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1. Population Genome Sequencing of the Scab Fungal Species Venturia inaequalis, Venturia pirina, Venturia aucupariae and Venturia asperata

Author

Bruno Le Cam, Dan Sargent, Jérôme Gouzy, Joëlle Amselem, Marie-Noëlle Bellanger, Olivier Bouchez, Spencer Brown, Valérie Caffier, Marie De Gracia, Robert Debuchy, Ludovic Duvaux, Thibaut Payen, Mélanie Sannier, Jason Shiller, Jérôme Collemare, and Christophe Lemaire

Subjects
Venturia, Fusicladium, formae specialis, transposable elements, effectors, apple scab, apple, pear, Genetics, QH426-470
Abstract

The Venturia genus comprises fungal species that are pathogens on Rosaceae host plants, including V. inaequalis and V. asperata on apple, V. aucupariae on sorbus and V. pirina on pear. Although the genetic structure of V. inaequalis populations has been investigated in detail, genomic features underlying these subdivisions remain poorly understood. Here, we report whole genome sequencing of 87 Venturia strains that represent each species and each population within V. inaequalis. We present a PacBio genome assembly for the V. inaequalis EU-B04 reference isolate. The size of selected genomes was determined by flow cytometry, and varied from 45 to 93 Mb. Genome assemblies of V. inaequalis and V. aucupariae contain a high content of transposable elements (TEs), most of which belong to the Gypsy or Copia LTR superfamilies and have been inactivated by Repeat-Induced Point mutations. The reference assembly of V. inaequalis presents a mosaic structure of GC-equilibrated regions that mainly contain predicted genes and AT-rich regions, mainly composed of TEs. Six pairs of strains were identified as clones. Single-Nucleotide Polymorphism (SNP) analysis between these clones revealed a high number of SNPs that are mostly located in AT-rich regions due to misalignments and allowed determining a false discovery rate. The availability of these genome sequences is expected to stimulate genetics and population genomics research of Venturia pathogens. Especially, it will help understanding the evolutionary history of Venturia species that are pathogenic on different hosts, a history that has probably been substantially influenced by TEs.

Published
2019
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2. Draft Genome Sequence of the Environmental Fungus Scedosporium dehoogii

Author

Amandine Gastebois, Jean-Philippe Bouchara, Christophe Lemaire, Amandine Rougeron, Jason Shiller, Bruno Le Cam, Thomas Dugé de Bernonville, Ludovic Duvaux, Patrick Vandeputte, Sandrine Giraud, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Groupe d'Étude des Interactions Hôte-Pathogène (GEIHP), Université d'Angers (UA), SFR UA 4208 Interactions Cellulaires et Applications Thérapeutiques (ICAT), Université de Tours (UT), Laboratoire de Parasitologie-Mycologie (CHU d'Angers), Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM)-PRES Université Nantes Angers Le Mans (UNAM), University of Angers (France), and Université de Tours

Subjects
Whole genome sequencing, 0303 health sciences, Genome, biology, 030306 microbiology, Veterinary (miscellaneous), Scedosporium boydii, Scedosporium apiospermum, Fungus, Environment, biology.organism_classification, Applied Microbiology and Biotechnology, Microbiology, Scedosporium dehoogii, 03 medical and health sciences, Scedosporium aurantiacum, Fungi, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Scedosporium minutisporum, Agronomy and Crop Science, 030304 developmental biology
Abstract

International audience; Today, the genus Scedosporium comprises at least ten species with four of them, Scedosporium apiospermum, Scedosporium boydii, Scedosporium aurantiacum and Scedosporium minutisporum capable of colonizing the lungs of patients with cystic fibrosis. Scedosporium dehoogii, which is also common in the soil, has never been reported as causing human pulmonary infections. Here we report the first genome sequence for S. dehoogii, an invaluable resource to understand the genetic bases of pathogenesis in the genus Scedosporium.

Published
2021
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3. Draft Genome Sequence of the Environmental Fungus Scedosporium dehoogii

Author

Jason, Shiller, Ludovic, Duvaux, Patrick, Vandeputte, Christophe, Lemaire, Amandine, Rougeron, Thomas Dugé, De Bernonville, Sandrine, Giraud, Bruno, Le Cam, Jean-Philippe, Bouchara, and Amandine, Gastebois

Subjects
Genome, Humans, Scedosporium
Abstract

Today, the genus Scedosporium comprises at least ten species with four of them, Scedosporium apiospermum, Scedosporium boydii, Scedosporium aurantiacum and Scedosporium minutisporum capable of colonizing the lungs of patients with cystic fibrosis. Scedosporium dehoogii, which is also common in the soil, has never been reported as causing human pulmonary infections. Here we report the first genome sequence for S. dehoogii, an invaluable resource to understand the genetic bases of pathogenesis in the genus Scedosporium.

Published
2021

4. Asian wild apples threatened by gene flow from domesticated apples and by their pestified pathogen

Author

M. De Gracia Coquerel, E. Guitton, B. Le Cam, Jason Shiller, Marie-Noëlle Bellanger, Valérie Caffier, Mélanie Sannier, A. Feurtey, Christophe Lemaire, Ludovic Duvaux, Tatiana Giraud, Pascale Expert, Ecologie Systématique et Evolution (ESE), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Noble Research Institut

Subjects
0106 biological sciences, Population, Introgression, Zoology, Population genetics, Biology, 010603 evolutionary biology, 01 natural sciences, Gene flow, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, education, Domestication, Hybridization, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, education.field_of_study, Venturia inaequalis, Apple, Venturia, 15. Life on land, biology.organism_classification, Center of origin, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Malus, Biological dispersal, Crop-to-wild gene flow, Secondary contact, Avirulence gene
Abstract

Massive gene flow between crops and their wild relatives may threaten the genetic integrity of wild species. Such threats are now well documented, but little is known about indirect consequences involving the spillover of crop pathogens to wild plants or introgression between crop and wild pathogens. To address these questions, we used population genetics approaches, demographic inference and pathogenicity tests on host-pathogen pairs composed of wild or domesticated apple trees of Central Asia and their fungal pathogen, Venturia inaequalis, itself showing differentiated agricultural-type and wild-type populations. We confirmed the occurrence of gene flow from cultivated to wild apple trees in Asian forests, threatening the Asian wild apple genetic integrity. SNP markers and demographic modeling revealed the occurrence of a secondary contact followed by hybridization between agricultural-type and wild-type fungal pathogen populations, and the dispersal of the agricultural-type pathogen in wild forests. We detected a SNP predicting the ability of the fungus to parasitize the different host populations, which induced an early stop codon in a gene coding for a small secreted protein in the agricultural-type fungal population, thus representing a putative avirulence gene which function loss would enable to parasitize cultivated apples. Pathogenicity tests in fact revealed the pestification of V. inaequalis, with higher virulence of the agricultural-type population on both wild and domesticated trees. Our findings highlight the threat posed by cultivating a crop near its center of origin, with the invasion of a pestified pathogen on wild plants and introgression in the wild-type pathogen.

Published
2020

5. Developing collaborative works for faster progress on fungal respiratory infections in cystic fibrosis

Author

Gilles Nevez, Joerg Steinmann, Laurence Delhaes, Ludovic Duvaux, Jean-Philippe Bouchara, Wieland Meyer, Ludwig Sedlacek, Maxime Fleury, Nicolas Papon, Loïc Favennec, Patrick Vandeputte, Javier Pemán, Amandine Gastebois, Françoise Botterel, Jose A. Vazquez, Stéphane Ranque, Sharon C.-A. Chen, Ana Alastruey-Izquierdo, Solène Le Gal, Craig Williams, Marie-Elisabeth Bougnoux, Carsten Schwarz, Françoise Symoens, Estrella Martin Mazuelos, Guillermo Quindós, Thomas Dugé de Bernonville, Josep Cano, Amparo Solé, Amandine Rougeron, Sandrine Giraud, María Teresa Martín-Gómez, Groupe d'Étude des Interactions Hôte-Pathogène (GEIHP), Université d'Angers (UA), Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), University of Sheffield [Sheffield], Facultat de Medicina i Ciències de la Salut, Universitat Rovira i Virgili, Anofel Cryptosporidium National Network, Laboratoire de Parasitologie-Mycologie, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Service de Microbiologie, Université Paris Descartes - Paris 5 (UPD5)-CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Service de Parasitologie et de Mycologie [Lille], Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Centre de recherche Cardio-Thoracique de Bordeaux [Bordeaux] (CRCTB), Université Bordeaux Segalen - Bordeaux 2-CHU Bordeaux [Bordeaux]-Institut National de la Santé et de la Recherche Médicale (INSERM), Appareil Digestif Environnement Nutrition (ADEN ), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Augusta University, University System of Georgia (USG), The Westmead Institute for Medical Research, Centre for Infectious Disease and Microbiology (CIDM), Hôpital de la Cavale Blanche - CHRU Brest (CHU - BREST ), APP1031943, National Health and Medical Research Council, 2010/IC1003, Vaincre la Mucoviscidose, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Groupe d'Etude des Interactions Hôte-Parasite (GEIHP), Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte - Clermont Auvergne (M2iSH), Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), Groupe d’Etude des Interactions Hôte-Pathogène, Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), and Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne)-Institut National de la Recherche Agronomique (INRA)

Subjects
Microbiological Techniques, 0301 basic medicine, medicine.medical_specialty, Antifungal Agents, Cystic Fibrosis, biological diagnosis, 030106 microbiology, Medizin, Context (language use), Disease, Drug resistance, Cystic fibrosis, pathogenic mechanisms, cystic fibrosis, Scedosporium, 03 medical and health sciences, fungal respiratory infections, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Drug Resistance, Multiple, Fungal, medicine, Humans, Microbiome, Intensive care medicine, Respiratory Tract Infections, Genotyping, treatment, business.industry, Fungi, Genomics, General Medicine, medicine.disease, 3. Good health, Infectious Diseases, Mycoses, Scedosporium species, Identification (biology), business
Abstract

International audience; Cystic fibrosis (CF) is the major genetic inherited disease in Caucasian populations. The respiratory tract of CF patients displays a sticky viscous mucus, which allows for the entrapment of airborne bacteria and fungal spores and provides a suitable environment for growth of microorganisms, including numerous yeast and filamentous fungal species. As a consequence, respiratory infections are the major cause of morbidity and mortality in this clinical context. Although bacteria remain the most common agents of these infections, fungal respiratory infections have emerged as an important cause of disease. Therefore, the International Society for Human and Animal Mycology (ISHAM) has launched a working group on Fungal respiratory infections in Cystic Fibrosis (Fri-CF) in October 2006, which was subsequently approved by the European Confederation of Medical Mycology (ECMM). Meetings of this working group, comprising both clinicians and mycologists involved in the follow-up of CF patients, as well as basic scientists interested in the fungal species involved, provided the opportunity to initiate collaborative works aimed to improve our knowledge on these infections to assist clinicians in patient management. The current review highlights the outcomes of some of these collaborative works in clinical surveillance, pathogenesis and treatment, giving special emphasis to standardization of culture procedures, improvement of species identification methods including the development of nonculture-based diagnostic methods, microbiome studies and identification of new biological markers, and the description of genotyping studies aiming to differentiate transient carriage and chronic colonization of the airways. The review also reports on the breakthrough in sequencing the genomes of the main Scedosporium species as basis for a better understanding of the pathogenic mechanisms of these fungi, and discusses treatment options of infections caused by multidrug resistant microorganisms, such as Scedosporium and Lomentospora species and members of the Rasamsonia argillacea species complex.

Published
2018
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6. Threat to Asian wild apple trees posed by gene flow from domesticated apple trees and their 'pestified' pathogens

Author

Alice Feurtey, Bruno Le Cam, Marie-Noëlle Bellanger, Christophe Lemaire, Ludovic Duvaux, Mélanie Sannier, Valérie Caffier, Marie De Gracia Coquerel, Pascale Expert, Tatiana Giraud, Jason Shiller, Ellen Guitton, Ecologie Systématique et Evolution (ESE), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Noble Research Institut, The INRAE-SPE Department (Escapades project), a Louis D. grant (Institut de France) to TG, a PhD grant from the Région Ile-de-France to AF, the 'Objectif Végétal, Research, Education and Innovation in Pays de la Loire' program supported by the French Region Pays de la Loire, Angers Loire Métropole, and and the European Regional Development Fund (Escapes project).

Subjects
0106 biological sciences, 0301 basic medicine, apple, crop-to-wild gene flow, hybridization, Malus, secondary contact, avirulence gene, Venturia, Gene Flow, Malus, [SDV]Life Sciences [q-bio], Population, Zoology, Introgression, apple, 010603 evolutionary biology, 01 natural sciences, Gene flow, 03 medical and health sciences, crop-to-wild gene flow, Genetics, secondary contact, education, hybridization, Ecology, Evolution, Behavior and Systematics, Plant Diseases, 2. Zero hunger, education.field_of_study, biology, Venturia inaequalis, Venturia, biology.organism_classification, Center of origin, Fungal Genus Venturia, 030104 developmental biology, Malus sieversii, Genetics, Population, avirulence gene, Biological dispersal
Abstract

Secondary contact between crops and their wild relatives poses a threat to wild species, not only through gene flow between plants, but also through the dispersal of crop pathogens and genetic exchanges involving these pathogens, particularly those that have become more virulent by indirect selection on resistant crops, a phenomenon known as “pestification”. Joint analyses of wild and domesticated hosts and their pathogens are essential to address this issue, but such analyses remain rare. We used population genetics approaches, demographic inference and pathogenicity tests on host-pathogen pairs of wild or domesticated apple trees from Central Asia and their main fungal pathogen, Venturia inaequalis, which itself has differentiated agricultural and wild-type populations. We confirmed the occurrence of gene flow from cultivated (Malus domestica) to wild (Malus sieversii) apple trees in Asian forests, potentially threatening the persistence of Asian wild apple trees. Pathogenicity tests demonstrated the pestification of V. inaequalis, the agricultural-type population being more virulent on both wild and domesticated trees. SNP markers and the demographic modeling of pathogen populations revealed hybridization following secondary contact between agricultural and wild-type fungal populations, and dispersal of the agricultural-type pathogen population in wild forests, increasing the threat of disease in the wild apple species. We detected a SNP potentially involved in pathogen pestification, generating an early stop codon in a gene encoding a small secreted protein in the agricultural-type fungal population. Our findings, based on joint analyses of paired host and pathogen datasets, highlight the threat posed by cultivating a crop near its center of origin, in terms of pestified pathogen invasions in wild plant populations and introgression in the wild-type pathogen population.

Published
2019
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7. Towards reproducible research: Evolve your practices

Author

Loic Desquilbet, Sabrina Granger, Boris Hejblum, Arnaud Legrand, Pascal Pernot, Rougier, Nicolas P., Elisa de Castro Guerra, Martine Courbin-Coulaud, Ludovic Duvaux, Pierre Gravier, Grégoire Le Campion, Solenne Roux, Frédéric Santos, École nationale vétérinaire d'Alfort (ENVA), Université de Bordeaux (UB), Statistics In System biology and Translational Medicine (SISTM), Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Epidémiologie et Biostatistique [Bordeaux], Université Bordeaux Segalen - Bordeaux 2-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Bordeaux Segalen - Bordeaux 2-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM), Performance analysis and optimization of LARge Infrastructures and Systems (POLARIS), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'Informatique de Grenoble (LIG), Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut National Polytechnique de Grenoble (INPG)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut National Polytechnique de Grenoble (INPG)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Laboratoire de Chimie Physique D'Orsay (LCPO), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Mnemonic Synergy (Mnemosyne), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut des Maladies Neurodégénératives [Bordeaux] (IMN), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), FLOSS Manuals (FM), Information et Édition Scientifiques (IES), Inria Siège, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Passages, Centre National de la Recherche Scientifique (CNRS)-Université Bordeaux Montaigne-Université de Pau et des Pays de l'Adour (UPPA)-Ministère de la Culture et de la Communication (MCC)-Université de Bordeaux (UB), Laboratoire de psychologie:Santé et qualité de vie, Université Bordeaux Segalen - Bordeaux 2, De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Unité régionale de formation à l'information scientifique et technique de Bordeaux, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)- Bordeaux population health (BPH), Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM), Performance analysis and optimization of LARge Infrastructures and Systems (POLARIS ), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'Informatique de Grenoble (LIG ), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Université Paris-Sud - Paris 11 (UP11)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Inria Bordeaux - Sud-Ouest, Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB)-Ministère de la Culture et de la Communication (MCC)-Université de Pau et des Pays de l'Adour (UPPA)-Université Bordeaux Montaigne-Centre National de la Recherche Scientifique (CNRS), École nationale vétérinaire - Alfort (ENVA), Institut de Chimie Physique (ICP), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest, Direction de la Culture et de l’Information Scientifiques (DCIS), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Inria Siège, and Université de Bordeaux (UB)-Ministère de la Culture et de la Communication (MCC)-Université de Pau et des Pays de l'Adour (UPPA)-Université Bordeaux Montaigne (UBM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Réutilisation des données, Crise de la réplication, Open data, [INFO.INFO-GL]Computer Science [cs]/General Literature [cs.GL], Transparence de la recherche, Open source, Replication crisis, Reproducible research, Recherche reproductible, Standardization, Data reusability, Science ouverte, Research transparency, Data sharing, [INFO]Computer Science [cs], Book sprint, Open science, Standardisation
Abstract

International audience; For a researcher, there is nothing more frustrating than the failure to reproduce major results obtained a few months back. The causes of such disappointments can be multiple and insidious. This phenomenon plays an important role in the so-called “research reproducibility crisis”.This book takes a current perspective onto a number of potentially dangerous situations and practices, to examplify and highlight the symptoms of non-reproducibility in research. Each time, it provides efficient solutions ranging from good-practices that are easily and immediately implementable to more technical tools, all of which are free and have been put to the test by the authors themselves.With this book written during a book sprint, students and engineers and researchers should find efficient and accessible ways leading them to improve their reproducible research practices.; Pour un chercheur, il n’y a rien de plus frustrant que l’impossibilité de reproduire des résultats majeurs obtenus quelques mois auparavant. Les causes de ce type de déconvenues sont multiples et parfois pernicieuses. Ce phénomène participe à ce que certains identifient comme une “crise de la reproductibilité de la recherche”.Cet ouvrage considère un ensemble de situations et de pratiques potentiellement dangereuses afin d’illustrer et de mettre en évidence les symptômes de la non-reproductibilité dans la recherche. À chaque fois, il propose un éventail de solutions allant de bonnes pratiques faciles et rapides à implémenter jusqu’à des outils plus techniques, tous gratuits et mis à l’épreuve par les auteurs eux-mêmes.Dans ce livre rédigé lors d’un book sprint, étudiants, ingénieurs et chercheurs devraient trouver des moyens efficaces et à leur portée pour améliorer leurs pratiques de la recherche reproductible.

Published
2019

8. Importance of incomplete lineage sorting and introgression in the origin of shared genetic variation between two closely related pines with overlapping distributions

Author

Yongfeng Zhou, Zhang Lr, Ludovic Duvaux, Jianquan Liu, Outi Savolainen, Guangpeng Ren, Department of Animal and Plant Sciences [Sheffield], and University of Sheffield [Sheffield]

Subjects
Gene Flow, 0106 biological sciences, 0301 basic medicine, China, DNA, Plant, Genetic Speciation, Population, Allopatric speciation, Population genetics, Introgression, Parapatric speciation, Biology, 010603 evolutionary biology, 01 natural sciences, Coalescent theory, 03 medical and health sciences, Human population genetics, Genetics, education, ComputingMilieux_MISCELLANEOUS, Genetics (clinical), education.field_of_study, Models, Genetic, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Genetic Variation, Bayes Theorem, Sequence Analysis, DNA, 15. Life on land, Pinus, Introns, Genetics, Population, 030104 developmental biology, Evolutionary biology, Original Article
Abstract

Genetic variation shared between closely related species may be due to retention of ancestral polymorphisms because of incomplete lineage sorting (ILS) and/or introgression following secondary contact. It is challenging to distinguish ILS and introgression because they generate similar patterns of shared genetic diversity, but this is nonetheless essential for inferring accurately the history of species with overlapping distributions. To address this issue, we sequenced 33 independent intron loci across the genome of two closely related pine species (Pinus massoniana Lamb. and Pinus hwangshanensis Hisa) from Southeast China. Population structure analyses revealed that the species showed slightly more admixture in parapatric populations than in allopatric populations. Levels of interspecific differentiation were lower in parapatry than in allopatry. Approximate Bayesian computation suggested that the most likely speciation scenario explaining this pattern was a long period of isolation followed by a secondary contact. Ecological niche modeling suggested that a gradual range expansion of P. hwangshanensis during the Pleistocene climatic oscillations could have been the cause of the overlap. Our study therefore suggests that secondary introgression, rather than ILS, explains most of the shared nuclear genomic variation between these two species and demonstrates the complementarity of population genetics and ecological niche modeling in understanding gene flow history. Finally, we discuss the importance of contrasting results from markers with different dynamics of migration, namely nuclear, chloroplast and mitochondrial DNA.

Published
2016
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9. Population Genome Sequencing of the Scab Fungal Species Venturia inaequalis, Venturiapirina, Venturia aucupariae and Venturia asperata

Author

Mélanie Sannier, Jérôme Collemare, Robert Debuchy, Spencer Brown, Christophe Lemaire, Jérôme Gouzy, Bruno Le Cam, Bouchez Olivier, Jason Shiller, Marie Noëlle Bellanger, Daniel Sargent, Thibaut Payen, Ludovic Duvaux, Joelle Amselem, Marie De Gracia, Valérie Caffier, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Différenciation sexuée et méiose chez les champignons (DSMC), Département Biologie des Génomes (DBG), 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)-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), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Laboratory of Phytopathology, Wageningen University and Research [Wageningen] (WUR), Plant Healt Department of INRA (ESCAPADES Project), Agence Nationale pour la Recherche (Bioadapt ANR) : ANR-12-ADAP-0009, ANR-09-GENM-028, French Region Pays de la Loire (ROAD MOVIE project), French Region Pays de la Loire, Angers Loire Metropole, European Regional Development Fund, University of Angers, Plant health Department of INRA, Region Pays de La Loire, France Genomique National infrastructure : ANR-10-INBS-09, France-BioImaging : ANR-10-INBS-04-01, Labex 'Saclay Plant Science' : ANR-11-IDEX-0003-02, AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), GeT PlaGe, Genotoul, Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Université de Bordeaux (UB)-Institut National de la Recherche Agronomique (INRA), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), URA 0083, Wageningen University and Research Centre [Wageningen] (WUR), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Westerdijk Fungal Biodiversity Institute, Westerdijk Fungal Biodiversity Institute - Fungal Natural Products, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), and Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
0106 biological sciences, [SDV]Life Sciences [q-bio], Population, MRP, apple, Genomics, QH426-470, 01 natural sciences, Genome, Venturia, DNA sequencing, Population genomics, 03 medical and health sciences, Transposable, Genetics, education, Molecular Biology, Gene, Genetics (clinical), 030304 developmental biology, 2. Zero hunger, Whole genome sequencing, 0303 health sciences, education.field_of_study, biology, Fusicladium, Venturia inaequalis, pear, Elements, biology.organism_classification, formae specialis, Apple scab, apple scab, transposable elements, 010606 plant biology & botany, effectors
Abstract

TheVenturiagenus comprises fungal species that are pathogens onRosaceaehost plants, includingV. inaequalisandV. asperataon apple,V. aucupariaeon sorbus andV. pirinaon pear. Although the genetic structure ofV. inaequalispopulations has been investigated in detail, genomic features underlying these subdivisions remain poorly understood. Here, we report whole genome sequencing of 87Venturiastrains that represent each species and each population withinV. inaequalis. We present a PacBio genome assembly for theV. inaequalisEU-B04 reference isolate. The size of selected genomes was determined by flow cytometry, and varied from 45 to 93 Mb. Genome assemblies ofV. inaequalisandV. aucupariaecontain a high content of transposable elements (TEs), most of which belong to the Gypsy or Copia LTR superfamilies and have been inactivated by Repeat-Induced Point mutations. The reference assembly ofV. inaequalispresents a mosaic structure of GC-equilibrated regions that mainly contain predicted genes and AT-rich regions, mainly composed of TEs. Six pairs of strains were identified as clones. Single-Nucleotide Polymorphism (SNP) analysis between these clones revealed a high number of SNPs that are mostly located in AT-rich regions due to misalignments and allowed determining a false discovery rate. The availability of these genome sequences is expected to stimulate genetics and population genomics research ofVenturiapathogens. Especially, it will help understanding the evolutionary history ofVenturiaspecies that are pathogenic on different hosts, a history that has probably been substantially influenced by TEs.

Published
2019
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10. Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity

Author

Ludovic Duvaux, Aurélie Cohas, John J. Welch, Bernd Timmermann, Markus Ralser, Peer Bork, Christophe Lemaire, Falk Hildebrand, Achchuthan Shanmugasundram, Sophia Schade, Toni I. Gossmann, Coraline Bichet, Stefan T. Börno, Julian L. Griffin, Lee D. Roberts, Jakob Vowinckel, Aleksej Zelezniak, Dominique Allainé, Michael Mülleder, Sven Klages, Enrica Calvani, Heiner Kuhl, Johanna M. Gostner, Department of Animal and Plant Sciences, University of Sheffield [Sheffield], Universität Bielefeld = Bielefeld University, The Francis Crick Institute [London], University of Liverpool, Max Planck Institute for Molecular Genetics (MPIMG), Max-Planck-Gesellschaft, Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Department of Ecophysiology and Aquaculture, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Leibnitz-Leibnitz, University of Cambridge [UK] (CAM), University of Leeds, Leopold Franzens Universität Innsbruck - University of Innsbruck, European Molecular Biology Laboratory (EMBL), Earlham Institute, Norwich Research Park, Institute of Avian Research, Department of Biochemistry, Chalmers University of Technology [Gothenburg, Sweden], Max Delbrück Centre for Molecular Medicine, 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), Department of Genetics, AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), University of Innsbruck, Griffin, Julian [0000-0003-1336-7744], Welch, John [0000-0001-7049-7129], Ralser, Markus [0000-0001-9535-7413], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, Marmota marmota, low genetic diversity, NUMT, Climate, [SDV]Life Sciences [q-bio], Adaptation, Biological, climate adaptation, Marmot, large population size, migration, General Biochemistry, Genetics and Molecular Biology, Article, ice age, 03 medical and health sciences, 0302 clinical medicine, Genetic variation, Animals, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 14. Life underwater, 11 Medical and Health Sciences, Phylogeny, reference genome, Population Density, Genetic diversity, Genome, biology, Ecology, Alpine marmot, Genetic Variation, 06 Biological Sciences, 15. Life on land, biology.organism_classification, 17 Psychology and Cognitive Sciences, 030104 developmental biology, Habitat, Cardiovascular and Metabolic Diseases, 13. Climate action, Marmota, [SDE]Environmental Sciences, Conservation status, lipidomics, pleistocene, Adaptation, General Agricultural and Biological Sciences, Niche adaptation, human activities, 030217 neurology & neurosurgery, Developmental Biology
Abstract

Summary Some species responded successfully to prehistoric changes in climate [1, 2], while others failed to adapt and became extinct [3]. The factors that determine successful climate adaptation remain poorly understood. We constructed a reference genome and studied physiological adaptations in the Alpine marmot (Marmota marmota), a large ground-dwelling squirrel exquisitely adapted to the “ice-age” climate of the Pleistocene steppe [4, 5]. Since the disappearance of this habitat, the rodent persists in large numbers in the high-altitude Alpine meadow [6, 7]. Genome and metabolome showed evidence of adaptation consistent with cold climate, affecting white adipose tissue. Conversely, however, we found that the Alpine marmot has levels of genetic variation that are among the lowest for mammals, such that deleterious mutations are less effectively purged. Our data rule out typical explanations for low diversity, such as high levels of consanguineous mating, or a very recent bottleneck. Instead, ancient demographic reconstruction revealed that genetic diversity was lost during the climate shifts of the Pleistocene and has not recovered, despite the current high population size. We attribute this slow recovery to the marmot’s adaptive life history. The case of the Alpine marmot reveals a complicated relationship between climatic changes, genetic diversity, and conservation status. It shows that species of extremely low genetic diversity can be very successful and persist over thousands of years, but also that climate-adapted life history can trap a species in a persistent state of low genetic diversity., Highlights • The Alpine marmot is among the least genomically diverse animal species • Its diversity was lost during consecutive ice-age climate-related events • An extreme lifestyle hampered the subsequent recovery of genetic variation • Alpine marmots show why large populations can coexist with very low genetic variation, Despite being highly abundant and well adapted, Gossmann et al. report that the Alpine marmot is among the least genetically diverse animal species. The low diversity is found to be the consequence of consecutive, climate-related events, including long-term extreme niche adaptation, that also greatly retarded the recovery of its genetic diversity.

Published
2019
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11. The genetic structure ofNautilus pompiliuspopulations surrounding Australia and the Philippines

Author

Terry Burke, William Sinclair, Ludovic Duvaux, Benjamin C. Jackson, Deborah A. Dawson, Rachel C. Williams, Department of Animal and Plant Sciences [Sheffield], and University of Sheffield [Sheffield]

Subjects
Gene Flow, Marine conservation, Conservation of Natural Resources, Genotype, Philippines, Molecular Sequence Data, Biology, Effective population size, Genetic drift, Genetics, Animals, 14. Life underwater, Nautilus, Reef, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, Population Density, Genetic diversity, geography, Extinction, geography.geographical_feature_category, Models, Genetic, Coral Reefs, Ecology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Genetic Drift, Australia, Bayes Theorem, biology.organism_classification, Genetics, Population, Genetic structure, Microsatellite Repeats
Abstract

Understanding the distribution of genetic diversity in exploited species is fundamental to successful conservation. Genetic structure and the degree of gene flow among populations must be assessed to design appropriate strategies to prevent the loss of distinct populations. The cephalopod Nautilus pompilius is fished unsustainably in the Philippines for the ornamental shell trade and has limited legislative protection, despite the species' recent dramatic decline in the region. Here, we use 14 microsatellite markers to evaluate the population structure of N. pompilius around Australia and the Philippines. Despite their relative geographical proximity, Great Barrier Reef individuals are genetically isolated from Osprey Reef and Shark Reef in the Coral Sea (FST = 0.312, 0.229, respectively). Conversely, despite the larger geographical distances between the Philippines and west Australian reefs, samples display a small degree of genetic structure (FST = 0.015). Demographic scenarios modelled using approximate Bayesian computation analysis indicate that this limited divergence is not due to contemporary gene flow between the Philippines and west Australia. Instead, present-day genetic similarity can be explained by very limited genetic drift that has occurred due to large average effective population sizes that persisted at both locations following their separation. The lack of connectivity among populations suggests that immigrants from west Australia would not facilitate natural recolonization if Philippine populations were fished to extinction. These data help to rectify the paucity of information on the species' biology currently inhibiting their conservation classification. Understanding population structure can allow us to facilitate sustainable harvesting, thereby preserving the diversity of genetically distinct stocks.

Published
2015
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12. Are assortative mating and genital divergence driven by reinforcement ?

Author

Johan Hollander, Ludovic Duvaux, Roger K. Butlin, Giuseppe Bianco, Anja M. Westram, Mauricio Montaño-Rendón, David G. Reid, Xi Yang, Lund University [Lund], Department of Animal and Plant Sciences, University of Sheffield [Sheffield], Institute of Science and Technology [Austria] (IST Austria), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Department of Life Sciences, Natural History Museum [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Department of Marine Sciences, and University of Connecticut (UCONN)

Subjects
0106 biological sciences, 0301 basic medicine, Letter, [SDV]Life Sciences [q-bio], Allopatric speciation, 010603 evolutionary biology, 01 natural sciences, Divergence, 03 medical and health sciences, Genetic algorithm, Littorinidae, reproductive interference, assortative mating, Genetics, Character displacement, gene‐flow, genitalia, reinforcement, reproductive character displacement, speciation, Littorinidae, Letters, Mating, Ecology, Evolution, Behavior and Systematics, biology, Assortative mating, biology.organism_classification, 030104 developmental biology, Mate choice, Evolutionary biology
Abstract

The evolution of assortative mating is a key part of the speciation process. Stronger assortment, or greater divergence in mating traits, between species pairs with overlapping ranges is commonly observed, but possible causes of this pattern of reproductive character displacement are difficult to distinguish. We use a multidisciplinary approach to provide a rare example where it is possible to distinguish among hypotheses concerning the evolution of reproductive character displacement. We build on an earlier comparative analysis that illustrated a strong pattern of greater divergence in penis form between pairs of sister species with overlapping ranges than between allopatric sister-species pairs, in a large clade of marine gastropods (Littorinidae). We investigate both assortative mating and divergence in male genitalia in one of the sister-species pairs, discriminating among three contrasting processes each of which can generate a pattern of reproductive character displacement: reinforcement, reproductive interference and the Templeton effect. We demonstrate reproductive character displacement in assortative mating, but not in genital form between this pair of sister species and use demographic models to distinguish among the different processes. Our results support a model with no gene flow since secondary contact and thus favor reproductive interference as the cause of reproductive character displacement for mate choice, rather than reinforcement. High gene flow within species argues against the Templeton effect. Secondary contact appears to have had little impact on genital divergence.

Published
2018
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13. The Response to Past Climate Perturbations Explains Extremely Low Genetic Diversity in the Genome of an Abundant Ice-Age Remnant, the Alpine Marmot

Author

Aleksej Zelezniak, Stefan T. Börno, Christophe Lemaire, John J. Welch, Johanna M. Gostner, Bernd Timmermann, Ludovic Duvaux, Aurélie Cohas, Sven Klages, Julian L. Griffin, Markus Ralser, Dominique Allainé, Jakob Vowinckel, Enrica Calvani, Peer Bork, Toni I. Gossmann, Coraline Bichet, Michael Mülleder, Heiner Kuhl, Falk Hildebrand, Lee D. Roberts, Sophia Schade, and Achchuthan Shanmugasundram

Subjects
Marmota marmota, Genetic diversity, biology, Pleistocene, Habitat, Ecology, Genetic variation, Ice age, Marmot, Adaptation, biology.organism_classification
Abstract

The Alpine Marmot (Marmota marmota) is a rodent remnant of the ‘ice-age’ climate of the Pleistocene steppe, and since the disappearance of this habitat, persists in the high altitude Alpine meadow. Sequencing its genome, we reveal that the long-term cold-climate adaptation has altered its metabolism, in particular biosynthesis and storage of fatty acids. Paradoxically, despite successful adaptation and a large population size, we detected levels of genetic variation that are among the lowest for mammals, and that purifying selection is ineffective. Reconstructing its demographic past revealed that the two apparently contradictory observations are, in fact, intimately interlinked. The climate-adaptive life history prevented genetic diversity to recover from Pleistocene perturbations. The case of the Alpine marmot demonstrates that populations of extremely low genetic diversity can be very successful and persist over thousands of years, but that a climate-adapted life history can deprive a species from the possibility to recover genetic diversity.

Published
2018
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14. Isolation and gene flow: inferring the speciation history of European house mice

Author

Khalid Belkhir, Ludovic Duvaux, Matthieu Boulesteix, and Pierre Boursot

Subjects
0106 biological sciences, 0303 health sciences, Allopatric speciation, Zoology, Subspecies, Biology, Incipient speciation, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, House mouse, Gene flow, 03 medical and health sciences, Hybrid zone, Genetic Speciation, Genetics, House mice, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology
Abstract

Inferring the history of isolation and gene flow during species differentiation can inform us on the processes underlying their formation. Following their recent expansion in Europe, two subspecies of the house mouse (Mus musculus domesticus and Mus musculus musculus) have formed a hybrid zone maintained by hybrid incompatibilities and possibly behavioural reinforcement, offering a good model of incipient speciation. We reconstruct the history of their divergence using an approximate Bayesian computation framework and sequence variation at 57 autosomal loci. We find support for a long isolation period preceding the advent of gene flow around 200,000 generations ago, much before the formation of the European hybrid zone a few thousand years ago. The duration of the allopatric episode appears long enough (74% of divergence time) to explain the accumulation of many post-zygotic incompatibilities expressed in the present hybrid zone. The ancient contact inferred could have played a role in mating behaviour divergence and laid the ground for further reinforcement. We suggest that both subspecies originally colonized the Middle East from the northern Indian subcontinent, domesticus settling on the shores of the Persian Gulf and musculus on those of the Caspian Sea. Range expansions during interglacials would have induced secondary contacts, presumably in Iran, where they must have also interacted with Mus musculus castaneus. Future studies should incorporate this possibility, and we point to Iran and its surroundings as a hot spot for house mouse diversity and speciation studies.

Published
2011
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15. Human-facilitated metapopulation dynamics in an emerging pest species, Cimex lectularius

Author

Ludovic Duvaux, Gavin J. Horsburgh, Roger K. Butlin, Toby Fountain, Klaus Reinhardt, Department of Animal and Plant Sciences [Sheffield], University of Sheffield [Sheffield], Biosciences, Centre of Excellence in Metapopulation Research, and Ecology and Evolutionary Biology

Subjects
BED-BUG, Bedbugs, approximate Bayesian computation analysis, education, Molecular Sequence Data, Population Dynamics, Population, Metapopulation, APPROXIMATE BAYESIAN COMPUTATION, Biology, microsatellites, SPATIAL GENETIC-STRUCTURE, Coalescent theory, Bed bug, Genetic drift, London, genetic structure, Genetics, Animals, Humans, POPULATION-STRUCTURE, PHALACRUS-SUBSTRIATUS, Research Articles, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Genetic diversity, education.field_of_study, Models, Genetic, Ecology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], fungi, metapopulation dynamics, Genetic Variation, Bayes Theorem, Cimex lectularius, biology.organism_classification, HEMIPTERA CIMICIDAE, pest management, Genetics, Population, MICROSATELLITE LOCI, Evolutionary biology, COMPUTER-PROGRAM, 1181 Ecology, evolutionary biology, INSECTICIDE RESISTANCE, BLATTELLA-GERMANICA, Biological dispersal, Microsatellite Repeats
Abstract

The number and demographic history of colonists can have dramatic consequences for the way in which genetic diversity is distributed and maintained in a metapopulation. The bed bug (Cimex lectularius) is a re-emerging pest species whose close association with humans has led to frequent local extinction and colonization, that is, to metapopulation dynamics. Pest control limits the lifespan of subpopulations, causing frequent local extinctions, and human-facilitated dispersal allows the colonization of empty patches. Founder events often result in drastic reductions in diversity and an increased influence of genetic drift. Coupled with restricted migration, this can lead to rapid population differentiation. We therefore predicted strong population structuring. Here, using 21 newly characterized microsatellite markers and approximate Bayesian computation (ABC), we investigate simplified versions of two classical models of metapopulation dynamics, in a coalescent framework, to estimate the number and genetic composition of founders in the common bed bug. We found very limited diversity within infestations but high degrees of structuring across the city of London, with extreme levels of genetic differentiation between infestations (FST = 0.59). ABC results suggest a common origin of all founders of a given subpopulation and that the numbers of colonists were low, implying that even a single mated female is enough to found a new infestation successfully. These patterns of colonization are close to the predictions of the propagule pool model, where all founders originate from the same parental infestation. These results show that aspects of metapopulation dynamics can be captured in simple models and provide insights that are valuable for the future targeted control of bed bug infestations. © 2013 John Wiley & Sons Ltd.

Published
2014
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16. Isolation and gene flow: inferring the speciation history of European house mice

Author

Ludovic, Duvaux, Khalid, Belkhir, Matthieu, Boulesteix, and Pierre, Boursot

Subjects
Gene Flow, Models, Genetic, Genetic Speciation, Molecular Sequence Data, Genetic Variation, Bayes Theorem, Sequence Analysis, DNA, Iran, Europe, Mice, Middle East, Phylogeography, Species Specificity, Genetic Loci, Animals, Hybridization, Genetic, Computer Simulation, Indian Ocean, Sequence Alignment, Alleles
Abstract

Inferring the history of isolation and gene flow during species differentiation can inform us on the processes underlying their formation. Following their recent expansion in Europe, two subspecies of the house mouse (Mus musculus domesticus and Mus musculus musculus) have formed a hybrid zone maintained by hybrid incompatibilities and possibly behavioural reinforcement, offering a good model of incipient speciation. We reconstruct the history of their divergence using an approximate Bayesian computation framework and sequence variation at 57 autosomal loci. We find support for a long isolation period preceding the advent of gene flow around 200,000 generations ago, much before the formation of the European hybrid zone a few thousand years ago. The duration of the allopatric episode appears long enough (74% of divergence time) to explain the accumulation of many post-zygotic incompatibilities expressed in the present hybrid zone. The ancient contact inferred could have played a role in mating behaviour divergence and laid the ground for further reinforcement. We suggest that both subspecies originally colonized the Middle East from the northern Indian subcontinent, domesticus settling on the shores of the Persian Gulf and musculus on those of the Caspian Sea. Range expansions during interglacials would have induced secondary contacts, presumably in Iran, where they must have also interacted with Mus musculus castaneus. Future studies should incorporate this possibility, and we point to Iran and its surroundings as a hot spot for house mouse diversity and speciation studies.

Published
2011

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