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1. 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 more...

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. more...

Published
2020
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2. 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. more...

Published
2018
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3. 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] more...

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 more...

Published
2020
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4. 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) more...

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. more...

Published
2019
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5. 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 more...

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. more...

Published
2019
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6. 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 more...

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. more...

Published
2018
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7. 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 more...

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. more...

Published
2018
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8. 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. more...

Published
2018

9. 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] more...

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. more...

Published
2018
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10. 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). more...

Published
2018

11. 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. more...

Published
2017

12. 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) more...

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. more...

Published
2016
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13. 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) more...

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. more...

Published
2016
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14. 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 more...

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. more...

Published
2016
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15. 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) more...

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). more...

Published
2015

16. 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) more...

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. more...

Published
2014
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17. 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) more...

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. more...

Published
2018
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