarchi and 'Tenacibaculum finnmarkense' Highlights Intricate Evolution of Fish-Pathogenic Species

15. Evolutionary constraints in fitness landscapes

16. The landscape of epilepsy-related GATOR1 variants

17. The neutral frequency spectrum of linked sites

18. Coalescent Processes with Skewed Offspring Distributions and Nonequilibrium Demography

19. Quiescence unveils a novel mutational force in fission yeast

20. Yeast de novo genes preferentially emerge from divergently transcribed, GC-rich intergenic regions

21. Properties of selected mutations and genotypic landscapes under Fisher's geometric model

22. Testing for independence between evolutionary processes

23. MicNeSs: genotyping microsatellite loci from a collection of (NGS) reads

24. ABGD, Automatic Barcode Gap Discovery for primary species delimitation

25. The Impact of Selection, Gene Conversion, and Biased Sampling on the Assessment of Microbial Demography

26. Decomposing the site frequency spectrum: the impact of tree topology on neutrality tests

27. Mutational pattern of a sample from a critical branching population

28. Mutations of DEPDC5 cause autosomal dominant focal epilepsies

29. Evolution of Coding Microsatellites in Primate Genomes

30. ViralORFeome: an integrated database to generate a versatile collection of viral ORFs

31. Hypermutability of genes in Homo sapiens due to the hosting of long mono-SSR

32. Population structure of the fish-pathogenic bacterium Flavobacterium psychrophilum

33. Novel insights into RNAi off-target effects using C. elegans paralogs

34. Kin discrimination and outer membrane exchange in Myxococcus xanthus : A comparative analysis among natural isolates

Catalog

Searchworks

Select search scope, currently: Articles Catalog books, media & more in Jio Institute collections Articles journal articles & other e-resources

Search

Search Constraints

Refine your results

Search Limiters

Topic

Publication Year Range

Language

Journal

Database

Publisher

34 results on '"Guillaume Achaz"'

Search Results

Catalog

Select search scope, currently: Articles

Catalog

books, media & more in Jio Institute collections

Articles

journal articles & other e-resources