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34 results on '"Natural History Museum [Geneva]"'

1. First chromosome scale genomes of ithomiine butterflies (Nymphalidae: Ithomiini): comparative models for mimicry genetic studies

Author: Jérémy Gauthier, Joana Meier, Fabrice Legeai, Melanie McClure, Annabel Whibley, Anthony Bretaudeau, Hélène Boulain, Hugues Parrinello, Sam T. Mugford, Richard Durbin, Chenxi Zhou, Shane McCarthy, Christopher W. Wheat, Florence Piron‐Prunier, Christelle Monsempes, Marie‐Christine François, Paul Jay, Camille Noûs, Emma Persyn, Emmanuelle Jacquin‐Joly, Camille Meslin, Nicolas Montagné, Claire Lemaitre, Marianne Elias, Natural History Museum [Geneva], Department of Zoology [Cambridge], University of Cambridge [UK] (CAM), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, 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 de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), 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), Laboratoire Ecologie, Evolution, Interactions des Systèmes amazoniens (LEEISA), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS), School of Biological Sciences [Auckland], University of Auckland [Auckland], Department of Ecology and Evolution [Lausanne], Université de Lausanne = University of Lausanne (UNIL), Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX), Institut de Génomique Fonctionnelle (IGF), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-BioCampus (BCM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), John Innes Centre [Norwich], Biotechnology and Biological Sciences Research Council (BBSRC), Department of Crop Genetics, Biotechnology and Biological Sciences Research Council (BBSRC)-Biotechnology and Biological Sciences Research Council (BBSRC), Department of Genetics [Cambridge], The Wellcome Trust Sanger Institute [Cambridge], Stockholm University, Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecologie Systématique et Evolution (ESE), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Laboratoire Cogitamus, Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ME acknowledges financial support from ANR (projects SPECREP, ANR-14-CE02-0011, and CLEARWING, ANR-16-CE02-0012) and HFSP (RGP0014/2016). MGX acknowledges financial support from France Génomique National infrastructure, funded as part of 'Investissement d’Avenir' program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-0009). RD, SM and CZ acknowledge financial support from Wellcome grant WT207492, and SM and work at the Wellcome Sanger Institute were also supported by Wellcome grant WT206194. We thank members of the Wellcome Sanger Institute Scientific Operations and Tree of Life core groups for their contributions to data production and assembly for the Melinaea genomes. We thank Mario Tuanama and Ronald Mori-Pezo for help with rearing and collecting butterflies. MM acknowledges a postdoctoral fellowship by the Fonds Québécois de la Recherche sur la Nature et les Technologies (FQRNT). STM acknowledges support from the BBSRC Institute Strategy Programme (BB/P012574/1). We thank the Peruvian authorities for research permits (236-2012-AG-DGFFS-DGEFFS, 201-2013-MINAGRI-DGFFS/DGEFFS, 002-2015-SERFOR-DGGSPFFS and 373-2017-SERFOR-DGGSPFFS), the Gobierno Regional San Martín PEHCBM (permit: 124-2016-GRSM/PEHCBM-DMA/EII-ANP/JARR) and the Museo de Historia Natural and Prof. Gerardo Lamas for their support. We thank the GenOuest BioInformatics Platform (http://www.genouest.org), which allowed the use of a computing cluster for bioinformatic analyses., ANR-14-CE02-0011,SPECREP,Répétabilité du processus de spéciation chez les papillons: replications naturelles dans une zone de suture(2014), ANR-16-CE02-0012,CLEARWING,La transparence : origine physique, fonctions adaptatives et évolution chez les papillons transparents(2016), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Gauthier, Jérémy [0000-0001-6666-1002], Meier, Joana [0000-0001-7726-2875], Whibley, Annabel [0000-0003-1878-7705], Parrinello, Hugues [0000-0002-1151-001X], Wheat, Christopher W [0000-0003-1863-2340], Apollo - University of Cambridge Repository, Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), International Aphid Genomics Consortium (IAGC), Department of Crop Genetics [Norwich], and Department of Zoology [Stockholm]
Subjects: ithomiine butterflies, Genomics, chromosome-level genome, Adaptation, Physiological, Chromosomes, Phenotype, Hi-C, Genetics, Animals, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Butterflies, Ecology, Evolution, Behavior and Systematics, mimicry, Biotechnology, Butterflies/genetics, Chromosomes/genetics, olfaction
Abstract: Funder: Human Frontier Science Program; Id: http://dx.doi.org/10.13039/501100000854, The ithomiine butterflies (Nymphalidae: Danainae) represent the largest known radiation of Müllerian mimetic butterflies. They dominate by number the mimetic butterfly communities, which include species such as the iconic neotropical Heliconius genus. Recent studies on the ecology and genetics of speciation in Ithomiini have suggested that sexual pheromones, colour pattern and perhaps hostplant could drive reproductive isolation. However, no reference genome was available for Ithomiini, which has hindered further exploration on the genetic architecture of these candidate traits, and more generally on the genomic patterns of divergence. Here, we generated high-quality, chromosome-scale genome assemblies for two Melinaea species, M. marsaeus and M. menophilus, and a draft genome of the species Ithomia salapia. We obtained genomes with a size ranging from 396 to 503 Mb across the three species and scaffold N50 of 40.5 and 23.2 Mb for the two chromosome-scale assemblies. Using collinearity analyses we identified massive rearrangements between the two closely related Melinaea species. An annotation of transposable elements and gene content was performed, as well as a specialist annotation to target chemosensory genes, which is crucial for host plant detection and mate recognition in mimetic species. A comparative genomic approach revealed independent gene expansions in ithomiines and particularly in gustatory receptor genes. These first three genomes of ithomiine mimetic butterflies constitute a valuable addition and a welcome comparison to existing biological models such as Heliconius, and will enable further understanding of the mechanisms of adaptation in butterflies.
Published: 2023

2. Functional and taxonomic responses of tropical moth communities to deforestation

Author: Sylvain Dolédec, Yenny Correa-Carmona, Marlucia Bonifacio Martins, Rodolphe Rougerie, Johan Oszwald, Patrick Lavelle, Jan Beck, Solen Le Clec'h, Jérôme Murienne, Sujeevan Ratnasingham, Chris Ho, Liliana Ballesteros-Mejia, Thibaud Decaëns, Pierre Arnal, Ian J. Kitching, Carlos Lopez-Vaamonde, Universidad de Antioquia = University of Antioquia [Medellín, Colombia], Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-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)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, 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)-Université de Montpellier (UM), Muséum national d'Histoire naturelle (MNHN), University of Basel (Unibas), Équipe 1 - Biodiversité et Adaptation dans les Hydrosystèmes (BAH), Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), University of Guelph, The Natural History Museum [London] (NHM), Université Sorbonne Paris Nord, Wageningen University and Research [Wageningen] (WUR), Unité de recherche Zoologie Forestière (URZF), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de recherche sur la biologie de l'insecte UMR7261 (IRBI), Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Museu Paraense Emílio Goeldi [Belém, Brésil] (MPEG), Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR), French Foundation for Research on Biodiversity. Grant Number: CESAB ACTIAS, Centre for Biodiversity Genomics, University of Guelph, ANR-16-CE02-0011,SPHINX,Comprendre et prédire l'adaptation des espèces aux changements environnementaux chez les insectes(2016), Beck, Jan [https://orcid.org/0000-0003-1170-4751], Dolédec, Sylvain [https://orcid.org/0000-0002-0280-7866], Le Clec’h, Solen [https://orcid.org/0000-0001-7886-2899], Lopez-Vaamonde, Carlos [https://orcid.org/0000-0003-2278-2368], Murienne, Jérôme [https://orcid.org/0000-0003-1474-7829], Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Grupo de Entomología Universidad de Antioquia (GEUA), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Centre de Synthèse et d’Analyse sur la Biodiversité (CESAB), Fondation pour la recherche sur la Biodiversité (FRB), Grupo de Investigacion Diseño, Imagen y Comunicacion, Universidad El Bosque [Bogota], University of Basel, Department of Environmental Sciences, University of Colorado Museum of Natural History, University of Colorado [Boulder], Biodiversity Institute of Ontario, Centre for Biodiversity Genomics, Department of Life Sciences, Natural History Museum [Geneva], Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Environmental Systems Analysis Group, Laboratorio de Ecologia de Invertebrados, Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Université de Toulouse, CNRS, IRD, UPS, Université de Tours-Centre National de la Recherche Scientifique (CNRS), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, Landscape ecology, 010603 evolutionary biology, 01 natural sciences, Neotropical insect decline, Lepidoptera genitalia, Deforestation, Community ecology, functional traits, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, landscape ecology, Community, Ecology, 010604 marine biology & hydrobiology, 15. Life on land, Lepidoptera, Environmental Systems Analysis, Geography, Milieusysteemanalyse, Insect Science, [SDE]Environmental Sciences, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Functional traits, community ecology
Abstract: International audience; Global insect decline has recently become a cause for major concern, particularly in the tropics where the vast majority of species occurs. Deforestation is suggested as being a major driver of this decline, but how anthropogenic changes in landscape structure affect tropical insect communities has rarely been addressed. We sampled Saturniidae and Sphingidae moths on 27 farms located in Brazilian Amazonia (Para state) and characterised by different deforestation histories. We used functional traits (forewing length, body mass, wing load, trophic niche breadth and resource use strategy), analysed by combining RLQ and null model analyses, to investigate the responses of their taxonomic and functional diversity to landscape change dynamics and current structure. We found that communities had a higher proportion of large and polyphagous species with low wing load in landscapes with low forest quality and relative cover and high land use turnover. This was mainly due to a significant response to deforestation by saturniids, whereas the more mobile sphingids showed no significant landscape-related pattern. We also observed an overall increase of species richness and functional dispersion in landscapes that have been deforested for a long time when compared with more recent agricultural settlements. Our results highlight the complex way in which landscape structure and historical dynamics interact to shape Neotropical moth communities and that saturniid moths respond clearly to the structure of the surrounding landscape, confirming their potential use as an indicator group for environmental monitoring programmes.
Published: 2022

3. Comparative osteology of the fossorial frogs of the genus Synapturanus (Anura, Microhylidae) with the description of three new species from the Eastern Guiana Shield

Author: Elodie A. Courtois, Maël Dewynter, Killian Leblanc, Antoine Fouquet, Marcelo Menin, Raffael Ernst, Miguel Trefaut Rodrigues, Pedro L. V. Peloso, Philippe J. R. Kok, Monique Hölting, Anne-Claire Fabre, Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Department of Life Sciences, Natural History Museum [Geneva], Departamento de Biologia, Universidade Federal do Amazonas, Manaus, Brazil (UFAM), NeoMedLight, Federal University of Para - Universidade Federal do Para [Belem - Brésil], Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Federal University of Para - Universidade Federal do Pará - UFPA [Belém, Brazil] (UFPA)
Subjects: 0106 biological sciences, Morphology, Microhylidae, 010607 zoology, Zoology, Morphology (biology), 010603 evolutionary biology, 01 natural sciences, Amphibia, Amazonia, Genus, MORFOLOGIA ANIMAL, medicine, Clade, Synapturanus, Tomography, ComputingMilieux_MISCELLANEOUS, biology, Osteology, Fossorial, biology.organism_classification, Skull, medicine.anatomical_structure, [SDE]Environmental Sciences, Integrative taxonomy, Animal Science and Zoology
Abstract: The genus Synapturanus includes three nominal species of fossorial Amazonian frogs. A previous study combining molecular, morphological and acoustic data suggested that there may be six times more species than currently recognized. Herein we describe and name three of these new species and compare their osteology. Synapturanus zombie sp. nov. occurs in French Guiana and Amapa (Brazil), Synapturanus mesomorphus sp. nov. in Guyana and adjacent Venezuela, and Synapturanus ajuricaba sp. nov. in the northern part of the Brazilian states of Amazonas and Para. These species are readily differentiated from congeners by a combination of external morphological characters such as body size, development of fringes on fingers and coloration, by advertisement call variables, and by osteological traits. Along with osteological reinforcement of the skull, atlas and scapular region, the reduction of the size of phalanges, more developed fringes on fingers, smaller eyes and larger body size, altogether suggest an overall increase of the fossorial habits in the easternmost species. In contrast, the relatively conserved morphology of the posterior part of the body across the genus suggests that fossoriality mostly involves the anterior part. Furthermore, the fusion of tarsal bones in the species of the western clade may indicate locomotory adaptation to more epigean habits. (C) 2021 Elsevier GmbH. All rights reserved.
Published: 2021

4. Reed warblers in the Marquesas Islands: song divergence and plumage convergence of two distinct lineages

Author: Alice Cibois, Nicholas R. Friedman, Tony Robillard, Laure Desutter-Grandcolas, Jean-Claude Thibault, Kevin E. Omland, Eric Pasquet, Dept. of Mammalogy and Ornithology, Natural History Museum [Geneva], Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)
Subjects: 0106 biological sciences, 0301 basic medicine, geography, Acrocephalidae, geography.geographical_feature_category, biology, Ecology, Zoology, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Gene flow, 03 medical and health sciences, 030104 developmental biology, Taxon, Plumage, Convergent evolution, Archipelago, Acrocephalus, Animal Science and Zoology, 14. Life underwater, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ornithology, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation
Abstract: The Pacific Ocean is the site of the most important diversification of insular reed warblers (Acrocephalus). In the Marquesas Islands (Eastern Polynesia), reed warblers belong to two distinct lineages that have reached the archipelago independently. We used mitochondrial sequences and microsatellite markers and found evidence of gene flow between the two lineages. One island in particular, Nuku Hiva, seems to act as the main contact zone between the two taxa. We then used reflectance spectrometry to evaluate the variation of carotenoid colouration among all populations. Marquesan reed warblers exhibit convergent evolution in carotenoid-based plumage colouration, but variation among islands was important. Having two different phylogenetic origins, the two lineages acquired their yellow colour independently and there is stochastic variation in plumage among islands. Finally, we analysed the songs of reed warblers from the main islands. Multifactorial analysis showed that vocalisations of Marquesan r...
Published: 2019

5. Size, microhabitat, and loss of larval feeding drive cranial diversification in frogs

Author: David C. Blackburn, Anne-Claire Fabre, Margot Bon, Julien Clavel, Edward L. Stanley, Carla Bardua, Kalpana Das, Anjali Goswami, Department of Life Sciences, Natural History Museum [Geneva], Department of Genetics, Evolution & Environment, University College of London [London] (UCL), Paläontologisches Institut und Museum der Universität Zürich, Karl-Schmid Strasse 4, CH-8006 Zürich, Switzerland (PALäONTOLOGISCHES INSTITUT UND MUSEUM DER UNIVERSITäT ZüRICH, KARL-SCHMID STRASSE 4, CH-8006 ZüRICH, SWITZERLAND), Universität Zürich [Zürich] = University of Zurich (UZH), Équipe 6 - Paléontologie, Paléoécologie, Paléobiogéographie, Évolution (P3E), Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), Museum für Naturkunde, Leibniz Institut für Evolutions und Biodiversitätsforschung, Department of Biology and Florida Museum of Natural History [USA], and University of Florida [Gainesville] (UF)
Subjects: 0106 biological sciences, 0301 basic medicine, Amphibian, Science, Ontogeny, Ecology (disciplines), General Physics and Astronomy, Zoology, Biology, Lissamphibia, Evolutionary ecology, 010603 evolutionary biology, 01 natural sciences, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Osteogenesis, biology.animal, medicine, Animals, Ecosystem, Phylogeny, Principal Component Analysis, Larva, Multidisciplinary, Herpetology, Skull, Fossorial, Feeding Behavior, General Chemistry, biology.organism_classification, Biological Evolution, Phylogenetics, 030104 developmental biology, medicine.anatomical_structure, Evolutionary developmental biology, Allometry, Anura, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Habitat is one of the most important factors shaping organismal morphology, but it may vary across life history stages. Ontogenetic shifts in ecology may introduce antagonistic selection that constrains adult phenotype, particularly with ecologically distinct developmental phases such as the free-living, feeding larval stage of many frogs (Lissamphibia: Anura). We test the relative influences of developmental and ecological factors on the diversification of adult skull morphology with a detailed analysis of 15 individual cranial regions across 173 anuran species, representing every extant family. Skull size, adult microhabitat, larval feeding, and ossification timing are all significant factors shaping aspects of cranial evolution in frogs, with late-ossifying elements showing the greatest disparity and fastest evolutionary rates. Size and microhabitat show the strongest effects on cranial shape, and we identify a “large size-wide skull” pattern of anuran, and possibly amphibian, evolutionary allometry. Fossorial and aquatic microhabitats occupy distinct regions of morphospace and display fast evolution and high disparity. Taxa with and without feeding larvae do not notably differ in cranial morphology. However, loss of an actively feeding larval stage is associated with higher evolutionary rates and disparity, suggesting that functional pressures experienced earlier in ontogeny significantly impact adult morphological evolution., The evolution of metamorphic species may be constrained by different ecologies of the larval and adult stages. Here, Bardua et al. show that in frogs, adult ecology is more important than larval ecology for skull evolution, but species that don’t feed as tadpoles evolve faster than those that do.
Published: 2021

6. EvoSheep : The Makeup of Sheep Breeds in the Ancient Near East

Author: Sofiane Bouzid, François Pompanon, Bea De Cupere, Camille Bader, Hossein Davoudi, Philippe Abrahami, Daniel Helmer, Catherine Breniquet, Azadeh Fatemeh Mohaseb, Thomas Cucchi, Rémi Berthon, Moussab Albesso, Oscar Estrada, Lionel Gourichon, Emmanuelle Vila, Marjan Mashkour, Daniel G. Bradley, Manon Vuillien, Jwana Chahoud, Ludovic Orlando, Jacqueline Studer, Wei Huangfu, Cécile Michel, Gilles Escarguel, Joséphine Lesur, Agraw Amane, ARCHEORIENT - Environnements et sociétés de l'Orient ancien (Archéorient), Université Lumière - Lyon 2 (UL2)-Centre National de la Recherche Scientifique (CNRS), Histoire, Archéologie et Littérature des Mondes Anciens - UMR 8164 (HALMA), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture (MC), Addis Ababa University (AAU), International Livestock Research Institute [CGIAR, Ethiopie] (ILRI), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Trinity College Dublin, Centre d'Histoire 'Espaces et Cultures' (CHEC), Université Clermont Auvergne (UCA), Lebanese University [Beirut] (LU), University of Tehran, Royal Belgian Institute of Natural Sciences (RBINS), Équipe 6 - Paléontologie, Paléoécologie, Paléobiogéographie, Évolution (P3E), Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Culture et Environnements, Préhistoire, Antiquité, Moyen-Age (CEPAM), 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), Maison de l'Orient et de la Méditerranée - Jean Pouilloux (MOM), École normale supérieure de Lyon (ENS de Lyon)-Université Lumière - Lyon 2 (UL2)-Université Jean Moulin - Lyon 3 (UJML), Université de Lyon-Université de Lyon-Aix Marseille Université (AMU)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Archéologies et Sciences de l'Antiquité (ArScAn), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Natural History Museum [Geneva], ANR-17-CE27-0004,EVOSHEEP,Exploration des premières innovations zootechniques dans les sociétés du sud-ouest asiatique (5e-1er millénaires av. J.-C.)(2017), Histoire Archéologie Littérature des Mondes Anciens - UMR 8164 (HALMA), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN), Archaeozoological section, Bioarchaeological laboratory, Directorate Earth & History of Life, Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Department of Archaeozoology, Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Ministère de la Culture (MC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Department of Microbial, Cellular and Molecular Biology, ILRI Ethiopia (ILRI), ILRI, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland, Department of Archaeology, Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA), École normale supérieure - Lyon (ENS Lyon)-Université Lumière - Lyon 2 (UL2)-Université Jean Moulin - Lyon 3 (UJML), Université de Lyon-Université de Lyon-Aix Marseille Université (AMU)-Université Jean Monnet [Saint-Étienne] (UJM)-Centre National de la Recherche Scientifique (CNRS), ARCHEORIENT - Environnements et sociétés de l'Orient ancien [Archéorient], Histoire, Archéologie et Littérature des Mondes Anciens - UMR 8164 [HALMA], Archéozoologie, archéobotanique : sociétés, pratiques et environnements [AASPE], Centre d'Histoire 'Espaces et Cultures' [CHEC], Anthropologie Moléculaire et Imagerie de Synthèse [AMIS], Archéologies et Sciences de l'Antiquité [ArScAn], Laboratoire d'Ecologie Alpine [LECA ], Culture et Environnements, Préhistoire, Antiquité, Moyen-Age [CEPAM], Centre National de la Recherche Scientifique (CNRS)-Université Lumière - Lyon 2 (UL2), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS), and Équipe 6 - Paléontologie, Paléoécologie, Paléobiogéographie, Évolution [P3E]
Subjects: Near East, 010506 paleontology, Archeology, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Textile production, 01 natural sciences, [SHS]Humanities and Social Sciences, 0601 history and archaeology, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Levant, Archaeozoology, 0105 earth and related environmental sciences, 2. Zero hunger, Morphometrics, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, [SDV.GEN]Life Sciences [q-bio]/Genetics, Geometric morphometrics, Middle East, Plateau, geography.geographical_feature_category, Africa, Sheep, 060102 archaeology, General Arts and Humanities, Mesopotamia, 06 humanities and the arts, Archaeology, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Geography, [SDE]Environmental Sciences, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; The EVOSHEEP project combines archaeozoology, geometric morphometrics and genetics to study archaeo- logical sheep assemblages dating from the sixth to the first millennia BC in eastern Africa, the Levant, the Ana- tolian South Caucasus, the Iranian Plateau and Mesopotamia. The project aims to understand changes in the physical appearance and phenotypic characteristics of sheep and how these related to the appearance of new breeds and the demand for secondary products to supply the textile industry.
Published: 2021

7. Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization

Author: Myriam Harry, Bernard Duvic, Anthony Bretaudeau, Hélène Boulain, Jetske G. de Boer, Jean-Marc Aury, Claire Capdevielle-Dulac, Annie Bézier, Diane Bigot, Natacha Kremer, Laure Kaiser, Lyam Baudry, Joke J.F.A. van Vugt, Jean-Michel Drezen, Georges Periquet, Stéphane Dupas, Romain Koszul, Aurélie Hua-Van, Jérémy Gauthier, Fabrice Legeai, Emma Persyn, Mahnaz Sabeti-Azad, Fernando Luis Cônsoli, Valérie Barbe, Joelle Amselem, Karine Labadie, Benjamin Noel, Frédérique Hilliou, Martine Maïbèche, Géraldine Dubreuil, Isabelle Luyten, Karine Musset, Martial Marbouty, Christophe Bressac, Isabelle Boulogne, Louise E. M. Vet, Thibaut Josse, Philippe Gayral, Hans M. Smid, Emmanuelle Jacquin-Joly, David Siaussat, James B. Whitfield, Elisabeth A. Herniou, Mohamed Amine Chebbi, Thomas Chertemps, Nicolas Montagné, Sébastien J. M. Moreau, Elisabeth Huguet, Bruna Laís Merlin, Gaëlle Le Goff, Sven Warris, Institut de recherche sur la biologie de l'insecte UMR7261 (IRBI), Université de Tours-Centre National de la Recherche Scientifique (CNRS), Natural History Museum [Geneva], Swiss Federal Insitute of Aquatic Science and Technology [Dübendorf] (EAWAG), Netherlands Institute of Ecology - NIOO-KNAW (NETHERLANDS), Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Collège doctoral [Sorbonne universités], Sorbonne Université (SU), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), 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-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-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-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), Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Wageningen University and Research [Wageningen] (WUR), Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] (DGIMI), Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), Evolution, génomes, comportement et écologie (EGCE), Institut de Recherche pour le Développement (IRD)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Recherche Génomique Info (URGI), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), Universidade de São Paulo (USP), Department of Entomology [Urbana], University of Illinois System, Department of Terrestrial Ecology [Wageningen], Netherlands Institute of Ecology (NIOO-KNAW), ANR-12-ADAP-0001, Agence Nationale de la Recherche, Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Collège Doctoral, Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO 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 Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Universidade de São Paulo = University of São Paulo (USP), ANR-12-ADAP-0001,ABC - PaPoGen,Adaptation en lutte biologique - Génomique des populations de parasitoïdes(2012), Evolutionary Genetics, Development & Behaviour, Terrestrial Ecology (TE), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1), and Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique)
Subjects: Genome evolution, food.ingredient, QH301-705.5, Bioinformatics, [SDV]Life Sciences [q-bio], Medicine (miscellaneous), macromolecular substances, Biology, Genome, Article, Evolutionary genetics, General Biochemistry, Genetics and Molecular Biology, Plan_S-Compliant-OA, Parasitoid wasp, 03 medical and health sciences, BIOS Applied Bioinformatics, 0302 clinical medicine, food, Bioinformatica, Life Science, Cotesia congregata, VÍRUS DE DNA, Biology (General), Laboratory of Entomology, Gene, 030304 developmental biology, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, Human evolutionary genetics, Chromosome, biology.organism_classification, PE&RC, Laboratorium voor Entomologie, Evolutionary biology, international, EPS, General Agricultural and Biological Sciences, Bracovirus, Entomology, 030217 neurology & neurosurgery
Abstract: Endogenous viruses form an important proportion of eukaryote genomes and a source of novel functions. How large DNA viruses integrated into a genome evolve when they confer a benefit to their host, however, remains unknown. Bracoviruses are essential for the parasitism success of parasitoid wasps, into whose genomes they integrated ~103 million years ago. Here we show, from the assembly of a parasitoid wasp genome at a chromosomal scale, that bracovirus genes colonized all ten chromosomes of Cotesia congregata. Most form clusters of genes involved in particle production or parasitism success. Genomic comparison with another wasp, Microplitis demolitor, revealed that these clusters were already established ~53 mya and thus belong to remarkably stable genomic structures, the architectures of which are evolutionary constrained. Transcriptomic analyses highlight temporal synchronization of viral gene expression without resulting in immune gene induction, suggesting that no conflicts remain between ancient symbiotic partners when benefits to them converge., Jeremy Gauthier et al. present the chromosome scale assembly of the genome of the parasitic wasp C. congregata and show that bracovirus genes have colonized all ten chromosomes. Comparison with genome scaffolds of another wasp reveals a striking stability of these regions over ~53 million years, suggesting strong evolutionary constraints.
Published: 2021

8. Linking seascape with landscape genetics: Oceanic currents favour colonization across the Galápagos Islands by a coastal plant

Author: Pablo Vargas, Miguel Navascués, Javier Fernández-López, Manuel Nogales, Yurena Arjona, Nadir Alvarez, Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Real Jardín Botánico de Madrid (RJB), Spanish National Research Council (CSIC), Instituto de Productos Naturales y Agrobiologia = Institute of Natural Products and Agrobiology (IPNA), Instituto de Investigación en Recursos Cinegéticos (IREC), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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), Museum d'Histoire Naturelle [Genève] (MHN), YA was funded by the Ministerio de Economía y Competitividad (Spain) (BES‐2013‐062843, EEBB‐I‐15‐10273, EEBB‐I‐16‐11437). This study is framed within a project also financed by the Ministerio de Economía y Competitividad (CGL2012‐C02‐01). The manuscript was edited by Guido Jones, currently funded by the Cabildo de Tenerife, under the TFinnova Programme supported by MEDI and FDCAN funds., Real Jardín Botanico, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Natural History Museum [Geneva], Island Ecology and Evolution Research Group, IPNA CSIC, Real Jardín Botánico (RJB–CSIC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), and Ministerio de Economía y Competitividad (España)
Subjects: Thalassochory, 0106 biological sciences, thalassochory, directional dispersal, Population genetics, Directional dispersal, [SDV]Life Sciences [q-bio], 010603 evolutionary biology, 01 natural sciences, salt bush, Salt bush, 03 medical and health sciences, Oceanic islands, Colonization, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, Isolation by resistance, 030304 developmental biology, Seascape, 0303 health sciences, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Ecology, Ocean current, oceanic islands, population genetics, 15. Life on land, isolation by resistance, Geography
Abstract: [Aim]: Coastal plants are terrestrial organisms for which ocean surface currents often act as long‐distance dispersal vectors (thalassochorous species) favouring broad distributions and connecting distant populations. However, few studies have statistically assessed the role of currents in modulating gene flow and species distributions of terrestrial organisms. Here we evaluate the hypothesis that some thalassochorous plants exhibit population connectivity, presumably due to effective seed dispersal driven by sea currents. Location Galápagos Islands (Ecuador). Taxon Salt bush (Cryptocarpus pyriformis Kunth), a Galápagos native and locally widespread coastal angiosperm. Methods Using 1806 SNPs obtained by ddRADseq, we evaluated the genetic structure and differentiation of the Galápagos salt bush. To assess the role of sea currents in modulating inter‐population gene flow, four explicit hypotheses were tested using reciprocal causal modelling and spatial eigenvector analysis: (a) isolation by sea resistance, considering that only sea dispersal is possible; (b) isolation by sea and inland resistance, considering that inland dispersal is also possible; (c) isolation by barrier, considering the sea as an obstacle to seed dispersal; and (d) isolation by geographical distance. Results Low differentiation and little genetic structure were detected among populations of C. pyriformis. Pairwise genetic distances between populations from different islands were significantly correlated with cost distances calculated from sea‐current direction and speed. Nonetheless, inland dispersal also accounted for some gene flow within each island. Main conclusion Extensive and frequent seed dispersal by sea has apparently favoured strong inter‐island genetic connectivity within Galápagos. A combination of methods developed for terrestrial and marine domains (landscape and seascape genetics) aids in understanding how landscape features modulate gene flow of coastal plant species, as these terrestrial organisms are highly dependent on the sea for seed dispersal., [Location]: Galápagos Islands (Ecuador)., [Taxon]: Salt bush (Cryptocarpus pyriformis Kunth), a Galápagos native and locally widespread coastal angiosperm., [Methods]: Using 1806 SNPs obtained by ddRADseq, we evaluated the genetic structure and differentiation of the Galápagos salt bush. To assess the role of sea currents in modulating inter‐population gene flow, four explicit hypotheses were tested using reciprocal causal modelling and spatial eigenvector analysis: (a) isolation by sea resistance, considering that only sea dispersal is possible; (b) isolation by sea and inland resistance, considering that inland dispersal is also possible; (c) isolation by barrier, considering the sea as an obstacle to seed dispersal; and (d) isolation by geographical distance., [Results]: Low differentiation and little genetic structure were detected among populations of C. pyriformis. Pairwise genetic distances between populations from different islands were significantly correlated with cost distances calculated from sea‐current direction and speed. Nonetheless, inland dispersal also accounted for some gene flow within each island. Main conclusion Extensive and frequent seed dispersal by sea has apparently favoured strong inter‐island genetic connectivity within Galápagos. A combination of methods developed for terrestrial and marine domains (landscape and seascape genetics) aids in understanding how landscape features modulate gene flow of coastal plant species, as these terrestrial organisms are highly dependent on the sea for seed dispersal., This study is framed within a project also financed by the Ministerio de Economía y Competitividad (CGL2012‐C02‐01).
Published: 2020

9. DiscoSnp-RAD: de novo detection of small variants for RAD-Seq population genomics

Author: Gauthier, Jérémy, Mouden, Charlotte, Suchan, Tomasz, Alvarez, Nadir, Arrigo, Nils, Riou, Chloé, Lemaitre, Claire, Peterlongo, Pierre, Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), W. Szafer Institute of Botany, Polska Akademia Nauk = Polish Academy of Sciences (PAN), Natural History Museum [Geneva], Department of Ecology and Evolution [Lausanne], Université de Lausanne (UNIL), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Université de Lausanne = University of Lausanne (UNIL), CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Université de Rennes (UNIV-RENNES)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Université de Rennes (UNIV-RENNES), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Polska Akademia Nauk (PAN), and Dpt of Ecology and Evolution [Lausanne]
Subjects: Insertions, Bioinformatics, Reference-free, lcsh:R, Variants, lcsh:Medicine, Genomics, De novo variant calling, RAD-seq, Next-generation sequencing, Deletions, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Population genomics, Molecular Biology, SNPs
Abstract: International audience; Restriction site Associated DNA Sequencing (RAD-Seq) is a technique characterized by the sequencing of specific loci along the genome that is widely employed in the field of evolutionary biology since it allows to exploit variants (mainly Single Nucleotide Polymorphism—SNPs) information from entire populations at a reduced cost. Common RAD dedicated tools, such as STACKS or IPyRAD, are based on all-vs-all read alignments, which require consequent time and computing resources. We present an original method, DiscoSnp-RAD, that avoids this pitfall since variants are detected by exploiting specific parts of the assembly graph built from the reads, hence preventing all-vs-all read alignments. We tested the implementation on simulated datasets of increasing size, up to 1,000 samples, and on real RAD-Seq data from 259 specimens of Chiastocheta flies, morphologically assigned to seven species. All individuals were successfully assigned to their species using both STRUCTURE and Maximum Likelihood phylogenetic reconstruction. Moreover, identified variants succeeded to reveal a within-species genetic structure linked to the geographic distribution. Furthermore, our results show that DiscoSnp-RAD is significantly faster than state-of-the-art tools. The overall results show that DiscoSnp-RAD is suitable to identify variants from RAD-Seq data, it does not require time-consuming parameterization steps and it stands out from other tools due to its completely different principle, making it substantially faster, in particular on large datasets.
Published: 2020

10. Report on the 2018 and 2019 Seasons of the Madâ'in Sâlih Archaeological Project

Author: Nehmé, Laïla, Bouchaud, Charlène, Delhopital, Nathalie, Durand, Caroline, Égal, Florent, Fiema, Zbigniew, Gatier, Pierre-Louis, Gazagne, Damien, Gerber, Yvonne, Al-Huwaytî, Ahmad, Al-Juhany, Maha, Leguilloux, Martine, Milon, Juliette, Al-Muqbil, Saad, Al-Mûsa, Maher, Al-Nawfal, Samar, Nenna, Marie-Dominique, Norris, Jérôme, Peillet, Marie, Al-Sabhân, Ibrahîm, Studer, Jacqueline, Al-Talhi, Daifallah, Humbert, Jean, Ilioglou, Ariadni, ORIENT ET MÉDITERRANÉE : Textes, Archéologie, Histoire (OM), Université Paris 1 Panthéon-Sorbonne (UP1)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN), Archéologies et Sciences de l'Antiquité (ArScAn), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Histoire et Sources des Mondes antiques (HiSoMA), Centre National de la Recherche Scientifique (CNRS)-Université Jean Monnet [Saint-Étienne] (UJM)-Université Jean Moulin - Lyon 3 (UJML), Université de Lyon-Université de Lyon-Université Lumière - Lyon 2 (UL2)-École normale supérieure - Lyon (ENS Lyon), University of Helsinki, Maison de l'Orient et de la Méditerranée - Jean Pouilloux (MOM), Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Aix Marseille Université (AMU)-Université Jean Monnet [Saint-Étienne] (UJM)-Université Jean Moulin - Lyon 3 (UJML), Université de Lyon-Université de Lyon-Université Lumière - Lyon 2 (UL2), EVEHA (Etudes et valorisations archeologiques), University of Basel (Unibas), King Saud University [Riyadh] (KSU), Centre Archéologique du Var, Saudi Commisssion for Tourism and Antiquities, Centre d'études Alexandrines (CEALEX), Centre National de la Recherche Scientifique (CNRS), Histoire et Cultures de l'Antiquité et du Moyen Âge (HISCANT-MA), Université de Lorraine (UL), Musées de la ville de Strasbourg, Natural History Museum [Geneva], University of Hail, CNRS, Université Paris 1 Panthéon-Sorbonne (UP1)-École Pratique des Hautes Études (EPHE), Équipe Mondes sémitiques (OM-MS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris 1 Panthéon-Sorbonne (UP1)-École Pratique des Hautes Études (EPHE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure de Lyon (ENS de Lyon)-Université Lumière - Lyon 2 (UL2)-Université Jean Moulin - Lyon 3 (UJML), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Université de Lyon-Université de Lyon-Aix Marseille Université (AMU)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Université Lumière - Lyon 2 (UL2)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris 1 Panthéon-Sorbonne (UP1)-École pratique des hautes études (EPHE), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS), and École normale supérieure - Lyon (ENS Lyon)-Université Lumière - Lyon 2 (UL2)-Université Jean Moulin - Lyon 3 (UJML)
Subjects: [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Hegra
Published: 2020

11. Contrasting genomic and phenotypic outcomes of hybridization between pairs of mimetic butterfly taxa across a suture zone

Author: Céline Houssin, James Mallet, Fabrice Legeai, Yann Le Poul, Jérémy Gauthier, Donna Lisa de Silva, Zachariah Gompert, Marianne Elias, Annabel Whibley, Melanie McClure, Claire Lemaitre, Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Natural History Museum [Geneva], 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), Department of Biology [Utah], University of Utah, School of Biological Sciences [Auckland], University of Auckland [Auckland], Institut für Soziologie Ludwig-Maximilians-Universität München (LMU), Ludwig-Maximilians-Universität München (LMU), Laboratoire Ecologie, Evolution, Interactions des Systèmes amazoniens (LEEISA), Centre National de la Recherche Scientifique (CNRS)-Université de Guyane (UG)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-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), Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University [Cambridge], CLEARWING ANR‐16‐CE02‐0012, Agence Nationale de la Recherche, RGP0014/2016, Human Frontier Science Program, Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO 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), Harvard University, and ANR-16-CE02-0012,CLEARWING,La transparence : origine physique, fonctions adaptatives et évolution chez les papillons transparents(2016)
Subjects: 0106 biological sciences, 0301 basic medicine, Reproductive Isolation, Genotype, Genetic Speciation, Population, Genome, Insect, introgression, Genetic admixture, Introgression, 010603 evolutionary biology, 01 natural sciences, Nymphalidae, Polymorphism, Single Nucleotide, 03 medical and health sciences, Peru, Genetics, Heliconius, Animals, Wings, Animal, education, Hybridization, Ecology, Evolution, Behavior and Systematics, Hybrid, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, education.field_of_study, biology, [SDV.BA]Life Sciences [q-bio]/Animal biology, Reproductive isolation, differentiation, biology.organism_classification, Ithomiini, 030104 developmental biology, admixture mapping, Genetics, Population, Phenotype, Evolutionary biology, Hybridization, Genetic, Butterflies, mimicry
Abstract: International audience; Hybrid zones, whereby divergent lineages come into contact and eventually hybridize, can provide insights on the mechanisms involved in population differentiation and reproductive isolation, and ultimately speciation. Suture zones offer the opportunity to compare these processes across multiple species. In this paper we use reduced-complexity genomic data to compare the genetic and phenotypic structure and hybridization patterns of two mimetic butterfly species, Ithomia salapia and Oleria onega (Nymphalidae: Ithomiini), each consisting of a pair of lineages differentiated for their wing colour pattern and that come into contact in the Andean foothills of Peru. Despite similarities in their life history, we highlight major differences, both at the genomic and phenotypic level, between the two species. These differences include the presence of hybrids, variations in wing phenotype, and genomic patterns of introgression and differentiation. In I. salapia, the two lineages appear to hybridize only rarely, whereas in O. onega the hybrids are not only more common, but also genetically and phenotypically more variable. We also detected loci statistically associated with wing colour pattern variation, but in both species these loci were not over-represented among the candidate barrier loci, suggesting that traits other than wing colour pattern may be important for reproductive isolation. Our results contrast with the genomic patterns observed between hybridizing lineages in the mimetic Heliconius butterflies, and call for a broader investigation into the genomics of speciation in Ithomiini - the largest radiation of mimetic butterflies.
Published: 2019

12. DiscoSnp-RAD: de novo detection of small variants for population genomics

Author: Nadir Alvarez, Pierre Peterlongo, Chloé Riou, Tomasz Suchan, Jérémy Gauthier, Claire Lemaitre, Charlotte Mouden, Nils Arrigo, Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), W. Szafer Institute of Botany, Polska Akademia Nauk (PAN), Natural History Museum [Geneva], Dpt of Ecology and Evolution [Lausanne], Université de Lausanne (UNIL), and Université de Bordeaux (UB)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, Genetics, 0303 health sciences, population genomics, Shotgun sequencing, Single-nucleotide polymorphism, Computational biology, Biology, 010603 evolutionary biology, 01 natural sciences, Genome, DNA sequencing, De Bruijn graph, Phylogenetic reconstruction, RAD-Seq, Population genomics, 03 medical and health sciences, Restriction site, symbols.namesake, symbols, next-generation sequencing, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], 030304 developmental biology, de novo variant calling
Abstract: We present an original method to de novo call variants for Restriction site associated DNA Sequencing (RAD-Seq). RAD-Seq is a technique characterized by the sequencing of specific loci along the genome, that is widely employed in the field of evolutionary biology since it allows to exploit variants (mainly SNPs) information from entire populations at a reduced cost. Common RAD dedicated tools, as STACKS or IPyRAD, are based on all-versus-all read comparisons, which require consequent time and computing resources. Based on the variant caller DiscoSnp, initially designed for shotgun sequencing, DiscoSnp-RAD avoids this pitfall as variants are detected by exploring the De Bruijn Graph built from all the read datasets. We tested the implementation on RAD data from 259 specimens of Chiastocheta flies, morphologically assigned to 7 species. All individuals were successfully assigned to their species using both STRUCTURE and Maximum Likelihood phylogenetic reconstruction. Moreover, identified variants succeeded to reveal a within species structuration and the existence of two populations linked to their geographic distributions. Furthermore, our results show that DiscoSnp-RAD is at least one order of magnitude faster than state-of-the-art tools. The overall results show that DiscoSnp-RAD is suitable to identify variants from RAD data, and stands out from other tools due to his completely different principle, making it significantly faster, in particular on large datasets.LicenseGNU Affero general public licenseAvailabilityhttps://github.com/GATB/DiscoSnpContactjeremy.gauthier@inria.fr
Published: 2019

13. Gene flow and genetic divergence among mainland and insular populations across the south-western range of the Eurasian treecreeper (Certhia familiaris , Aves)

Author: Georges Olioso, Jean-Marc Pons, Jean-Claude Thibault, Alice Cibois, Jérôme Fuchs, Jérôme Fournier, 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), Dept. of Mammalogy and Ornithology, Natural History Museum [Geneva], Centre d'Ecologie et des Sciences de la COnservation (CESCO), and Muséum national d'Histoire naturelle (MNHN)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Mitochondrial DNA, Population, Allopatric speciation, Corsica, Mediterranean islands, mitochondrial DNA, 010603 evolutionary biology, 01 natural sciences, microsatellites, Gene flow, parasitic diseases, education, Ecology, Evolution, Behavior and Systematics, education.field_of_study, biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], population structure, Certhia familiaris, 15. Life on land, biology.organism_classification, Genetic divergence, Evolutionary biology, Genetic structure, Treecreeper, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, gene flow, geographic locations
Abstract: International audience; The Eurasian treecreeper (Certhia familiaris) comprises two mitochondrial lineages that diverged during the mid-Pleistocene. One palaeoendemic lineage has an allopatric range currently restricted to the island of Corsica and the Caucasus region, whereas the second one has a very large Eurasian range. Here, we used microsatellites (N = 6) and mitochondrial DNA (COI) to assess the genetic structure of insular and mainland populations from Corsica, mainland France and Central Italy (N = 258) and the level of mitochondrial and nuclear gene flow among these populations. Concordant with the mitochondrial DNA signal, the results for microsatellites clearly demonstrate that the Corsican population (Certhia familiaris corsa) is strongly divergent from nearby mainland populations (Certhia familiaris macrodactyla). Microsatellite data also support significant divergence and low gene flow between the Central Italian and mainland French populations. Our results suggest low nuclear gene flow from the mainland into Corsica and no mitochondrial gene flow. Sporadic gene flow from the nearby mainland might explain the presence of continental nuclear alleles in the genome of 5% of sampled insular birds. Our study confirms the existence of an endemic Corsican treecreeper lineage with important conservation value. Our results also imply that Eurasian treecreepers from Central Italy constitute a distinct management unit.
Published: 2019

14. Population expansion, current and past gene flow in Gould’s petrel: implications for conservation

Author: Nicholas Carlile, S. Ruault, A. Iglesias-Vasquez, Vicki L. Friesen, Vincent Bretagnolle, David Priddel, Cécile Ribout, Benoit Gangloff, Alice Cibois, Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université de La Rochelle (ULR), New South Wales Office of Environment and Heritage, Department of Biology, Queen's University, Deparment of Mammalogy and Ornithology, Natural History Museum [Geneva], and Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, 0301 basic medicine, Conservation genetics, Demographic history, Population, 010603 evolutionary biology, 01 natural sciences, Extended Bayesian Skyline plot, 03 medical and health sciences, Genetics, 14. Life underwater, education, Ecology, Evolution, Behavior and Systematics, Pterodroma leucoptera, Leucoptera, education.field_of_study, biology, Ecology, Seabird, 15. Life on land, biology.organism_classification, Phylogeography, 030104 developmental biology, Procellariiformes, [SDE]Environmental Sciences, Threatened species, Isolation with Migration
Abstract: Seabird life-history traits such as long generation time, low annual fecundity and delayed sexual maturation make them more prone to population loss and consequently to extinction; petrels are indeed amongst the most threatened birds. Based on coalescence and multiloci inference this study examines the extent of genetic differentiation of a vulnerable New Caledonia (caledonica) and Australia (leucoptera) subspecies of Pterodroma leucoptera (Gould’s Petrel), and whether the genetic relationship between them results from the influence of past events like variation in sea level, or is dominated by contemporary gene flow. Sequences of two mitochondrial genes and five nuclear introns were obtained from 86 individuals from both populations. Haplotype networks were used to infer relationships between the haplotypes of both populations. The demographic history of the P. leucoptera complex was studied using neutrality tests and Extended Bayesian Skyline Plots. A weak population differentiation was revealed. The Extended Bayesian Skyline plot suggested a population expansion approximately 80,000 years before present (bp) for caledonica and 30,000 years bp for leucoptera. The split was dated to 30,000 years bp by means of multilocus inference through *BEAST. Despite genetic similarity of the two taxa, we advocate to consider them as independent units for conservation management, given their strong ecological distinctiveness (foraging distribution, winter distribution, breeding phenology and breeding distribution).
Published: 2016

15. Modern alongside traditional taxonomy-Integrative systematics of the genera Gymnangium Hincks, 1874 and Taxella Allman, 1874 (Hydrozoa, Aglaopheniidae)

Author: Bautisse Postaire, Emilie Boissin, Chloé A.-F. Bourmaud, Nicole Gravier-Bonnet, Peter Schuchert, Marta Ronowicz, Department of Marine Ecology, Polska Akademia Nauk = Polish Academy of Sciences (PAN)-Institute of Oceanology, Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-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 d'Excellence CORAIL (LabEX CORAIL), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de La Réunion (UR)-Université de la Polynésie Française (UPF)-Université de la Nouvelle-Calédonie (UNC)-Institut d'écologie et environnement-Université des Antilles (UA), Ecologie marine tropicale dans les Océans Pacifique et Indien (ENTROPIE [Réunion]), Centre National de la Recherche Scientifique (CNRS)-Université de La Réunion (UR)-Institut de Recherche pour le Développement (IRD), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Natural History Museum [Geneva], Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École Pratique des Hautes Études (EPHE), Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS), and Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Internodes, Teeth, Gene Expression, lcsh:Medicine, Plant Science, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, Mathematical and Statistical Techniques, Genus, Oceans, Medicine and Health Sciences, Clade, lcsh:Science, Indian Ocean, Phylogeny, Hydrozoa, Data Management, Multidisciplinary, Phylogenetic analysis, biology, Phylogenetic tree, Aglaopheniidae, Plant Anatomy, Phylogenetics, Physical Sciences, Taxonomy (biology), Anatomy, New species reports, Statistics (Mathematics), Research Article, Systematics, Computer and Information Sciences, Genetic Speciation, Rare species, Principal component analysis, Research and Analysis Methods, 010603 evolutionary biology, DNA, Mitochondrial, 03 medical and health sciences, Calmodulin, Indian Ocean Islands, Bodies of water, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Animals, Evolutionary Systematics, 14. Life underwater, Statistical Methods, Taxonomy, Evolutionary Biology, lcsh:R, Biology and Life Sciences, Stem Anatomy, biology.organism_classification, Marine and aquatic sciences, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Earth sciences, 030104 developmental biology, Jaw, Evolutionary biology, Multivariate Analysis, lcsh:Q, Animal Distribution, Digestive System, Head, Mathematics
Abstract: International audience; We studied the diversity within the former genus Gymnangium in the South West Indian Ocean by using an integrative approach of both traditional (morphology-based) and modern molecular taxonomy. Nine species were recorded in the material collected. A total of 97 16S mitochondrial DNA sequences and 54 Calmodulin nuclear sequences from eight Gymnangium/Taxella species were analyzed. We found both morphological and molecular differences in the studied Gymnangium species that make it necessary to split the genus. It is proposed to revalidate the genus Taxella which is currently regarded as a synonym of Gymnangium. Two species of the genus Taxella (T. eximia and T. gracilicaulis), until now regarded as distinct species based on morphological characteristics, cluster together in one phylogenetic clade. Possible explanations are discussed. Two species from Madagascar new to science are herein described and rare species from the Indian Ocean islands are re-described.
Published: 2017

16. Molecular analysis of a storm petrel specimen from the Marquesas Islands, with comments on specimens of Fregetta lineata and F. guttata

Author: Cibois, Alice, Thibault, Jean-Claude, Lecroy, Mary, Bretagnolle, Vincent, Dept. of Mammalogy and Ornithology, Natural History Museum [Geneva], Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Ornithology, American Museum of Natural History (AMNH), Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de la Recherche Agronomique (INRA)-Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), and Lacalle, Martine
Subjects: [SDE] Environmental Sciences, [SDE]Environmental Sciences
Abstract: International audience; An old museum specimen of a storm petrel from the MarquesasIslands (French Polynesia) was sampled genetically. This specimen has beenalternatively attributed to Black-bellied Storm Petrel Fregetta tropica, or describedas a new taxon. Its plumage also recalls the recently rediscovered New ZealandStorm Petrel F. maoriana. However, molecular phylogenetic analysis revealed thatthis specimen is closely related to some individuals of White-bellied Storm PetrelF. grallaria, which species is apparently non-monophyletic.
Published: 2015

17. Dynamic evolution of size and colour in the highly specialized Zodarion ant-eating spiders.

Author: Ortiz D, Pekár S, Bilat J, Shafaie S, Alvarez N, and Gauthier J
Subjects: Animals, Phylogeny, Color, Predatory Behavior, Genomics, Spiders genetics
Abstract: Ecological specialists constitute relevant case studies for understanding the mechanisms, potential and limitations of evolution. The species-rich and strictly myrmecophagous spiders of the genus Zodarion show diversified defence mechanisms, including myrmecomorphy of different ant species and nocturnality. Through Hybridization Capture Using RAD Probes (hyRAD), a phylogenomic technique designed for sequencing poorly preserved specimens, we reconstructed a phylogeny of Zodarion using 52 (approx. a third of the nominal) species that cover its phylogenetic and distributional diversity. We then estimated the evolution of body size and colour, traits that have diversified noticeably and are linked to defence mechanisms, across the group. Our genomic matrix of 300 loci led to a well-supported phylogenetic hypothesis that uncovered two main clades inside Zodarion . Ancestral state estimation revealed the highly dynamic evolution of body size and colour across the group, with multiple transitions and convergences in both traits, which we propose is likely indicative of multiple transitions in ant specialization across the genus. Our study will allow the informed targeted selection of Zodarion taxa of special interest for research into the group's remarkable adaptations to ant specialization. It also exemplifies the utility of hyRAD for phylogenetic studies using museum material.
Published: 2023
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18. A global survey of tapeworms (Cestoda: Proteocephalidae) of 'true' frogs (Amphibia: Ranidae), including a tabulated list of all proteocephalids parasitising amphibians.

Author: Scholz T, de Chambrier A, Kudlai O, Tkach VV, and McAllister CT
Subjects: Animals, Ranidae, North America, Cestode Infections epidemiology, Cestode Infections veterinary, Cestoda
Abstract: Proteocephalid tapeworms of frogs of the family Ranidae ('true' frogs) are reviewed with emphasis on their species diversity, host specificity and geographical distribution. New molecular data (nuclear lsrDNA and mitochondrial COI sequences) are presented for tapeworms of four species of ranid frogs in North America, including the poorly known Ophiotaenia saphena Osler, 1931 of Rana clamitans Latreille and R. catesbeiana (Shaw), which is redescribed using new material from Arkansas, USA. Tapeworms of R. sphenocephala (Cope) and R. pipiens Schreber, the latter previously identified as O. saphena, represent another, putative new species, but are not formally described due to insufficient available material. Proteocephalus papuensis Bursey, Goldberg et Kraus, 2008 from Sylvirana supragrisea (Menzies) is transferred to Ophiotaenia La Rue, 1911 as a new combination. After a critical review of the literature, only nine nominal species of Ophiotaenia are recognised as valid, which is in contrast to the large number of ranid frogs (> 440 spp.). The reasons for this striking disparity are briefly discussed, and a key based on morphology is presented for the identification of all species of Ophiotaenia from the Ranidae. Molecular data are available for only two taxa from North America that form a monophyletic group. The relationships among tapeworms of ranid frogs occurring in other zoogeographical regions are not yet known. The taxonomic status of Batrachotaenia Rudin, 1917, which was erected to accommodate proteocephalids from amphibians, is also discussed. To facilitate future studies, a tabulated summary of all 32 species of proteocephalids belonging to three genera reported from amphibians (frogs and salamanders) is presented, with information on their hosts, distribution, and taxonomically important characters, including key measurements.
Published: 2023
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19. Hybridization fuelled diversification in Spialia butterflies.

Author: Hinojosa JC, Dapporto L, Pitteloud C, Koubínová D, Hernández-Roldán J, Vicente JC, Alvarez N, and Vila R
Subjects: Animals, DNA, Mitochondrial genetics, Gene Flow, Genomics, Hybridization, Genetic, Male, Phylogeny, Butterflies genetics
Abstract: The importance of hybridization and introgression is well documented in the evolution of plants but, in insects, their role is not fully understood. Given the fact that insects are the most diverse group of organisms, assessing the impact of reticulation events on their evolution may be key to comprehend the emergence of such remarkable diversity. Here, we used an insect model, the Spialia butterflies, to gather genomic evidence of hybridization as a promoter of novel diversity. By using double-digest RADseq (ddRADseq), we explored the phylogenetic relationships between Spialia orbifer, S. rosae and S. sertorius, and documented two independent events of interspecific gene flow. Our data support that the Iberian endemism S. rosae probably received genetic material from S. orbifer in both mitochondrial and nuclear DNA, which could have contributed to a shift in the ecological preferences of S. rosae. We also show that admixture between S. sertorius and S. orbifer probably occurred in Italy. As a result, the admixed Sicilian populations of S. orbifer are differentiated from the rest of populations both genetically and morphologically, and display signatures of reproductive character displacement in the male genitalia. Additionally, our analyses indicated that genetic material from S. orbifer is present in S. sertorius along the Italian Peninsula. Our findings add to the view that hybridization is a pervasive phenomenon in nature and in butterflies in particular, with important consequences for evolution due to the emergence of novel phenotypes., (© 2022 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)
Published: 2022
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20. A fossil assemblage from the mid-late Maastrichtian of Gavdos Island, Greece, provides insights into the pre-extinction pelagic ichthyofaunas of the Tethys.

Author: Argyriou T, Alexopoulos A, Carrillo-Briceño JD, and Cavin L
Subjects: Animals, Biological Evolution, Fishes, Greece, Vertebrates, Water, Fossils, Gastropoda
Abstract: The global body-fossil record of marine 'fishes' from the time interval immediately preceding the Cretaceous-Paleogene Extinction is markedly poor. This deficiency appears to be further exacerbated with regards to offshore and deep-water taxa, obscuring our understanding of the state and composition of corresponding vertebrate faunas at the onset of this major extinction event. Recent fieldwork in the mid-late Maastrichtian exposures of the Pindos Unit in Gavdos Island, Greece, yielded a small but informative sample of fossil 'fishes', which inhabited the Tethys approximately three to four million years before the extinction. In this work we describe this sample, which comprises between eight and nine discrete morphotypes of various size classes, belonging to †Ichthyodectoidei, Aulopiformes (†Dercetidae, †Enchodontidae, †Ichthyotringidae), cf. †Sardinioididae, as well as the hexanchid shark †Gladioserratus sp. The new material expands the faunal list for the Maastrichtian of Gavdos Island, and the Pindos Unit as a whole, and further allows for the description of a new genus and species of †Enchodontidae and a new species of †Ichthyotringidae. The two new taxa are found to be widespread in the Maastrichtian of the Pindos Unit. The overall character of the assemblage agrees with previous interpretations of an offshore and rather deep depositional environment for the fossiliferous horizons. Furthermore, it exhibits a higher diversity than, and little taxonomic overlap with penecontemporaneous teleost assemblages from the Tethys, and informs on the otherwise poorly known Maastrichtian offshore and deep-water marine ichthyofaunas of the region., Competing Interests: The authors have declared that no competing interests exist.
Published: 2022
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21. Brazilian cave heritage under siege.

Author: Ferreira RL, Bernard E, da Cruz Júnior FW, Piló LB, Calux A, Souza-Silva M, Barlow J, Pompeu PS, Cardoso P, Mammola S, García AM, Jeffery WR, Shear W, Medellín RA, Wynne JJ, Borges PAV, Kamimura Y, Pipan T, Hajna NZ, Sendra A, Peck S, Onac BP, Culver DC, Hoch H, Flot JF, Stoch F, Pavlek M, Niemiller ML, Manchi S, Deharveng L, Fenolio D, Calaforra JM, Yager J, Griebler C, Nader FH, Humphreys WF, Hughes AC, Fenton B, Forti P, Sauro F, Veni G, Frumkin A, Gavish-Regev E, Fišer C, Trontelj P, Zagmajster M, Delic T, Galassi DMP, Vaccarelli I, Komnenov M, Gainett G, da Cunha Tavares V, Kováč Ľ, Miller AZ, Yoshizawa K, Di Lorenzo T, Moldovan OT, Sánchez-Fernández D, Moutaouakil S, Howarth F, Bilandžija H, Dražina T, Kuharić N, Butorac V, Lienhard C, Cooper SJB, Eme D, Strauss AM, Saccò M, Zhao Y, Williams P, Tian M, Tanalgo K, Woo KS, Barjakovic M, McCracken GF, Simmons NB, Racey PA, Ford D, Labegalini JA, Colzato N, Ramos Pereira MJ, Aguiar LMS, Moratelli R, Du Preez G, Pérez-González A, Reboleira ASPS, Gunn J, Mc Cartney A, Bobrowiec PED, Milko D, Kinuthia W, Fischer E, Meierhofer MB, and Frick WF
Published: 2022
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22. The first late cretaceous mawsoniid coelacanth (Sarcopterygii: Actinistia) from North America: Evidence of a lineage of extinct 'living fossils'.

Author: Cavin L, Toriño P, Van Vranken N, Carter B, Polcyn MJ, and Winkler D
Subjects: Animals, North America, Phylogeny, Biological Evolution, Extinction, Biological, Bone and Bones anatomy & histology, Fossils, Fishes anatomy & histology, Fishes classification
Abstract: Today, the only living genus of coelacanth, Latimeria is represented by two species along the eastern coast of Africa and in Indonesia. This sarcopterygian fish is nicknamed a "living fossil", in particular because of its slow evolution. The large geographical distribution of Latimeria may be a reason for the great resilience to extinction of this lineage, but the lack of fossil records for this genus prevents us from testing this hypothesis. Here we describe isolated bones (right angular, incomplete basisphenoid, fragments of parasphenoid and pterygoid) found in the Cenomanian Woodbine Formation in northeast Texas that are referred to the mawsoniid coelacanth Mawsonia sp. In order to assess the impact of this discovery on the alleged characteristic of "living fossils" in general and of coelacanths in particular: 1) we compared the average time duration of genera of ray-finned fish and coelacanth in the fossil record; 2) we compared the biogeographic signal from Mawsonia with the signal from the rest of the vertebrate assemblage of the Woodbine formation; and 3) we compared these life traits with those of Latimeria. The stratigraphical range of Mawsonia is at least 50 million years. Since Mawsonia was a fresh, brackish water fish with probably a low ability to cross large sea barriers and because most of the continental components of the Woodbine Fm vertebrate assemblage exhibit Laurasian affinities, it is proposed that the Mawsonia's occurrence in North America is more likely the result of a vicariant event linked to the break-up of Pangea rather than the result of a dispersal from Gondwana. The link between a wide geographic distribution and the resilience to extinction demonstrated here for Mawsonia is a clue that a similar situation existed for Latimeria, which allowed this genus to live for tens of millions of years., Competing Interests: The authors have declared that no competing interests exist.
Published: 2021
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23. Comparative transcriptome analysis at the onset of speciation in a mimetic butterfly-The Ithomiini Melinaea marsaeus.

Author: Piron-Prunier F, Persyn E, Legeai F, McClure M, Meslin C, Robin S, Alves-Carvalho S, Mohammad A, Blugeon C, Jacquin-Joly E, Montagné N, Elias M, and Gauthier J
Subjects: Animals, Gene Expression Profiling, Reproductive Isolation, Transcriptome, Wings, Animal, Butterflies genetics
Abstract: Ecological speciation entails divergent selection on specific traits and ultimately on the developmental pathways responsible for these traits. Selection can act on gene sequences but also on regulatory regions responsible for gene expression. Mimetic butterflies are a relevant system for speciation studies because wing colour pattern (WCP) often diverges between closely related taxa and is thought to drive speciation through assortative mating and increased predation on hybrids. Here, we generate the first transcriptomic resources for a mimetic butterfly of the tribe Ithomiini, Melinaea marsaeus, to examine patterns of differential expression between two subspecies and between tissues that express traits that likely drive reproductive isolation; WCP and chemosensory genes. We sequenced whole transcriptomes of three life stages to cover a large catalogue of transcripts, and we investigated differential expression between subspecies in pupal wing discs and antennae. Eighteen known WCP genes were expressed in wing discs and 115 chemosensory genes were expressed in antennae, with a remarkable diversity of chemosensory protein genes. Many transcripts were differentially expressed between subspecies, including two WCP genes and one odorant receptor. Our results suggest that in M. marsaeus the same genes as in other mimetic butterflies are involved in traits causing reproductive isolation, and point at possible candidates for the differences in those traits between subspecies. Differential expression analyses of other developmental stages and body organs and functional studies are needed to confirm and expand these results. Our work provides key resources for comparative genomics in mimetic butterflies, and more generally in Lepidoptera., (© 2021 European Society for Evolutionary Biology.)
Published: 2021
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24. The origins and spread of domestic horses from the Western Eurasian steppes.

Author: Librado P, Khan N, Fages A, Kusliy MA, Suchan T, Tonasso-Calvière L, Schiavinato S, Alioglu D, Fromentier A, Perdereau A, Aury JM, Gaunitz C, Chauvey L, Seguin-Orlando A, Der Sarkissian C, Southon J, Shapiro B, Tishkin AA, Kovalev AA, Alquraishi S, Alfarhan AH, Al-Rasheid KAS, Seregély T, Klassen L, Iversen R, Bignon-Lau O, Bodu P, Olive M, Castel JC, Boudadi-Maligne M, Alvarez N, Germonpré M, Moskal-Del Hoyo M, Wilczyński J, Pospuła S, Lasota-Kuś A, Tunia K, Nowak M, Rannamäe E, Saarma U, Boeskorov G, Lōugas L, Kyselý R, Peške L, Bălășescu A, Dumitrașcu V, Dobrescu R, Gerber D, Kiss V, Szécsényi-Nagy A, Mende BG, Gallina Z, Somogyi K, Kulcsár G, Gál E, Bendrey R, Allentoft ME, Sirbu G, Dergachev V, Shephard H, Tomadini N, Grouard S, Kasparov A, Basilyan AE, Anisimov MA, Nikolskiy PA, Pavlova EY, Pitulko V, Brem G, Wallner B, Schwall C, Keller M, Kitagawa K, Bessudnov AN, Bessudnov A, Taylor W, Magail J, Gantulga JO, Bayarsaikhan J, Erdenebaatar D, Tabaldiev K, Mijiddorj E, Boldgiv B, Tsagaan T, Pruvost M, Olsen S, Makarewicz CA, Valenzuela Lamas S, Albizuri Canadell S, Nieto Espinet A, Iborra MP, Lira Garrido J, Rodríguez González E, Celestino S, Olària C, Arsuaga JL, Kotova N, Pryor A, Crabtree P, Zhumatayev R, Toleubaev A, Morgunova NL, Kuznetsova T, Lordkipanize D, Marzullo M, Prato O, Bagnasco Gianni G, Tecchiati U, Clavel B, Lepetz S, Davoudi H, Mashkour M, Berezina NY, Stockhammer PW, Krause J, Haak W, Morales-Muñiz A, Benecke N, Hofreiter M, Ludwig A, Graphodatsky AS, Peters J, Kiryushin KY, Iderkhangai TO, Bokovenko NA, Vasiliev SK, Seregin NN, Chugunov KV, Plasteeva NA, Baryshnikov GF, Petrova E, Sablin M, Ananyevskaya E, Logvin A, Shevnina I, Logvin V, Kalieva S, Loman V, Kukushkin I, Merz I, Merz V, Sakenov S, Varfolomeyev V, Usmanova E, Zaibert V, Arbuckle B, Belinskiy AB, Kalmykov A, Reinhold S, Hansen S, Yudin AI, Vybornov AA, Epimakhov A, Berezina NS, Roslyakova N, Kosintsev PA, Kuznetsov PF, Anthony D, Kroonen GJ, Kristiansen K, Wincker P, Outram A, and Orlando L
Subjects: Animals, Archaeology, Asia, DNA, Ancient, Europe, Genome, Grassland, Phylogeny, Domestication, Genetics, Population, Horses genetics
Abstract: Domestication of horses fundamentally transformed long-range mobility and warfare 1 . However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling 2-4 at Botai, Central Asia around 3500 BC 3 . Other longstanding candidate regions for horse domestication, such as Iberia 5 and Anatolia 6 , have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 BC, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association 7 between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 BC 8,9 driving the spread of Indo-European languages 10 . This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium BC Sintashta culture 11,12 ., (© 2021. The Author(s).)
Published: 2021
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25. Poor performance of DNA barcoding and the impact of RAD loci filtering on the species delimitation of an Iberian ant-eating spider.

Author: Ortiz D, Pekár S, Bilat J, and Alvarez N
Subjects: Animals, Cell Nucleus genetics, Cluster Analysis, Electron Transport Complex IV genetics, Genetics, Population, Genomics, Geography, Likelihood Functions, Mitochondria genetics, Species Specificity, Spiders classification, DNA Barcoding, Taxonomic, Genetic Loci, Phylogeny, Restriction Mapping, Sequence Analysis, DNA, Spiders genetics
Abstract: Genomic data provide unprecedented power for species delimitation. However, current implementations are still time and resource consuming. In addition, bioinformatic processing is contentious and its impact on downstream analyses is insufficiently understood. Here we employ ddRAD sequencing and a thorough sampling for species delimitation in Zodarion styliferum, a widespread Iberian ant-eating spider. We explore the influence of the loci filtering strategy on the downstream phylogenetic analyses, genomic clustering and coalescent species delimitation. We also assess the accuracy of one mitochondrial (COI) and one nuclear (ITS) barcode for fast and inexpensive species delineation in the group. Our genomic data strongly support two morphologically cryptic but ecologically divergent lineages, mainly restricted to the central-eastern and western parts of the Iberian Peninsula, respectively. Larger matrices with more missing data showed increased genomic diversity, supporting that bioinformatic strategies to maximize matrix completion disproportionately exclude loci with the highest mutation rates. Moderate loci filtering gave the best results across analyses: although larger matrices returned concatenated phylogenies with higher support, middle-sized matrices performed better in genetic structure analyses. COI displayed high diversity and a conspicuous barcode gap, revealing 13 mitochondrial lineages. Mitonuclear discordance is consistent with ancestral isolation in multiple groups, probably in glacial refugia, followed by range expansion and secondary contact that produced genomic homogenization. Several apparently (unidirectionally) introgressed specimens further challenge the accuracy of species identification through mitochondrial barcodes in the group. Conversely, ITS failed to separate both lineages of Z. styliferum. This study shows an extreme case of mitonuclear discordance that highlights the limitations of single molecular barcodes for species delimitation, even in presence of distinct barcode gaps, and brings new light on the effects of parameterization on shallow-divergence studies using RAD data., (Copyright © 2020 Elsevier Inc. All rights reserved.)
Published: 2021
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26. Museomics identifies genetic erosion in two butterfly species across the 20th century in Finland.

Author: Gauthier J, Pajkovic M, Neuenschwander S, Kaila L, Schmid S, Orlando L, and Alvarez N
Subjects: Animals, Biodiversity, Ecosystem, Finland, Genetic Variation, Museums, Population Dynamics, Butterflies classification, Butterflies genetics, Evolution, Molecular
Abstract: Erosion of biodiversity generated by anthropogenic activities has been studied for decades and in many areas at the species level, using taxa monitoring. In contrast, genetic erosion within species has rarely been tracked, and is often studied by inferring past population dynamics from contemporaneous estimators. An alternative to such inferences is the direct examination of past genes, by analysing museum collection specimens. While providing direct access to genetic variation over time, historical DNA is usually not optimally preserved, and it is necessary to apply genotyping methods based on hybridization-capture to unravel past genetic variation. In this study, we apply such a method (i.e., HyRAD), to large time series of two butterfly species in Finland, and present a new bioinformatic pipeline, namely PopHyRAD, that standardizes and optimizes the analysis of HyRAD data at the within-species level. In the localities for which the data retrieved have sufficient power to accurately examine genetic dynamics through time, we show that genetic erosion has increased across the last 100 years, as revealed by signatures of allele extinctions and heterozygosity decreases, despite local variations. In one of the two butterflies (Erebia embla), isolation by distance also increased through time, revealing the effect of greater habitat fragmentation over time., (© 2020 John Wiley & Sons Ltd.)
Published: 2020
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27. Contrasting genomic and phenotypic outcomes of hybridization between pairs of mimetic butterfly taxa across a suture zone.

Author: Gauthier J, de Silva DL, Gompert Z, Whibley A, Houssin C, Le Poul Y, McClure M, Lemaitre C, Legeai F, Mallet J, and Elias M
Subjects: Animals, Butterflies classification, Genetic Speciation, Genome, Insect, Genotype, Peru, Phenotype, Polymorphism, Single Nucleotide, Reproductive Isolation, Wings, Animal anatomy & histology, Butterflies genetics, Genetics, Population, Hybridization, Genetic
Abstract: Hybrid zones, whereby divergent lineages come into contact and eventually hybridize, can provide insights on the mechanisms involved in population differentiation and reproductive isolation, and ultimately speciation. Suture zones offer the opportunity to compare these processes across multiple species. In this paper we use reduced-complexity genomic data to compare the genetic and phenotypic structure and hybridization patterns of two mimetic butterfly species, Ithomia salapia and Oleria onega (Nymphalidae: Ithomiini), each consisting of a pair of lineages differentiated for their wing colour pattern and that come into contact in the Andean foothills of Peru. Despite similarities in their life history, we highlight major differences, both at the genomic and phenotypic level, between the two species. These differences include the presence of hybrids, variations in wing phenotype, and genomic patterns of introgression and differentiation. In I. salapia, the two lineages appear to hybridize only rarely, whereas in O. onega the hybrids are not only more common, but also genetically and phenotypically more variable. We also detected loci statistically associated with wing colour pattern variation, but in both species these loci were not over-represented among the candidate barrier loci, suggesting that traits other than wing colour pattern may be important for reproductive isolation. Our results contrast with the genomic patterns observed between hybridizing lineages in the mimetic Heliconius butterflies, and call for a broader investigation into the genomics of speciation in Ithomiini - the largest radiation of mimetic butterflies., (© 2020 John Wiley & Sons Ltd.)
Published: 2020
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28. Evolutionary history of the Cameroon radiation of puddle frogs (Phrynobatrachidae: Phrynobatrachus ), with descriptions of two critically endangered new species from the northern Cameroon Volcanic Line.

Author: Gvoždík V, Nečas T, Dolinay M, Zimkus BM, Schmitz A, and Fokam EB
Abstract: The Cameroon Volcanic Line, a mountain chain located between West and Central Africa, is a region of numerous endemic diversifications, including of puddle frogs ( Phrynobatrachus ). This study reviews the phylogeny and taxonomy of puddle frogs of the "Cameroon radiation," which is a clade containing mainly montane but also at least three lowland species. Molecular data revealed a novel evolutionary lineage from high altitudes in the northern part of the mountains. Puddle frogs from the new, minute-sized (SVL < 20 mm) lineage are identified using molecular, morphological and acoustic data and described as two new species, Phrynobatrachus arcanus sp. nov. (Gotel Mountains, Cameroon-Nigeria) and P. mbabo sp. nov. (Tchabal Mbabo, Cameroon). The tadpole of the first species is also described. Phylogenetic analyses placed the new lineage to the proximity of the recently described lowland small-sized taxa ( P. horsti , P. ruthbeateae ). Based on the inferred phylogeny, we propose five species groups within the Cameroon radiation: P. arcanus , P. chukuchuku , P. ruthbeateae , P. steindachneri , and P. werneri . The taxonomically enigmatic P. hylaios is proposed to be a member of the P. ruthbeateae species group. The basal radiation evolved during the late Miocene with subsequent diversifications occurring during the Pliocene, while closely related terminal taxa originated during the Pleistocene. We recommend that the newly described species are categorized as Critically Endangered due to their limited ranges and because recent surveys did not identify any individuals at the type localities. This further supports the need for conservation interventions in the mountains of Cameroon and Nigeria., Competing Interests: The authors declare that they have no competing interests., (© 2020 Gvoždík et al.)
Published: 2020
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29. Untangling convoluted taxonomy of Chambriella Rego, Chubb & Pavanelli, 1999 (Cestoda: Proteocephalidae), with erection of Riggenbachiella n. g. and the description of a new species from pimelodid catfishes in the Neotropical Region.

Author: Alves PV, de Chambrier A, Luque JL, and Scholz T
Subjects: Animals, Brazil, Cestoda anatomy & histology, Cestoda genetics, DNA, Helminth genetics, Intestines parasitology, Rivers, Species Specificity, Catfishes parasitology, Cestoda classification
Abstract: As part of a complex revision of proteocephalid cestodes parasitic in freshwater bony fishes of the Neotropical Region, the genus Chambriella Rego, Chubb & Pavanelli, 1999 is redefined based on detailed examination of type-specimens and newly collected material of both nominal species of the genus. This examination revealed that the type-species C. agostinhoi (Pavanelli & Santos, 1992) from Zungaro jahu (Ihering) (type-host) and Z. zungaro (Humboldt) is indistinguishable from Lenhataenia megacephala (Woodland, 1934) from Sorubimichthys planiceps (Spix & Agassiz) (all hosts Siluriformes: Pimelodidae), the type- and only species of the genus. New molecular data (partial sequences of the large subunit nuclear ribosomal RNA gene) support the conspecificity of these taxa. As a result, Lenhataenia de Chambrier & Scholz, 2008 becomes a junior synonym of Chambriella and its type-species, C. agostinhoi, a junior synonym of C. megacephala (Woodland, 1934) n. comb. The second species of Chambriella, C. paranaensis (Pavanelli & Rego, 1989) from Hemisorubim platyrhynchos (Valenciennes), is transferred to a new genus, Riggenbachiella n. g., as R. paranaense (Pavanelli & Rego, 1989) n. comb. Riggenbachiella amazonense n. sp. (syn. Chambriella sp. of de Chambrier & Scholz, 2008) from S. planiceps (type-host), Phractocephalus hemioliopterus (Bloch & Schneider) and Z. zungaro is described and designated as the type-species of the new genus. Riggenbachiella n. g. is placed in the subfamily Monticelliinae Mola, 1929, because of the cortical position of the testes, ovary, vitelline follicles and uterus, and is mainly characterised by the possession of a sigmoid cirrus-sac with voluminous, chambered internal seminal vesicle, and bi-loculate suckers.
Published: 2017
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30. A new genus and species of proteocephalidean tapeworm (Cestoda), first parasite found in the driftwood catfish Tocantinsia piresi (Siluriformes: Auchenipteridae) from Brazil.

Author: Alves PV, Chambrier Ad, Scholz T, and Luque JL
Abstract: Frezella gen. n. is proposed to accommodate Frezella vaucheri sp. n. from poorly known auchenipterid fish, Tocantinsia piresi (Miranda Ribeiro), from the Xingú River, one of the principal tributaries of the lower Amazon River in Brazil. The new genus belongs to the Proteocephalinae because of the medullary position of the testes, ovary (yet some follicles penetrate to the cortex on the dorsal side), vitelline follicles and uterus. It differs from other proteocephaline genera in the morphology of the scolex, which includes a metascolex composed of two distinct zones: anterior, strongly wrinkled part posterior to the suckers, and posterior, sparsely folded zone. Frezella can also be differentiated by having the internal longitudinal musculature hypertrophied laterally on both sides, the presence of some ovarian follicles in the cortex on the dorsal side and the presence of additional pair of tiny, thin-walled osmoregulatory canals situated slightly dorsomedian to ventral canals. Frezella vaucheri is the first helminth parasite reported from T. piresi, which occurs in the lower reaches of the Amazon and Tocantins River basins in Brazil.
Published: 2015
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31. A new genus of the family Hymenolepididae (Cestoda) from Sephanoides sephaniodes (Apodiformes, Trochilidae) in Northern Patagonia (Chile).

Author: Widmer VC, Georgiev BB, and Mariaux J
Subjects: Animals, Bird Diseases epidemiology, Birds, Cestoda genetics, Cestode Infections epidemiology, Cestode Infections parasitology, Chile epidemiology, Phylogeny, Species Specificity, Bird Diseases parasitology, Cestoda anatomy & histology, Cestoda classification, Cestode Infections veterinary
Abstract: A new species of hymenolepidid cestodes from Sephanoides sephaniodes (Trochilidae) found in Chile is described. The most characteristic features of Colibrilepis pusilla gen. nov., sp. nov. are the lack of rostellum, a cirrus sac with a thick-walled distal end (separated by a constriction) and protruding into genital atrium, a thick-walled saccular uterus filling entire median field of the gravid proglottis and the small number of eggs containing thick walled embryophores with polar swellings. Staphylepis is the most similar genus but differs in its apical structure because of the presence of a rudimentary rostellum. Moreover, molecular phylogenetic analyses show that Staphylepis and Colibrilepis are not sister taxa.
Published: 2013
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32. Cretaceous stem chondrichthyans survived the end-Permian mass extinction.

Author: Guinot G, Adnet S, Cavin L, and Cappetta H
Subjects: Animals, Biodiversity, Biological Evolution, Ecosystem, Extinction, Biological, Oceans and Seas, Sharks classification, Sharks physiology, Time Factors, Tooth physiology, Adaptation, Physiological, Fossils, Paleontology, Phylogeny, Sharks anatomy & histology, Tooth anatomy & histology
Abstract: Cladodontomorph sharks are Palaeozoic stem chondrichthyans thought to go extinct at the end-Permian mass extinction. This extinction preceded the diversification of euselachians, including modern sharks. Here we describe an outer-platform cladodontomorph shark tooth assemblage from the Early Cretaceous of southern France, increasing the fossil record of this group by circa 120 million years. Identification of this material rests on new histological observations and morphological evidence. Our finding shows that this lineage survived mass extinctions most likely by habitat contraction, using deep-sea refuge environments during catastrophic events. The recorded gap in the cladodontomorph lineage represents the longest gap in the fossil record for an extinct marine vertebrate group. This discovery demonstrates that the deep-sea marine diversity, poorly known during most of the fish evolutionary history, contains essential data for a complete understanding of the long-term evolution of marine fish paleobiodiversity.
Published: 2013
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33. Paleontology. On giant filter feeders.

Author: Cavin L
Subjects: Animals, Biodiversity, Biological Evolution, Climate, Extinction, Biological, Feeding Behavior, Food Chain, Geologic Sediments, Phylogeny, Diatoms, Fishes anatomy & histology, Fishes classification, Fishes physiology, Fossils, Whales anatomy & histology, Whales classification, Whales physiology
Published: 2010
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34. Redescription of Testudotaenia testudo (Magath, 1924) (Eucestoda: Proteocephalidea), a parasite of Apalone spinifera (Le Sueur) (Reptilia: Trionychidae) and Amia calva L. (Pisces: Amiidae) in North America and erection of the Testudotaeniinae n. subfam.

Author: de Chambrier A, Coquille SC, Mariaux J, and Tkach V
Subjects: Animals, Cestoda genetics, DNA genetics, Phylogeny, Cestoda classification, Cestoda ultrastructure, Fishes parasitology, Turtles parasitology
Abstract: Testudotaenia testudo (Magath, 1924) is redescribed from the intestine of the softshell turtle Apalone spinifera (Le Sueur) (Trionychidae) and the bowfin Amia calva Linnaeus (Amiidae) from Reelfoot Lake, Tennessee, United States. A new subfamily, the Testudotaeniinae, is erected. The new taxon differs from all proteocephalidean subfamilies in the position of the genital organs in relation to the longitudinal internal musculature, i.e. the testes are cortical, rarely medullary; the ovary is partly medullary, with cortical lobes; the vitelline follicles are mainly medullary, with some follicles in the cortex; and the uterus is cortical. A key to the subfamilies of the order Proteocephalidea Mola, 1928 is provided. The most characteristic features of T. testudo are the precocious uterine aperture, the presence of internal uterine pores (as previously described for Proteocephalus paraguayensis (Rudin, 1917)), the eggs laid unripe, the very long strobila (up to 970 mm), and the presence of an anterior circular musculature in the suckers, which is considered as a good differential character. Three other species were found in Amia calva: Proteocephalus perplexus La Rue, 1911, P. ambloplitis (Leidy, 1887) and a new, undescribed form. Sequences of the partial nuclear 28S rRNA gene of specimens of T. testudo from Apalone spinulifera and Amia calva confirm the conspecificity of samples from these two very distinct hosts, which may represent a capture phenomenon. As the subfamily Adenobrechmoinae Bursey, Goldberg & Kraus, 2006 and the genus Adenobrechmos Bursey, Goldberg & Kraus, 2006 are based on the presence of an apical organ, a character which reflects a rather common convergence, we consider the Adenobrechmoinae to be a junior synonym of the Proteocephalinae La Rue, 1911 and Adenobrechmos a junior synonym of Ophiotaenia La Rue, 1911. Adenobrechmos greeri Bursey, Goldberg & Kraus, 2006 thus becomes Ophiotaenia greeri (Bursey, Goldberg & Kraus, 2006) n. comb.
Published: 2009
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34 results on '"Natural History Museum [Geneva]"'

1. First chromosome scale genomes of ithomiine butterflies (Nymphalidae: Ithomiini): comparative models for mimicry genetic studies

2. Functional and taxonomic responses of tropical moth communities to deforestation

3. Comparative osteology of the fossorial frogs of the genus Synapturanus (Anura, Microhylidae) with the description of three new species from the Eastern Guiana Shield

4. Reed warblers in the Marquesas Islands: song divergence and plumage convergence of two distinct lineages

5. Size, microhabitat, and loss of larval feeding drive cranial diversification in frogs

6. EvoSheep : The Makeup of Sheep Breeds in the Ancient Near East

7. Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization

8. Linking seascape with landscape genetics: Oceanic currents favour colonization across the Galápagos Islands by a coastal plant

9. DiscoSnp-RAD: de novo detection of small variants for RAD-Seq population genomics

10. Report on the 2018 and 2019 Seasons of the Madâ'in Sâlih Archaeological Project

11. Contrasting genomic and phenotypic outcomes of hybridization between pairs of mimetic butterfly taxa across a suture zone

12. DiscoSnp-RAD: de novo detection of small variants for population genomics

13. Gene flow and genetic divergence among mainland and insular populations across the south-western range of the Eurasian treecreeper (Certhia familiaris , Aves)

14. Population expansion, current and past gene flow in Gould’s petrel: implications for conservation

15. Modern alongside traditional taxonomy-Integrative systematics of the genera Gymnangium Hincks, 1874 and Taxella Allman, 1874 (Hydrozoa, Aglaopheniidae)

16. Molecular analysis of a storm petrel specimen from the Marquesas Islands, with comments on specimens of Fregetta lineata and F. guttata

17. Dynamic evolution of size and colour in the highly specialized Zodarion ant-eating spiders.

18. A global survey of tapeworms (Cestoda: Proteocephalidae) of 'true' frogs (Amphibia: Ranidae), including a tabulated list of all proteocephalids parasitising amphibians.

19. Hybridization fuelled diversification in Spialia butterflies.

20. A fossil assemblage from the mid-late Maastrichtian of Gavdos Island, Greece, provides insights into the pre-extinction pelagic ichthyofaunas of the Tethys.

21. Brazilian cave heritage under siege.

22. The first late cretaceous mawsoniid coelacanth (Sarcopterygii: Actinistia) from North America: Evidence of a lineage of extinct 'living fossils'.

23. Comparative transcriptome analysis at the onset of speciation in a mimetic butterfly-The Ithomiini Melinaea marsaeus.

24. The origins and spread of domestic horses from the Western Eurasian steppes.

25. Poor performance of DNA barcoding and the impact of RAD loci filtering on the species delimitation of an Iberian ant-eating spider.

26. Museomics identifies genetic erosion in two butterfly species across the 20th century in Finland.

27. Contrasting genomic and phenotypic outcomes of hybridization between pairs of mimetic butterfly taxa across a suture zone.

28. Evolutionary history of the Cameroon radiation of puddle frogs (Phrynobatrachidae: Phrynobatrachus ), with descriptions of two critically endangered new species from the northern Cameroon Volcanic Line.

29. Untangling convoluted taxonomy of Chambriella Rego, Chubb & Pavanelli, 1999 (Cestoda: Proteocephalidae), with erection of Riggenbachiella n. g. and the description of a new species from pimelodid catfishes in the Neotropical Region.

30. A new genus and species of proteocephalidean tapeworm (Cestoda), first parasite found in the driftwood catfish Tocantinsia piresi (Siluriformes: Auchenipteridae) from Brazil.

31. A new genus of the family Hymenolepididae (Cestoda) from Sephanoides sephaniodes (Apodiformes, Trochilidae) in Northern Patagonia (Chile).

32. Cretaceous stem chondrichthyans survived the end-Permian mass extinction.

33. Paleontology. On giant filter feeders.

34. Redescription of Testudotaenia testudo (Magath, 1924) (Eucestoda: Proteocephalidea), a parasite of Apalone spinifera (Le Sueur) (Reptilia: Trionychidae) and Amia calva L. (Pisces: Amiidae) in North America and erection of the Testudotaeniinae n. subfam.

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34 results on '"Natural History Museum [Geneva]"'

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