Descriptor: "MESH: Biological Evolution" - Searchworks@Jio Institute Digital Library Search Results

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170 results on '"MESH: Biological Evolution"'

1. Telomeres, the loop tying cancer to organismal life‐histories

Author: Beata Ujvari, Nynke Raven, Thomas Madsen, Marcel Klaassen, Antoine M. Dujon, Aaron G. Schultz, Leonard Nunney, Jean‐François Lemaître, Mathieu Giraudeau, Frédéric Thomas, Deakin University [Burwood], University of California [Riverside] (UC Riverside), University of California (UC), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM), LIttoral ENvironnement et Sociétés (LIENSs), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherches Ecologiques et Evolutives sur le Cancer (MIVEGEC-CREEC), Processus Écologiques et Évolutifs au sein des Communautés (PEEC), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM), Deakin LES Entrepreneurship Funds (2020-2021), MAVA Foundation, ARC Linkage, Grant/Award Number: LP170101105, Deakin SEBE, Centre National de la Recherche Scientifique, ANR TRANSCAN, Grant/Award Number: ANR- 18- CE35- 0009, HolsworthWildlifeResearchEndowment, and ANR-18-CE35-0009,TRANSCAN,ECOLOGIE ET EVOLUTION DES CANCERS TRANSMISSIBLES(2018)
Subjects: [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, Mate-choice, MESH: Humans, MESH: Biological Evolution, [SDV.CAN]Life Sciences [q-bio]/Cancer, Predator-prey interactions, Pollution, Peto's paradox, Parental effect, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MESH: Telomere Shortening, Genetics, Parasites, MESH: Ecosystem, MESH: Neoplasms, MESH: Telomere, Cell proliferation, Ecology, Evolution, Behavior and Systematics
Abstract: International audience; Recent developments in telomere and cancer evolutionary ecology demonstrate a very complex relationship between the need of tissue repair and controlling the emergence of abnormally proliferating cells. The trade-off is balanced by natural and sexual selection and mediated via both intrinsic and environmental factors. Here, we explore the effects of telomere-cancer dynamics on life history traits and strategies as well as on the cumulative effects of genetic and environmental factors. We show that telomere-cancer dynamics constitute an incredibly complex and multifaceted process. From research to date, it appears that the relationship between telomere length and cancer risk is likely nonlinear with good evidence that both (too) long and (too) short telomeres can be associated with increased cancer risk. The ability and propensity of organisms to respond to the interplay of telomere dynamics and oncogenic processes, depends on the combination of its tissue environments, life history strategies, environmental challenges (i.e., extreme climatic conditions), pressure by predators and pollution, as well as its evolutionary history. Consequently, precise interpretation of telomere-cancer dynamics requires integrative and multidisciplinary approaches. Finally, incorporating information on telomere dynamics and the expression of tumour suppressor genes and oncogenes could potentially provide the synergistic overview that could lay the foundations to study telomere-cancer dynamics at ecosystem levels.
Published: 2022

2. A phylogenetic study to assess the link between biome specialization and diversification in swallowtail butterflies

Author: Gamboa, Sara, Condamine, Fabien L., Cantalapiedra, Juan L., Varela, Sara, Pelegrín, Jonathan S., Menéndez, Iris, Blanco, Fernando, Hernández Fernández, Manuel, Universidade de Vigo, Instituto de Geociencias [Madrid] (IGEO), Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), 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)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Universidad de Alcalá - University of Alcalá (UAH), Universidad santiago de cali, Universidad del Valle [Cali] (Univalle), Museum für Naturkunde [Berlin], and Leibniz Institut für Evolutions und Biodiversitätsforschung
Subjects: resource-use, Antarctic Regions, MESH: Biological Evolution, Paleontología, MESH: Antarctic Regions, Environmental Chemistry, Animals, MESH: Animals, MESH: Ecosystem, MESH: Phylogeny, Ecosystem, Phylogeny, General Environmental Science, macroevolution, Global and Planetary Change, Ecology, Papilionidae, MESH: Butterflies, Biological Evolution, ecological specialization, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, 2401.06 Ecología Animal, speciation, macroecology, [SDV.EE.BIO]Life Sciences [q-bio]/Ecology, environment/Bioclimatology, bioclimatology, Butterflies
Abstract: Financiado para publicación en acceso aberto: Universidade de Vigo/CISUG The resource-use hypothesis, proposed by E.S. Vrba, states that habitat fragmentation caused by climatic oscillations would affect particularly biome specialists (species inhabiting only one biome), which might show higher speciation and extinction rates than biome generalists. If true, lineages would accumulate biome-specialist species. This effect would be particularly exacerbated for biomes located at the periphery of the global climatic conditions, namely, biomes that have high/low precipitation and high/low temperature such as rainforest (warm-humid), desert (warm-dry), steppe (cold-dry) and tundra (cold-humid). Here, we test these hypotheses in swallowtail butterflies, a clade with more than 570 species, covering all the continents but Antarctica, and all climatic conditions. Swallowtail butterflies are among the most studied insects, and they are a model group for evolutionary biology and ecology studies. Continental macroecological rules are normally tested using vertebrates, this means that there are fewer examples exploring terrestrial invertebrate patterns at global scale. Here, we compiled a large Geographic Information System database on swallowtail butterflies' distribution maps and used the most complete time-calibrated phylogeny to quantify diversification rates (DRs). In this paper, we aim to answer the following questions: (1) Are there more biome-specialist swallowtail butterflies than biome generalists? (2) Is DR related to biome specialization? (3) If so, do swallowtail butterflies inhabiting extreme biomes show higher DRs? (4) What is the effect of species distribution area? Our results showed that swallowtail family presents a great number of biome specialists which showed substantially higher DRs compared to generalists. We also found that biome specialists are unevenly distributed across biomes. Overall, our results are consistent with the resource-use hypothesis, species climatic niche and biome fragmentation as key factors promoting isolation. Agence Nationale de la Recherche https://doi.org/10.13039/501100001665 | Ref. ANR‐10‐LABX‐25‐01 Alexander von Humboldt-Stiftung https://doi.org/10.13039/100005156 | Ref. AOBJ: 637491 Centre National de la Recherche Scientifique https://doi.org/10.13039/501100004794 Consejería de Educación, Juventud y Deporte, Comunidad de Madrid https://doi.org/10.13039/501100008433 | Ref. 2017‐P1/AMB‐5298 Deutsche Forschungsgemeinschaft https://doi.org/10.13039/501100001659 | Ref. LO 2368/1‐1 Ministerio de Ciencia e Innovación https://doi.org/10.13039/501100004837 | Ref. PGC2018‐094955‐A‐100 Universidad Complutense de Madrid https://doi.org/10.13039/501100002911 | Ref. CT27/16‐CT28/16
Published: 2022

3. Small-RNA-mediated transgenerational silencing of histone genes impairs fertility in piRNA mutants

Author: Blaise Li, Martino Ugolini, Damarys Loew, Germano Cecere, Aleksei Samolygo, Céline Didier, Eric Cornes, Meetali Singh, Giorgia Barucci, Piergiuseppe Quarato, Florent Dingli, Mécanismes de l'Hérédité épigénétique / Mechanisms of epigenetic inheritance, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Scuola Normale Superiore di Pisa (SNS), Moscow Institute of Physics and Technology [Moscow] (MIPT), Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie [Paris], This project has received funding from the Institut Pasteur, the CNRS and the European Research Council (ERC) under the EU Horizon 2020 research and innovation programme under grant agreement no. ERC-StG- 679243. G.B. is part of the Pasteur–Paris University (PPU) International PhD Program and has received funding from the EU Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 665807. E.C. was supported by a Pasteur-Cantarini Fellowship program. F.D. and D.L. have received funding from Région Ile-de-France and Fondation pour la Recherche Médicale grants to support this study, We thank the members of the Cecere laboratory, D. Canzio, N. Iovino, R. Sawarkar and P. Andersen for discussions of the manuscript, the Miska, the Mello, the Kennedy, the Seydoux, the Claycomb, the Strome and the Dumont laboratories for sharing strains and/or antibodies. Some strains were provided by the CGC, funded by NIH Office of Research Infrastructure Programs (P40 OD010440)., and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: MESH: Gene Editing, MESH: CRISPR-Cas Systems, Small RNA, MESH: Argonaute Proteins / deficiency, MESH: Caenorhabditis elegans Proteins / metabolism, Inheritance Patterns, MESH: RNA, Small Interfering / genetics, MESH: Argonaute Proteins / metabolism, medicine.disease_cause, MESH: RNA, Antisense / genetics, MESH: Argonaute Proteins / genetics, Animals, Genetically Modified, Histones, 0302 clinical medicine, MESH: Histones / metabolism, MESH: Animals, RNA, Small Interfering, MESH: Caenorhabditis elegans / genetics, Caenorhabditis elegans, Gene Editing, 0303 health sciences, Mutation, MESH: RNA, Messenger / metabolism, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Biological Evolution, Cell biology, Histone, MESH: Fertility / genetics, 030220 oncology & carcinogenesis, Argonaute Proteins, Piwi RNAs, MESH: RNA, Messenger / genetics, MESH: Gene Silencing, Epigenetic memory, endocrine system, MESH: Mutation, MESH: Caenorhabditis elegans / metabolism, Piwi-interacting RNA, MESH: Biological Evolution, Biology, Article, MESH: Animals, Genetically Modified, 03 medical and health sciences, medicine, Animals, Gene silencing, RNA, Antisense, Gene Silencing, RNA, Messenger, MESH: RNA, Antisense / metabolism, Caenorhabditis elegans Proteins, Gene, Repetitive Sequences, Nucleic Acid, 030304 developmental biology, MESH: RNA, Small Interfering / metabolism, MESH: Repetitive Sequences, Nucleic Acid, MESH: Histones / genetics, urogenital system, RNA, Cell Biology, biology.organism_classification, Fertility, RNAi, biology.protein, MESH: Caenorhabditis elegans Proteins / genetics, MESH: Inheritance Patterns, CRISPR-Cas Systems
Abstract: International audience; PIWI-interacting RNAs (piRNAs) promote fertility in many animals. However, whether this is due to their conserved role in repressing repetitive elements (REs) remains unclear. Here, we show that the progressive loss of fertility in Caenorhabditis elegans lacking piRNAs is not caused by derepression of REs or other piRNA targets but, rather, is mediated by epigenetic silencing of all of the replicative histone genes. In the absence of piRNAs, downstream components of the piRNA pathway relocalize from germ granules and piRNA targets to histone mRNAs to synthesize antisense small RNAs (sRNAs) and induce transgenerational silencing. Removal of the downstream components of the piRNA pathway restores histone mRNA expression and fertility in piRNA mutants, and the inheritance of histone sRNAs in wild-type worms adversely affects their fertility for multiple generations. We conclude that sRNA-mediated silencing of histone genes impairs the fertility of piRNA mutants and may serve to maintain piRNAs across evolution.
Published: 2020

4. Uridine Catabolism Breaks the Bonds of Commensalism

Author: Julien Royet, Manish Joshi, Institut de Biologie du Développement de Marseille (IBDM), and Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Centre National de la Recherche Scientifique (CNRS)
Subjects: MESH: Uridine, [SDV]Life Sciences [q-bio], viruses, Cell, MESH: Biological Evolution, Biology, Microbiology, Article, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Symbiosis, Virology, Ribose, medicine, Humans, MESH: Alphavirus Infections, Uracil, Uridine, Pathogen, 030304 developmental biology, MESH: Uracil, 0303 health sciences, MESH: Humans, MESH: Symbiosis, Binding Sites, Alphavirus Infections, Host (biology), digestive, oral, and skin physiology, virus diseases, Commensalism, Biological Evolution, medicine.anatomical_structure, MESH: Binding Sites, chemistry, Biochemistry, Parasitology, 030217 neurology & neurosurgery
Abstract: Alphaviruses are emerging, mosquito-transmitted RNA viruses with poorly understood cellular tropism and species selectivity. Mxra8 is an entry receptor for multiple alphaviruses including chikungunya virus (CHIKV). We discovered that while expression of mouse, rat, chimpanzee, dog, horse, goat, sheep, and human Mxra8 enables alphavirus infection in cell culture, cattle Mxra8 does not. Cattle Mxra8 encodes a 15-amino acid insertion in its ectodomain that prevents Mxra8 binding to CHIKV. Identical insertions are present in zebu, yak, and the extinct auroch. As other Bovinae lineages contain related Mxra8 sequences, this insertion likely occurred at least 5 million years ago. Removing the Mxra8 insertion in Bovinae enhances alphavirus binding and infection, while introducing the insertion into mouse Mxra8 blocks CHIKV binding, prevents infection by multiple alphaviruses in cells, and mitigates CHIKV-induced pathogenesis in mice. Our studies showing this insertion provides resistance to CHIKV infection could facilitate countermeasures that disrupt Mxra8 interactions with alphaviruses.
Published: 2020

5. Human Immunology through the Lens of Evolutionary Genetics

Author: Lluis Quintana-Murci, Génétique Evolutive Humaine - Human Evolutionary Genetics, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Research in the Quintana-Murci lab is funded by the Institut Pasteur, the Centre National de la Recherche Scientifique (CNRS), the Agence Nationale de la Recherche (ANR-14-CE14-0008-02, ANR-14-CE14-0007-02, ANR-14-CE02-0003-01), the French Government’s Investissement d’Avenir program, Laboratoires d’Excellence ‘‘Integrative Biology of Emerging Infectious Diseases’’ (ANR-10- LABX-62-IBEID) and ‘‘Milieu Intérieur’’ (ANR-10-LABX-69-01), and the Fondation pour la Recherche Médicale (Equipe FRMDEQ20180339214), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-10-LABX-0069,MILIEU INTERIEUR,GENETIC & ENVIRONMENTAL CONTROL OF IMMUNE PHENOTYPE VARIANCE: ESTABLISHING A PATH TOWARDS PERSONALIZED MEDICINE(2010), ANR-14-CE14-0003,ORBiMP,Déjouer la résistance aux beta-lactamines des méningocoques et pneumocoques(2014), ANR-14-CE14-0007,TBPATHGEN,Dissection de la pathogenèse de la tuberculose par l'identification de défauts monogéniques de l'immunité dans les formes pédiatriques sévères de la maladie(2014), ANR-14-CE14-0008,IEIHSEER,L'encéphalite Herpétique de l'enfant résulte de déficits héréditaires d'immunité contre l'HSV-1: une exception ou une règle?(2014), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: MESH: Selection, Genetic, MESH: Genetics, Population, Population genetics, MESH: Biological Evolution, Biology, General Biochemistry, Genetics and Molecular Biology, Evolution, Molecular, Immune System Phenomena, 03 medical and health sciences, 0302 clinical medicine, Genetic variation, Humans, MESH: Genetic Variation, Selection, Genetic, MESH: Evolution, Molecular, MESH: Immunity, Selection (genetic algorithm), MESH: Immune System Phenomena, 030304 developmental biology, 0303 health sciences, Genetic diversity, MESH: Humans, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Human evolutionary genetics, Systems Biology, Immunity, Genetic Variation, Adaptation, Physiological, Biological Evolution, MESH: Adaptation, Physiological, 3. Good health, Genetics, Population, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Human evolution, Evolutionary biology, MESH: Systems Biology, Human genome, Adaptation, 030217 neurology & neurosurgery
Abstract: International audience; Pathogen-imposed selection pressures have been paramount during human evolution. Detecting such selection signatures in ancient and modern human genomes can thus help us to identify genes of temporal and spatial immunological relevance. Admixture with ancient hominins and between human populations has been a source of genetic diversity open to selection by infections. Furthermore, cultural transitions, such as the advent of agriculture, have exposed humans to new microbial threats, with impacts on host defense mechanisms. The integration of population genetics and systems immunology holds great promise for the increased understanding of the factors driving immune response variation between individuals and populations.
Published: 2019

6. The neural correlates of ongoing conscious thought

Author: Theodoros Karapanagiotidis, Giulia L. Poerio, Deniz Vatansever, Robert Leech, Elizabeth Jefferies, Daniel S. Margulies, Nerissa S.P. Ho, Mahiko Konishi, Jonathan W. Schooler, Jonathan Smallwood, Brontë Mckeown, Meichao Zhang, Danilo Bzdok, Hao-Ting Wang, Boris C. Bernhardt, Delali Konu, Adam Turnbull, Paul Seli, Charlotte Murphy, University of York [York, UK], University of California [Santa Barbara] (UC Santa Barbara), University of California (UC), University of Rochester [USA], University of Sussex, University of Essex, Cardiff University, Fudan University [Shanghai], McGill University = Université McGill [Montréal, Canada], Laboratoire de sciences cognitives et psycholinguistique (LSCP), Département d'Etudes Cognitives - ENS Paris (DEC), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École des hautes études en sciences sociales (EHESS)-Centre National de la Recherche Scientifique (CNRS), King‘s College London, Duke University [Durham], Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Université Pierre et Marie Curie - Paris 6 (UPMC)-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)-Centre National de la Recherche Scientifique (CNRS), and Margulies, Daniel
Subjects: 0301 basic medicine, Cognitive Neuroscience, MESH: Biological Evolution, Context (language use), 02 engineering and technology, Cognitive neuroscience, Experiential learning, Task (project management), MESH: Brain, 03 medical and health sciences, Techniques in Neuroscience, Psychology, MESH: Animals, MESH: Neuroimaging, lcsh:Science, Control (linguistics), Default mode network, Cognitive science, Neural correlates of consciousness, MESH: Humans, Multidisciplinary, MESH: Anatomy, Comparative, Perspective (graphical), [SDV.NEU.SC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Cognitive Sciences, 021001 nanoscience & nanotechnology, 3. Good health, MESH: Primates, 030104 developmental biology, Perspective, lcsh:Q, 0210 nano-technology, [SDV.NEU.SC] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Cognitive Sciences
Abstract: Summary A core goal in cognitive neuroscience is identifying the physical substrates of the patterns of thought that occupy our daily lives. Contemporary views suggest that the landscape of ongoing experience is heterogeneous and can be influenced by features of both the person and the context. This perspective piece considers recent work that explicitly accounts for both the heterogeneity of the experience and context dependence of patterns of ongoing thought. These studies reveal that systems linked to attention and control are important for organizing experience in response to changing environmental demands. These studies also establish a role of the default mode network beyond task-negative or purely episodic content, for example, implicating it in the level of vivid detail in experience in both task contexts and in spontaneous self-generated experiential states. Together, this work demonstrates that the landscape of ongoing thought is reflected in the activity of multiple neural systems, and it is important to distinguish between processes contributing to how the experience unfolds from those linked to how these experiences are regulated., Cognitive Neuroscience; Psychology; Techniques in Neuroscience
Published: 2021

7. The many bits of positional information

Author: Thomas Gregor, Gašper Tkačik, Institute of Science and Technology [Austria] (IST Austria), Department of Physics, Princeton University (DPPU), Princeton University, Physique des fonctions biologiques / Physics of Biological Functions, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), This work was supported in part by the National Science Foundation, through the Center for the Physics of Biological Function (PHY-1734030), by the National Institutes of Health (R01GM097275) and by the Fonds zur Förderung der wissenschaftlichen Forschung (FWF P28844)., Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/Imaging, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Information Theory, Subject (philosophy), MESH: Biological Evolution, Review, Space (commercial competition), Biology, Information theory, Models, Biological, 03 medical and health sciences, Lewis Wolpert, 0302 clinical medicine, Developmental biology, Animals, Humans, MESH: Animals, Molecular Biology, Body Patterning, 030304 developmental biology, Cognitive science, 0303 health sciences, MESH: Humans, Interpretation (philosophy), Perspective (graphical), MESH: Models, Biological, MESH: Information Theory, [SDV.BDD.MOR]Life Sciences [q-bio]/Development Biology/Morphogenesis, Drosophila embryo, Biological Evolution, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Field (geography), Focus (linguistics), Variable (computer science), Pattern formation, Shannon information, 030217 neurology & neurosurgery, MESH: Body Patterning
Abstract: Half a century after Lewis Wolpert's seminal conceptual advance on how cellular fates distribute in space, we provide a brief historical perspective on how the concept of positional information emerged and influenced the field of developmental biology and beyond. We focus on a modern interpretation of this concept in terms of information theory, largely centered on its application to cell specification in the early Drosophila embryo. We argue that a true physical variable (position) is encoded in local concentrations of patterning molecules, that this mapping is stochastic, and that the processes by which positions and corresponding cell fates are determined based on these concentrations need to take such stochasticity into account. With this approach, we shift the focus from biological mechanisms, molecules, genes and pathways to quantitative systems-level questions: where does positional information reside, how it is transformed and accessed during development, and what fundamental limits it is subject to?
Published: 2021

8. Genomic and fossil windows into the secret lives of the most ancient fungi

Author: Paul Kenrick, Christine Strullu-Derrien, Pierre-Marc Delaux, Paul K. Strother, Marc-André Selosse, John W. Taylor, Mary L. Berbee, University of British Columbia (UBC), The Natural History Museum [London] (NHM), 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), Evolution des Interactions Plantes-Microorganismes, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Boston College (BC), University of Gdańsk (UG), University of California [Berkeley], University of California, ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-17-CE20-0006,EVOLSYM,Découverte de réseaux moléculaires symbiotiques chez les plantes par des approches basée sur l'évolution(2017), ANR-10-LABX-0003,BCDiv,Biological and Cultural Diversities : Origins, Evolution, Interactions, Future(2010), European Project: 298735,EC:FP7:PEOPLE,FP7-PEOPLE-2011-IEF,SYMBIONTS(2012), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), University of California [Berkeley] (UC Berkeley), and University of California (UC)
Subjects: Earth, Planet, Fresh Water, MESH: History, Ancient, Freshwater ecosystem, MESH: Plants / microbiology, Decomposer, Oxidative Phosphorylation, Chlorophyta, Fungal genomics, MESH: Fungi / metabolism, MESH: Ecosystem, MESH: Phylogeny, History, Ancient, Phylogeny, MESH: Earth, Planet, 0303 health sciences, Environmental microbiology, Ecology, Fossils, MESH: Genomics, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], MESH: Sterols / biosynthesis, food and beverages, Genomics, Plants, Biological Evolution, MESH: Fresh Water / microbiology, MESH: Fossils / history, Sterols, Infectious Diseases, MESH: Fungi / classification, MESH: Fossils / ultrastructure, Evolution of fungi, MESH: Biological Evolution, Biology, Microbiology, MESH: Symbiosis / physiology, 03 medical and health sciences, Microbial ecology, MESH: Oxidative Phosphorylation, Ecosystem, MESH: Chlorophyta / microbiology, Symbiosis, Fungal ecology, Deep time, Fossil Record, General Immunology and Microbiology, 030306 microbiology, fungi, MESH: Fungi / growth & development, Fungi, 15. Life on land, MESH: Fungi / genetics, Earth system science, 13. Climate action, Fungal evolution, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: Fungi have crucial roles in modern ecosystems as decomposers and pathogens, and they engage in various mutualistic associations with other organisms, especially plants. They have a lengthy geological history, and there is an emerging understanding of their impact on the evolution of Earth systems on a large scale. In this Review, we focus on the roles of fungi in the establishment and early evolution of land and freshwater ecosystems. Today, questions of evolution over deep time are informed by discoveries of new fossils and evolutionary analysis of new genomes. Inferences can be drawn from evolutionary analysis by comparing the genes and genomes of fungi with the biochemistry and development of their plant and algal hosts. We then contrast this emerging picture against evidence from the fossil record to develop a new, integrated perspective on the origin and early evolution of fungi. Fungi originated in a freshwater environment and their evolution accompanied the rise of algae and land plants. In this Review, Berbee and colleagues examine the fossil and genomic record of ancient fungi and the inferences we can make about their lifestyle.
Published: 2020

9. On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference

Author: Criscuolo, Alexis, Institut Pasteur [Paris], Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), The author thanks Pascal Campagne for his meaningful comments on the manuscript. The author is also obliged to Sylvain Brisse and to the Hub de Bioinformatique et Biostatistique, Institut Pasteur, Paris (France), for their support. This work used the computational and storage services (TARS cluster) provided by the IT department at Institut Pasteur, Paris, Institut Pasteur [Paris] (IP), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Computational Biology, substitution model, MESH: Biological Evolution, Articles, simulation, Biological Evolution, Quantitative Biology::Genomics, p-distance, evolutionary distance, Evolution, Molecular, phylogenetics, ComputingMethodologies_PATTERNRECOGNITION, MinHash, MESH: Genome, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], MESH: Phylogeny, genome, Phylogeny, MESH: Evolution, Molecular, Research Article, MESH: Computational Biology
Abstract: International audience; Recently developed MinHash-based techniques were proven successful in quickly estimating the level of similarity between large nucleotide sequences. This article discusses their usage and limitations in practice to approximating uncorrected distances between genomes, and transforming these pairwise dissimilarities into proper evolutionary distances. It is notably shown that complex distance measures can be easily approximated using simple transformation formulae based on few parameters. MinHash-based techniques can therefore be very useful for implementing fast yet accurate alignment-free phylogenetic reconstruction procedures from large sets of genomes. This last point of view is assessed with a simulation study using a dedicated bioinformatics tool.
Published: 2020

10. Evolutionary and population (epi)genetics of immunity to infection

Author: Lluis Quintana-Murci, Luis B. Barreiro, The University of Chicago Medicine [Chicago], Génétique Evolutive Humaine - Human Evolutionary Genetics, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), This work has been supported by grants NIH R01-GM115656 and R01-GM134376 to L.B.B, and by the Institut Pasteur, the French Government’s Investissement d’Avenir program, Laboratoires d’Excellence 'Integrative Biology of Emerging Infec-tious Diseases' (ANR-10- LABX-62-IBEID) and 'Milieu Intérieur' (ANR-10-LABX-69-01), and the Fondation pour la Recherche Médi-cale (Equipe FRM DEQ20180339214) to L.Q.-M, ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-10-LABX-0069,MILIEU INTERIEUR,GENETIC & ENVIRONMENTAL CONTROL OF IMMUNE PHENOTYPE VARIANCE: ESTABLISHING A PATH TOWARDS PERSONALIZED MEDICINE(2010), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Collège de France - Chaire Génomique humaine et évolution, and Collège de France (CdF (institution))
Subjects: MESH: Selection, Genetic, Population, Population genetics, MESH: Genetics, Population, MESH: Biological Evolution, Biology, Infections, Article, Epigenesis, Genetic, 03 medical and health sciences, Immune system, Genetics, Animals, Humans, MESH: Animals, MESH: Epigenesis, Genetic, MESH: Genetic Variation, Selection, Genetic, education, Genetics (clinical), MESH: Genome, Human, 030304 developmental biology, 0303 health sciences, education.field_of_study, Natural selection, MESH: Humans, Genome, Human, 030305 genetics & heredity, MESH: Infections, Genetic Variation, Biological Evolution, Human genetics, Genetics, Population, Human evolution, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Adaptation, Functional genomics
Abstract: International audience; Immune response is one of the functions that have been more strongly targeted by natural selection during human evolution. The evolutionary genetic dissection of the immune system has greatly helped to distinguish genes and functions that are essential, redundant or advantageous for human survival. It is also becoming increasingly clear that admixture between early Eurasians with now-extinct hominins such as Neanderthals or Denisovans, or admixture between modern human populations, can be beneficial for human adaptation to pathogen pressures. In this review, we discuss how the integration of population genetics with functional genomics in diverse human populations can inform about the changes in immune functions related to major lifestyle transitions (e.g., from hunting and gathering to farming), the action of natural selection to the evolution of the immune system, and the history of past epidemics. We also highlight the need of expanding the characterization of the immune system to a larger array of human populations-particularly neglected human groups historically exposed to different pathogen pressures-to fully capture the relative contribution of genetic, epigenetic, and environmental factors to immune response variation in humans.
Published: 2020

11. Tracing the Evolutionary History and Global Expansion of Candida auris Using Population Genomic Analyses

Author: Ana Belén Araúz, Elizabeth L. Berkow, Oliver Kurzai, Christopher H. Heath, Rodney Adam, Sahar Althawadi, Xiao Li, Shawn R. Lockhart, Patricia Escandón, Ronen Ben-Ami, Anastasia P. Litvintseva, Lalitha Gade, Alexandre Alanio, Revathi Gunturu, Kaitlin Forsberg, Ana Alastruey-Izquierdo, Nancy A. Chow, Christina A. Cuomo, Amrita Bharat, Marie Desnos-Ollivier, Dianne Gardam, Belinda Calvo, Ronny Martin, José F. Muñoz, Rory M. Welsh, Centers for Disease Control and Prevention (CDC), Broad Institute [Cambridge], Massachusetts Institute of Technology (MIT)-Harvard University [Cambridge], Aga Khan University Hospital (AKUH), Nairobi, Mycologie moléculaire - Molecular Mycology, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Centre National de Référence Mycoses Invasives et Antifongiques - National Reference Center Invasive Mycoses & Antifungals (CNRMA), Institut Pasteur [Paris], Laboratoire de Parasitologie-Mycologie [CHU Saint Louis, Paris], Groupe Hospitalier Saint Louis - Lariboisière - Fernand Widal [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Université de Paris (UP), Instituto de Salud Carlos III [Madrid] (ISC), King Faisal Specialist Hospital and Research Centre, Riyadh, Hospital Santo Tomás, Tel Aviv Sourasky Medical Center [Te Aviv], Tel Aviv University [Tel Aviv], Public Health Agency of Canada (PHAC), Universidad del Zulia (LUZ), Instituto Nacional de Salud [Bogota], Fiona Stanley Hospital [Murdoch], Royal Perth Hospital, The University of Western Australia (UWA), Leibniz Institute for Natural Product Research and Infection Biology (Hans Knoell Institute), University of Würzburg = Universität Würzburg, This project has been funded in part with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under award U19AI110818 to the Broad Institute. C.A.C. is a CIFAR fellow in the Fungal Kingdom Program. This work was also made possible through support from the Advanced Molecular Detection (AMD) initiative at CDC., National Institute of Allergy and Infectious Diseases (United States), Harvard University-Massachusetts Institute of Technology (MIT), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP), Université Paris Cité (UPCité), King Faisal Specialist Hospital and Research Centre (KFSH & RC), and Tel Aviv University (TAU)
Subjects: Azoles, Antifungal Agents, Population genetics, Emerging species, Echinocandins, MESH: Azoles, Molecular clock, Clade, MESH: Phylogeny, Fluconazole, Phylogeny, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Candida, genome analysis, emerging species, 0303 health sciences, education.field_of_study, Molecular Epidemiology, Candida auris, antifungal resistance, Biological Evolution, QR1-502, 3. Good health, Phylogeography, MESH: Phylogeography, MESH: Genome, Fungal, MESH: Fluconazole, Genome, Fungal, MESH: Metagenomics, MESH: Whole Genome Sequencing, Research Article, MESH: Mutation, Population, Genes, Fungal, MESH: Genetics, Population, Context (language use), MESH: Biological Evolution, Ecological and Evolutionary Science, Biology, Microbiology, MESH: Drug Resistance, Fungal, 03 medical and health sciences, Phylogenetics, Drug Resistance, Fungal, MESH: Candida, Virology, Humans, MESH: Molecular Epidemiology, Candidiasis, Invasive, education, 030304 developmental biology, MESH: Humans, Molecular epidemiology, Whole Genome Sequencing, 030306 microbiology, MESH: Echinocandins, population genetics, Antifungal resistance, Genome analysis, MESH: Antifungal Agents, MESH: Candidiasis, Invasive, Genetics, Population, Evolutionary biology, Mutation, Metagenomics, MESH: Genes, Fungal
Abstract: In less than a decade, C. auris has emerged in health care settings worldwide; this species is capable of colonizing skin and causing outbreaks of invasive candidiasis. In contrast to other Candida species, C. auris is unique in its ability to spread via nosocomial transmission and its high rates of drug resistance. As part of the public health response, whole-genome sequencing has played a major role in characterizing transmission dynamics and detecting new C. auris introductions. Through a global collaboration, we assessed genome evolution of isolates of C. auris from 19 countries. Here, we described estimated timing of the expansion of each C. auris clade and of fluconazole resistance, characterized discrete phylogeographic population structure of each clade, and compared genome data to sensitivity measurements to describe how antifungal resistance mechanisms vary across the population. These efforts are critical for a sustained, robust public health response that effectively utilizes molecular epidemiology., Candida auris has emerged globally as a multidrug-resistant yeast that can spread via nosocomial transmission. An initial phylogenetic study of isolates from Japan, India, Pakistan, South Africa, and Venezuela revealed four populations (clades I, II, III, and IV) corresponding to these geographic regions. Since this description, C. auris has been reported in more than 30 additional countries. To trace this global emergence, we compared the genomes of 304 C. auris isolates from 19 countries on six continents. We found that four predominant clades persist across wide geographic locations. We observed phylogeographic mixing in most clades; clade IV, with isolates mainly from South America, demonstrated the strongest phylogeographic substructure. C. auris isolates from two clades with opposite mating types were detected contemporaneously in a single health care facility in Kenya. We estimated a Bayesian molecular clock phylogeny and dated the origin of each clade within the last 360 years; outbreak-causing clusters from clades I, III, and IV originated 36 to 38 years ago. We observed high rates of antifungal resistance in clade I, including four isolates resistant to all three major classes of antifungals. Mutations that contribute to resistance varied between the clades, with Y132F in ERG11 as the most widespread mutation associated with azole resistance and S639P in FKS1 for echinocandin resistance. Copy number variants in ERG11 predominantly appeared in clade III and were associated with fluconazole resistance. These results provide a global context for the phylogeography, population structure, and mechanisms associated with antifungal resistance in C. auris.
Published: 2020

12. An ancestral signalling pathway is conserved in intracellular symbioses-forming plant lineages

Author: Anna-Malin Linde, Fay-Wei Li, Jean Keller, Mélanie K. Rich, Nicolas Vigneron, Pierre-Marc Delaux, Duchesse Lacour Mbadinga Mbadinga, Shifeng Cheng, Giles E. D. Oldroyd, Ludovic Cottret, Ulf Lagercrantz, Guru V. Radhakrishnan, Hélène San Clemente, Tatiana Vernié, D. Magnus Eklund, Gane Ka-Shu Wong, Jitender Cheema, Cyril Libourel, John Innes Centre [Norwich], Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Uppsala University, Chinese Academy of Agricultural Sciences (CAAS), Beijing Genomics Institute [Shenzhen] (BGI), University of Alberta, Boyce Thompson Institute [Ithaca], University of Cambridge [UK] (CAM), Evolution des Interactions Plantes-Microorganismes, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Bill and Melinda Gates Foundation as Engineering the Nitrogen Symbiosis for Africa : OPP1172165, Biotechnology and Biological Sciences Research Council (BBSRC) : BB/L014130/1, National Science Foundation (NSF) : DEB1831428, Swedish Research Council : 2011-5609, 2014-522, 2016-05180, Biotechnology and Biological Sciences Research Council Discovery Fellowship : BB/S011005/1, ANR-17-CE20-0006,EVOLSYM,Découverte de réseaux moléculaires symbiotiques chez les plantes par des approches basée sur l'évolution(2017), and ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010)
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], MESH: Biological Evolution, Plant Science, Cyanobacteria, 01 natural sciences, Genome, MESH: Symbiosis / physiology, MESH: Plants / microbiology, 03 medical and health sciences, Symbiosis, Phylogenetics, Phylogenomics, Mycorrhizae, Ectomycorrhizae, Colonization, Plant Physiological Phenomena, Plant evolution, MESH: Transcriptome, biology, MESH: Fungi / physiology, fungi, Fungi, MESH: Plant Physiological Phenomena, food and beverages, 15. Life on land, Plants, biology.organism_classification, Biological Evolution, MESH: Signal Transduction, Arbuscular mycorrhiza, 030104 developmental biology, Evolutionary biology, MESH: Mycorrhizae, Transcriptome, Genome, Plant, MESH: Genome, Plant, 010606 plant biology & botany, Signal Transduction, MESH: yanobacteria / physiology
Abstract: International audience; Plants are the foundation of terrestrial ecosystems, and their colonization of land was probably facilitated by mutualistic associations with arbuscular mycorrhizal fungi. Following this founding event, plant diversification has led to the emergence of a tremendous diversity of mutualistic symbioses with microorganisms, ranging from extracellular associations to the most intimate intracellular associations, where fungal or bacterial symbionts are hosted inside plant cells. Here, through analysis of 271 transcriptomes and 116 plant genomes spanning the entire land-plant diversity, we demonstrate that a common symbiosis signalling pathway co-evolved with intracellular endosymbioses, from the ancestral arbuscular mycorrhiza to the more recent ericoid and orchid mycorrhizae in angiosperms and ericoid-like associations of bryophytes. By contrast, species forming exclusively extracellular symbioses, such as ectomycorrhizae, and those forming associations with cyanobacteria, have lost this signalling pathway. This work unifies intracellular symbioses, revealing conservation in their evolution across 450 million yr of plant diversification.An extensive phylogenomics study based on hundreds of genomes and transcriptomes provides a new interpretation of the evolution of different types of symbiotic associations in land plants, and reveals a conserved ancestral symbiosis pathway.
Published: 2020

13. Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts

Author: Isabel Monte, Pierre-Marc Delaux, Zheng Li, Dolf Weijers, Noe Fernandez-Pozo, Jan de Vries, Alexander Kirbis, Shifeng Cheng, Tanner A. Robison, Keiko Sakakibara, Jill C. Harrison, Sumanth K. Mutte, Péter Szövényi, Stefan A. Rensing, Tomoaki Nishiyama, Sophie de Vries, Masaki Shimamura, Tom Bennett, Miguel A. Blázquez, Eftychios Frangedakis, Jorge Hernández-García, Manuel Waller, Duncan A. Hauser, Juan Carlos Villarreal, John C. Meeks, Gane Ka-Shu Wong, Jean Keller, Dietmar Quandt, Michael S. Barker, Fay-Wei Li, Susann Wicke, Andrew C. Cuming, Issa S. Diop, Anna Neubauer, Boyce Thompson Institute [Ithaca], Cornell University [New York], Kanazawa University (KU), Universität Zürich [Zürich] = University of Zurich (UZH), Department of Plant, University of Oxford [Oxford], Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Orange Labs, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Campus de Teatinos s/n, Universidad de Málaga [Málaga] = University of Málaga [Málaga], Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Instituto de Biología Molecular y Celular de Plantas, Chinese Academy of Agricultural Sciences (CAAS), Evolution des Interactions Plantes-Microorganismes, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), University of Bristol [Bristol], Nees Institut for Plant Biodiversity, Rheinische Friedrich-Wilhelms-Universität Bonn, Faculty of Biology, University of Freiburg [Freiburg], Wageningen University and Research Centre (WUR), Department of Systematic and Evolutionary Botany, University of Vienna [Vienna], Li, Fay-Wei [0000-0002-0076-0152], Nishiyama, Tomoaki [0000-0003-1279-7806], Keller, Jean [0000-0002-5198-0331], Fernandez-Pozo, Noe [0000-0002-6489-5566], Barker, Michael S [0000-0001-7173-1319], Bennett, Tom [0000-0003-1612-4019], Blázquez, Miguel A [0000-0001-5743-0448], Cuming, Andrew C [0000-0003-2562-2052], de Vries, Jan [0000-0003-3507-5195], de Vries, Sophie [0000-0002-5267-8935], Delaux, Pierre-Marc [0000-0002-6211-157X], Hernández-García, Jorge [0000-0003-2526-8639], Monte, Isabel [0000-0002-7058-8343], Mutte, Sumanth K [0000-0003-3376-2354], Rensing, Stefan A [0000-0002-0225-873X], Villarreal, Juan Carlos [0000-0002-0770-1446], Weijers, Dolf [0000-0003-4378-141X], Wicke, Susann [0000-0001-5785-9500], Wong, Gane K-S [0000-0001-6108-5560], Sakakibara, Keiko [0000-0003-4420-9351], Szövényi, Péter [0000-0002-0324-4639], Apollo - University of Cambridge Repository, University of Zurich, and Li, Fay-Wei
Subjects: MESH: Genome, Plant, Crop and Pasture Production, 0106 biological sciences, Anthoceros, Evolution, [SDV]Life Sciences [q-bio], Lineage (evolution), Biochemie, Plant Biology, MESH: Biological Evolution, Anthocerotophyta, Plant Science, 580 Plants (Botany), Biology, Biochemistry, 01 natural sciences, Genome, Article, Pyrenoid, UFSP13-7 Evolution in Action: From Genomes to Ecosystems, Hornwort, 03 medical and health sciences, 1110 Plant Science, Genetics, Life Science, 10211 Zurich-Basel Plant Science Center, MESH: Anthocerotophyta / genetics, Clade, Life History Traits, 030304 developmental biology, 0303 health sciences, MESH: Life History Traits, Sporophyte, Plant, Genomics, 15. Life on land, biology.organism_classification, Biological Evolution, 10121 Department of Systematic and Evolutionary Botany, Evolutionary biology, Embryophyta, Bryophyte, MESH: Embryophyta / physiology, EPS, Plant sciences, Genome, Plant, 010606 plant biology & botany
Abstract: Hornworts comprise a bryophyte lineage that diverged from other extant land plants >400 million years ago and bears unique biological features, including a distinct sporophyte architecture, cyanobacterial symbiosis and a pyrenoid-based carbon-concentrating mechanism (CCM). Here, we provide three high-quality genomes of Anthoceros hornworts. Phylogenomic analyses place hornworts as a sister clade to liverworts plus mosses with high support. The Anthoceros genomes lack repeat-dense centromeres as well as whole-genome duplication, and contain a limited transcription factor repertoire. Several genes involved in angiosperm meristem and stomatal function are conserved in Anthoceros and upregulated during sporophyte development, suggesting possible homologies at the genetic level. We identified candidate genes involved in cyanobacterial symbiosis and found that LCIB, a Chlamydomonas CCM gene, is present in hornworts but absent in other plant lineages, implying a possible conserved role in CCM function. We anticipate that these hornwort genomes will serve as essential references for future hornwort research and comparative studies across land plants., Analyses of three high-quality genomes of Anthoceros hornworts place hornworts as a sister clade to the lineage including liverworts and mosses, and provide insights into the unique biological features of hornworts.
Published: 2020

14. Evolutionary Dynamics of Wild Populations

Author: Simon Blanchet, Delphine Legrand, Station d'écologie théorique et expérimentale (SETE), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), and Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)
Subjects: MESH: Biodiversity, [SDE.MCG]Environmental Sciences/Global Changes, Population Dynamics, QH426-470, Environment, Biology, MESH: Phenotype, MESH: Population Dynamics, MESH: Biological Evolution, 03 medical and health sciences, 0302 clinical medicine, Genetics, Humans, MESH: Environment, skin and connective tissue diseases, Evolutionary dynamics, Genetics (clinical), 030304 developmental biology, 0303 health sciences, MESH: Humans, Biodiversity, 15. Life on land, Biological Evolution, [SDE.ES]Environmental Sciences/Environmental and Society, n/a, Editorial, Phenotype, 13. Climate action, Evolutionary biology, 030220 oncology & carcinogenesis, sense organs, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Wild populations are facing rapid and sometimes extreme environmental changes that are currently exacerbated by pressing human activities. A major scientific endeavor is to reveal the evolutionary processes allowing wild populations to generate adaptive responses to these rapid and drastic environmental changes. In the recent decades, the accumulation of empirical data as well as the development of new theories and molecular tools have largely improved our ability to tackle such a major question. In particular, there is now growing evidence that evolutionary processes (gene flow, drift, mutation, and natural selection) interact in sometimes complex ways to shape the rapid responses of organisms to changing environments, and this can lead to unexpected feedback between evolutionary and ecological dynamics. These rapid responses are sustained by genetic determinants in addition to alternative inheritance systems, including those that are epigenetically controlled. Revealing these underlying molecular mechanisms of adaptation may change the way wild populations are managed and conserved.
Published: 2021

15. Diversification of giant and large eukaryotic dsDNA viruses predated the origin of modern eukaryotes

Author: Julien Guglielmini, Morgan Gaia, Patrick Forterre, Anthony C. Woo, Mart Krupovic, Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Biologie Cellulaire des Archées (ARCHEE), Département Microbiologie (Dpt Microbio), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), This work was supported by a European Research Council grant from the European Union’s Seventh Framework Program (FP/2007-2013)/Project EVOMOBIL-ERC Grant Agreement 340440., We thank Alexis Criscuolo for his expert support in computational analyses and the development of the online platform, and Violette Da Cunha for assistance., European Project: 340440,EC:FP7:ERC,ERC-2013-ADG,EVOMOBIL(2014), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris]
Subjects: [SDV]Life Sciences [q-bio], MESH: DNA-Directed RNA Polymerases / genetics, Biology, MESH: Eukaryotic Cells / metabolism, proto-eukaryotes, MESH: Biological Evolution, 03 medical and health sciences, chemistry.chemical_compound, RNA polymerase, evolution, MESH: Eukaryota / genetics, Human virome, Giant Virus, MESH: DNA-Directed RNA Polymerases / metabolism, Clade, MESH: Phylogeny, Gene, giant viruses, Polymerase, MESH: Evolution, Molecular, 030304 developmental biology, 0303 health sciences, Mimivirus, MESH: Cytoplasm / virology, Multidisciplinary, Phylogenetic tree, 030306 microbiology, MESH: Giant Viruses / genetics, RNA, DNA virus, Biological Sciences, biology.organism_classification, chemistry, Evolutionary biology, biology.protein, MESH: Cell Nucleus / genetics, NCLDV, MESH: Giant Viruses / metabolism, MESH: DNA Viruses / genetics
Abstract: Comment in :Reply to Ku and Sun: Ancestors of modern giant and large eukaryotic dsDNA viruses infected proto-eukaryotes./ Guglielmini J, Woo AC, Krupovic M, Forterre P, Gaia M. Proc Natl Acad Sci U S A. 2020 Feb 11;117(6):2749-2750./ doi: 10.1073/pnas.1920855117. Epub 2020 Jan 28. PMID: 31992645.Did giant and large dsDNA viruses originate before their eukaryotic hosts?Ku C, Sun TW. Proc Natl Acad Sci U S A. 2020 Feb 11;117(6):2747-2748. doi: 10.1073/pnas.1919860117. Epub 2020 Jan 28. PMID: 31992646; International audience; Giant and large eukaryotic double-stranded DNA viruses from the Nucleo-Cytoplasmic Large DNA Virus (NCLDV) assemblage represent a remarkably diverse and potentially ancient component of the eukaryotic virome. However, their origin(s), evolution, and potential roles in the emergence of modern eukaryotes remain subjects of intense debate. Here we present robust phylogenetic trees of NCLDVs, based on the 8 most conserved proteins responsible for virion morphogenesis and informational processes. Our results uncover the evolutionary relationships between different NCLDV families and support the existence of 2 superclades of NCLDVs, each encompassing several families. We present evidence strongly suggesting that the NCLDV core genes, which are involved in both informational processes and virion formation, were acquired vertically from a common ancestor. Among them, the largest subunits of the DNA-dependent RNA polymerase were transferred between 2 clades of NCLDVs and proto-eukaryotes, giving rise to 2 of the 3 eukaryotic DNA-dependent RNA polymerases. Our results strongly suggest that these transfers and the diversification of NCLDVs predated the emergence of modern eukaryotes, emphasizing the major role of viruses in the evolution of cellular domains.
Published: 2019

16. Genes Involved in the Development and Physiology of Both the Peripheral and Central Auditory Systems

Author: Nicolas Michalski, Christine Petit, Génétique et Physiologie de l'Audition, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Institut de la Vision, Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Chaire Génétique et physiologie cellulaire, Collège de France (CdF (institution)), This work was supported by the Prix Emergence of the Agir Pour l'Audition foundation to N.M. and by grants from the French Agence Nationale pour la Recherche (ANR), as part of the second Investissements d'Avenir program (ANR-15-RHUS-0001), the LabEx Lifesenses (ANR-10-LABX-65), the European Research Council (ERC-2011-ADG_294570), the BNP Paribas Foundation, the FAUN Stiftung, and the LHW-Stiftung to C.P., ANR-15-RHUS-0001,LIGHT4DEAF,ECLAIRER LA SURDITÉ : UNE APPROCHE HOLISTIQUE DU SYNDROME D'USHER(2015), ANR-10-LABX-0065,LIFESENSES,DES SENS POUR TOUTE LA VIE(2010), European Project: 294570,EC:FP7:ERC,ERC-2011-ADG_20110310,HAIRBUNDLE(2012), michalski, nicolas, ECLAIRER LA SURDITÉ : UNE APPROCHE HOLISTIQUE DU SYNDROME D'USHER - - LIGHT4DEAF2015 - ANR-15-RHUS-0001 - RHUS - VALID, DES SENS POUR TOUTE LA VIE - - LIFESENSES2010 - ANR-10-LABX-0065 - LABX - VALID, Assembling the puzzle of the operating auditory hair bundle - HAIRBUNDLE - - EC:FP7:ERC2012-12-01 - 2017-11-30 - 294570 - VALID, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and Collège de France - Chaire Génétique et physiologie cellulaire
Subjects: 0301 basic medicine, MESH: Gene Ontology, Auditory Pathways, [SDV]Life Sciences [q-bio], [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, cochlea, Gene regulatory network, MESH: Hearing Disorders, Ion Channels, 0302 clinical medicine, MESH: Sensory Receptor Cells, MESH: Cochlea, MESH: Gene Expression Regulation, Developmental, auditory cortex, MESH: Hair Cells, Auditory, MESH: Animals, MESH: Nerve Tissue Proteins, Hearing Disorders, auditory hindbrain, General Neuroscience, Gene Expression Regulation, Developmental, MESH: Rhombencephalon, MESH: Transcription Factors, Biological Evolution, MESH: Genes, [SDV] Life Sciences [q-bio], medicine.anatomical_structure, MESH: Auditory Pathways, Brainstem, Hair cell, Sensory Receptor Cells, Neurogenesis, Nerve Tissue Proteins, MESH: Biological Evolution, Biology, Auditory cortex, hair cell, 03 medical and health sciences, Hair Cells, Auditory, evolution, medicine, Auditory system, Animals, Humans, Transcription factor, gene regulatory networks, Cochlea, MESH: Humans, [SDV.NEU.NB] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, MESH: Neurogenesis, Rhombencephalon, 030104 developmental biology, Gene Ontology, Genes, MESH: Ion Channels, Neuroscience, 030217 neurology & neurosurgery, Function (biology), Transcription Factors
Abstract: International audience; The genetic approach, based on the study of inherited forms of deafness, has proven to be particularly effective for deciphering the molecular mechanisms underlying the development of the peripheral auditory system, the cochlea and its afferent auditory neurons, and how this system extracts the physical parameters of sound. Although this genetic dissection has provided little information about the central auditory system, scattered data suggest that some genes may have a critical role in both the peripheral and central auditory systems. Here, we review the genes controlling the development and function of the peripheral and central auditory systems, focusing on those with demonstrated intrinsic roles in both systems and highlighting the current underappreciation of these genes. Their encoded products are diverse, from transcription factors to ion channels, as are their roles in the central auditory system, mostly evaluated in brainstem nuclei. We examine the on-togenetic and evolutionary mechanisms that may underlie their expression at different sites.
Published: 2019

17. Origin of viruses: primordial replicators recruiting capsids from hosts

Author: Mart Krupovic, Eugene V. Koonin, Valerian V. Dolja, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), Department of Botany and Plant Pathology, Oregon State University (OSU), National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health [Bethesda] (NIH)-National Center for Biotechnology Information (NCBI), E.V.K. is supported through the intramural programme of the US National Institutes of Health. M.K. was supported by the Agence Nationale de la Recherche (France) project ENVIRA (no. ANR-17-CE15-0005-01)., Nature Reviews Microbiology thanks Raul Andino, Purificación López-García, Didier Raoult and Yong-Zhen Zhang for their contribution to the peer review of this work., ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), and Institut Pasteur [Paris]
Subjects: viruses, [SDV]Life Sciences [q-bio], Morphogenesis, MESH: Capsid/metabolism, Biology, Microbiology, Genome, MESH: Biological Evolution, 03 medical and health sciences, Capsid, Polyphyly, Replicon, Viral evolution, Gene, 0303 health sciences, Host Microbial Interactions, General Immunology and Microbiology, 030306 microbiology, MESH: Host Microbial Interactions, Viral proteins, Virus structures, Biological Evolution, Infectious Diseases, MESH: Viruses/growth & development, Evolutionary biology, Viruses, MESH: Viruses/genetics, Viral genome replication
Abstract: International audience; Viruses are ubiquitous parasites of cellular life and the most abundant biological entities on Earth. It is widely accepted that viruses are polyphyletic, but a consensus scenario for their ultimate origin is still lacking. Traditionally, three scenarios for the origin of viruses have been considered: descent from primordial, precellular genetic elements, reductive evolution from cellular ancestors and escape of genes from cellular hosts, achieving partial replicative autonomy and becoming parasitic genetic elements. These classical scenarios give different timelines for the origin(s) of viruses and do not explain the provenance of the two key functional modules that are responsible, respectively, for viral genome replication and virion morphogenesis. Here, we outline a 'chimeric' scenario under which different types of primordial, selfish replicons gave rise to viruses by recruiting host proteins for virion formation. We also propose that new groups of viruses have repeatedly emerged at all stages of the evolution of life, often through the displacement of ancestral structural and genome replication genes.
Published: 2019

18. Defining the genetic and evolutionary architecture of alternative splicing in response to infection

Author: Lluis Quintana-Murci, Hélène Quach, Maxime Rotival, Génétique Evolutive Humaine - Human Evolutionary Genetics, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), This project was funded by the European Research Council under the European Union’s Seventh Framework Programme (FP/2007–2013)/ERC grant agreement 281297 (to L.Q.-M.). The Quintana-Murci lab is funded by the French Government’s Investissement d’Avenir program, Laboratoires d’Excellence 'Integrative Biology of Emerging Infectious Diseases' (ANR-10-LABX-62-IBEID) and the Fondation pour la Recherche Médicale (Equipe FRM DEQ20180339214). M.R. was supported by a Marie Skłodowska-Curie fellowship (DLV-655417)., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), European Project: 281297,EC:FP7:ERC,ERC-2011-StG_20101109,EVOIMMUNOPOP(2012), European Project: 655417,H2020,H2020-MSCA-IF-2014,GATTACA(2015), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Male, MESH: Selection, Genetic, General Physics and Astronomy, 02 engineering and technology, MESH: Protein Isoforms, MESH: Sequence Analysis, RNA, Protein Isoforms, MESH: Animals, MESH: Genetic Variation, MESH: Healthy Volunteers, lcsh:Science, MESH: Immunity, Neanderthals, MESH: Neanderthals, education.field_of_study, Multidisciplinary, Repertoire, MESH: Alternative Splicing, MESH: Polymorphism, Single Nucleotide, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], MESH: Infections, MESH: European Continental Ancestry Group, 021001 nanoscience & nanotechnology, Biological Evolution, Healthy Volunteers, RNA splicing, 0210 nano-technology, Gene isoform, Science, Population, Quantitative Trait Loci, Introgression, Black People, MESH: Biological Evolution, Biology, Infections, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, White People, Article, 03 medical and health sciences, Immune system, MESH: Whole Exome Sequencing, Exome Sequencing, Animals, Humans, Selection, Genetic, education, Local adaptation, MESH: Humans, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Sequence Analysis, RNA, MESH: Transcriptome, Alternative splicing, Immunity, Genetic Variation, General Chemistry, MESH: Male, MESH: Quantitative Trait Loci, Alternative Splicing, 030104 developmental biology, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Evolutionary biology, lcsh:Q, MESH: African Continental Ancestry Group, Transcriptome
Abstract: Host and environmental factors contribute to variation in human immune responses, yet the genetic and evolutionary drivers of alternative splicing in response to infection remain largely uncharacterised. Leveraging 970 RNA-sequencing profiles of resting and stimulated monocytes from 200 individuals of African- and European-descent, we show that immune activation elicits a marked remodelling of the isoform repertoire, while increasing the levels of erroneous splicing. We identify 1,464 loci associated with variation in isoform usage (sQTLs), 9% of them being stimulation-specific, which are enriched in disease-related loci. Furthermore, we detect a longstanding increased plasticity of immune gene splicing, and show that positive selection and Neanderthal introgression have both contributed to diversify the splicing landscape of human populations. Together, these findings suggest that differential isoform usage has been an important substrate of innovation in the long-term evolution of immune responses and a more recent vehicle of population local adaptation., Genetic ancestry might influence immunological response to infection at different regulatory levels. Here, the authors use RNA-Seq to investigate the variability of alternative splicing patterns in resting and stimulated monocytes of African- and European-descent.
Published: 2019

19. An updated structural classification of replicative DNA polymerases

Author: Pierre Raia, Marc Delarue, Ludovic Sauguet, Dynamique structurale des Macromolécules / Structural Dynamics of Macromolecules, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU), ANR-17-CE11-0005,ARCHAPOL,Spécificités structurales et potentiel biotechnologique de la PolD, une ADN polymérase atypique d'archée(2017), and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: DNA polymerase, Protein Conformation, MESH: Biological Evolution, MESH: DNA Replication, DNA-Directed DNA Polymerase, DNA replication, Biochemistry, Genome, 03 medical and health sciences, DNA polymerases, 0302 clinical medicine, MESH: Protein Conformation, proofreading, evolution, MESH: DNA-Directed DNA Polymerase, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Polymerase, 030304 developmental biology, Genetics, 0303 health sciences, biology, Bacteria, Eukaryota, Processivity, biology.organism_classification, Archaea, Biological Evolution, genomic DNA, MESH: Bacteria, MESH: Eukaryota, classification, MESH: Archaea, biology.protein, Proofreading, PolD, 030217 neurology & neurosurgery
Abstract: Replicative DNA polymerases are nano-machines essential to life, which have evolved the ability to copy the genome with high fidelity and high processivity. In contrast with cellular transcriptases and ribosome machines, which evolved by accretion of complexity from a conserved catalytic core, no replicative DNA polymerase is universally conserved. Strikingly, four different families of DNA polymerases have evolved to perform DNA replication in the three domains of life. In Bacteria, the genome is replicated by DNA polymerases belonging to the A- and C-families. In Eukarya, genomic DNA is copied mainly by three distinct replicative DNA polymerases, Polα, Polδ, and Polε, which all belong to the B-family. Matters are more complicated in Archaea, which contain an unusual D-family DNA polymerase (PolD) in addition to PolB, a B-family replicative DNA polymerase that is homologous to the eukaryotic ones. PolD is a heterodimeric DNA polymerase present in all Archaea discovered so far, except Crenarchaea. While PolD is an essential replicative DNA polymerase, it is often underrepresented in the literature when the diversity of DNA polymerases is discussed. Recent structural studies have shown that the structures of both polymerase and proofreading active sites of PolD differ from other structurally characterized DNA polymerases, thereby extending the repertoire of folds known to perform DNA replication. This review aims to provide an updated structural classification of all replicative DNAPs and discuss their evolutionary relationships, both regarding the DNA polymerase and proofreading active sites.
Published: 2019

20. Genomic Imprinting and Physiological Processes in Mammals

Author: Valter Tucci, Anthony R. Isles, Gavin Kelsey, Anne C. Ferguson-Smith, Marisa S. Bartolomei, Nissim Benvenisty, Déborah Bourc’his, Marika Charalambous, Catherine Dulac, Robert Feil, Juliane Glaser, Lisa Huelsmann, Rosalind M. John, Gráinne I. McNamara, Kim Moorwood, Francoise Muscatelli, Hiroyuki Sasaki, Beverly I. Strassmann, Claudius Vincenz, Jon Wilkins, Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Génétique Moléculaire de Montpellier (IGMM), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)
Subjects: [SDV]Life Sciences [q-bio], MESH: Biological Evolution, MESH: Physiological Phenomena, Biology, General Biochemistry, Genetics and Molecular Biology, Chromosomes, MESH: Mammals, Epigenesis, Genetic, 03 medical and health sciences, Genomic Imprinting, 0302 clinical medicine, MESH: DNA Methylation, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: Animals, Epigenetics, MESH: Epigenesis, Genetic, Imprinting (psychology), Allele, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Alleles, Physiological Phenomena, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Epigenesis, Genetics, Mammals, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, MESH: Alleles, DNA Methylation, Phenotype, Biological Evolution, MESH: Genomic Imprinting, Multicellular organism, DNA methylation, MESH: Chromosomes, Genomic imprinting, 030217 neurology & neurosurgery
Abstract: International audience; Complex multicellular organisms, such as mammals, express two complete sets of chromosomes per nucleus, combining the genetic material of both parents. However, epigenetic studies have demonstrated violations to this rule that are necessary for mammalian physiology; the most notable parental allele expression phenomenon is genomic imprinting. With the identification of endogenous imprinted genes, genomic imprinting became well-established as an epigenetic mechanism in which the expression pattern of a parental allele influences phenotypic expression. The expanding study of genomic imprinting is revealing a significant impact on brain functions and associated diseases. Here, we review key milestones in the field of imprinting and discuss mechanisms and systems in which imprinted genes exert a significant role.
Published: 2019

21. Mesencephalic origin of the inferior lobe in zebrafish

Author: Manon Thomas, Elodie Machado, Sonya Galant, Kei Yamamoto, Arnim Jenett, Solal Bloch, Ingrid Colin, Pierre Affaticati, Institut des Neurosciences Paris-Saclay (NeuroPSI), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Transgénèse pour les Etudes Fonctionnelles sur les Organismes Modèles (TEFOR), Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Recherche Agronomique (INRA), CNRS Universite Paris Sud, Universite Paris-Saclay, Agence National de la Recherche (ANR PALL-E-NODY), Fondation pour la Recherche Medicale en France (Equipe FRM & Fin de these de sciences) [FDT201805005408], TEFOR - Investissement d’avenir ANR-II-INBS-0014, and ANR-11-INBS-0014,TEFOR,Transgenèse pour les Etudes Fonctionnelles sur les Organismes modèles(2011)
Subjects: MESH: Neural Stem Cells, Lateral hypothalamus, Physiology, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Teleost, poisson zèbre, Plant Science, Midbrain, MESH: Prosencephalon, 0302 clinical medicine, Neural Stem Cells, teleost, midbrain, forebrain, evolution, homology, vertebrate, comparative neuroanatomy, development, cell lineage, ventricle, poisson, Structural Biology, Mesencephalon, cyprinidae, lobe occipital, MESH: Animals, hypothalamus, ventricule cérébral, Zebrafish, lcsh:QH301-705.5, 0303 health sciences, [SDV.NEU.PC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Psychology and behavior, Vertebrate, [SDV.NEU.SC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Cognitive Sciences, Biological Evolution, mesencéphale, Hypothalamus, danio rerio, cerveau, General Agricultural and Biological Sciences, Biotechnology, Research Article, Sarcopterygii, Evolution, ventricule, Sensory system, MESH: Biological Evolution, Biology, Development, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Prosencephalon, biology.animal, Animals, MESH: Zebrafish, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Cell lineage, Cell Biology, MESH: Mesencephalon, Comparative neuroanatomy, MESH: Cell Lineage, biology.organism_classification, Homology, lcsh:Biology (General), plasticité neuronale, Forebrain, Ventricle, Neuroscience, 030217 neurology & neurosurgery, Developmental Biology
Abstract: Background Although the overall brain organization is shared in vertebrates, there are significant differences within subregions among different groups, notably between Sarcopterygii (lobe-finned fish) and Actinopterygii (ray-finned fish). Recent comparative studies focusing on the ventricular morphology have revealed a large diversity of the hypothalamus. Here, we study the development of the inferior lobe (IL), a prominent structure forming a bump on the ventral surface of the teleost brain. Based on its position, IL has been thought to be part of the hypothalamus (therefore forebrain). Results Taking advantage of genetic lineage-tracing techniques in zebrafish, we reveal that cells originating from her5-expressing progenitors in the midbrain-hindbrain boundary (MHB) participate in the formation of a large part of the IL. 3D visualization demonstrated how IL develops in relation to the ventricular system. We found that IL is constituted by two developmental components: the periventricular zone of hypothalamic origin and the external zone of mesencephalic origin. The mesencephalic external zone grows progressively until adulthood by adding new cells throughout development. Conclusion Our results disprove a homology between the IL and the mammalian lateral hypothalamus. We suggest that the IL is likely to be involved in multimodal sensory integration rather than feeding motivation. The teleost brain is not a simpler version of the mammalian brain, and our study highlights the evolutionary plasticity of the brain which gives rise to novel structures. Electronic supplementary material The online version of this article (10.1186/s12915-019-0631-y) contains supplementary material, which is available to authorized users.
Published: 2019

22. Genomic signature of successful colonization of Eurasia by the allopolyploid shepherd's purse (Capsella bursa-pastoris)

Author: Karl Holm, Stephen I. Wright, Martin Lascoux, Amandine Cornille, Sylvain Glémin, Adriana Salcedo, Dmytro Kryvokhyzha, Department of Ecology and Genetics [Uppsala] (EBC), Uppsala University, Evolutionary Biology Centre (EBC), Department of Ecology and Evolutionary Biology [University of Toronto] (EEB), University of Toronto, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), and 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
Subjects: bottleneck, 0301 basic medicine, MESH: Sequence Analysis, DNA, Plant Weeds, invasive species, Gene flow, MESH: Genotype, Colonization, MESH: Models, Genetic, MESH: Plant Weeds, biology, MESH: Asia, Ecology, MESH: Polymorphism, Single Nucleotide, Capsella, Genomic signature, Capsella bursa-pastoris, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Biological Evolution, Europe, MESH: Capsella, unphased SNP, Asia, Genotype, Demographic history, MESH: Bayes Theorem, MESH: Genetics, Population, MESH: Biological Evolution, Polymorphism, Single Nucleotide, time estimation, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, Polyploidy, Middle East, 03 medical and health sciences, MESH: Spatial Analysis, Capsella orientalis, MESH: Polyploidy, Genetics, dispersal, disomic inheritance, Ecology, Evolution, Behavior and Systematics, Spatial Analysis, Models, Genetic, Selfing, Bayes Theorem, Sequence Analysis, DNA, biology.organism_classification, MESH: Hybridization, Genetic, Genetics, Population, 030104 developmental biology, MESH: Middle East, Evolutionary biology, Brassicaceae, Hybridization, Genetic, MESH: Europe
Abstract: International audience; Polyploidization is a dominant feature of flowering plant evolution. However, detailed genomic analyses of the interpopulation diversification of polyploids following genome duplication are still in their infancy, mainly because of methodological limits, both in terms of sequencing and computational analyses. The shepherd's purse (Capsella bursa-pastoris) is one of the most common weed species in the world. It is highly self-fertilizing, and recent genomic data indicate that it is an allopolyploid, resulting from hybridization between the ancestors of the diploid species Capsella grandiflora and Capsella orientalis. Here, we investigated the genomic diversity of C. bursa-pastoris, its population structure and demographic history, following allopolyploidization in Eurasia. To that end, we genotyped 261 C. bursa-pastoris accessions spread across Europe, the Middle East and Asia, using genotyping-by-sequencing, leading to a total of 4274 SNPs after quality control. Bayesian clustering analyses revealed three distinct genetic clusters in Eurasia: one cluster grouping samples from Western Europe and Southeastern Siberia, the second one centred on Eastern Asia and the third one in the Middle East. Approximate Bayesian computation (ABC) supported the hypothesis that C. bursa-pastoris underwent a typical colonization history involving low gene flow among colonizing populations, likely starting from the Middle East towards Europe and followed by successive human-mediated expansions into Eastern Asia. Altogether, these findings bring new insights into the recent multistage colonization history of the allotetraploid C. bursa-pastoris and highlight ABC and genotyping-by-sequencing data as promising but still challenging tools to infer demographic histories of selfing allopolyploids.
Published: 2016

23. Evolutionary diversification of the HAP2 membrane insertion motifs to drive gamete fusion across eukaryotes

Author: Thomas Krey, Ahmed Haouz, Mark A. Johnson, Félix A. Rey, Juliette Fedry, Gérard Pehau-Arnaudet, Pierre Legrand, Jennifer Forcina, Virologie Structurale - Structural Virology, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université Paris Descartes - Paris 5 (UPD5), Hannover Medical School [Hannover] (MHH), Brown University, Synchrotron SOLEIL (SSOLEIL), Centre National de la Recherche Scientifique (CNRS), Microscopie ultrastructurale - Ultrapole (CITECH), Institut Pasteur [Paris] (IP), Protéopole, German Center for Infection Research - partner site Hannover-Braunschweig (DZIF), ERC Advanced grant CelCelFus (grant number 340371) received by FAR. Recurrent funding from the CNRS received by FAR. Recurrent funding from the Institut Pasteur received by FAR. Allocation ministerielle pour l’Ecole Polytechnique AMX received by JFe. National Science Foundation (NSF) (grant number IOS-1353798). Received by MJ. National Science Foundation (NSF) (grant number IOS-1540019). Received by MJ. National Institutes of Health Training Grant (grant number #T32-GM007601). Received by JFo., and European Project: 340371,EC:FP7:ERC,ERC-2013-ADG,CELCELFUS(2014)
Subjects: Protein Structure Comparison, 0301 basic medicine, MESH: Sequence Homology, Amino Acid, [SDV]Life Sciences [q-bio], Cell Membranes, Arabidopsis, Chlamydomonas reinhardtii, MESH: Chlamydomonas, Membrane Fusion, Biochemistry, Macromolecular Structure Analysis, MESH: Arabidopsis, MESH: Genetic Variation, Biology (General), Flowering Plants, Fusion, General Neuroscience, Eukaryota, Plants, Biological Evolution, Transmembrane protein, Cell biology, MESH: Eukaryota, Experimental Organism Systems, Cellular Structures and Organelles, General Agricultural and Biological Sciences, Research Article, Protein Structure, QH301-705.5, Arabidopsis Thaliana, MESH: Biological Evolution, MESH: Carrier Proteins, Brassica, MESH: Arabidopsis Proteins, Viral Structure, Biology, Research and Analysis Methods, MESH: Membrane Fusion, Microbiology, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Model Organisms, Plant and Algal Models, Virology, Vesicles, Molecular Biology, Sequence Homology, Amino Acid, General Immunology and Microbiology, Arabidopsis Proteins, Chlamydomonas, Organisms, Biology and Life Sciences, Membrane Proteins, Proteins, Genetic Variation, Lipid bilayer fusion, Cell Biology, biology.organism_classification, Fusion protein, MESH: Germ Cells, Germ Cells, 030104 developmental biology, Membrane protein, Liposomes, Helix, Carrier Proteins
Abstract: HAPLESS2 (HAP2) is a broadly conserved, gamete-expressed transmembrane protein that was shown recently to be structurally homologous to viral class II fusion proteins, which initiate fusion with host cells via insertion of fusion loops into the host membrane. However, the functional conformation of the HAP2 fusion loops has remained unknown, as the reported X-ray structure of Chlamydomonas reinhardtii HAP2 lacked this critical region. Here, we report a structure-guided alignment that reveals diversification of the proposed HAP2 fusion loops. Representative crystal structures show that in flowering plants, HAP2 has a single prominent fusion loop projecting an amphipathic helix at its apex, while in trypanosomes, three small nonpolar loops of HAP2 are poised to interact with the target membrane. A detailed structure-function analysis of the Arabidopsis HAP2 amphipathic fusion helix defines key residues that are essential for membrane insertion and for gamete fusion. Our study suggests that HAP2 may have evolved multiple modes of membrane insertion to accommodate the diversity of membrane environments it has encountered during eukaryotic evolution., Author summary The fusion of gamete plasma membranes is the fundamental cellular event that brings two parental cells together to form a new individual, yet we know surprisingly little about this process at the molecular level. HAPLESS 2 (HAP2) is a conserved sperm plasma membrane protein that is essential for gamete fusion in a diverse array of eukaryotes. It was recently shown to share a common ancestor with viral proteins that drive fusion of the viral envelope with host membranes, but its mechanism of action remained elusive, since the reported structure did not resolve the proposed membrane interaction surface. Here, we report two new HAP2 structures revealing that HAP2 has evolved diverse membrane interaction surfaces. In the flowering plants, HAP2 uses an amphipathic helix that presents nonpolar residues to the target membrane; in trypanosomes, the membrane interaction surface comprises three shallow nonpolar loops.
Published: 2018

24. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

Author: Emmanuel Paradis, Klaus Schliep, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), 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), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), 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)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Statistics and Probability, Computer science, Big data, Context (language use), MESH: Biological Evolution, Biochemistry, MESH: Biodiversity, 03 medical and health sciences, MESH: Software, Software, Phylogenetics, MESH: Phylogeny, Molecular Biology, Phylogeny, 030304 developmental biology, Flexibility (engineering), 0303 health sciences, business.industry, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], 030302 biochemistry & molecular biology, Usability, Biodiversity, Biological Evolution, Data science, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Computer Science Applications, Computational Mathematics, Computational Theory and Mathematics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business
Abstract: Summary After more than fifteen years of existence, the R package ape has continuously grown its contents, and has been used by a growing community of users. The release of version 5.0 has marked a leap towards a modern software for evolutionary analyses. Efforts have been put to improve efficiency, flexibility, support for ‘big data’ (R’s long vectors), ease of use and quality check before a new release. These changes will hopefully make ape a useful software for the study of biodiversity and evolution in a context of increasing data quantity. Availability and implementation ape is distributed through the Comprehensive R Archive Network: http://cran.r-project.org/package=ape. Further information may be found at http://ape-package.ird.fr/.
Published: 2018

25. Editorial overview: Host–pathogen interactions shaped through evolutionary and regulatory processes

Author: Carmen Buchrieser, Joan Mecsas, Biologie des Bactéries intracellulaires - Biology of Intracellular Bacteria, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Tufts University School of Medicine [Boston], and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Microbiology (medical), 0303 health sciences, MESH: Humans, Bacteria, 030306 microbiology, Host (biology), Microbiota, MESH: Host-Pathogen Interactions, MESH: Biological Evolution, Computational biology, Biology, Biological Evolution, Microbiology, 03 medical and health sciences, MESH: Bacteria, Infectious Diseases, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Host-Pathogen Interactions, Humans, bacteria, MESH: Microbiota, Pathogen, 030304 developmental biology
Abstract: Comment on Bacterial microbiota of the nasal passages across the span of human life. [Curr Opin Microbiol. 2018] Evolution of virulence in Enterococcus faecium, a hospital-adapted opportunistic pathogen. [Curr Opin Microbiol. 2018] The challenges of integrating two genomes in one cell. [Curr Opin Microbiol. 2018]; International audience
Published: 2018

26. Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes

Author: Panagiotis S. Adam, Simonetta Gribaldo, Guillaume Borrel, Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Institut Pasteur [Paris] (IP), Université Paris Diderot - Paris 7 (UPD7), P.S.A. is supported by a PhD fellowship from Paris Diderot University and by funds from the PhD Programme 'Frontières du Vivant (FdV)–Programme Bettencourt.' G.B. is a recipient of a Roux-Cantarini fellowship from the Institut Pasteur. S.G. acknowledges funding from the French National Agency for Research Grant ArchEvol (ANR-16-CE02-0005-01)., We thank Alexander Probst for feedback on an earlier version of the paper, and two anonymous reviewers whose comments helped improve clarity and correctness of the manuscript., ANR-16-CE02-0005,Arch-Evol,Approches phylogenomiques pour étudier l'origine et évolution des Archées(2016), and Institut Pasteur [Paris]
Subjects: 0301 basic medicine, Enzyme complex, MESH: Genome, Archaeal, LUCA, [SDV]Life Sciences [q-bio], MESH: Genome, Bacterial, Genome, Corrections, chemistry.chemical_compound, Genome, Archaeal, MESH: Multienzyme Complexes/genetics, methanogens, Phylogeny, MESH: Phylogeny, Genetics, Carbon Monoxide, Multidisciplinary, Last universal ancestor, Carbon fixation, Acetyl-CoA, MESH: Carbon Cycle, Aldehyde Oxidoreductases, Biological Evolution, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, PNAS Plus, MESH: Bacteria/enzymology, Wood–Ljungdahl pathway, Wood-Ljungdahl pathway, MESH: Aldehyde Oxidoreductases/metabolism, Carbon monoxide dehydrogenase, 030106 microbiology, MESH: Bacteria/genetics, Acetate-CoA Ligase, Bacterial genome size, Biology, MESH: Biological Evolution, MESH: Aldehyde Oxidoreductases/genetics, Carbon Cycle, 03 medical and health sciences, MESH: Carbon Monoxide/metabolism, Multienzyme Complexes, MESH: Archaea/genetics, evolution, MESH: Acetate-CoA Ligase/metabolism, MESH: Multienzyme Complexes/metabolism, MESH: Archaea/enzymology, Bacteria, MESH: Acetate-CoA Ligase/genetics, Archaea, acetogens, 030104 developmental biology, chemistry, biology.protein, Genome, Bacterial
Abstract: Erratum in : Correction for Adam et al., Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes. [Proc Natl Acad Sci U S A. 2018]; International audience; Carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ ACS) is a five-subunit enzyme complex responsible for the carbonyl branch of the Wood-Ljungdahl (WL) pathway, considered one of the most ancient metabolisms for anaerobic carbon fixation, but its origin and evolutionary history have been unclear. While traditionally associated with methanogens and acetogens, the presence of CODH/ACS homologs has been reported in a large number of un-cultured anaerobic lineages. Here, we have carried out an exhaustive phylogenomic study of CODH/ACS in over 6,400 archaeal and bacterial genomes. The identification of complete and likely functional CODH/ACS complexes in these genomes significantly expands its distribution in microbial lineages. The CODH/ACS complex displays astounding conservation and vertical inheritance over geological times. Rare intradomain and interdomain transfer events might tie into important functional transitions, including the acquisition of CODH/ACS in some archaeal methanogens not known to fix carbon, the tinkering of the complex in a clade of model bacterial acetogens, or emergence of archaeal-bacterial hybrid complexes. Once these transfers were clearly identified, our results allowed us to infer the presence of a CODH/ACS complex with at least four subunits in the last universal common ancestor (LUCA). Different scenarios on the possible role of ancestral CODH/ACS are discussed. Despite common assumptions, all are equally compatible with an autotrophic, mixotrophic, or heterotrophic LUCA. Functional characterization of CODH/ACS from a larger spectrum of bacterial and archaeal lineages and detailed evolutionary analysis of the WL methyl branch will help resolve this issue.
Published: 2018

27. Host Genetic Variation Does Not Determine Spatio-Temporal Patterns of European Bat 1 Lyssavirus

Author: Troupin, Cécile, Picard-Meyer, Evelyne, Dellicour, Simon, Casademont, Isabelle, Kergoat, Lauriane, Lepelletier, Anthony, Dacheux, Laurent, Baele, Guy, Monchâtre-Leroy, Elodie, Cliquet, Florence, Lemey, Philippe, Bourhy, Hervé, Centre Collaborateur de l'OMS pour la Rage - Dynamique des lyssavirus et adaptation à l'hôte (CC-OMS), Institut Pasteur [Paris] (IP), Laboratoire de la rage et de la faune sauvage de Nancy (LRFSN), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Rega Institute for Medical Research [Leuven, België], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Génétique fonctionnelle des maladies infectieuses - Functional Genetics of Infectious Diseases, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), This work was supported by European Union Seventh Framework Programme (FP7/2007-2013) PREDEMICS (under grant agreement number 278433), Santé Publique France and the Institut Pasteur. SD is funded by the Fonds Wetenschappelijk Onderzoek (FWO, Flanders, Belgium). PL acknowledges the Research Foundation - Flanders (G0D5117N & G066215) and the Research Fund KU Leuven (OT/14/115)., The author want to acknowledge Karin Eiglmeier from Unit of Insect Vector Genetics and Genomics for access and help on ABI Prism 3730 for microsatellite genotyping. We would like to thank the SFEPM group (Societe Francaise pour l’Etude et la Protection des Mammiferes, groupe Chiropteres), and especially the bat naturalists, for their collaboration in the surveillance of bat rabies in France., European Project: 278433,EC:FP7:HEALTH,FP7-HEALTH-2011-two-stage,PREDEMICS(2011), Institut Pasteur [Paris], and Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris]
Subjects: MESH: Cell Nucleus, MESH: Lyssavirus, MESH: Selection, Genetic, genome sequence, Chiroptera -- genetics -- virology, MESH: Biological Evolution, Genome, Viral, DNA, Mitochondrial, European bat 1 lyssavirus (EBLV-1), Chiroptera, Lyssavirus -- classification -- genetics -- isolation & purification, Animals, MESH: Animals, Selection, Genetic, Cell Nucleus, next generation sequencing, MESH: Host-Pathogen Interactions, MESH: DNA, Mitochondrial, MESH: Chiroptera, Sciences bio-médicales et agricoles, Biological Evolution, Europe, Cell Nucleus -- genetics, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Host-Pathogen Interactions, RNA virus evolution, Lyssavirus, MESH: Europe, MESH: Microsatellite Repeats, MESH: Genome, Viral, DNA, Mitochondrial -- genetics, serotine bat, Microsatellite Repeats, Research Article
Abstract: The majority of bat rabies cases in Europe are attributed to European bat 1 lyssavirus (EBLV-1), circulating mainly in serotine bats (Eptesicus serotinus). Two subtypes have been defined (EBLV-1a and EBLV-1b), each associated with a different geographical distribution. In this study, we undertake a comprehensive sequence analysis based on 80 newly obtained EBLV-1 nearly complete genome sequences from nine European countries over a 45-year period to infer selection pressures, rates of nucleotide substitution, and evolutionary time scale of these two subtypes in Europe. Our results suggest that the current lineage of EBLV-1 arose in Europe ∼600 years ago and the virus has evolved at an estimated average substitution rate of ∼4.19×10-5 subs/site/year, which is among the lowest recorded for RNA viruses. In parallel, we investigate the genetic structure of French serotine bats at both the nuclear and mitochondrial level and find that they constitute a single genetic cluster. Furthermore, Mantel tests based on interindividual distances reveal the absence of correlation between genetic distances estimated between viruses and between host individuals. Taken together, this indicates that the genetic diversity observed in our E. serotinus samples does not account for EBLV-1a and -1b segregation and dispersal in Europe., info:eu-repo/semantics/published
Published: 2017

28. Microbiome intestinal ancien et problématiques médicales contemporaines

Author: Philippe, Charlier, Anaïs, Augias, Philippe, Sansonetti, Céline, Bon, Sean, Kennedy, Laure, Segurel, Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Hôpital Max Fourestier, Institut de la précarité et de l’exclusion sociale, Pathogénie Microbienne Moléculaire, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Chaire Microbiologie et Maladies infectieuses, Collège de France (CdF (institution)), Eco-Anthropologie et Ethnobiologie (EAE), Muséum national d'Histoire naturelle (MNHN)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Centre d'Innovation et Recherche Technologique / Center for Innovation and Technological Research, and Institut Pasteur [Paris]
Subjects: MESH: Humans, MESH: Immune System, MESH: Intestines/parasitology, Paleontology, MESH: Paleontology, MESH: Biological Evolution, Feeding Behavior, Environment, MESH: History, Ancient, Biological Evolution, Gastrointestinal Microbiome, Intestines, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Immune System, MESH: Feeding Behavior, Humans, MESH: Gastrointestinal Microbiome/physiology, MESH: Environment, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, History, Ancient
Abstract: International audience; Human gut microbiome composition and diversity increasingly appear as a reliable marker of human evolution within his environment, and of health and its alteration (concept of dysbiosis); as a matter of fact, it can be considered as a strong marker of the disease status of individuals. Thus, in retrospect, the capacity to profile the gut microbiome would offer a great opportunity to identify individual and societal changes to which ancient populations were exposed. A global and diachronic view of the gut microbiome evolution is necessary in order to highlight the potential role of environmental factors or human habits in this process. However, to make the most of its contribution, archaeo-microbiology should aim at being as exhaustive as possible, encompassing parasites which have likely played a major role in the development of the mammalian immune system, and viruses.; La composition et la diversité du microbiote intestinal humain apparaissent de plus en plus comme un marqueur fiable de l’évolution de l’homme dans son environnement, mais aussi de la santé et de son altération (c’est le concept de dysbiose). Il peut donc être considéré comme un marqueur puissant de l’état d’une pathologie rencontrée chez un individu. Ainsi, rétrospectivement, la possibilité de caractériser le microbiote intestinal des individus offrirait une excellente occasion d’identifier les changements individuels et sociétaux auxquels les populations anciennes ont été exposées. Une vision globale et environnementale de l’évolution du microbiote intestinal est donc nécessaire afin de mettre en évidence le rôle potentiel des facteurs environnementaux ou des habitudes humaines possiblement impliquées dans ces modifications évolutives. Cependant, pour tirer le meilleur parti de sa contribution, l’archéo-microbiologie doit être aussi exhaustive que possible, englobant virus et parasites qui ont vraisemblablement joué un rôle majeur dans le développement du système immunitaire des mammifères.
Published: 2017

29. Spontaneous Loss of Virulence in Natural Populations of Listeria monocytogenes

Author: Mariela Scortti, Alexandra Moura, Lei Han, Guillaume Vales, Alexandre Leclercq, Olivier Disson, Marc Lecuit, Hélène Bracq-Dieye, Mylène M. Maury, Edith Gouin, José A. Vázquez-Boland, Viviane Chenal-Francisque, Centre collaborateur de l'OMS Listeria / WHO Collaborating Centre Listeria (CC-OMS / WHO-CC), Institut Pasteur [Paris] (IP)-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Centre National de Référence Listeria - National Reference Center Listeria (CNRL), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), University of Edinburgh, Biologie des Infections - Biology of Infection, Interactions Bactéries-Cellules (UIBC), Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Descartes - Paris 5 (UPD5), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Work in M.L.'s laboratory was supported by Institut Pasteur, Inserm, LabEx IBEID, the European Research Council, and Santé Publique France. Work in J.A.V.-B.'s laboratory was supported by the Wellcome Trust (program grant WT074020MA) and partially by core Roslin Institute funding from BBSRC (BB/J004227/1), We acknowledge Anne Morvan, Thomas Cantinelli, Nathalie Tessaud-Rita and Laetitia Bellon for their help in strain collection and isolation at the National Reference Centre for Listeria. We thank Pascale Cossart for providing antibodies against LLO and the Institut Pasteur P2M platform for genome sequencing., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), DIAKITE, andrée, Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID, Institut Pasteur [Paris]-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Centre collaborateur de l'OMS Listeria - Biologie des Infections (CCOMS), Centre National de Référence Listeria - Biologie des Infections (CNRL), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris]-Institut National de la Recherche Agronomique (INRA), Institut des Maladies Génétiques Imagine [Paris], and ANR-10-LABX-62-IBEID,IBEID,Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases'(2010)
Subjects: 0301 basic medicine, Erythrocytes, MESH: Selection, Genetic, Mutant, MESH: Heat-Shock Proteins, MESH: Virulence, medicine.disease_cause, MESH: Listeria monocytogenes, Severity of Illness Index, MESH: Recombinant Proteins, Hemolysin Proteins, Mice, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Listeriosis, MESH: Animals, Cloning, Molecular, MESH: Phylogeny, Pathogen, MESH: Bacterial Proteins, Heat-Shock Proteins, Phylogeny, Mice, Inbred BALB C, MESH: Gene Expression Regulation, Bacterial, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, MESH: Erythrocytes, Listeriolysin O, Biological Evolution, spontaneous mutations, MESH: Amino Acid Substitution, MESH: Hemolysis, Recombinant Proteins, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, MESH: Hemolysin Proteins, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Peptide Termination Factors, Peptide Termination Factors, Transposable element, MESH: Mutation, Bacterial Toxins, 030106 microbiology, Immunology, MESH: Mice, Inbred BALB C, Virulence, Molecular Genomics, MESH: Biological Evolution, Biology, Microbiology, Frameshift mutation, 03 medical and health sciences, Bacterial Proteins, Listeria monocytogenes, MESH: Severity of Illness Index, medicine, genomics, Animals, Humans, MESH: Cloning, Molecular, Selection, Genetic, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Gene, MESH: Mice, MESH: Humans, Gene Expression Regulation, Bacterial, biochemical phenomena, metabolism, and nutrition, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, virulence, Amino Acid Substitution, MESH: Bacterial Toxins, MESH: Listeriosis, Mutation, Parasitology, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, hemolysis, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: The pathogenesis of Listeria monocytogenes depends on the ability of this bacterium to escape from the phagosome of the host cells via the action of the pore-forming toxin listeriolysin O (LLO). Expression of the LLO-encoding gene ( hly ) requires the transcriptional activator PrfA, and both hly and prfA genes are essential for L. monocytogenes virulence. Here, we used the hemolytic activity of LLO as a phenotypic marker to screen for spontaneous virulence-attenuating mutations in L. monocytogenes . Sixty nonhemolytic isolates were identified among a collection of 57,820 confirmed L. monocytogenes strains isolated from a variety of sources (0.1%). In most cases (56/60; 93.3%), the nonhemolytic phenotype resulted from nonsense, missense, or frameshift mutations in prfA . Five strains carried hly mutations leading to a single amino acid substitution (G299V) or a premature stop codon causing strong virulence attenuation in mice. In one strain, both hly and gshF (encoding a glutathione synthase required for full PrfA activity) were missing due to genomic rearrangements likely caused by a transposable element. The PrfA/LLO loss-of-function (PrfA − /LLO − ) mutants belonged to phylogenetically diverse clades of L. monocytogenes , and most were identified among nonclinical strains (57/60). Consistent with the rare occurrence of loss-of-virulence mutations, we show that prfA and hly are under purifying selection. Although occurring at a low frequency, PrfA − /LLO − mutational events in L. monocytogenes lead to niche restriction and open an evolutionary path for obligate saprophytism in this facultative intracellular pathogen.
Published: 2017

30. Emergence and maintenance of menopause in humans: A game theory model

Author: Michel Raymond, Valentin Thouzeau, 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, Eco-Anthropologie et Ethnobiologie (EAE), and Muséum national d'Histoire naturelle (MNHN)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Statistics and Probability, MESH: Menopause, media_common.quotation_subject, [SDV]Life Sciences [q-bio], MESH: Biological Evolution, Kin selection, Biology, MESH: Reproduction, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Reproductive senescence, Game Theory, medicine, MESH: Family Characteristics, Humans, ESS, Grandmothering, Ovulation, media_common, Pleiotropy, Family Characteristics, MESH: Humans, General Immunology and Microbiology, Life span, Applied Mathematics, Reproduction, Conflict over resources, [SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology, General Medicine, medicine.disease, Biological Evolution, Menopause, 030104 developmental biology, Pleiotropy (drugs), MESH: Game Theory, Modeling and Simulation, Maternity cost, Female, General Agricultural and Biological Sciences, Game theory, MESH: Female, Demography
Abstract: International audience; Menopause, the permanent cessation of ovulation, occurs in women well before the end of their expected life span. Several adaptive hypotheses have been proposed to solve this evolutionary puzzle, each based on a possible fitness benefit derived from an early reproductive senescence, but no consensus has emerged. The construction of a game theory model allowed us to jointly study the main adaptive hypotheses in emergence and maintenance of menopause. Four classical hypotheses on the benefits of menopause were considered (decreased maternal mortality, increased grandmothering, decreased conflict over reproductive resources between older and younger females, and changes in their relatedness) plus a fifth one derived from a possible pleiotropic trade-off. Interestingly, the conditions for the emergence of menopause are more restrictive than those for its maintenance due to the social and familial changes induced by the occurrence of non-reproductive older women.
Published: 2017

31. The early life of a fly glial cell

Author: Angela Giangrande, Benjamin Altenhein, Pierre B. Cattenoz, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Cattenoz, Pierre, University of Cologne, and Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: MESH: Cell Differentiation, MESH: Neural Stem Cells, 0301 basic medicine, MESH: Drosophila Proteins, Cell, MESH: Biological Evolution, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Biology, MESH: Drosophila melanogaster, 03 medical and health sciences, Neural Stem Cells, MESH: Gene Expression Regulation, Developmental, [SDV.BC.BC] Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], medicine, Animals, Drosophila Proteins, Humans, Regeneration, MESH: Animals, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Molecular Biology, ComputingMilieux_MISCELLANEOUS, Gliogenesis, MESH: Humans, Regeneration (biology), MESH: Regeneration, Gene Expression Regulation, Developmental, Cell Differentiation, Embryo, Cell Biology, Anatomy, biology.organism_classification, Biological Evolution, Early life, Drosophila melanogaster, 030104 developmental biology, medicine.anatomical_structure, Larva, MESH: Neuroglia, Neuroglia, MESH: Larva, Neuroscience, Neural development, Function (biology), Developmental Biology
Abstract: International audience; Throughout evolution, glia have key regulatory roles in neural development and function. Typically, they control the response to developmental and/or pathological signals, thereby affecting neural proliferation, remodeling, survival, and regeneration. Such complex biology depends on the plastic features of glial cells, but also on the presence of different classes of glial cells, hence the importance of understanding the cellular and the molecular mechanisms underlying their development. The fly community has made major breakthroughs by characterizing the bases of gliogenesis and here we describe the glial lineages as well as the glial promoting factor active in the embryo of Drosophila melanogaster. WIREs Dev Biol 2016, 5:67-84. doi: 10.1002/wdev.200 For further resources related to this article, please visit the WIREs website.
Published: 2015

32. Origins and evolution of viruses of eukaryotes: The ultimate modularity

Author: Eugene V. Koonin, Mart Krupovic, Valerian V. Dolja, National Center for Biotechnology Information (NCBI), Oregon State University (OSU), Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], EVK is supported by the intramural funds of the US Department of Health and Human Services (National Library of Medicine)., The authors thank David Karlin and Tero Ahola for the kind permission to cite the results of their work before publication., and Institut Pasteur [Paris] (IP)
Subjects: [SDV]Life Sciences [q-bio], viruses, MESH: Biological Evolution, Biology, Genome, Article, MESH: Viruses, 03 medical and health sciences, Evolution of viruses, Virology, Functional gene modules, Bacteriophages, Human virome, Giant Virus, MESH: Genetic Variation, Non-cellular life, Gene, 030304 developmental biology, Genetics, 0303 health sciences, Polintons, 030306 microbiology, Eukaryota, Genetic Variation, RNA, Biological Evolution, Recombination, MESH: Eukaryota, Viral replication, Viral evolution, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Transposable elements
Abstract: International audience; Viruses and other selfish genetic elements are dominant entities in the biosphere, with respect to both physical abundance and genetic diversity. Various selfish elements parasitize on all cellular life forms. The relative abundances of different classes of viruses are dramatically different between prokaryotes and eukaryotes. In prokaryotes, the great majority of viruses possess double-stranded (ds) DNA genomes, with a substantial minority of single-stranded (ss) DNA viruses and only limited presence of RNA viruses. In contrast, in eukaryotes, RNA viruses account for the majority of the virome diversity although ssDNA and dsDNA viruses are common as well. Phylogenomic analysis yields tangible clues for the origins of major classes of eukaryotic viruses and in particular their likely roots in prokaryotes. Specifically, the ancestral genome of positive-strand RNA viruses of eukaryotes might have been assembled de novo from genes derived from prokaryotic retroelements and bacteria although a primordial origin of this class of viruses cannot be ruled out. Different groups of double-stranded RNA viruses derive either from dsRNA bacteriophages or from positive-strand RNA viruses. The eukaryotic ssDNA viruses apparently evolved via a fusion of genes from prokaryotic rolling circle-replicating plasmids and positive-strand RNA viruses. Different families of eukaryotic dsDNA viruses appear to have originated from specific groups of bacteriophages on at least two independent occasions. Polintons, the largest known eukaryotic transposons, predicted to also form virus particles, most likely, were the evolutionary intermediates between bacterial tectiviruses and several groups of eukaryotic dsDNA viruses including the proposed order "Megavirales" that unites diverse families of large and giant viruses. Strikingly, evolution of all classes of eukaryotic viruses appears to have involved fusion between structural and replicative gene modules derived from different sources along with additional acquisitions of diverse genes.
Published: 2015
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33. Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage

Author: Sabine Rüsch-Gerdes, Hans P eter Beck, Vladyslav Nikolayevskyy, Irina Kontsevaya, Petras Stakenas, Kadri Toit, Shinji Maeda, Eman Aleksic, Marie Ballif, Stefano Mona, Troels Lillebaek, Maryline Bonnet, Caroline Allix-Béguec, Sophie Lecher, Robin M. Warren, Isdore Chola Shamputa, Francesca Barletta, Isolina Campos-Herrero, Wei wei Jiao, Thomas Kohl, Suzanne M. Crowe, Ewa Augustynowicz-Kopeć, Solomon Ghebremichael, Branislava Savic, Francis Varaine, Dragana Vuković, Camille Blin, Annick Antierens, Li Hwei Sng, Maryse Fauville-Dufaux, Céline Wahl, Thierry Wirth, Stefan Niemann, Eve Willery, Helen Cox, Valeriu Crudu, Emanuele Borroni, Sebastien Gagneux, Philip Supply, Sven Hoffner, Adong Shen, Stobdan Kalon, Michael Rasmussen, Francis Drobniewski, Igor Mokrousov, Michael G. B. Blum, Madeleine Hanekom, Sofía Samper, Matthias Merker, Clifton E. Barry, Nicolas Duforet-Frebourg, Roland Diel, Nalin Rastogi, Daniela Maria Cirillo, Elisabeth Sanchez-Padilla, Molecular Mycobacteriology, Research Center Borstel - Leibniz Lung Center [Germany], 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), Laboratoire Biologie Intégrative des Population, Evolution Moléculaire, École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Biologie Computationnelle et Mathématique (TIMC-IMAG-BCM), Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble - UMR 5525 (TIMC-IMAG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-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 Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-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), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), National Reference Center for Mycobacteria, Institut Pasteur de Saint-Pétersbourg, Réseau International des Instituts Pasteur (RIIP), Centre for Biomedical Research, Burnet Institute [Melbourne, Victoria], genoscreen, GenoScreen, Medical Department, Médecins sans Frontières [Genève] (MSF), Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, Institute of Social and Preventive Medicine, Universität Bern [Bern] (UNIBE), Instituto de Medicina Tropical Alexander von Humboldt, Molecular Epidemiology Unit–Tuberculosis, Instituto de Medicina Tropical 'Alexander von Humboldt' (IMT AvH), Universidad Peruana Cayetano Heredia (UPCH)-Universidad Peruana Cayetano Heredia (UPCH), Medical Parasitology and Infection Biology [Basel, Suisse] (MPI), Swiss Tropical and Public Health Institute [Basel], Laboratoire de Recherche en Informatique d'Amiens (LaRIA), Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Epicentre [Paris] [Médecins Sans Frontières], Emerging Bacterial Pathogen Unit, San Raffaele Scientific Institute, hospital Universitario de Gran Canaria Dr Negrin, Macfarlane Burnet Institute for Medical Research, Laboratoire Jean Alexandre Dieudonné (LJAD), 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 Côte d'Azur (UCA), PHE National Mycobacterial Reference Laboratory and Clinical TB and HIV Group, Queen Mary's School of Medicine and Dentistry, Division of Infectious Diseases, Imperial College London, Centre national de Référence et Laboratoire Tuberculose et Mycobactéries = National Reference Centre of Tuberculosis and Mycobacteria [Brussels] (CNR), Institut Scientifique de Santé Publique [Belgique] - Scientific Institute of Public Health [Belgium] (WIV-ISP), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), MRC National Institute for Medical Research, Department of Preparedness, Swedish Institute for Infectious Disease Control, Faculty of Medicine and Health Sciences, stellen, Key Laboratory of Major Diseases in Children, Beijing Children's Hospital affiliated to Capital Medical University-Beijing Pediatric Research Institute-Chine - Ministry of Education, Samara Oblast TB Service, Research institute of Tuberculosis, Anti-tuberculosis Association, Institut Pasteur de la Guadeloupe, LAboratoire de Recherche en Mécanique Appliquée (LARMAUR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Mycobacteriology Unit, Prince Leopold Institute of Tropical Medicine, Microbiology Unit, Tropical Diseases Research Centre [Zambia] (TDRC), Alcatel-Thalès III-V lab (III-V Lab), THALES [France]-ALCATEL, Central Tuberculosis Laboratory, Singapore General Hospital, Medecins Sans Frontieres (Medecins Sans Frontieres), Médecins Sans Frontières, DTU Fotonik - Department of Photonics Engineering, Danmarks Tekniske Universitet = Technical University of Denmark (DTU), molecular biology and human genetics, Stell, Molecular Mycobacteriology Group, National Reference Center for Mycobacyeria, Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), We acknowledge J. Peh for her assistance and support in the study andI. Comas for statistical advice. Parts of this work have been supported by grantsfrom the European Community’s Seventh Framework Programme (FP7/2007-2013) under grant agreement 278864 in the framework of the European UnionPathoNGenTrace project and grant agreement 223681 in the framework of theTB-PAN-NET project. We also thank Action Transversale du Muséum Nationald’Histoire Naturelle ‘Les Microorganismes, Acteurs Clés dans les Ecosystèmes’for financial support, European Project: 223681,EC:FP7:HEALTH,FP7-HEALTH-2007-B,TB PAN-NET(2009), European Project: 278864,FP7/2007- 2013, 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 pratique des hautes études (EPHE), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Universität Bern [Bern], Laboratoire Jean Alexandre Dieudonné (JAD), Université Côte d'Azur (UCA)-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 de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), THALES-ALCATEL, and Technical University of Denmark [Lyngby] (DTU)
Subjects: Tuberculosis, Lineage (genetic), MESH: Mutation, MESH: Mycobacterium tuberculosis, Genotype, MESH: Biological Evolution, MESH: Global Health, Biology, MESH: Genome, Bacterial, Global Health, Genetic analysis, Mycobacterium tuberculosis, MESH: Genotype, Evolution, Molecular, Phylogenetics, Tuberculosis, Multidrug-Resistant, Genetics, Global health, medicine, Humans, MESH: Phylogeny, MESH: Evolution, Molecular, MESH: Tuberculosis, Multidrug-Resistant, Phylogeny, MESH: Humans, Ecology, Population size, medicine.disease, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Biological Evolution, 3. Good health, Mycobacterium tuberculosis/classification/genetics/isolation & purification, Evolutionary biology, Mutation, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Tuberculosis, Multidrug-Resistant/epidemiology/microbiology, Genome, Bacterial, purl.org/pe-repo/ocde/ford#1.06.07 [https]
Abstract: International audience; Mycobacterium tuberculosis strains of the Beijing lineage are globally distributed and are associated with the massive spread of multidrug-resistant (MDR) tuberculosis in Eurasia. Here we reconstructed the biogeographical structure and evolutionary history of this lineage by genetic analysis of 4,987 isolates from 99 countries and whole-genome sequencing of 110 representative isolates. We show that this lineage initially originated in the Far East, from where it radiated worldwide in several waves. We detected successive increases in population size for this pathogen over the last 200 years, practically coinciding with the Industrial Revolution, the First World War and HIV epidemics. Two MDR clones of this lineage started to spread throughout central Asia and Russia concomitantly with the collapse of the public health system in the former Soviet Union. Mutations identified in genes putatively under positive selection and associated with virulence might have favored the expansion of the most successful branches of the lineage.
Published: 2015
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34. Whole-genome analyses resolve early branches in the tree of life of modern birds

Author: Bhanu Rekepalli, Jaime Huerta-Cepas, David Haussler, Beth Shapiro, Frank E. Rheindt, Bo Li, Per Alström, Oliver A. Ryder, Salvador Capella-Gutierrez, Jianwen Li, José Alfredo Samaniego, Binghang Liu, Paula F. Campos, David P. Mindell, Xiangjiang Zhan, An Pas, Yinhua Huang, Liang Liu, Scott V. Edwards, Dave Burt, David A. Ray, Andrew Dixon, Hui Li, Toni Gabaldón, Bastien Boussau, Cai Li, Hans Ellegren, Carsten Rahbek, Shengbin Li, Michael J. Braun, Peter Houde, Peter V. Lovell, Alexandros Stamatakis, Claudia C. Weber, Yong Zhang, Jian Wang, Thomas Sicheritz-Pontén, Volodymyr Zavidovych, Alexander Suh, Xiong Yinqi, Maria Paula Cruz Schneider, Stephen J. O'Brien, Ganesh Ganapathy, Shamsuzzoha Bayzid, Huanming Yang, Guojie Zhang, Alonzo Alfaro-Núñez, Claudio V. Mello, Michael Bunce, Amy C. Driskell, Francisco Prosdocimi, Zijun Xiong, Joel Cracraft, Long Zhou, Mikkel H. Schierup, Brant C. Faircloth, Gary R. Graves, F. Keith Barker, Jon Fjeldså, Benoit Nabholz, Bent E. K. Lindow, Frederick H. Sheldon, Robb T. Brumfield, Nitish Narula, Bent O. Petersen, Kasper Munch, Klaus-Peter Koepfli, Rute R. da Fonseca, Thomas L. Bailey, Kui Wu, Quiemei Zheng, Tandy Warnow, John E. McCormack, Elizabeth P. Derryberry, Linnéa Smeds, Simon Y. W. Ho, Polina L. Perelman, Siavash Mirarab, Qi Zhou, Michael William Bruford, Knud A. Jønsson, M. Thomas P. Gilbert, Ning Li, Richard E. Green, Edward L. Braun, R. Paul Scofield, Wesley C. Warren, Zhenyu Li, Fang Zhang Zhang, Warren E. Johnson, Morgan Wirthlin, Jason T. Howard, Travis C. Glenn, Ludovic Orlando, Mads F. Bertelsen, David M. Lambert, Andre J. Aberer, Erich D. Jarvis, Sankar Subramanian, Amhed Missael Vargas Velazquez, Yongli Zeng, Eske Willerslev, Jin Xiao, Shiping Liu, Wang Jun, Howard Hughes Medical Institute (HHMI), Duke University Medical Center, University of Texas at Austin [Austin], Heidelberg Institute for Theoretical Studies (HITS ), Beijing Genomics Institute [Shenzhen] (BGI), Xi'an Jiaotong University (Xjtu), Natural History Museum of Denmark, Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), New Mexico State University, The University of Sydney, University of California, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), 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), Evolutionary Biology Centre (EBC), Uppsala University, Okinawa Institute of Science and Technology Graduate University, University of Georgia [USA], 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), Griffith University [Brisbane], Centre for Genomic Regulation [Barcelona] (CRG), Universitat Pompeu Fabra [Barcelona] (UPF)-Centro Nacional de Analisis Genomico [Barcelona] (CNAG), Institució Catalana de Recerca i Estudis Avançats (ICREA), Joint Institute for Computational Sciences [Knoxville] (JICS), The University of Tennessee [Knoxville], Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC, Aarhus University [Aarhus], The McDonnell Genome Institute (MGI), Washington University in Saint Louis (WUSTL), Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology [Mstate, USA] (BCH-EPP), Mississippi State University [Mississippi], Department of Biological Sciences [Lubbock], Texas Tech University [Lubbock] (TTU), Department of Ecology and Evolutionary Biology [Santa Cruz], University of California [Santa Cruz] (UCSC), University of California-University of California, School of Biosciences [Cardiff], Cardiff University, Kunming Institute of Zoology, Chinese Academy of Sciences [Beijing] (CAS), International Wildlife Consultants Ltd, China Agricultural University (CAU), Tulane University, Louisiana State University (LSU), Copenhagen Zoo, Oregon Health and Science University [Portland] (OHSU), Federal University of Para - Universidade Federal do Para [Belem - Brésil], Technical University of Denmark [Lyngby] (DTU), Breeding Centre for Endangered Arabian Wildlife, Dubai Hospital, Canterbury Museum, Curtin University [Perth], Planning and Transport Research Centre (PATREC), Department of Integrative Biology [Berkeley] (IB), University of California [Berkeley], National Cancer Institute Frederick, Novosibirsk State University (NSU), Smithsonian Institution, Department of Biological Sciences [Singapore], National University of Singapore (NUS), Bell Museum of Natural History, University of Minnesota [Twin Cities] (UMN), University of Minnesota System-University of Minnesota System, Department of Life Sciences, Imperial College London, Smithsonian Conservation Biology Institute, Theodosius Dobzhansky Center for Genome Bioinformatics, St Petersburg State University (SPbU), Nova Southeastern University (NSU), Center for Biomolecular Science and Engineering, San Diego Zoo Global Institute for Conservation Research, Occidental College, The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Key Laboratory of Zoological Systematics and Evolution, Chinese Academy of Agricultural Sciences (CAAS), Swedish Species Information Centre, Swedish University of Agricultural Sciences (SLU), Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University [Cambridge], Institute of Theoretical Informatics, Karlsruhe Institute of Technology (KIT), Department of Biochemistry and Biophysics [San Francisco], American Museum of Natural History (AMNH), University of Florida [Gainesville] (UF), University of Illinois at Urbana-Champaign [Urbana], University of Illinois System, University of Copenhagen = Københavns Universitet (KU), King Abdulaziz University, Macau University of Science and Technology (MUST), The University of Hong Kong (HKU), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), University of California (UC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), University of California [Santa Cruz] (UC Santa Cruz), University of California (UC)-University of California (UC), Kunming Institute of Zoology (KIZ), Federal University of Para - Universidade Federal do Pará - UFPA [Belém, Brazil] (UFPA), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), University of California [Berkeley] (UC Berkeley), Biotechnology and Biological Sciences Research Council (BBSRC), Harvard University, and University of Copenhagen = Københavns Universitet (UCPH)
Subjects: Palaeognathae, MESH: Sequence Analysis, DNA, Genetic Speciation, MESH: Introns, Zoology, MESH: Biological Evolution, MESH: Base Sequence, Article, Coalescent theory, Avian Proteins, Birds, MESH: INDEL Mutation, INDEL Mutation, MESH: Avian Proteins, Animals, MESH: Animals, MESH: Genome, MESH: Phylogeny, Clade, Phylogeny, MESH: Genetic Speciation, Genome, Multidisciplinary, Columbea, Base Sequence, biology, Phylogenetic tree, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Sequence Analysis, DNA, Passerea, biology.organism_classification, Biological Evolution, Introns, MESH: Genes, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Genes, MESH: DNA Transposable Elements, Neognathae, MESH: Birds, DNA Transposable Elements, Neoaves
Abstract: International audience; To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
Published: 2014

35. Evolution of a Biomass-Fermenting Bacterium To Resist Lignin Phenolics

Author: Volker Döring, Magali Boutard, Marcel Salanoubat, Ivan Dubois, Tiffany Souterre, Wahiba Berrabah, Andrew C. Tolonen, Ismael Torres-Romero, Julien Patrouix, Tristan Cerisy, Karine Labadie, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), This work was funded by the Genoscope-CEA, a CNRS Chaire d'Excellence (to A.C.T.), and the Agence Nationale de la Recherche Grant ANR-16-CE05-0020 (to A.C.T.)., We thank P. Marlière for the GM3, E. Darii for mass spectrometry, and the Genoscope-CEA sequencing platform for DNA and RNA sequencing., ANR-16-CE05-0020,Phytocell,Développement des bactéries cellulolytiques Clostridium phytofermentans et Clostridium cellulolyticum comme biocatalyseurs pour la conversion de la biomasse végétale en alcools supérieurs(2016), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Lignocellulosic biomass, MESH: Biological Evolution, MESH: Bacterial Proteins/genetics, MESH: Clostridium/genetics, Lignin, 7. Clean energy, Applied Microbiology and Biotechnology, MESH: Biodegradation, Environmental, MESH: Fermentation, Clostridia, Ferulic acid, 03 medical and health sciences, chemistry.chemical_compound, Bacterial Proteins, MESH: Biomass, Botany, evolution, Environmental Microbiology, genomics, Biomass, Food science, MESH: Cellulose/metabolism, Cellulose, Clostridium, 2. Zero hunger, [SDV.GEN]Life Sciences [q-bio]/Genetics, Phenol, Ecology, biology, food and beverages, Plants, Clostridium phytofermentans, biology.organism_classification, Biological Evolution, Biodegradation, Environmental, 030104 developmental biology, chemistry, Fermentation, clostridia, MESH: Bacterial Proteins/metabolism, Bacteria, Food Science, Biotechnology
Abstract: Increasing the resistance of plant-fermenting bacteria to lignocellulosic inhibitors is useful to understand microbial adaptation and to develop candidate strains for consolidated bioprocessing. Here, we study and improve inhibitor resistance in Clostridium phytofermentans (also called Lachnoclostridium phytofermentans ), a model anaerobe that ferments lignocellulosic biomass. We survey the resistance of this bacterium to a panel of biomass inhibitors and then evolve strains that grow in increasing concentrations of the lignin phenolic, ferulic acid, by automated, long-term growth selection in an anaerobic GM3 automat. Ultimately, strains resist multiple inhibitors and grow robustly at the solubility limit of ferulate while retaining the ability to ferment cellulose. We analyze genome-wide transcription patterns during ferulate stress and genomic variants that arose along the ferulate growth selection, revealing how cells adapt to inhibitors through changes in gene dosage and regulation, membrane fatty acid structure, and the surface layer. Collectively, this study demonstrates an automated framework for in vivo directed evolution of anaerobes and gives insight into the genetic mechanisms by which bacteria survive exposure to chemical inhibitors. IMPORTANCE Fermentation of plant biomass is a key part of carbon cycling in diverse ecosystems. Further, industrial biomass fermentation may provide a renewable alternative to fossil fuels. Plants are primarily composed of lignocellulose, a matrix of polysaccharides and polyphenolic lignin. Thus, when microorganisms degrade lignocellulose to access sugars, they also release phenolic and acidic inhibitors. Here, we study how the plant-fermenting bacterium Clostridium phytofermentans resists plant inhibitors using the lignin phenolic, ferulic acid. We examine how the cell responds to abrupt ferulate stress by measuring changes in gene expression. We evolve increasingly resistant strains by automated, long-term cultivation at progressively higher ferulate concentrations and sequence their genomes to identify mutations associated with acquired ferulate resistance. Our study develops an inhibitor-resistant bacterium that ferments cellulose and provides insights into genomic evolution to resist chemical inhibitors.
Published: 2017

36. Biotic Host–Pathogen Interactions As Major Drivers of Plastid Endosymbiosis

Author: Agathe Subtil, Debashish Bhattacharya, Andreas P.M. Weber, Ugo Cenci, Christophe Colleoni, Steven G. Ball, Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Rutgers University [Camden], Rutgers University System (Rutgers), Rheinische Friedrich-Wilhelms-Universität Bonn, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf]-Max Planck Institute for Plant Breeding Research (MPIPZ)-Universität zu Köln = University of Cologne, Biologie cellulaire de l'infection microbienne, Institut Pasteur [Paris] (IP), U.C., S.B., C.C., and A.S. were supported by the CNRS, the Université de Lille CNRS, the Institut Pasteur and the ANR grants ‘Expendo’ and ‘Ménage à Trois’. D.B. was supported by NSF grants MGSP 0625440 and MCB 0946528, and A.W. was supported by German Research Foundation grants CRC-TR1, CRC 1208, and EXC 1028., ANR-14-CE11-0024,Expendo,Vers l'endosymbiose expérimentale(2014), ANR-12-BSV2-0009,Ménage à trois,Une symbiose tripartite explique l'origine du plaste et son intégration métabolique(2012), Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Rutgers University, Universität zu Köln-Heinrich-Heine-Universität Düsseldorf [Düsseldorf]-Max Planck Institute for Plant Breeding Research (MPIPZ), Institut Pasteur [Paris], Institut National de la Recherche Agronomique (INRA)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Universität zu Köln-Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf]-Max Planck Institute for Plant Breeding Research (MPIPZ), and Université de Lille-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Symbiogenesis, MESH: Glycogen, chlamydia, MESH: Biological Evolution, Plant Science, Biology, glycogen metabolism, Microbiology, 03 medical and health sciences, MESH: Chlamydia, evolution of plastids, [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], Plastids, Plastid, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Symbiosis, Pathogen, Gene, Genetics, MESH: Symbiosis, Endosymbiosis, Obligate, Host (biology), MESH: Host-Pathogen Interactions, MESH: Plastids, biology.organism_classification, Biological Evolution, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], T3SS, bacterial conjugation, 030104 developmental biology, Host-Pathogen Interactions, Eukaryote, tryptophan synthesis, Glycogen
Abstract: International audience; The plastid originated 1.5 billion years ago through a primary endosymbiosis involving a heterotrophic eukaryote and an ancient cyanobacterium. Phylogenetic and biochemical evidence suggests that the incipient endosymbiont interacted with an obligate intracellular chlamydial pathogen that housed it in an inclusion. This aspect of the ménage-à-trois hypothesis (MATH) posits that Chlamydiales provided critical novel transporters and enzymes secreted by the pathogens in the host cytosol. This initiated the efflux of photosynthate to both the inclusion lumen and host cytosol. Here we review the experimental evidence supporting the MATH and focus on chlamydial genes that replaced existing cyanobacterial functions. The picture emerging from these studies underlines the importance of chlamydial host-pathogen interactions in the metabolic integration of the primary plastid.
Published: 2017

37. Biological Diversity and Evolution of Type IV Secretion Systems

Author: Peter J. Christie, Laura Gomez Valero, Carmen Buchrieser, McGovern Medical School [Houston, Texas], Biologie des Bactéries intracellulaires - Biology of Intracellular Bacteria, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, DNA transfer, Multiprotein complex, 030106 microbiology, MESH: Biological Evolution, Computational biology, Pathogenesis, Effector translocation, Legionella Dot/Icm, Legionella pneumophila, Article, MESH: Biodiversity, Type IV Secretion Systems, 03 medical and health sciences, chemistry.chemical_compound, Type IV secretion, Type (biology), Bacterial Proteins, Phylogenomics, Secretion, MESH: Bacterial Secretion Systems, Bacterial Secretion Systems, MESH: Bacterial Proteins, MESH: Type IV Secretion Systems, biology, Conjugation, MESH: Agrobacterium tumefaciens, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Agrobacterium tumefaciens, Biodiversity, biology.organism_classification, Biological Evolution, Traffic ATPases, MESH: Legionella pneumophila, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Coupling protein, chemistry, Bacteria, DNA
Abstract: International audience; The bacterial type IV secretion systems (T4SSs) are a highly functionally and structurally diverse superfamily of secretion systems found in many species of gram-negative and-positive bacteria. Collectively, the T4SSs can translocate DNA and monomeric and multimeric protein substrates to a variety of bacterial and eukaryotic cell types. Detailed phylogenomics analyses have established that the T4SSs evolved from ancient conjugation machines whose original functions were to disseminate mobile DNA elements within and between bacterial species. How members of the T4SS superfamily evolved to recognize and translocate specific substrate repertoires to prokaryotic or eukaryotic target cells is a fascinating question from evolutionary, biological, and structural perspectives. In this chapter, we will summarize recent findings that have shaped our current view of the biological diversity of the T4SSs. We focus mainly on two subtypes, designated as the types IVA (T4ASS) and IVB (T4BSS) systems that respectively are represented by the paradigmatic Agrobacterium tumefaciens VirB/VirD4 and Legionella pneumophila Dot/Icm T4SSs. We present current information about the composition and architectures of these representative systems. We also describe how these and a few related T4ASS and T4BSS members evolved as specialized nanomachines through acquisition of novel domains or subunits, a process that ultimately generated extensive genetic and structural mosaicism among this secretion superfamily. Finally, we present new phylogenomics information establishing that the T4BSSs are much more broadly distributed than initially envisioned.
Published: 2017

38. The Ancient Gamete Fusogen HAP2 Is a Eukaryotic Class II Fusion Protein

Author: Fedry, Juliette, Liu, Yanjie, Pehau-Arnaudet, Gerard, Pei, Jimin, Li, Wenhao, Tortorici, M Alejandra, Traincard, François, Meola, Annalisa, Bricogne, Gérard, Grishin, Nick, Snell, William, Rey, Felix, Krey, Thomas, Virologie Structurale - Structural Virology, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Hannover Medical School [Hannover] (MHH), University of Texas Southwestern Medical Center, Microscopie ultrastructurale - Ultrapole (CITECH), Institut Pasteur [Paris] (IP), Ingénierie des Anticorps (plate-forme) - Antibody Engineering (Platform), Global Phasing Ltd, Global Phasing, German Center for Infection Research - partner site Hannover-Braunschweig (DZIF), F.A.R. acknowledges funding from the ERC Advanced grant project (340371) CelCelFus for this work, which also used general support from Institut Pasteur and CNRS. W.J.S. was supported by a grant from the NIH (GM56778) and acknowledges funding from the UTSW HI/HR Program. N.V.G. is funded, in part, by a grant from the NIH (GM094575) and the Welch Foundation (I-1505). J.F. benefitted from an Allocation ministérielle pour l'Ecole Polytechnique AMX., We thank Francis-André Wollmann and Sandrine Bujaldon for discussions and help with initial experiments, Fredrick Grinnell, Saikat Mukhopadhyay, Michael Henne, and Margaret Phillips of UT Southwestern for helpful discussions, the crystallization platform of the Pasteur Proteopole for technical help, Remi Fronzes for help with native PAGE experiments, Vincent Olieric and the staff of synchrotron beamlines PX-III at the Swiss Light Source, Proxima-1 and -2 at SOLEIL and ID29 and ID30-3 at the European Synchrotron Radiation Facility for help during data collection, members of the Rey and Snell labs for discussions, and M. Nilges and the Equipement d’excellence CACSICE for providing the Falcon II direct electron detector., European Project: 340371,EC:FP7:ERC,ERC-2013-ADG,CELCELFUS(2014), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris]
Subjects: Plasmodium, crystal structure, transmission-blocking malaria vaccine, sexual reproduction, [SDV]Life Sciences [q-bio], membrane fusion, Protozoan Proteins, MESH: Sequence Alignment, MESH: Biological Evolution, MESH: Amino Acid Sequence, virus entry, Crystallography, X-Ray, gamete fusion, MESH: Chlamydomonas, Article, MESH: Recombinant Proteins, Protein Domains, lipid insertion, HAP2, Humans, Amino Acid Sequence, MESH: Membrane Fusion Proteins, MESH: Protozoan Proteins, Membrane Fusion Proteins, Plant Proteins, class II fusion protein, MESH: Plant Proteins, Biochemistry, Genetics and Molecular Biology(all), MESH: Plasmodium, Chlamydomonas, Eukaryota, MESH: Crystallography, X-Ray, Biological Evolution, Recombinant Proteins, MESH: Germ Cells, Germ Cells, Virus Diseases, MESH: Protein Domains, Sequence Alignment, Chlamydomonas reinhardtii
Abstract: Summary Sexual reproduction is almost universal in eukaryotic life and involves the fusion of male and female haploid gametes into a diploid cell. The sperm-restricted single-pass transmembrane protein HAP2-GCS1 has been postulated to function in membrane merger. Its presence in the major eukaryotic taxa—animals, plants, and protists (including important human pathogens like Plasmodium)—suggests that many eukaryotic organisms share a common gamete fusion mechanism. Here, we report combined bioinformatic, biochemical, mutational, and X-ray crystallographic studies on the unicellular alga Chlamydomonas reinhardtii HAP2 that reveal homology to class II viral membrane fusion proteins. We further show that targeting the segment corresponding to the fusion loop by mutagenesis or by antibodies blocks gamete fusion. These results demonstrate that HAP2 is the gamete fusogen and suggest a mechanism of action akin to viral fusion, indicating a way to block Plasmodium transmission and highlighting the impact of virus-cell genetic exchanges on the evolution of eukaryotic life., Graphical Abstract, Highlights • The primordial gamete fusogen HAP2 exhibits homology to class II viral fusion proteins • HAP2 inserts into the target gamete membrane via a hydrophobic fusion loop • HAP2 links virus entry into target cells and the origins of sexual reproduction • HAP2 is a sex-specific target for blocking fertilization in multiple kingdoms, Gamete fusion across eukaryotic branches uses an ancient factor homologous to viral fusion proteins.
Published: 2017

39. Special Issue: Mathematical and Computational Evolutionary Biology-2015

Author: David Bryant, Olivier Gascuel, University of Otago [Dunedin, Nouvelle-Zélande], Bioinformatique évolutive - Evolutionary Bioinformatics, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris]
Subjects: 0106 biological sciences, 0301 basic medicine, MEDLINE, Library science, MESH: Biological Evolution, Biological evolution, Biology, 010603 evolutionary biology, 01 natural sciences, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 03 medical and health sciences, MESH: Classification, Editorial, 030104 developmental biology, Genetics, Ecology, Evolution, Behavior and Systematics, MESH: Congresses as Topic, Introductory Journal Article, MESH: Computational Biology
Abstract: International audience; This special issue of Systematic Biology contains review articles contributed by keynote speakers at the “Mathematical and Computational EvolutionaryBiology” conference (MCEB; see web sites below), held in 2015. This is the seventh conference in this series, the first being held in Paris in 2003 with keynote addresses from such notables as Joe Felsenstein, Ziheng Yang, and Walter Fitch. Oxford University Press published two books based on the 2003 and 2005 Paris meetings (Gascuel 2005; Gascuel and Steel 2007).
Published: 2017

40. Mitogenomic phylogeny, diversification, and biogeography of South American spiny rats

Author: Ana Carolina Loss, Pierre-Henri Fabre, Emmanuel J. P. Douzery, Louise H. Emmons, Ludovic Orlando, Marie-Ka Tilak, Nathan S. Upham, Bruce D. Patterson, Yuri L. R. Leite, Fabienne Justy, 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, Smithsonian Institution, Department of Ecology and Evolutionary Biology [New Haven], Yale University [New Haven], Field Museum of Natural History [Chicago, USA], Federal University of Espírito Santo, Centre for GeoGenetics, Natural History Museum of Denmark, Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), 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), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Science [Copenhagen], and University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)
Subjects: 0106 biological sciences, 0301 basic medicine, MESH: Sequence Analysis, DNA, Range (biology), MESH: Rodentia, MESH: Base Sequence, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, MESH: Animals, MESH: Genetic Variation, MESH: Phylogeny, Phylogeny, MESH: Evolution, Molecular, Phylogenetic tree, Carterodon, Nuclear DNA, Biological Evolution, Mitochondria, Phylogeography, Biogeography, MESH: Phylogeography, Diversification, MESH: Genome, Mitochondrial, Neotropics, MESH: Rats, MESH: Mitochondria, MESH: Bayes Theorem, Zoology, Rodentia, MESH: Biological Evolution, Biology, 010603 evolutionary biology, DNA, Mitochondrial, Evolution, Molecular, 03 medical and health sciences, Phylogenetics, Genetics, Vicariance, Animals, Molecular Biology, Fast-evolving gene, Ecology, Evolution, Behavior and Systematics, Mitogenomics, Base Sequence, MESH: DNA, Mitochondrial, Genetic Variation, Bayes Theorem, Echimyidae, Sequence Analysis, DNA, MESH: South America, 15. Life on land, South America, biology.organism_classification, Rats, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, 030104 developmental biology, Taxon, Evolutionary biology, Genome, Mitochondrial, Biological dispersal
Abstract: International audience; Echimyidae is one of the most speciose and ecologically diverse rodent families in the world, occupying a wide range of habitats in the Neotropics. However, a resolved phylogeny at the genus-level is still lacking for these 22 genera of South American spiny rats, including the coypu (Myocastorinae), and 5 genera of West Indian hutias (Capromyidae) relatives. Here, we used Illumina shotgun sequencing to assemble 38 new complete mitogenomes, establishing Echimyidae, and Capromyidae as the first major rodent families to be completely sequenced at the genus-level for their mitochondrial DNA. Combining mitogenomes and nuclear exons, we inferred a robust phylogenetic framework that reveals several newly supported nodes as well as the tempo of the higher level diversification of these rodents. Incorporating the full generic diversity of extant echimyids leads us to propose a new higher level classification of two subfamilies: Euryzygomatomyinae and Echimyinae. Of note, the enigmatic Carterodon displays fast-evolving mitochondrial and nuclear sequences, with a long branch that destabilizes the deepest divergences of the echimyid tree, thereby challenging the sister-group relationship between Capromyidae and Euryzygomatomyinae. Biogeographical analyses involving higher level taxa show that several vicariant and dispersal events impacted the evolutionary history of echimyids. The diversification history of Echimyidae seems to have been influenced by two major historical factors, namely (1) recurrent connections between Atlantic and Amazonian Forests and (2) the Northern uplift of the Andes.
Published: 2017

41. Microbiome intestinal ancien et problématiques médicales contemporaines: Fæces vivos docent

Author: Charlier, Philippe, Augias, Anaïs, Sansonetti, Philippe, Bon, Céline, Kennedy, Sean, Ségurel, Laure, Kennedy, Sean, Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Hôpital Max Fourestier, Institut de la précarité et de l’exclusion sociale, Pathogénie Microbienne Moléculaire, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Collège de France - Chaire Microbiologie et Maladies infectieuses, Collège de France (CdF (institution)), Eco-Anthropologie et Ethnobiologie (EAE), Muséum national d'Histoire naturelle (MNHN)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Centre d'Innovation et Recherche Technologique / Center for Innovation and Technological Research, and Institut Pasteur [Paris] (IP)
Subjects: MESH: Humans, MESH: Immune System, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, MESH: Intestines/parasitology, MESH: Feeding Behavior, MESH: Paleontology, MESH: Biological Evolution, MESH: Gastrointestinal Microbiome/physiology, [SDU.STU.PG] Sciences of the Universe [physics]/Earth Sciences/Paleontology, MESH: History, Ancient, MESH: Environment, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology
Abstract: Human gut microbiome composition and diversity increasingly appear as a reliable marker of human evolution within his environment, and of health and its alteration (concept of dysbiosis); as a matter of fact, it can be considered as a strong marker of the disease status of individuals. Thus, in retrospect, the capacity to profile the gut microbiome would offer a great opportunity to identify individual and societal changes to which ancient populations were exposed. A global and diachronic view of the gut microbiome evolution is necessary in order to highlight the potential role of environmental factors or human habits in this process. However, to make the most of its contribution, archaeo-microbiology should aim at being as exhaustive as possible, encompassing parasites which have likely played a major role in the development of the mammalian immune system, and viruses., La composition et la diversité du microbiote intestinal humain apparaissent de plus en plus comme un marqueur fiable de l’évolution de l’homme dans son environnement, mais aussi de la santé et de son altération (c’est le concept de dysbiose). Il peut donc être considéré comme un marqueur puissant de l’état d’une pathologie rencontrée chez un individu. Ainsi, rétrospectivement, la possibilité de caractériser le microbiote intestinal des individus offrirait une excellente occasion d’identifier les changements individuels et sociétaux auxquels les populations anciennes ont été exposées. Une vision globale et environnementale de l’évolution du microbiote intestinal est donc nécessaire afin de mettre en évidence le rôle potentiel des facteurs environnementaux ou des habitudes humaines possiblement impliquées dans ces modifications évolutives. Cependant, pour tirer le meilleur parti de sa contribution, l’archéo-microbiologie doit être aussi exhaustive que possible, englobant virus et parasites qui ont vraisemblablement joué un rôle majeur dans le développement du système immunitaire des mammifères.
Published: 2017

42. Genetic Diversity and the Efficacy of Purifying Selection across Plant and Animal Species

Author: Jun Chen, Martin Lascoux, Sylvain Glémin, Department of Ecology and Genetics [Uppsala] (EBC), Uppsala University, Evolutionary Biology Centre (EBC), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), 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), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE)
Subjects: 0106 biological sciences, 0301 basic medicine, Nonsynonymous substitution, MESH: Genome, Plant, Mutation rate, MESH: Selection, Genetic, 01 natural sciences, Nucleotide diversity, Effective population size, MESH: Genetic Fitness, Purifying selection, MESH: Animals, MESH: Genetic Variation, MESH: Models, Genetic, MESH: Phylogeny, Phylogeny, MESH: Evolution, Molecular, Genome, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Biological Evolution, MESH: Silent Mutation, Distribution of fitness effects, Genome, Plant, MESH: Mutation, MESH: Population Density, MESH: Biological Evolution, Biology, 010603 evolutionary biology, Life history theory, Evolution, Molecular, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, MESH: Polymorphism, Genetic, Genetics, Animals, MESH: Genome, Selection, Genetic, Nearly neutral theory, Molecular Biology, Silent Mutation, Ecology, Evolution, Behavior and Systematics, Population Density, Genetic diversity, Polymorphism, Genetic, Models, Genetic, business.industry, Genetic Variation, Life history traits, 15. Life on land, Mating system, Biotechnology, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, 030104 developmental biology, Evolutionary biology, Mutation, Nearly neutral theory of molecular evolution, Genetic Fitness, business
Abstract: International audience; A central question in evolutionary biology is why some species have more genetic diversity than others and a no less important question is why selection efficacy varies among species. Although these questions have started to be tackled in animals, they have not been addressed to the same extent in plants. Here, we estimated nucleotide diversity at synonymous, πS, and nonsynonymous sites, πN, and a measure of the efficacy of selection, the ratio πN/πS, in 34 animal and 28 plant species using full genome data. We then evaluated the relationship of nucleotide diversity and selection efficacy with effective population size, the distribution of fitness effect and life history traits. In animals, our data confirm that longevity and propagule size are the variables that best explain the variation in πS among species. In plants longevity also plays a major role as well as mating system. As predicted by the nearly neutral theory of molecular evolution, the log of πN/πS decreased linearly with the log of πS but the slope was weaker in plants than in animals. This appears to be due to a higher mutation rate in long lived plants, and the difference disappears when πS is rescaled by the mutation rate. Differences in the distribution of fitness effect of new mutations also contributed to variation in πN/πS among species.
Published: 2017

43. Multiple origins of viral capsid proteins from cellular ancestors

Author: Mart Krupovic, Eugene V. Koonin, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], National Center for Biotechnology Information (NCBI), and Institut Pasteur [Paris] (IP)
Subjects: Models, Molecular, 0301 basic medicine, Structure analysis, viruses, [SDV]Life Sciences [q-bio], origin of viruses, MESH: Biological Evolution, Genome, Viral, Biology, Genome, Virus, capsid proteins, nucleocapsids, MESH: Viruses, 03 medical and health sciences, Animals, Humans, MESH: Animals, MESH: Phylogeny, Gene, Phylogeny, Host protein, MESH: Capsid Proteins, Evolutionary genomics, Genetics, virus evolution, primordial replicons, Multidisciplinary, MESH: Humans, Eukaryota, Archaea, Biological Evolution, MESH: Eukaryota, 030104 developmental biology, PNAS Plus, Capsid, Viral evolution, MESH: Archaea, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, MESH: Genome, Viral, MESH: Models, Molecular
Abstract: International audience; Viruses are the most abundant biological entities on earth and show remarkable diversity of genome sequences, replication and expression strategies, and virion structures. Evolutionary genomics of viruses revealed many unexpected connections but the general scenario(s) for the evolution of the virosphere remains a matter of intense debate among proponents of the cellular regression, escaped genes, and primordial virus world hypotheses. A comprehensive sequence and structure analysis of major virion proteins indicates that they evolved on about 20 independent occasions, and in some of these cases likely ancestors are identifiable among the proteins of cellular organisms. Virus genomes typically consist of distinct structural and replication modules that recombine frequently and can have different evolutionary trajectories. The present analysis suggests that, although the replication modules of at least some classes of viruses might descend from primordial selfish genetic elements, bona fide viruses evolved on multiple, independent occasions throughout the course of evolution by the recruitment of diverse host proteins that became major virion components.
Published: 2017

44. The Envelope Proteins of the Bunyavirales

Author: Pablo Guardado-Calvo, Félix A. Rey, Virologie Structurale - Structural Virology, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, MESH: Phlebovirus, viruses, MESH: Protein Folding, MESH: Virus Internalization, Membrane fusion, MESH: Biological Evolution, Alphavirus, MESH: Bunyaviridae Infections, 03 medical and health sciences, Virus entry, Viral envelope, Viral entry, MESH: Animals, MESH: Phylogeny, MESH: Structural Homology, Protein, Genetics, MESH: Humans, biology, MESH: Alphavirus, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Membrane fusion protein, MESH: Hantavirus, RNA, biology.organism_classification, Herpesvirus glycoprotein B, Fusion protein, Virus evolution, 3. Good health, 030104 developmental biology, Class II fusion proteins, MESH: Endosomes, Viral evolution, MESH: RNA, Viral, MESH: Viral Fusion Proteins, Bunyavirus, MESH: Genome, Viral, MESH: Models, Molecular
Abstract: International audience; The Bunyavirales Order encompasses nine families of enveloped viruses containing a single-stranded negative-sense RNA genome divided into three segments. The small (S) and large (L) segments encode proteins participating in genome replication in the infected cell cytoplasm. The middle (M) segment encodes the viral glycoproteins Gn and Gc, which are derived from a precursor polyprotein by host cell proteases. Entry studies are available only for a few viruses in the Order, and in each case they were shown to enter cells via receptor-mediated endocytosis. The acidic endosomal pH triggers the fusion of the viral envelope with the membrane of an endosome. Structural studies on two members of this Order, the phleboviruses and the hantaviruses, have shown that the membrane fusion protein Gc displays a class II fusion protein fold and is homologous to its counterparts in flaviviruses and alphaviruses, which are positive-sense, single-stranded RNA viruses. We analyze here recent data on the structure and function of the structure of the phlebovirus Gc and hantavirus Gn and Gc glycoproteins, and extrapolate common features identified in the amino acid sequences to understand also the structure and function of their counterparts in other families of the Bunyavirales Order. Our analysis also identified clear structural homology between the hantavirus Gn and alphavirus E2 glycoproteins, which make a heterodimer with the corresponding fusion proteins Gc and E1, respectively, revealing that not only the fusion protein has been conserved across viral families.
Published: 2017

45. Evolutionary history of tuberculosis shaped by conserved mutations in the PhoPR virulence regulator

Author: Charlotte Passemar, Alexandre Pawlik, Wladimir Malaga, Flavie Moreau, Mamadou Daffé, Carlos Martin, Roland Brosch, Christophe Guilhot, Catherine Astarie-Dequeker, Françoise Laval, Jesús Gonzalo-Asensio, University of Zaragoza - Universidad de Zaragoza [Zaragoza], Institut de pharmacologie et de biologie structurale (IPBS), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Pathogénomique mycobactérienne intégrée - Integrated Mycobacterial Pathogenomics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), This work was supported in part by the Juan de la Cierva Programme JCI-2009-03799 from the Spanish Ministry of Science and Innovation (to J.G.-A.), the Centre National de la Recherche Scientifique, the Fondation pour la Recherche Médicale ('Equipe FRM' DEQ20090515399 and DEQ20130326471), the European Union 7th Framework Programme (Contracts NEWTBVAC 241745, MM4TB 260872, and FEDER/POCTEFA/REFBIO EFA237/11), the Spanish Ministry of Economy and Competitiveness (Contracts BIO2011-23555 and FIS12/1970), and the Région Midi-Pyrénées (CPER 2007-2013) for the scientific project and for the ASB3 animal facility., We thank Dr. Geanncarlo Lugo-Villarino and Dr. Stephen V. Gordon for critical reading of the manuscript. We thank the members of the Genotoul platforms TRI and ANEXPLO (Institut de Pharmacologie et de Biologie Structurale) for epifluorescence microscopy imaging and for animal experiments, respectively, and Dr. Marie-Agnès Dillies and Dr. Jean-Yves Coppée from the Transcriptome Platform PF2 at the Institut Pasteur for advice., European Project: 241745,EC:FP7:HEALTH,FP7-HEALTH-2009-single-stage,NEWTBVAC(2010), European Project: 260872,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,MM4TB(2011), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: adaptation, MESH: Animals, MESH: Phylogeny, Conserved Sequence, Phylogeny, Genetics, Mycobacterium bovis, Multidisciplinary, Virulence, Genetic transfer, Biological Sciences, Biological Evolution, 3. Good health, MESH: Cattle, Host-Pathogen Interactions, MESH: Mycobacterium tuberculosis / genetics, MESH: Conserved Sequence / genetics, Locus (genetics), MESH: Mycobacterium tuberculosis / pathogenicity, Biology, Polymorphism, Single Nucleotide, MESH: Biological Evolution, Mycobacterium, Microbiology, Mycobacterium tuberculosis, Bacterial Proteins, evolution, MESH: Virulence / genetics, Animals, Humans, Tuberculosis, Secretion, MESH: Mycobacterium bovis / pathogenicity, MESH: Bacterial Proteins / metabolism, Alleles, Antigens, Bacterial, MESH: Humans, MESH: Alleles, MESH: Host-Pathogen Interactions, zoonosis, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: Mycobacterium / genetics, Mutagenesis, Insertional, Regulon, MESH: Mutagenesis, Insertional, MESH: Bacterial Proteins / genetics, MESH: Gene Deletion, MESH: Mutation / genetics, MESH: Mycobacterium bovis / genetics, Mutation, Cattle, MESH: Polymorphism, Single Nucleotide / genetics, MESH: Tuberculosis / microbiology, MESH: Tuberculosis / genetics, Mycobacterium africanum, MESH: Antigens, Bacterial, Gene Deletion
Abstract: International audience; Although the bovine tuberculosis (TB) agent, Mycobacterium bovis, may infect humans and cause disease, long-term epidemiological data indicate that humans represent a spill-over host in which infection with M. bovis is not self-maintaining. Indeed, human-to-human transmission of M. bovis strains and other members of the animal lineage of the tubercle bacilli is very rare. Here, we report on three mutations affecting the two-component virulence regulation system PhoP/PhoR (PhoPR) in M. bovis and in the closely linked Mycobacterium africanum lineage 6 (L6) that likely account for this discrepancy. Genetic transfer of these mutations into the human TB agent, Mycobacterium tuberculosis, resulted in down-regulation of the PhoP regulon, with loss of biologically active lipids, reduced secretion of the 6-kDa early antigenic target (ESAT-6), and lower virulence. Remarkably, the deleterious effects of the phoPR mutations were partly compensated by a deletion, specific to the animal-adapted and M. africanum L6 lineages, that restores ESAT-6 secretion by a PhoPR-independent mechanism. Similarly, we also observed that insertion of an IS6110 element upstream of the phoPR locus may completely revert the phoPR-bovis-associated fitness loss, which is the case for an exceptional M. bovis human outbreak strain from Spain. Our findings ultimately explain the long-term epidemiological data, suggesting that M. bovis and related phoPR-mutated strains pose a lower risk for progression to overt human TB, with major impact on the evolutionary history of TB.
Published: 2014

46. Mating systems and selection efficacy: a test using chloroplastic sequence data in Angiosperms

Author: Aline Muyle, Sylvain Glémin, Sexe et évolution, Département PEGASE [LBBE] (PEGASE), 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)-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), 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), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), 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), École pratique des hautes études (EPHE), and 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
Subjects: 0106 biological sciences, MESH: Mutation, Chloroplasts, MESH: Selection, Genetic, [SDV]Life Sciences [q-bio], Population, selection, deleterious mutations, MESH: Biological Evolution, Outcrossing, Biology, 010603 evolutionary biology, 01 natural sciences, dN/dS ratio, Magnoliopsida, 03 medical and health sciences, Negative selection, Data sequences, chloroplast, MESH: Computer Simulation, Reproduction, Asexual, selfing, Computer Simulation, Selection, Genetic, education, MESH: Reproduction, Asexual, Crosses, Genetic, Ecology, Evolution, Behavior and Systematics, Selection (genetic algorithm), 030304 developmental biology, Genetics, MESH: Magnoliopsida, [SDV.GEN]Life Sciences [q-bio]/Genetics, 0303 health sciences, education.field_of_study, MESH: Chloroplasts, Extinction, Selfing, Mating system, MESH: Crosses, Genetic, Biological Evolution, mating systems, Mutation
Abstract: International audience; Selfing is assumed to reduce selection efficacy, especially purifying selection. This can be tested using molecular data, for example by comparing the Dn/Ds ratio between selfing and outcrossing lineages. So far, little evidence of relaxed selection against weakly deleterious mutations (as inferred by a higher Dn/Ds ratio) in selfers as compared to outcrossers has been found, contrary to the pattern often observed between asexual and sexual lineages. However, few groups have been studied to date. To further test this hypothesis, we compiled and analysed chloroplastic sequence data sets in several plant groups. We found a general trend towards relaxed selection in selfers in our data sets but with weak statistical support. Simulations suggested that the results were compatible with weak-to-moderate Dn/Ds ratio differences in selfing lineages. Simple theoretical predictions also showed that the ability to detect relaxed selection in selfers could strongly depend on the distribution of the effects of deleterious mutations on fitness. Our results are compatible with a recent origin of selfing lineages whereby deleterious mutations potentially have a strong impact on population extinction or with a more ancient origin but without a marked effect of deleterious mutations on the extinction dynamics.
Published: 2014

47. MOLECULAR EVOLUTION OF GPCRS: Kisspeptin/kisspeptin receptors

Author: Jérémy Pasquier, Nédia Kamech, Karine Rousseau, Anne-Gaëlle Lafont, Hubert Vaudry, Sylvie Dufour, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), and Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)
Subjects: MESH: Signal Transduction, receptor, MESH: Amino Acid Sequence, MESH: Receptors, G-Protein-Coupled, Bioinformatics, Receptors, G-Protein-Coupled, MESH: Structure-Activity Relationship, 0302 clinical medicine, Endocrinology, Kisspeptin, Gene Duplication, Gene duplication, MESH: Animals, MESH: Genetic Variation, Neoplasm Metastasis, MESH: Evolution, Molecular, Conserved Sequence, Kisspeptins, 0303 health sciences, MESH: Conserved Sequence, MESH: Kisspeptins, biology, Phylogenetic tree, MESH: Gene Duplication, Vertebrate, MESH: Receptors, Kisspeptin-1, Biological Evolution, Signal Transduction, endocrine system, MESH: Biological Evolution, kisspeptin, Evolution, Molecular, Structure-Activity Relationship, 03 medical and health sciences, Molecular evolution, biology.animal, evolution, Animals, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, Molecular Biology, Gene, 030304 developmental biology, MESH: Humans, Genetic Variation, MESH: Neoplasm Metastasis, Evolutionary biology, vertebrates, human activities, 030217 neurology & neurosurgery, Function (biology), Receptors, Kisspeptin-1
Abstract: Following the discovery of kisspeptin (Kiss) and its receptor (GPR54 or KissR) in mammals, phylogenetic studies revealed up to three Kiss and four KissR paralogous genes in other vertebrates. The multiplicity of Kiss and KissR types in vertebrates probably originated from the two rounds of whole-genome duplication (1R and 2R) that occurred in early vertebrates. This review examines compelling recent advances on molecular diversity and phylogenetic evolution of vertebrate Kiss and KissR. It also addresses, from an evolutionary point of view, the issues of the structure–activity relationships and interaction of Kiss with KissR and of their signaling pathways. Independent gene losses, during vertebrate evolution, have shaped the repertoire ofKissandKissRin the extant vertebrate species. In particular, there is no conserved combination of a givenKisstype with aKissRtype, across vertebrate evolution. The striking conservation of the biologically active ten-amino-acid C-terminal sequence of all vertebrate kisspeptins, probably allowed this evolutionary flexibility of Kiss/KissR pairs. KissR mutations, responsible for hypogonadotropic hypogonadism in humans, mostly occurred at highly conserved amino acid positions among vertebrate KissR. This further highlights the key role of these amino acids in KissR function. In contrast, less conserved KissR regions, notably in the intracellular C-terminal domain, may account for differential intracellular signaling pathways between vertebrate KissR. Cross talk between evolutionary and biomedical studies should contribute to further understanding of the Kiss/KissR structure–activity relationships and biological functions.
Published: 2014

48. Halorhabdus tiamatea: proteogenomics and glycosidase activity measurements identify the first cultivated euryarchaeon from a deep-sea anoxic brine lake as potential polysaccharide degrader

Author: Manuel Ferrer, Alexander J. Mann, Hanno Teeling, Tran Hai, Peter N. Golyshin, Marco Taborda, Johannes Werner, Frank Oliver Glöckner, Silvia Juárez, Olga V. Golyshina, Violetta La Cono, Milton S. da Costa, Gurvan Michel, Sergio Ciordia, André Antunes, Sixing Huang, María Alcaide, Michail M. Yakimov, Juan Pablo Albar, Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Association pour la Formation Professionnelle des Adultes (AFPA), Association pour la Formation Professionnelle des Adultes, Princeton University, Biogéochimie et écologie des milieux continentaux (Bioemco), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Proteomics facility, Centro Nacional de Biotecnología, Insitute for Coastal Marine Environment, Consiglio Nazionale delle Ricerche (CNR), Centro Interdisciplinar de Investigação Marinha e Ambiental (CIMAR/CIIMAR), Universidade do Porto, Departamento de Biologia, Institute for Biotechnology and Bioengineering (IBB), Technical University of Lisbon, Universidade de Coimbra [Coimbra], State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences [Beijing], Sino-French Laboratory LABIOCEM, Jacobs University [Bremen], Microbial genomics and bioinformatics research group, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, School of Biological Sciences [Bangor], Bangor University, European Commission, Ministerio de Economía y Competitividad (España), Max Planck Society, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Centro Nacional de Biotecnología [Madrid] (CNB-CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Universidade do Porto = University of Porto, Universidade do Minho, Consejo Superior de Investigaciones Científicas [Spain] (CSIC), and Universidade do Porto [Porto]
Subjects: MESH: Genome, Archaeal, [SDV]Life Sciences [q-bio], MESH: Indian Ocean, Sodium Chloride, Genome, Archaeal, Utah, Glycoside hydrolase, MESH: Ecosystem, Anaerobiosis, MESH: Phylogeny, Indian Ocean, extremophiles, Research Articles, Phylogeny, 0303 health sciences, Halobacteriaceae, biology, Ecology, Salt Tolerance, Anoxic waters, Adaptation, Physiological, Biological Evolution, Halorhabdus, Proteome, MESH: Lakes, MESH: Metagenomics, Water Microbiology, MESH: Oxygen, MESH: Sodium Chloride, Glycoside Hydrolases, MESH: Biological Evolution, Microbiology, 03 medical and health sciences, MESH: Halobacteriaceae, Phylogenetics, MESH: Enzyme Assays, Polysaccharides, Botany, MESH: Anaerobiosis, MESH: Glycoside Hydrolases, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, Ecosystem, 030304 developmental biology, Enzyme Assays, Science & Technology, MESH: Salt-Tolerance, 030306 microbiology, Thermophile, MESH: Utah, deep sea brine, biology.organism_classification, MESH: Adaptation, Physiological, MESH: Water Microbiology, Oxygen, Lakes, MESH: Polysaccharides, euryarchaeon, 13. Climate action, Metagenomics, Archaea
Abstract: Summary: Euryarchaea from the genus Halorhabdus have been found in hypersaline habitats worldwide, yet are represented by only two isolates: Halorhabdus utahensisAX-2T from the shallow Great Salt Lake of Utah, and Halorhabdus tiamateaSARL4BT from the Shaban deep-sea hypersaline anoxic lake (DHAL) in the Red Sea. We sequenced the H.tiamatea genome to elucidate its niche adaptations. Among sequenced archaea, H.tiamatea features the highest number of glycoside hydrolases, the majority of which were expressed in proteome experiments. Annotations and glycosidase activity measurements suggested an adaptation towards recalcitrant algal and plant-derived hemicelluloses. Glycosidase activities were higher at 2% than at 0% or 5% oxygen, supporting a preference for low-oxygen conditions. Likewise, proteomics indicated quinone-mediated electron transport at 2% oxygen, but a notable stress response at 5% oxygen. Halorhabdus tiamatea furthermore encodes proteins characteristic for thermophiles and light-dependent enzymes (e.g. bacteriorhodopsin), suggesting that H.tiamatea evolution was mostly not governed by a cold, dark, anoxic deep-sea habitat. Using enrichment and metagenomics, we could demonstrate presence of similar glycoside hydrolase-rich Halorhabdus members in the Mediterranean DHAL Medee, which supports that Halorhabdus species can occupy a distinct niche as polysaccharide degraders in hypersaline environments., This study was supported by the EU FP7 project MAMBA (‘Marine Metagenomics for New Biotechnological Applications’, FP7‐KBBE‐2008–226977, the Spanish Ministry of Economy and Competitiveness (grant BIO2011–25012) and the Max Planck Society. H.T., O.V.G. and P.N.G. acknowledge the support of EU FP7 for the project MicroB3 (OCEAN‐2011‐287589).
Published: 2014

49. An evolutionary conserved interaction between the Gcm transcription factor and the SF1 nuclear receptor in the female reproductive system

Author: Angela Giangrande, Wael Bazzi, Claude Delaporte, Pierre B. Cattenoz, 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), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), and Cattenoz, Pierre
Subjects: 0301 basic medicine, Receptors, Steroid, Exocrine gland, Regulator, Female reproductive system, [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Mice, 0302 clinical medicine, Drosophila Proteins, MESH: Animals, Reproductive system, ComputingMilieux_MISCELLANEOUS, Genetics, 030219 obstetrics & reproductive medicine, Multidisciplinary, MESH: Infertility, Female, [SDV.BDD.EO] Life Sciences [q-bio]/Development Biology/Embryology and Organogenesis, Cell Differentiation, Genitalia, Female, MESH: Transcription Factors, Biological Evolution, DNA-Binding Proteins, Drosophila melanogaster, medicine.anatomical_structure, Female, RNA Splicing Factors, Infertility, Female, Protein Binding, Infertility, MESH: Cell Differentiation, endocrine system, MESH: Drosophila Proteins, MESH: Biological Evolution, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Article, MESH: Drosophila melanogaster, 03 medical and health sciences, Spermatheca, medicine, Animals, MESH: Protein Binding, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, Transcription factor, MESH: Mice, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, medicine.disease, MESH: RNA Splicing Factors, 030104 developmental biology, [SDV.BDD.EO]Life Sciences [q-bio]/Development Biology/Embryology and Organogenesis, Nuclear receptor, MESH: Genitalia, Female, MESH: Female, MESH: DNA-Binding Proteins, Transcription Factors, MESH: Receptors, Steroid
Abstract: NR5A1 is essential for the development and for the function of steroid producing glands of the reproductive system. Moreover, its misregulation is associated with endometriosis, which is the first cause of infertility in women. Hr39, the Drosophila ortholog of NR5A1, is expressed and required in the secretory cells of the spermatheca, the female exocrine gland that ensures fertility by secreting substances that attract and capacitate the spermatozoids. We here identify a direct regulator of Hr39 in the spermatheca: the Gcm transcription factor. Furthermore, lack of Gcm prevents the production of the secretory cells and leads to female sterility in Drosophila. Hr39 regulation by Gcm seems conserved in mammals and involves the modification of the DNA methylation profile of mNr5a1. This study identifies a new molecular pathway in female reproductive system development and suggests a role for hGCM in the progression of reproductive tract diseases in humans.
Published: 2016

50. The phenetic structure of Aedes albopictus

Author: Takashi Tsunoda, Ronald Enrique Morales Vargas, Noppawan Phumala-Morales, Jean-Pierre Dujardin, Chamnan Apiwathnasorn, Mahidol University [Bangkok], Institut National d'Hygiène et d'Épidémiologie de Hanoi (NIHE), Réseau International des Instituts Pasteur (RIIP), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), This research was funded by the PHC-SIAM Grant No. 25646ZL, as well as by IRD Grant Nos. HC3165-3R165-GABI-ENT2 and HC3165-3R165-NV00-THA1., and Collections of specimens in Kanchanaburi (Thailand) were greatly helped by Dr. Jinrapa Phothikasikorn (Mahidol University, Fac. of Sciences). Dr. Sungsit Sungvornyothin and Ms. Thipruethai Phanitchat contributed to the collection of Ae. albopictus in the South of Thailand. Insects from Kyoto (Japan) and Fukuoka (Japan) were obtained thanks to Dr. Jorge Jose Garcia Polo (Kyoto University) and Dr. Tomomitsu Satho (Fukuoka University, Fac. of Pharmaceutical Sciences). We thank Dr. Sébastien Boyer (MIVEGEC, IRD) and Jean-Sébastien Dehecq (ARS, La Réunion) for their invaluable help during the Reunion Island collections. We are indebted to Didier Fontenille (MIVEGEC, IRD) for his critical reading of the manuscript.
Subjects: MESH: Aedes / genetics, MESH: Geography, Climate, MESH: Insect Vectors / genetics, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 0302 clinical medicine, Japan, Aedes, Ae. riversi, Body Size, Cluster Analysis, Wings, Animal, MESH: Animals, MESH: Wings, Animal / anatomy & histology, Phenetics, MESH: Japan, 0303 health sciences, Geography, Ecology, Thailand, Aedes albopictus, MESH: Climate, Biological Evolution, Infectious Diseases, Vietnam, MESH: Hawaii, Florida, Microbiology (medical), MESH: Aedes / anatomy & histology, Quantitative Trait Loci, 030231 tropical medicine, MESH: Biological Evolution, Biology, Southeast asian, Microbiology, Hawaii, 03 medical and health sciences, Genetic drift, Genetics, Animals, MESH: Thailand, Molecular Biology, Ae. flavopictus, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Morphometrics, Geometric morphometrics, MESH: Body Size, MESH: Aedes / classification, MESH: Insect Vectors / anatomy & histology, Interspecific competition, biology.organism_classification, MESH: Cluster Analysis, MESH: Quantitative Trait Loci, Insect Vectors, MESH: Florida, Vector (epidemiology), Chikungunya, MESH: Vietnam, Founder effect
Abstract: International audience; The large and recent migrations of the main vector of the Chikungunya virus, Aedes albopictus, raise questions about the epidemiological impact of possible microevolutionary changes in new territories. Quantitative traits are suitable to detect such changes as induced by environmental adaptations, local competition and founder effects. Using landmark-based geometric morphometrics, we compared the size and shape of 22 populations (1572 females) of Ae. albopictus. The collection sites covered five countries around the world, with special emphasis on Asia, which is assumed to be the origin of the vector. Some collections came from places where an important epidemic outbreak of Chikungunya has recently occurred.Quantitative comparisons were based on 18 anatomical landmarks on the wing. To contrast geographic and possible interspecific shape variation, close species were introduced in the sample, namely five Aedes riversi and nine Ae. flavopictus from Japan. The three species had similar size, but they were clearly separated by shape.Within Ae. albopictus, there was general agreement on size variation with the available climatic data. Shape variation was less related to climatic data than to either geography or a known itinerary of past territorial expansion. Thus, two main clusters were distinguished by wing shape variation: the first one composed of the Southeast Asian sample, the second one grouping Japan, Florida, Hawaii and the Reunion Island samples.The Southeast Asian countries, assumed to be at the origin of the geographic expansion of the mosquito, had similar wings and constituted a distinct group where localities clustered into northern and southern localities. Contrasting with this homogeneous group, very distant localities such as United States (US) and Japan shared a common shape pattern. The US Ae. albopictus samples (Hawaii and Florida) were indeed very similar to the Japanese samples, with Florida behaving exactly like a northern Japanese locality, close to Tokyo and Yokohama. Shape proximity among these distant areas could be explained by a common and relatively recent ancestor, as generally suggested in the literature. The three Reunion Island samples conformed a group external to the Southeast Asian countries, loosely connected to the remaining localities.Thus, areas where recent epidemics took place, the Reunion Island and the southernmost localities of Thailand, did not cluster together, but represented separate groups.In sum, the size of the wing was apparently under the influence of climatic factors, while its shape could contribute information on species and geographic differences. Apparent departures from expectations based on geography were explained by known past and present migratory routes. These patterns of shape variation were compatible with genetic drift, suggesting microevolutionary changes probably induced by the expansion of the Ae. albopictus mosquito.
Published: 2013

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