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4,194 results on '"Department of Genetics, Evolution '

1. Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses (a response to Vilella et al.’s correspondence)

Author: University of Geneva - Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, UNamur - SBIO_URBM (unité de recherche en biologie moléculaire), CRG - Centre de Regulació Genòmica, Milinkovitch, Michel C., Helaers, Raphaël, Depiereux, Eric, Tzika, Athanasia C., Gabaldon, Toni, University of Geneva - Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, UNamur - SBIO_URBM (unité de recherche en biologie moléculaire), CRG - Centre de Regulació Genòmica, Milinkovitch, Michel C., Helaers, Raphaël, Depiereux, Eric, Tzika, Athanasia C., and Gabaldon, Toni
Abstract: a response to Vilella et al.’s correspondence (A response to 2x genomes - depth does matter by MC Milinkovitch, R Helaers, E Depiereux, AC Tzika and T Gabaldón. Genome Biol 2010, 11:R16.)
Published: 2010

2. Mapping gene gains and losses among metazoan full genomes using an integrated phylogenetic framework

Author: University of Geneva - Laboratory of Natural and Artificial Evolution, Department of Genetics and Evolution, UNamur - SBIO_URBM (unité de recherche en biologie moléculaire), Tzika, Athanasia C., Helaers, Raphaël, Milinkovitch, Michel C., University of Geneva - Laboratory of Natural and Artificial Evolution, Department of Genetics and Evolution, UNamur - SBIO_URBM (unité de recherche en biologie moléculaire), Tzika, Athanasia C., Helaers, Raphaël, and Milinkovitch, Michel C.
Abstract: Gene duplication has long been believed to have played a major role in the rise of biological novelty through evolution of new function and gene expression patterns. The first book to examine gene duplication across all levels of biological organization, Evolution after Gene Duplication presents a comprehensive picture of the mechanistic process by which gene duplication may have played a role in generating biodiversity. Key Features: Explores comparative genomics, genome evolution studies and analysis of multi-gene families such as Hox, globins, olfactory receptors and MHC (immune system) A complete post-genome treatment of the topic originally covered by Ohno's 1970 classic, this volume extends coverage to include the fate of associated regulatory pathways Taps the significant increase in multi-gene family data that has resulted from comparative genomics Comprehensive coverage that includes opposing theoretical viewpoints, comparative genomics data, theoretical and empirical evidence and the role of bioinformatics in the study of gene duplication This up-to-date overview of theory and mathematical models along with practical examples is suitable for scientists across various levels of biology as well as instructors and graduate students.
Published: 2010

3. Benthic protists: the under-charted majority

Author: Diana Sarno, Nathalie Simon, John R. Dolan, Adriana Zingone, Patrick Wincker, Jan Pawlowski, Wiebe H. C. F. Kooistra, Bente Edvardsen, Marina Montresor, Fabrice Not, Colomban de Vargas, Thorsten Stoeck, Ramiro Logares, Elianne Egge, Sarah Romac, Stéphane Audic, Thomas A. Richards, Micah Dunthorn, Wenche Eikrem, Ramon Massana, Johan Decelle, Richard Christen, Hiroyuki Ogata, Dominik Forster, Kamran Shalchian-Tabrizi, Massimo C. Pernice, Raffaele Siano, Lucie Bittner, Jean-Michel Claverie, Frédéric Mahé, Daniel Vaulot, Angélique Gobet, David Bass, Christophe Boutte, Sébastien Santini, University of Kaiserslautern [Kaiserslautern], Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), The Natural History Museum [London] (NHM), Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (Cefas), Analyse des Données à Haut Débit en Génomique (ADHDG), Evolution Paris Seine, Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC), Symbiose Marine (SM), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), University of Oslo (UiO), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Stazione Zoologica Anton Dohrn (SZN), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Diversité et Interactions au sein du Plancton Océanique (DIPO), Kyoto University [Kyoto], Department of Genetics and Evolution [Genève], University of Geneva [Switzerland], University of Exeter, Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER Centre de Bretagne), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Stipendienstiftung Rheinland-Pfalz, European Commission, German Research Foundation, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Kyoto University, Université de Genève = University of Geneva (UNIGE), Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of ecology, Universität Kaiserslautern, Microbial Ecology, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Paris-Seine, Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de biologie virtuelle, COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA), Max Planck Institute for Biological Cybernetics, Max-Planck-Gesellschaft, Marine Botany, Consejo Superior de Investigaciones Científicas [Spain] (CSIC), Department of genetics and evolution, School of Geography and Environmental, Monash University, Monash University [Clayton], Dynamiques de l'Environnement Côtier (DYNECO), Commissariat à l'Energie Atomique, and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)
Subjects: 0106 biological sciences, 0301 basic medicine, Aquatic Organisms, Geologic Sediments, Foraminifera, medicine.disease_cause, 01 natural sciences, Applied Microbiology and Biotechnology, 18S ribosomal RNA, Benthic microbial communities, Sequence Read Archive, Phylogeny, High-throughput sequencing, Ecology, Protist, high-throughput sequencing, Biodiversity, Plankton, respiratory system, protist diversity, Benthic zone, geographic locations, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, Microbiology, [SDV.MP.PRO]Life Sciences [q-bio]/Microbiology and Parasitology/Protistology, 03 medical and health sciences, Hydrothermal Vents, benthic microbial communities, coastal environments, parasitic diseases, RNA, Ribosomal, 18S, medicine, 14. Life underwater, Ecosystem, Diatoms, Base Sequence, 010604 marine biology & hydrobiology, fungi, DNA, Sequence Analysis, DNA, 030104 developmental biology, Taxon, Protist diversity, Reference database, Coastal environments, Species richness, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, human activities
Abstract: Forster, Dominik ... et al.-- 11 pages, 6 figures, 1 table, supplementary data http://femsec.oxfordjournals.org/content/suppl/2016/06/05/fiw120.DC1, Marine protist diversity inventories have largely focused on planktonic environments, while benthic protists have received relatively little attention. We therefore hypothesize that current diversity surveys have only skimmed the surface of protist diversity in marine sediments, which may harbor greater diversity than planktonic environments. We tested this by analyzing sequences of the hypervariable V4 18S rRNA from benthic and planktonic protist communities sampled in European coastal regions. Despite a similar number of OTUs in both realms, richness estimations indicated that we recovered at least 70% of the diversity in planktonic protist communities, but only 33% in benthic communities. There was also little overlap of OTUs between planktonic and benthic communities, as well as between separate benthic communities. We argue that these patterns reflect the heterogeneity and diversity of benthic habitats. A comparison of all OTUs against the Protist Ribosomal Reference database showed that a higher proportion of benthic than planktonic protist diversity is missing from public databases; similar results were obtained by comparing all OTUs against environmental references from NCBI's Short Read Archive. We suggest that the benthic realm may therefore be the world's largest reservoir of marine protist diversity, with most taxa at present undescribed, This work was supported by the European Commission and is part of the EU-FP7 ERA-net program BiodivERsA, under the project BioMarKs [2008-6530]. Dominik Forster was supported by a graduate scholarship of Stipendienstiftung Rheinland-Pfalz. Micah Dunthorn and Frédéric Mahé were supported by the Deutsche Forschungsgemeinschaft [grant #DU1319/1-1]. Thorsten Stoeck was supported by the Deutsche Forschungsgemeinschaft [grant #STO414/11-1]. Daniel Vaulot was supported by the European Union [grants MicroB3/FP7-287589, MaCuMBA/FP7-KBBE-2012-6-311975]
Published: 2016
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4. Automatic landmarking identifies new loci associated with face morphology and implicates Neanderthal introgression in human nasal shape

Author: Qing Li, Jieyi Chen, Pierre Faux, Miguel Eduardo Delgado, Betty Bonfante, Macarena Fuentes-Guajardo, Javier Mendoza-Revilla, J. Camilo Chacón-Duque, Malena Hurtado, Valeria Villegas, Vanessa Granja, Claudia Jaramillo, William Arias, Rodrigo Barquera, Paola Everardo-Martínez, Mirsha Sánchez-Quinto, Jorge Gómez-Valdés, Hugo Villamil-Ramírez, Caio C. Silva de Cerqueira, Tábita Hünemeier, Virginia Ramallo, Sijie Wu, Siyuan Du, Andrea Giardina, Soumya Subhra Paria, Mahfuzur Rahman Khokan, Rolando Gonzalez-José, Lavinia Schüler-Faccini, Maria-Cátira Bortolini, Victor Acuña-Alonzo, Samuel Canizales-Quinteros, Carla Gallo, Giovanni Poletti, Winston Rojas, Francisco Rothhammer, Nicolas Navarro, Sijia Wang, Kaustubh Adhikari, Andrés Ruiz-Linares, Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University [Shanghai]-Collaborative Innovation Center for Genetics and Development, CAS Key Laboratory of Computational Biology, Chinese Academy of Sciences [Beijing] (CAS)-University of Chinese Academy of Sciences [Beijing] (UCAS)-Shanghai Institute of Nutrition and Health, Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), División Antropología [La Plata] (DA), Facultad de Ciencias Naturales y Museo [La Plata] (FCNyM), Universidad Nacional de la Plata [Argentine] (UNLP)-Universidad Nacional de la Plata [Argentine] (UNLP), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Departamento de Tecnología Médica, Universidad de Tarapaca, Laboratorios de Investigación y Desarrollo (LID), Universidad Peruana Cayetano Heredia (UPCH), Génétique Evolutive Humaine - Human Evolutionary Genetics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Division of Vertebrates and Anthropology, The Natural History Museum [London] (NHM), Laboratorio de Genética Molecular, Universidad de Antioquia = University of Antioquia [Medellín, Colombia], Molecular Genetics Laboratory, National School of Anthropology and History [Mexico City, Mexico] (NSAH), Department of Archaeogenetics [Jena] (DAG), Max Planck Institute for the Science of Human History (MPI-SHH), Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Forensic Science, Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM), Unidad de Genomica de Poblaciones Aplicada a la Salud, Scientific Police of São Paulo State [Ourinhos, Brazil], Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo = University of São Paulo (USP), Departamento de Genética, Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS), Instituto Patagónico de Ciencias Sociales y Humanas, School of Mathematics and Statistics [Milton Keynes], Faculty of Science, Technology, Engineering and Mathematics [Milton Keynes], The Open University [Milton Keynes] (OU)-The Open University [Milton Keynes] (OU), Facultad de Medicina & Instituto de Alta Investigacion, Universidad de Tarapaca-Universidade de Chile, Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL), Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College of London [London] (UCL), the National Natural Science Foundation of China (#31771393), the Scientific and Technology Committee of Shanghai Municipality (18490750300), Ministry of Science and Technology of China (2020YFE0201600), Shanghai Municipal Science and Technology Major Project (2017SHZDZX01) and the 111 Project (B13016), the Leverhulme Trust (F/07 134/DF), BBSRC (BB/I021213/1), Universidad de Antioquia (CODI sostenibilidad de grupos 2013- 2014 and MASO 2013-2014), Conselho Nacional de Desenvolvimento Científico e Tecnológico, Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul (Apoio a Núcleos de Excelência Program), Fundação de Aperfeiçoamento de Pessoal de Nível Superior and the National Institute of Dental and Craniofacial Research (R01-DE027023, U01-DE020078, R01-DE016148, X01-HG007821), Santander Research & Scholarship Award. B.B. is supported by a doctoral scholarship from Ecole Doctorale 251 Aix-Marseille Université., and ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011)
Subjects: MESH: Neanderthals, MESH: Cell Differentiation, MESH: Humans, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, MESH: Nose, Medicine (miscellaneous), Sitios de Carácter Cuantitativo, Quantitative trait, Genome-wide association studies, General Biochemistry, Genetics and Molecular Biology, Estudio de Asociación del Genoma Completo, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, MESH: Genome-Wide Association Study, MESH: Animals, General Agricultural and Biological Sciences, MESH: Mice
Abstract: e report a genome-wide association study of facial features in >6000 Latin Americans based on automatic landmarking of 2D portraits and testing for association with inter-landmark distances. We detected significant associations (P-value
Published: 2023
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5. Parallel evolution of amphioxus and vertebrate small-scale gene duplications

Author: Marina Brasó-Vives, Ferdinand Marlétaz, Amina Echchiki, Federica Mantica, Rafael D. Acemel, José L. Gómez-Skarmeta, Diego A. Hartasánchez, Lorlane L. Targa, Pierre Pontarotti, Juan J. Tena, Ignacio Maeso, Hector Escriva, Manuel Irimia, Marc Robinson-Rechavi, Department of Ecology and Evolution [Lausanne], Université de Lausanne = University of Lausanne (UNIL), Dept of Genetics, Evolution and Environment [London] (UCL-GEE), University College of London [London] (UCL), Centre for Genomic Regulation [Barcelona] (CRG), Universitat Pompeu Fabra [Barcelona] (UPF)-Centro Nacional de Analisis Genomico [Barcelona] (CNAG), Andalusian Centre for Developmental Biology (CABD), Department of Computational Biology, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Department of Genetics, Microbiology and Statistics, and IRBio, University of Barcelona, Barcelona, Spain, Biologie intégrative des organismes marins (BIOM), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Swiss Institute of Bioinformatics [Lausanne] (SIB), MRR acknowledges support from the Swiss National Science Foundation grant 31003A/173048, and from the Etat de Vaud. FMar acknowledges support from the Royal Society grant URF\R1\191161. MI acknowledges support from European Research Council ERC‑StG‑LS2‑637591. HE acknowledges support from the Centre National de la Recherche Scientifique and Agence Nationale de la Recherche (ANR‑16‑CE12‑0008‑01 and ANR‑19‑CE13‑0011). PP acknowledges support from the French Government under the 'Investissements d’avenir' program managed by the Agence Nationale de la Recherche (Méditerranée Infection 10‑IAHU‑03). IM acknowledges support from the Spanish Ministry of Science and Innovation and the European Union (RYC‑2016‑20089 and PGC2018‑099392‑A‑I00). JJT acknowledges support from the ERC (Grant Agreement No. 740041) and the Spanish Ministerio de Ciencia e Innovación (PID2019‑103921GB‑I00)., ANR-16-CE12-0008,CHORELAND,Détermination de la conservation du landscape génomique de régulation au cours de l'embryogenèse des chordés(2016), ANR-19-CE13-0011,NEUCECHO,Dynamique de l'induction neurale au niveau de la cellule unique chez les chordés(2019), Swiss National Science Foundation, Royal Society (UK), European Research Council, Centre National de la Recherche Scientifique (France), Agence Nationale de la Recherche (France), Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), and Agencia Estatal de Investigación (España)
Subjects: animal structures, Amphioxus, Genome assembly, Gene duplication, Vertebrate, Comparative genomics, [SDV]Life Sciences [q-bio], Genomics, Animals, Lancelets/genetics, Gene Duplication, Phylogeny, Vertebrates/genetics, Vertebrates/metabolism, Evolution, Molecular, Branchiostoma lanceolatum, Ohnolog, Small-scale duplication, Genòmica, Amfiox, Genes, Vertebrats, Vertebrates, Gens, Lancelets
Abstract: [Background]: Amphioxus are non-vertebrate chordates characterized by a slow morphological and molecular evolution. They share the basic chordate body-plan and genome organization with vertebrates but lack their 2R whole-genome duplications and their developmental complexity. For these reasons, amphioxus are frequently used as an outgroup to study vertebrate genome evolution and Evo-Devo. Aside from whole-genome duplications, genes continuously duplicate on a smaller scale. Small-scale duplicated genes can be found in both amphioxus and vertebrate genomes, while only the vertebrate genomes have duplicated genes product of their 2R whole-genome duplications. Here, we explore the history of small-scale gene duplications in the amphioxus lineage and compare it to small- and large-scale gene duplication history in vertebrates. [Results]: We present a study of the European amphioxus (Branchiostoma lanceolatum) gene duplications thanks to a new, high-quality genome reference. We find that, despite its overall slow molecular evolution, the amphioxus lineage has had a history of small-scale duplications similar to the one observed in vertebrates. We find parallel gene duplication profiles between amphioxus and vertebrates and conserved functional constraints in gene duplication. Moreover, amphioxus gene duplicates show levels of expression and patterns of functional specialization similar to the ones observed in vertebrate duplicated genes. We also find strong conservation of gene synteny between two distant amphioxus species, B. lanceolatum and B. floridae, with two major chromosomal rearrangements. [Conclusions]: In contrast to their slower molecular and morphological evolution, amphioxus’ small-scale gene duplication history resembles that of the vertebrate lineage both in quantitative and in functional terms., RR acknowledges support from the Swiss National Science Foundation grant 31003A/173048, and from the Etat de Vaud. FMar acknowledges support from the Royal Society grant URF\R1\191161. MI acknowledges support from European Research Council ERC-StG-LS2-637591. HE acknowledges support from the Centre National de la Recherche Scientifique and Agence Nationale de la Recherche (ANR-16-CE12-0008-01 and ANR-19-CE13-0011). PP acknowledges support from the French Government under the “Investissements d’avenir” program managed by the Agence Nationale de la Recherche (Méditerranée Infection 10-IAHU-03). IM acknowledges support from the Spanish Ministry of Science and Innovation and the European Union (RYC-2016-20089 and PGC2018-099392-A-I00). JJT acknowledges support from the ERC (Grant Agreement No. 740041) and the Spanish Ministerio de Ciencia e Innovación (PID2019-103921GB-I00).
Published: 2022
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6. Exact renormalization group and Φ-derivable approximations

Author: Blaizot, Jean-Paul, Pawlowski, Jan M., Reinosa, Urko, Pawlowski, Jan, Département de Physique des Particules (ex SPP) (DPP), Institut de Recherches sur les lois Fondamentales de l'Univers (IRFU), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Department of genetics and evolution, University of Geneva [Switzerland], Service de Physique Théorique (SPhT), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Department of Genetics and Evolution, Université de Genève (UNIGE), Département de Physique des Particules (ex SPP) (DPhP), and Université de Genève = University of Geneva (UNIGE)
Subjects: Physics, High Energy Physics - Theory, [PHYS]Physics [physics], Nuclear and High Energy Physics, 010308 nuclear & particles physics, Truncation, [PHYS.HTHE]Physics [physics]/High Energy Physics - Theory [hep-th], Density matrix renormalization group, FOS: Physical sciences, Renormalization group, 01 natural sciences, Condensed Matter - Other Condensed Matter, High Energy Physics - Phenomenology, High Energy Physics - Phenomenology (hep-ph), Flow (mathematics), High Energy Physics - Theory (hep-th), Simple (abstract algebra), Quantum electrodynamics, 0103 physical sciences, Functional renormalization group, Applied mathematics, Initial value problem, 010306 general physics, Effective action, Other Condensed Matter (cond-mat.other)
Abstract: We show that the so-called Phi-derivable approximations can be combined with the exact renormalization group to provide efficient non-perturbative approximation schemes. On the one hand, the Phi-derivable approximations allow for a simple truncation of the infinite hierarchy of the renormalization group flow equations. On the other hand, the flow equations turn the non linear equations that derive from the Phi-derivable approximations into an initial value problem, offering new practical ways to solve these equations., 15 pages, 2 figures
Published: 2011
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7. Fertility preservation in patients of childbearing age treated for breast cancer: A nationwide cohort study

Author: Martha Duraes, Gauthier Rathat, Sophie Bringer-Deutsch, Noémie Ranisavljevic, Sophie Brouillet, Christine Defez-Fougeron, Claire Duflos, Hôpitaux Universitaires Paris Sud, Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Hôpital Arnaud de Villeneuve [CHRU Montpellier], Université de Montpellier (UM), Génétique et Biologie du Développement, Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Dept of Genetics, Evolution and Environment [London] (UCL-GEE), University College of London [London] (UCL), CHU Montpellier, Institut Desbrest de santé publique (IDESP), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)
Subjects: Cohort Studies, Cryopreservation, Pregnancy, [SDV]Life Sciences [q-bio], Fertility Preservation, Humans, Oocyte Retrieval, Surgery, Breast Neoplasms, Female, General Medicine, ComputingMilieux_MISCELLANEOUS, Retrospective Studies
Abstract: Approximately 7% of breast cancers are diagnosed in women under 40. Question of subsequent fertility has become fundamental. We aimed to evaluate the rate of fertility preservation (FP) by oocyte retrieval (OR) after ovarian stimulation in patients of childbearing age, managed for breast cancer with adjuvant chemotherapy in France, reuse rate of frozen gametes and live births rate (LBR) after treatment.We included 15,774 women between 18 and 40 years old, managed by surgery and adjuvant chemotherapy for breast cancer, between January 2011 and December 2020 from a French health registry. Patients with OR after breast surgery and before chemotherapy were considered as FP group; those with no OR as no FP group. To compare LBR with French population independently of age, we calculated Standardized Incidence Rates (SIR) of live births using indirect standardization method.FP rate increased gradually since 2011, reaching 17% in 2019. A decrease in use was observed in 2020 (13,9%). Among patients with at least 2 years of follow-up, gamete reuse rate was 5,6%. Births after cancer were mostly from spontaneous pregnancies. Among patients with at least 3 years of follow-up, LBR was 19,6% in FP group, 3,9% in second group. SIR of live births was of 1,05 (95% CI = 0.91-1.19) and 0.33 (95% CI = 0.30-0.36) in FP and no FP group respectively.Oncofertility activity increased until 2019 in France, reaching 17%. Gamete reuse rate was low. Births resulted mainly from spontaneous pregnancies. SIR of live births was lower in no FP group.
Published: 2022
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8. The trophectoderm acts as a niche for the inner cell mass through C/EBPα-regulated IL-6 signaling

Author: Marcos Plana-Carmona, Gregoire Stik, Romain Bulteau, Carolina Segura-Morales, Noelia Alcázar, Chris D.R. Wyatt, Antonios Klonizakis, Luisa de Andrés-Aguayo, Maxime Gasnier, Tian V. Tian, Guillem Torcal Garcia, Maria Vila-Casadesús, Nicolas Plachta, Manuel Serrano, Mirko Francesconi, Thomas Graf, Institut Català de la Salut, [Plana-Carmona M, Stik G, Segura-Morales C] Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. Universitat Pompeu Fabra (UPF), Barcelona, Spain. [Bulteau R] Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, Lyon, France. [Alcázar N] Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain. Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain. [Wyatt CDR] Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. Universitat Pompeu Fabra (UPF), Barcelona, Spain. Department of Genetics, Evolution & Environment, University College London, London, UK. [Tian TV] Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. Universitat Pompeu Fabra (UPF), Barcelona, Spain. Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain. [Vila-Casadesús M] Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain, and Vall d'Hebron Barcelona Hospital Campus
Subjects: Embryology, factores biológicos::péptidos y proteínas de señalización intercelular::citocinas::interleucinas::interleucina-6 [COMPUESTOS QUÍMICOS Y DROGAS], INNER CELL MASS, Embryonic Development, Pre-implantation embryo development, Biochemistry, Morula, Interleucina-6, Genetics, CCAAT-Enhancer-Binding Protein-alpha, TRANSDIFFERENTIATION, Gene Regulation, Physiological Phenomena::Growth and Development::Morphogenesis::Embryonic and Fetal Development::Embryonic Development [PHENOMENA AND PROCESSES], Fisiologia cel·lular, Transdifferentiation, C/EBP transcription factor, Embriologia, Interleukin-6, somatic cell reprogramming, Cell Biology, Gene regulation, Blastocyst, pre-implantation embryo development, Biological Factors::Intercellular Signaling Peptides and Proteins::Cytokines::Interleukins::Interleukin-6 [CHEMICALS AND DRUGS], estructuras embrionarias::mórula [ANATOMÍA], Trophectoderm, IL-6 signaling, Inner cell mass, Embryonic Structures::Morula [ANATOMY], fenómenos fisiológicos::crecimiento y desarrollo::morfogénesis::desarrollo embrionario y fetal::desarrollo embrionario [FENÓMENOS Y PROCESOS], Somatic cell reprogramming, Developmental Biology
Abstract: Gene regulation; Somatic cell reprogramming; Trophectoderm Regulación de genes; Reprogramación de células somáticas; Trofoectodermo Regulació de gens; Reprogramació de cèl·lules somàtiques; Trofectoderma IL-6 has been shown to be required for somatic cell reprogramming into induced pluripotent stem cells (iPSCs). However, how Il6 expression is regulated and whether it plays a role during embryo development remains unknown. Here, we describe that IL-6 is necessary for C/EBPα-enhanced reprogramming of B cells into iPSCs but not for B cell to macrophage transdifferentiation. C/EBPα overexpression activates both Il6 and Il6ra genes in B cells and in PSCs. In embryo development, Cebpa is enriched in the trophectoderm of blastocysts together with Il6, while Il6ra is mostly expressed in the inner cell mass (ICM). In addition, Il6 expression in blastocysts requires Cebpa. Blastocysts secrete IL-6 and neutralization of the cytokine delays the morula to blastocyst transition. The observed requirement of C/EBPα-regulated IL-6 signaling for pluripotency during somatic cell reprogramming thus recapitulates a physiologic mechanism in which the trophectoderm acts as niche for the ICM through the secretion of IL-6. We thank C. Berenguer for help with B cell reprogramming and bone marrow collection; S. Nakagawa and B. Pernaute for advice on pre-implantation embryo culture and manipulation, and Kyle M. Loh for his valuable discussions; the flow cytometry and microscopy units of UPF-CRG for technical assistance; the CRG genomics core facility for sequencing and Graf laboratory members for critical discussions. Work in the laboratory of T.G. was supported by the Spanish Ministry of Economy, Industry and Competitiveness (Plan Estatal PID2019-109354GB-I00), the CRG, AGAUR (SGR 726), and a European Research Council Synergy grant (4D-Genome). M.P.-C. was supported by an FPI fellowship (BES-2016-076900). Work in the laboratory of M.S. was funded by the IRB and by grants from the Spanish Ministry of Economy co-funded by the European Regional Development Fund (SAF2017-82613-R), ERC (ERC-2014-AdG/669622), la Caixa Foundation, and Secretaria d’Universitats i Recerca del Departament d’Empresa i Coneixement of Catalonia (Grup de Recerca consolidat 2017 SGR 282).
Published: 2022

9. Blood groups of Neandertals and Denisova decrypted

Author: Andres Ruiz-Linares, Pierre Faux, Pascal Bailly, Caroline Costedoat, Jacques Chiaroni, Silvana Condemi, Stéphane Mazières, Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Dept of Genetics, Evolution and Environment [London] (UCL-GEE), University College of London [London] (UCL), School of Life Sciences [Fudan University], Fudan University [Shanghai], Etablissement Français du Sang Provence-Alpes Côte-d'Azur et Corse (EFS), and Mazières, Stéphane
Subjects: 0301 basic medicine, Neanderthal, Hominids, Heredity, Physiology, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Social Sciences, Homozygosity, 0302 clinical medicine, INDEL Mutation, Medicine and Health Sciences, Neanderthals, education.field_of_study, Multidisciplinary, biology, Fossils, Paleogenetics, Hominidae, Body Fluids, [SHS.ANTHRO-BIO] Humanities and Social Sciences/Biological anthropology, Genetic Mapping, Blood, Phenotype, Blood Group Antigens, Medicine, Physical Anthropology, Anatomy, Research Article, Genotype, Science, Population, Variant Genotypes, 03 medical and health sciences, Archaic Humans, ABO blood group system, biology.animal, Paleoanthropology, Genetic variation, Genetics, Hominins, Animals, Allele, education, Denisovan, Alleles, Evolutionary Biology, Polymorphism, Genetic, Population Biology, Haplotype, Biology and Life Sciences, Paleontology, Genetic Variation, biology.organism_classification, 030104 developmental biology, Haplotypes, Evolutionary biology, Genetic Loci, Anthropology, Earth Sciences, Blood Groups, 030217 neurology & neurosurgery, Population Genetics
Abstract: International audience; Red cell blood group systems are crucial for safe transfusion, transplantation, and pregnancy monitoring. In addition, blood groups have long been investigated to decipher the origin of human populations, migration, adaptation, and admixture. However, since the extensive use of DNA polymorphisms in Anthropology, blood groups have been relegated to their primary application, blood transfusion. The finer genomic mapping of some Neanderthal and Denisova individuals about modern humans has provided significant evidence on the evolutionary history of both archaic and modern humans. However, despite their medical and anthropological interest, little is known about blood groups in archaic populations. To better understand the origin, expansion and encounter with Homo sapiens, we reappraised the available high-quality sequences of three Neanderthals (Vindija 33.19, Chagyrskaya 8, Altai Neandertal) and one Denisovan (Denisova 3) for 11 genes of the 7 blood group systems that are routinely screened in transfusion: ABO including H/ Se, Rh (Rhesus), Kell, Duffy, Kidd, MNS, and Diego. We show that Neanderthals and Denisova were polymorphic for ABO and shared blood group alleles recurrent in modern Sub-Saharan populations. Furthermore, we found ABO-related alleles currently preventing viral gut infection and all Neanderthal shared RHD and RHCE alleles nowadays associated with a high risk of hemolytic disease of the fetus and newborn. Such a common blood group pattern across time and space is coherent with a Neanderthal population of low genetic diversity exposed to possible pregnancies with complications. Lastly, we connect the Neanderthal RHD allele to two present-day Aboriginal Australians and Papuan, suggesting that a segment of the archaic genome was introgressed in this gene in non-Eurasian populations before their expansion towards Oceania. While contributing to both the origin and late evolutionary history of Neanderthal and Denisova, our results further illustrate that blood group systems remain effective anthropological markers.
Published: 2021
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10. SPART: A versatile and standardized data exchange format for species partition information

Author: Tomas Flouri, Jeet Sukumaran, Sophie Brouillet, Nicolas Puillandre, Paschalia Kapli, Miguel Vences, Jacques Ducasse, Aurélien Miralles, Sangeeta Kumari, Alexandros Stamatakis, Tomochika Fujisawa, L. Lacey Knowles, Sarah Lutteropp, 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 Genetics, Evolution and Environment [London] (UCL-GEE), University College of London [London] (UCL), University of Shiga Prefecture, University of Michigan [Ann Arbor], University of Michigan System, Technische Universität Braunschweig = Technical University of Braunschweig [Braunschweig], Heidelberg Institute for Theoretical Studies (HITS ), and San Diego State University (SDSU)
Subjects: 0106 biological sciences, Computer science, Interoperability, Biology, 010603 evolutionary biology, 01 natural sciences, Data type, Terminology, 03 medical and health sciences, Species delimitation programs, Robustness (computer science), Genetics, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Block (data storage), 0303 health sciences, Information retrieval, Syntax (programming languages), [SDE.IE]Environmental Sciences/Environmental Engineering, Partition (database), Species partition format, Data exchange, SPART, Integrative taxonomy, LIMES v2.0, Biotechnology, Merge (linguistics)
Abstract: International audience; A wide range of data types can be used to delimit species and various computer-based tools dedicated to this task are now available. Although these formalized approaches have significantly contributed to increase the objectivity of species delimitation (SD) under different assumptions, they are not routinely used by alpha-taxonomists. One obvious shortcoming is the lack of interoperability among the various independently developed SD programs. Given the frequent incongruences between species partitions inferred by different SD approaches, researchers applying these methods often seek to compare these alternative species partitions to evaluate the robustness of the species boundaries. This procedure is excessively time consuming at present, and the lack of a standard format for species partitions is a major obstacle. Here, we propose a standardized format, SPART, to enable compatibility between different SD tools exporting or importing partitions. This format reports the partitions and describes, for each of them, the assignment of individuals to the “inferred species”. The syntax also allows support values to be optionally reported, as well as original trees and the full command lines used in the respective SD analyses. Two variants of this format are proposed, overall using the same terminology but presenting the data either optimized for human readability (matricial SPART) or in a format in which each partition forms a separate block (SPART.XML). ABGD, DELINEATE, GMYC, PTP and TR2 have already been adapted to output SPART files and a new version of LIMES has been developed to import, export, merge and split them.
Published: 2021
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11. CeLaVi: an interactive cell lineage visualization tool

Author: Maximilian J. Telford, Marco Grillo, Michalis Averof, Irepan Salvador-Martínez, Dept of Genetics, Evolution and Environment [London] (UCL-GEE), University College of London [London] (UCL), and Centre National de la Recherche Scientifique (CNRS)
Subjects: Cell type, AcademicSubjects/SCI00010, Lineage (evolution), Gene Expression, Trees (plant), Cell lineage, Computational biology, Biology, 03 medical and health sciences, 0302 clinical medicine, Crustacea, Genetics, Animals, Cell Lineage, Caenorhabditis elegans, [SDV.BDD]Life Sciences [q-bio]/Development Biology, 030304 developmental biology, 0303 health sciences, Gastrula, Ciona intestinalis, Visualization, Tree (data structure), Larva, Web Server Issue, Software, 030217 neurology & neurosurgery
Abstract: Recent innovations in genetics and imaging are providing the means to reconstruct cell lineages, either by tracking cell divisions using live microscopy, or by deducing the history of cells using molecular recorders. A cell lineage on its own, however, is simply a description of cell divisions as branching events. A major goal of current research is to integrate this description of cell relationships with information about the spatial distribution and identities of the cells those divisions produce. Visualizing, interpreting and exploring these complex data in an intuitive manner requires the development of new tools. Here we present CeLaVi, a web-based visualization tool that allows users to navigate and interact with a representation of cell lineages, whilst simultaneously visualizing the spatial distribution, identities and properties of cells. CeLaVi’s principal functions include the ability to explore and manipulate the cell lineage tree; to visualise the spatial distribution of cell clones at different depths of the tree; to colour cells in the 3D viewer based on lineage relationships; to visualise various cell qualities on the 3D viewer (e.g. gene expression, cell type) and to annotate selected cells/clones. All these capabilities are demonstrated with four different example data sets. CeLaVi is available at http://www.celavi.pro., Graphical Abstract Graphical AbstractCeLaVi is a web-based tool that allows users to explore and annotate cell lineages, whilst simultaneously visualizing the spatial distribution, identities and properties of cells.
Published: 2021
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12. 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
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13. A GWAS in Latin Americans identifies novel face shape loci, implicating VPS13B and a Denisovan introgressed region in facial variation

Author: Tábita Hünemeier, Andres Ruiz-Linares, Samuel Canizales-Quinteros, Christel Thauvin-Robinet, Betty Bonfante, Juan Camilo Chacón-Duque, Laurence Duplomb, Charlotte Montillot, Sagnik Palmal, Javier Mendoza-Revilla, Justin Cotney, Laurence Faivre, Seth M. Weinberg, Victor Acuña-Alonzo, Emma Wentworth, Philip H. Jones, Claudia Jaramillo, Caroline Costedoat, Morgane Dubied, David J. Balding, Manfred Kayser, Pierre Faux, Francisco Rothhammer, Mirsha Sánchez-Quinto, Carla Gallo, Paola Everardo-Martínez, Macarena Fuentes-Guajardo, Evie Stergiakouli, Pirro G. Hysi, Ziyi Xiong, Giovanni Poletti, Ceferino Varón-González, Rodrigo Barquera, Maria Cátira Bortolini, Laurence J. Howe, Lauriane Poloni, Rolando González-José, Valeria Villegas, Malena Hurtado, Kaustubh Adhikari, William Arias, Vanessa Granja, Lavinia Schuler-Faccini, Virginia Ramallo, John R. Shaffer, Timothy C. Cox, Tim D. Spector, Gabriel Bedoya, Hugo Villamil-Ramírez, Caio Cesar Silva de Cerqueira, Fan Liu, Binnaz Yalcin, Jorge Gómez-Valdés, Nicolas Navarro, Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL), Universidad Peruana Cayetano Heredia (UPCH), Génétique Evolutive Humaine - Human Evolutionary Genetics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Equipe GAD (LNC - U1231), Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Agro Dijon, 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 Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Agro Dijon, 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), University of Connecticut Health Center [Farmington], Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), University College of London [London] (UCL), Erasmus University Medical Center [Rotterdam] (Erasmus MC), Universidad de Tarapaca, The Natural History Museum [London] (NHM), Universidad de Antioquia = University of Antioquia [Medellín, Colombia], National School of Anthropology and History [Mexico City, Mexico] (NSAH), Max Planck Institute for the Science of Human History (MPI-SHH), Max-Planck-Gesellschaft, Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM), Instituto Nacional de Medicina Genomica, Scientific Police of São Paulo State [Ourinhos, Brazil], Universidade de São Paulo = University of São Paulo (USP), Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS), Centro Nacional Patagónico (CENPAT), Beijing Genomics Institute [Shenzhen] (BGI), University of Chinese Academy of Sciences [Beijing] (UCAS), University of Pittsburgh (PITT), Pennsylvania Commonwealth System of Higher Education (PCSHE), University of Bristol [Bristol], King‘s College London, FHU TRANSLAD (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), University of Melbourne, University of Missouri [Kansas City] (UMKC), University of Missouri System, The Open University [Milton Keynes] (OU), Fudan University [Shanghai], Work leading to this publication was funded by grants from the National Natural Science Foundation of China (#31771393), the Scientific and Technology Committee of Shanghai Municipality (18490750300), the Ministry of Science and Technology of China (2020YFE0201600), the Shanghai Municipal Science and Technology Major Project (2017SHZDZX01) and the 111 Project (B13016), the Leverhulme Trust (F/07 134/DF), BBSRC (BB/I021213/1), the Excellence Initiative of Aix-Marseille University–A*MIDEX (a French 'Investissements d’Avenir' program), Universidad de Antioquia (CODI sostenibilidad de grupos 2013-2014 and MASO 2013-2014), Conselho Nacional de Desenvolvimento Científico e Tecnológico, Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul (Apoio a Núcleos de Excelência Program), Fundação de Aperfeiçoamento de Pessoal de Nível Superior, the National Institute of Dental and Craniofacial Research (R01-DE027023, U01-DE020078, R01-DE016148, and X01-HG007821), and a Santander Research and Scholarship Award. B.B. is supported by a doctoral scholarship from Ecole Doctorale 251 Aix-Marseille Université., ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, École pratique des hautes études (EPHE), Laboratorios de Investigación y Desarrollo (LID), Unit of Human Evolutionary Genetics, Centre de génétique - Centre de référence des maladies rares, anomalies du développement et syndromes malformatifs (CHU de Dijon), Department of Genetics and Genome Sciences, University of Connecticut (UCONN), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, Department of Genetic Identification, Departamento de Tecnología Médica, Division of Vertebrates and Anthropology, Genética Molecular (GENMOL), Molecular Genetics Laboratory, National School of Anthropology and History, Department of Archaeogenetics [Jena] (DAG), Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Forensic Science, Universidad Nacional Autónoma de México (UNAM), Unidad de Genomica de Poblaciones Aplicada a la Salud, Universidad Nacional Autónoma de México (UNAM)-Instituto Nacional de Medicina Genomica, Scientific Police of São Paulo State, Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo (USP), Departamento de Genética, Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS)-Instituto de Biociencias, Instituto Patagónico de Ciencias Sociales y Humanas, Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Key Laboratory of Genomic and Precision Medicine [Beijing, China], Beijing Genomics Institute [Shenzhen] (BGI)-University of Chinese Academy of Sciences [Beijing] (UCAS), Center for Craniofacial and Dental Genetics, University of Pittsburgh School of Medicine, Pennsylvania Commonwealth System of Higher Education (PCSHE)-Pennsylvania Commonwealth System of Higher Education (PCSHE), Department of Human Genetics, Department of Anthropology, Medical Research Council Integrative Epidemiology Unit, University of the West of England [Bristol] (UWE Bristol), School of Oral and Dental Sciences, Department of Twin Research & Genetic Epidemiology, King's College London, Facultad de Medicina & Instituto de Alta Investigacion, Universidad de Tarapaca-Universidade de Chile, Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne-University of Melbourne, Department of Oral and Craniofacial Sciences, University of Missouri System-University of Missouri System, School of Mathematics and Statistics [Milton Keynes], Faculty of Science, Technology, Engineering and Mathematics [Milton Keynes], The Open University [Milton Keynes] (OU)-The Open University [Milton Keynes] (OU), State Key Laboratory of Genetics Engineering & MOE Key Laboratory of Contemporary Anthropology, Fudan University [Shanghai]-School of Life Sciences, Work leading to this publication was funded by grantsfrom the National Natural Science Foundation of China (#31771393), the Scientific andTechnology Committee of Shanghai Municipality (18490750300), the Ministry ofScience and Technology of China (2020YFE0201600), the Shanghai Municipal Scienceand Technology Major Project (2017SHZDZX01) and the 111 Project (B13016), theLeverhulme Trust (F/07 134/DF), BBSRC (BB/I021213/1), the Excellence Initiative ofAix-Marseille University–A*MIDEX (a French 'Investissements d’Avenir' program),Universidad de Antioquia (CODI sostenibilidad de grupos 2013-2014 and MASO 2013-2014), Conselho Nacional de Desenvolvimento Científico e Tecnológico,Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul (Apoio a Núcleos deExcelência Program), Fundação de Aperfeiçoamento de Pessoal de Nível Superior, theNational Institute of Dental and Craniofacial Research (R01-DE027023, U01-DE020078,R01-DE016148, and X01-HG007821), and a Santander Research and Scholarship Award.B.B. is supported by a doctoral scholarship from Ecole Doctorale 251 Aix-MarseilleUniversité., and Genetic Identification
Subjects: haplotype, Latin Americans, [SDV]Life Sciences [q-bio], [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Vesicular Transport Proteins, Genome-wide association study, Genome-wide association studies, Regulatory sequences, purl.org/becyt/ford/1 [https], Mice, 0302 clinical medicine, Native Americans, single nucleotide polymorphism, GWAS, 10. No inequality, Two-dimensional profiles, Research Articles, Mammals, 0303 health sciences, Multidisciplinary, biology, adult, article, SciAdv r-articles, Genomic regions, Hispanic or Latino, craniofacial development, VPS13B, GENÉTICA, Phenotype, American Indian, regulatory sequence, HUMAN POPULATION, Research Article, Morphology, Latin americans, Genotype, animal experiment, introgression, Introgression, Polymorphism, Single Nucleotide, Homo denisovan, 03 medical and health sciences, male, Animals, Humans, controlled study, human, Craniofacial, Facial feature, purl.org/becyt/ford/1.6 [https], Denisovan, Gene, mouse, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, nonhuman, genome-wide association study, Haplotype, face, Human Genetics, Single nucleotide polymorphisms, biology.organism_classification, photography, thickness, purl.org/pe-repo/ocde/ford#3.01.02 [https], facies, DENOSIVAN HAPLOTYPE, Evolutionary biology, Anthropology, Face, 030217 neurology & neurosurgery, purl.org/pe-repo/ocde/ford#1.06.07 [https], Genome-Wide Association Study
Abstract: We carried out a genome-wide association study in Latin Americans and identified novel face morphology loci.., To characterize the genetic basis of facial features in Latin Americans, we performed a genome-wide association study (GWAS) of more than 6000 individuals using 59 landmark-based measurements from two-dimensional profile photographs and ~9,000,000 genotyped or imputed single-nucleotide polymorphisms. We detected significant association of 32 traits with at least 1 (and up to 6) of 32 different genomic regions, more than doubling the number of robustly associated face morphology loci reported until now (from 11 to 23). These GWAS hits are strongly enriched in regulatory sequences active specifically during craniofacial development. The associated region in 1p12 includes a tract of archaic adaptive introgression, with a Denisovan haplotype common in Native Americans affecting particularly lip thickness. Among the nine previously unidentified face morphology loci we identified is the VPS13B gene region, and we show that variants in this region also affect midfacial morphology in mice.
Published: 2021
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14. Non-native Species Surrounding Protected Areas Influence the Community of Non-native Species Within Them

Author: Tim M. Blackburn, Anne Charpentier, Kevin G. Smith, Kathrin Holenstein, William D. Simonson, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), 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), United Nations Environment Programme (UNEP) World Conservation Monitoring Center (WCMC) (UNEP WCMC), International Union for Conservation of Nature (IUCN), Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College of London [London] (UCL), Institute of Zoology, Zoological Society of London, London, Université Paul-Valéry - Montpellier 3 (UPVM)-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 de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, and 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)
Subjects: 0106 biological sciences, Species distribution, lcsh:Evolution, Biodiversity, alien species, 010603 evolutionary biology, 01 natural sciences, Population density, Invasive species, invasive species, Abundance (ecology), lcsh:QH540-549.5, lcsh:QH359-425, 14. Life underwater, Alien species, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Ecology, 010604 marine biology & hydrobiology, protected area boundaries, non-native species, 15. Life on land, Geography, Habitat, species distribution, protected areas, lcsh:Ecology, Species richness, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Protected areas (PAs) are a key element of global conservation strategies aiming to protect habitats and species from various threats such as non-natives species (NNS) with negative ecological impacts. Yet little is known about the mechanisms by which PAs are colonized by NNS, and more specifically the role of colonizing events from surrounding areas. Here, we compared terrestrial and freshwater non-native plants and animals recorded in Norwegian PAs and in 5-km belts around them, using the database of the Norwegian Biodiversity Information Centre Species Map Service. Our analysis included 1,602 NNS and 671 PAs. We found that NNS were recorded in only 23% of the PAs, despite the fact that 90% of the 5-km belts were colonized by at least one NNS. A Zero-inflated negative binomial regression model showed that the number of NNS in the 5-km belts was a strong explanatory variable of the NNS richness inside PAs. Other significant variables included the surface area of the PA, mean human population density in the PA, main type of habitat and accessibility of PAs. We also observed similarity in the species in and around the PAs, with, on average, two thirds of the NNS present in a specific PA also present in its 5-km belt. Furthermore, NNS were recorded in PAs on average 4.5 years after being recorded in the 0–5 km belts, suggesting a dynamic of rapid colonization from the belts to the PAs. Invasive NNS represented 12% of NNS in the belts but 40% in the PAs. This difference was related to the higher abundance of invasive NNS in the belts. Our results highlight the necessity of expanding the focus of NNS management in PAs beyond their boundaries, in particular to prevent incursions of NNS with high negative ecological impact.
Published: 2021
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15. A generalized deep learning-based framework for assistance to the human malaria diagnosis from microscopic images

Author: Ziheng Yang, Karim Hammoudi, Ruiwen He, Feryal Windal, Halim Benhabiles, Dominique Collard, Department of Genetics, Evolution and Environment, University College of London [London] (UCL), Institut d’Électronique, de Microélectronique et de Nanotechnologie - UMR 8520 (IEMN), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL), JUNIA (JUNIA), Université catholique de Lille (UCL), Bio-Micro-Electro-Mechanical Systems - IEMN (BIOMEMS - IEMN), Université catholique de Lille (UCL)-Université catholique de Lille (UCL)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-JUNIA (JUNIA), Institut de Recherche en Informatique Mathématiques Automatique Signal (IRIMAS), Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA)), Laboratory for Integrated Micro Mechatronics Systems (LIMMS), The University of Tokyo (UTokyo)-Centre National de la Recherche Scientifique (CNRS), This project has received funding from the Interreg 2 Seas programme 2014-2020 co-funded by the European Regional Development Fund under subsidy contract No. 2S05-043 H4DC., and Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-JUNIA (JUNIA)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF)-JUNIA (JUNIA)
Subjects: Computer science, Machine learning, computer.software_genre, Plasmodium, World health, 03 medical and health sciences, [SPI]Engineering Sciences [physics], 0302 clinical medicine, Artificial Intelligence, parasitic diseases, medicine, Computational Science and Engineering, 030304 developmental biology, 0303 health sciences, biology, business.industry, Deep learning, Plasmodium parasite, biology.organism_classification, medicine.disease, 3. Good health, Blood smear, Infectious disease (medical specialty), 030220 oncology & carcinogenesis, Artificial intelligence, business, computer, Software, Malaria
Abstract: International audience; Malaria is an infectious disease caused by Plasmodium parasites and is potentially human life-threatening. Children under 5 years old are the most vulnerable group with approximately one death every two minutes, accounting for more than 65% of all malaria deaths. The World Health Organization (WHO) encourages the research of appropriate methods to treat malaria through rapid and economical diagnostic. In this paper, we present a deep learning-based framework for diagnosing human malaria infection from microscopic images of thin blood smears. The framework is based on a direct segmentation and classification approach which relies on the analysis of the parasite itself. The framework permits to segment the Plasmodium parasite in the images and to predict its species among four dominant classes: P. Falciparum, P. Malaria, P. Ovale, and P. Vivax. A high potential of generalization with a competitive performance of our framework on inter-class data is demonstrated through an experimental study considering several datasets. Our source code is publicly available on https://github.com/Benhabiles-JUNIA/MalariaNet.
Published: 2021
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16. Lack of support for Deuterostomia prompts reinterpretation of the first Bilateria

Author: Nadia Jeffrie, Hervé Philippe, Maximilian Fursman, Richard R. Copley, Paschalis Natsidis, Paschalia Kapli, Imran A. Rahman, Maximilian J. Telford, Daniel J. Leite, Dept of Genetics, Evolution and Environment [London] (UCL-GEE), University College of London [London] (UCL), Oxford University Museum of Natural History, and University of Oxford [Oxford]
Subjects: 0106 biological sciences, Paraphyly, [SDV]Life Sciences [q-bio], Lophotrochozoa, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, Evolution, Molecular, 03 medical and health sciences, Monophyly, Common descent, Animals, Bilateria, Phylogeny, Research Articles, 030304 developmental biology, Reinterpretation, Synapomorphy, 0303 health sciences, Evolutionary Biology, Multidisciplinary, Deuterostome, biology, Embryonic cleavage, SciAdv r-articles, biology.organism_classification, Invertebrates, Xenacoelomorpha, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Evolutionary biology, Ecdysozoa, Research Article
Abstract: The deuterostome animal groups (Chordata and Xenambulacraria) may not be each other’s closest relatives., The bilaterally symmetric animals (Bilateria) are considered to comprise two monophyletic groups, Protostomia (Ecdysozoa and the Lophotrochozoa) and Deuterostomia (Chordata and the Xenambulacraria). Recent molecular phylogenetic studies have not consistently supported deuterostome monophyly. Here, we compare support for Protostomia and Deuterostomia using multiple, independent phylogenomic datasets. As expected, Protostomia is always strongly supported, especially by longer and higher-quality genes. Support for Deuterostomia, however, is always equivocal and barely higher than support for paraphyletic alternatives. Conditions that cause tree reconstruction errors—inadequate models, short internal branches, faster evolving genes, and unequal branch lengths—coincide with support for monophyletic deuterostomes. Simulation experiments show that support for Deuterostomia could be explained by systematic error. The branch between bilaterian and deuterostome common ancestors is, at best, very short, supporting the idea that the bilaterian ancestor may have been deuterostome-like. Our findings have important implications for the understanding of early animal evolution.
Published: 2020
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17. Genome-wide mapping of brain phenotypes in extended pedigrees with strong genetic loading for bipolar disorder

Author: Margarita Ramirez, Juliana Gomez-Franco, Barbara Kremeyer, Todd A. Tishler, Julio Bejarano, Carmen Araya, Ileana Aldana, Andres Ruiz-Linares, Gabriel Montoya, Nelson B. Freimer, Victor I. Reus, Carlos López-Jaramillo, Maria Jalbrzikowski, Terri M. Teshiba, Gabriel Castrillón, Carrie E. Bearden, Javier I. Escobar, Patricia Montoya, María Cecilia López, Scott C. Fears, Rita M. Cantor, Chiara Sabatti, Noor B. Al-Sharif, Xinia Araya, Gabriel Macaya, Julio Molina, State Key Laboratory of Genetics Engineering & MOE Key Laboratory of Contemporary Anthropology, Fudan University [Shanghai]-School of Life Sciences, Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Dept of Genetics, Evolution and Environment [London] (UCL-GEE), and University College of London [London] (UCL)
Subjects: 0301 basic medicine, Bipolar Disorder, Genetic Linkage, Quantitative Trait Loci, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Single-nucleotide polymorphism, Pedigree chart, Quantitative trait locus, Biology, Corpus callosum, 03 medical and health sciences, Cellular and Molecular Neuroscience, 0302 clinical medicine, medicine, Humans, Bipolar disorder, Molecular Biology, ComputingMilieux_MISCELLANEOUS, Genetic association, Genetics, Brain morphometry, Brain, medicine.disease, Pedigree, Psychiatry and Mental health, 030104 developmental biology, Phenotype, Brain size, 030217 neurology & neurosurgery
Abstract: Bipolar disorder is a highly heritable illness, associated with alterations of brain structure. As such, identification of genes influencing inter-individual differences in brain morphology may help elucidate the underlying pathophysiology of bipolar disorder (BP). To identify quantitative trait loci (QTL) that contribute to phenotypic variance of brain structure, structural neuroimages were acquired from family members (n = 527) of extended pedigrees heavily loaded for bipolar disorder ascertained from genetically isolated populations in Latin America. Genome-wide linkage and association analysis were conducted on the subset of heritable brain traits that showed significant evidence of association with bipolar disorder (n = 24) to map QTL influencing regional measures of brain volume and cortical thickness. Two chromosomal regions showed significant evidence of linkage; a QTL on chromosome 1p influencing corpus callosum volume and a region on chromosome 7p linked to cortical volume. Association analysis within the two QTLs identified three SNPs correlated with the brain measures.
Published: 2020
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18. Detection and Replication of Moku Virus in Honey Bees and Social Wasps

Author: Jessica L. Kevill, Gideon J. Mordecai, Jade Hunt, Daniel Sauvard, John Feltwell, Andrea Highfield, Seirian Sumner, Summer Henderson, Declan C. Schroeder, Stephen J. Martin, Marine Biological Association of the United Kingdom (MBA), University of Salford, College of Veterinary Medicine, University of Minnesota, St Paul, MN United States, University of British Columbia (UBC), Unité de recherche Zoologie Forestière (URZF), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Wildlife Matters, Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College of London [London] (UCL), School of Biological Sciences [Reading], and University of Reading (UOR)
Subjects: 0106 biological sciences, 0301 basic medicine, China, [SDV]Life Sciences [q-bio], Wasps, lcsh:QR1-502, Zoology, Vespula vulgaris, Insect Viruses, Genome, Viral, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Virus Replication, 010603 evolutionary biology, 01 natural sciences, lcsh:Microbiology, Predation, 03 medical and health sciences, Virology, honey bee, Animals, hornet, Phylogeny, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Vespidae, biology, Communication, Moku virus, Honey bee, Bees, biology.organism_classification, Brood, 3. Good health, Vespula pensylvanica, Europe, 030104 developmental biology, Infectious Diseases, Robbing, [SDE]Environmental Sciences, wasp, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Transmission of honey bee viruses to other insects, and vice versa, has previously been reported and the true ecological importance of this phenomenon is still being realized. Members of the family Vespidae interact with honey bees via predation or through the robbing of brood or honey from colonies, and these activities could result in virus transfer. In this study we screened Vespa velutina and Vespa crabro collected from Europe and China and also honey bees and Vespula vulgaris from the UK for Moku virus (MV), an Iflavirus first discovered in the predatory social wasp Vespula pensylvanica in Hawaii. MV was found in 71% of Vespula vulgaris screened and was also detected in UK Vespa crabro. Only seven percent of Vespa velutina individuals screened were MV-positive and these were exclusively samples from Jersey. Of 69 honey bee colonies screened, 43% tested positive for MV. MV replication was confirmed in Apis mellifera and Vespidae species, being most frequently detected in Vespula vulgaris. MV sequences from the UK were most similar to MV from Vespula pensylvanica compared to MV from Vespa velutina in Belgium. The implications of the transfer of viruses between the Vespidae and honey bees are discussed.
Published: 2020
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19. Predicting haplogroups using a versatile machine learning program (PredYMaLe) on a new mutationally balanced 32 Y-STR multiplex (CombYplex): Unlocking the full potential of the human STR mutation rate spectrum to estimate forensic parameters

Author: Bouakaze, Caroline, Delehelle, Franklin, Saenz-Oyhéréguy, Nancy, Moreira, Andreia, Schiavinato, Stéphanie, Croze, Myriam, Delon, Solène, Fortes-Lima, Cesar, Gibert, Morgane, Bujan, Louis, Huyghe, Eric, Bellis, Gil, Calderon, Rosario, Hernández, Candela Lucia, Avendaño-Tamayo, Efren, Bedoya, Gabriel, Salas, Antonio, Mazières, Stéphane, Charioni, Jacques, Migot-Nabias, Florence, Ruiz-Linares, Andres, Dugoujon, Jean-Michel, Thèves, Catherine, Mollereau-Manaute, Catherine, Noûs, Camille, Poulet, Nicolas, King, Turi, D'Amato, Maria Eugenia, Balaresque, Patricia, D’Amato, Maria Eugenia, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Etablissement Français du Sang Provence-Alpes Côte-d'Azur et Corse (EFS), Laboratoire d'Anthropologie Moléculaire, Institut de Médecine Légale, Strasbourg, France (IML), Université Louis Pasteur - Strasbourg I, Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Éco-Anthropologie (EA), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), UMR 6578 : Anthropologie Bio-Culturelle (UAABC), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Groupe d'Activité de Médecine de la Reproduction [CHU Toulouse] (CECOS Toulouse), Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Département d'Urologie-Andrologie et Transplantation Rénale [CHU Toulouse], Pôle Urologie - Néphrologie - Dialyse - Transplantations - Brûlés - Chirurgie plastique - Explorations fonctionnelles et physiologiques [CHU Toulouse], Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Institut national d'études démographiques (INED), Departamento de Zoologia y Antropologia Fisica, Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Laboratorio de Genética Molecular, Universidad de Antioquia = University of Antioquia [Medellín, Colombia], Archaeogenetics Laboratory, Mère et enfant en milieu tropical : pathogènes, système de santé et transition épidémiologique (MERIT - UMR_D 216), Institut de Recherche pour le Développement (IRD)-Université Paris Descartes - Paris 5 (UPD5), Dept of Genetics, Evolution and Environment [London] (UCL-GEE), University College of London [London] (UCL), Laboratoire Cogitamus, Office national de l'eau et des milieux aquatiques (ONEMA), Ministère de l'écologie, du développement durable et de l'énergie, Department of Oncology, Real Expression Artificial Life (IRIT-REVA), Institut de recherche en informatique de Toulouse (IRIT), Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), UMR 6578 : Adaptabilité Biologique et Culturelle (UAABC), Groupe de recherche en fertilité humaine ( GRFH), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Service d'Urologie - Transplantation Rénale - Andrologie, CHU Toulouse [Toulouse]-Hôpital de Rangueil, CHU Toulouse [Toulouse], Universidad Complutense de Madrid [Madrid] (UCM), Mère et enfant face aux infections tropicales (MERIT - UMR_D 216), Hydrobiologie - antenne de Montpellier (UR HYAX), Centre national du machinisme agricole, du génie rural, des eaux et forêts (CEMAGREF), Department of Genetics [Leicester], University of Leicester, Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Éco-Anthropologie (EAE), CECOS Midi-Pyrénées, centre de sterilité masculine et équipe d'accueil Fertilité Humaine, Hôpital Paule de Viguier, and CHU Toulouse [Toulouse]-CHU Toulouse [Toulouse]
Subjects: 0301 basic medicine, Forensic Genetics, Male, Mutation rate, [SDV]Life Sciences [q-bio], Bayesian probability, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Machine learning, computer.software_genre, Polymorphism, Single Nucleotide, Haplogroup, Pathology and Forensic Medicine, 03 medical and health sciences, 0302 clinical medicine, Mutation Rate, (Hg prediction), Genetics, Humans, Y-STR, 030216 legal & forensic medicine, Genetik, ComputingMilieux_MISCELLANEOUS, Mathematics, Chromosomes, Human, Y, Artificial neural network, business.industry, Statistical parameter, DNA Fingerprinting, Random forest, Assignation accuracy and haplogroup prediction (Hg prediction), Support vector machine, 030104 developmental biology, Haplotypes, Assignation accuracy and haplogroup prediction, Incremental mutation rates, Artificial intelligence, business, computer, Multiplex Polymerase Chain Reaction, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Microsatellite Repeats
Abstract: International audience; We developed a new mutationally well-balanced 32 Y-STR multiplex ( CombYplex) together with a machine learning (ML) program PredYMa Le to assess the impact of STR mutability on haplogourp prediction, while respecting forensic community criteria (high DC/HD). We designed CombYplex around two sub-panels M1 and M2 characterized by average and high-mutation STR panels. Using these two sub-panels, we tested how our program PredYmale reacts to mutability when considering basal branches and, moving down, terminal branches. We tested first the discrimination capacity of CombYplex on 996 human samples using various forensic and statistical parameters and showed that its resolution is sufficient to separate haplogroup classes. In parallel, Pred YMa Le was designed and used to test whether a ML approach can predict haplogroup classes from Y-STR profiles. Applied to our kit, SVM and Random Forest classifiers perform very well (average 97 %), better than Neural Network (average 91 %) and Bayesian methods (< 90 %). We observe heterogeneity in haplogroup assignation accuracy among classes, with most haplogroups having high prediction scores (99–100 %) and two (E1b1b and G) having lower scores (67 %). The small sample sizes of these classes explain the high tendency to misclassify the Y-profiles of these haplogroups; results were measurably improved as soon as more training data were added. We provide evidence that our ML approach is a robust method to accurately predict haplogroups when it is combined with a sufficient number of markers, well-balanced mutation rate Y-STR panels, and large ML training sets. Further research on confounding factors (such as CNV-STR or gene conversion) and ideal STR panels in regard to the branches analysed can be developed to help classifiers further optimize prediction scores.
Published: 2020
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20. Cdk9 and H2Bub1 signal to Clr6-CII/Rpd3S to suppress aberrant antisense transcription

Author: Danny A. Bitton, Robert P. Fisher, Viviane Pagé, Miriam Sansó, J. Peter Svensson, Elena Hidalgo, Pabitra K. Parua, Sarah MacKinnon, Jürg Bähler, Daniel Pinto, Patrícia Garcia, Jason C. Tanny, Institut Català de la Salut, [Sansó M] Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Cancer Genomics Group, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain. [Parua PK] Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. [Pinto D, Pagé V] Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada. [Svensson JP] Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden. [Bitton DA] Research Department of Genetics, Evolution & Environment, University College, London, UK, and Vall d'Hebron Barcelona Hospital Campus
Subjects: Transcription Elongation, Genetic, enzimas y coenzimas::enzimas::enzimas multifuncionales::cinasa 9 dependiente de la ciclina [COMPUESTOS QUÍMICOS Y DROGAS], AcademicSubjects/SCI00010, Enzymes and Coenzymes::Enzymes::Multifunctional Enzymes::Cyclin-Dependent Kinase 9 [CHEMICALS AND DRUGS], RNA polymerase II, Cell Cycle Proteins, fenómenos químicos::fenómenos bioquímicos::transcripción genética::elongación de la transcripción genética [FENÓMENOS Y PROCESOS], Histones, 03 medical and health sciences, 0302 clinical medicine, Gene interaction, Transcription (biology), Schizosaccharomyces, Genetics, Histone H2B, Phosphorylation, Gene, 030304 developmental biology, 0303 health sciences, Natural Science Disciplines::Biological Science Disciplines::Biology::Computational Biology::Genomics [DISCIPLINES AND OCCUPATIONS], biology, Gene regulation, Chromatin and Epigenetics, Ubiquitination, Chemical Phenomena::Biochemical Phenomena::Transcription, Genetic::Transcription Elongation, Genetic [PHENOMENA AND PROCESSES], Cyclin-Dependent Kinase 9, Gene regulation, Chromatin, Cell biology, Quinases dependents de ciclina, Genòmica, Histone, Chromatin and epigenetics, disciplinas de las ciencias naturales::disciplinas de las ciencias biológicas::biología::biología computacional::genómica [DISCIPLINAS Y OCUPACIONES], biology.protein, Histone deacetylase, RNA Polymerase II, Schizosaccharomyces pombe Proteins, Transcriptional Elongation Factors, Transcripció genètica - Regulació, 030217 neurology & neurosurgery
Abstract: Regulació gènica Regulación genética Gene Regulation Mono-ubiquitylation of histone H2B (H2Bub1) and phosphorylation of elongation factor Spt5 by cyclin-dependent kinase 9 (Cdk9) occur during transcription by RNA polymerase II (RNAPII), and are mutually dependent in fission yeast. It remained unclear whether Cdk9 and H2Bub1 cooperate to regulate the expression of individual genes. Here, we show that Cdk9 inhibition or H2Bub1 loss induces intragenic antisense transcription of ∼10% of fission yeast genes, with each perturbation affecting largely distinct subsets; ablation of both pathways de-represses antisense transcription of over half the genome. H2Bub1 and phospho-Spt5 have similar genome-wide distributions; both modifications are enriched, and directly proportional to each other, in coding regions, and decrease abruptly around the cleavage and polyadenylation signal (CPS). Cdk9-dependence of antisense suppression at specific genes correlates with high H2Bub1 occupancy, and with promoter-proximal RNAPII pausing. Genetic interactions link Cdk9, H2Bub1 and the histone deacetylase Clr6-CII, while combined Cdk9 inhibition and H2Bub1 loss impair Clr6-CII recruitment to chromatin and lead to decreased occupancy and increased acetylation of histones within gene coding regions. These results uncover novel interactions between co-transcriptional histone modification pathways, which link regulation of RNAPII transcription elongation to suppression of aberrant initiation. National Institutes of Health [R35GM127289 to R.P.F.]; Canadian Institutes of Health Research [MOP-130362 to J.C.T.]; Natural Sciences and Engineering Council of Canada [RGPIN 03661-15 to J.C.T.]; Wellcome Trust Senior Investigator Award [095598/Z/11/Z to J.B.]; Swedish Research Council [VR2015-02312]; Cancerfonden [CAN2016/576 awards to P.S.]; J.C.T. is supported by a fellowship from Fond de recherche Quebec Santé [33115]. Funding for open access charge: National Institutes of Health (USA); Canadian Institutes of Health Research.
Published: 2020

21. Re-evaluating the phylogenetic position of the enigmatic early Cambrian deuterostome Yanjiahella

Author: Oldřich Fatka, Przemysław Gorzelak, Samuel Zamora, Imran A. Rahman, Bertrand Lefebvre, Jeffrey R. Thompson, Rich Mooi, Timothy A. M. Ewin, Martina Nohejlová, James Sprinkle, Bruno David, Thomas E. Guensburg, Colin D. Sumrall, Elise Nardin, David F. Wright, Selina R. Cole, Mike Reich, Aaron W. Hunter, Instituto Geológico y Minero de España (IGME), Grupo Aragosaurus-IUCA, University of Zaragoza - Universidad de Zaragoza [Zaragoza], Division of Paleontology (Invertebrates), American Museum of Natural History (AMNH), Department of Paleobiology [Washington], Smithsonian Institution, Department of Invertebrate Zoology & Geology, California Academy of Sciences, Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement [Lyon] (LGL-TPE), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Integrative Research Center, Field Museum of Natural History [Chicago, USA], Institute of Paleobiology [Warsaw], Polska Akademia Nauk = Polish Academy of Sciences (PAN), Muséum national d'Histoire naturelle (MNHN), Department of Earth and Planetary Sciences [Knoxville], The University of Tennessee [Knoxville], Department of Earth Sciences [Cambridge, UK], University of Cambridge [UK] (CAM), School of Earth Sciences [Perth], The University of Western Australia (UWA), Department of Geological Sciences [Austin], Jackson School of Geosciences (JSG), University of Texas at Austin [Austin]-University of Texas at Austin [Austin], Department of Genetics, Evolution and Environment, University College of London [London] (UCL), The Natural History Museum [London] (NHM), Department of Geology and Palaeontology, Faculty of Science, Charles University, Géosciences Environnement Toulouse (GET), Institut national des sciences de l'Univers (INSU - CNRS)-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-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Staatliche Naturwissenschaftliche Sammlungen Bayerns (SNSB), Paleontology and Geobiology, Ludwig-Maximilians-Universität München (LMU), GeoBio-CenterLMU, Czech Geological Survey [Praha], Oxford University Museum of Natural History, University of Oxford [Oxford], Work supported by the Spanish Ministry of Science, Innovation and Universities [grant number CGL2017-87631], cofinanced by the European Regional Development Fund, project 'Aragosaurus: recursos geológicos y paleoambientales' (ref: E18_17R) funded by the Government of Aragón, by Gerstner Scholar and Lerner-Gray postdoctoral fellowships at the American Museum of Natural History (AMNH), by a Kathryn W. Davis postdoctoral fellowship at the AMNH, by a Royal Society Newton International Fellowship. I.A.R. is supported by the Oxford University Museum of Natural History., Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement (LGL-TPE), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Oxford University Museum of Natural History (OUMNH), University of Oxford, Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon)
Subjects: 0301 basic medicine, Geologic Sediments, China, 010506 paleontology, Science, Starfish, General Physics and Astronomy, 02 engineering and technology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Monophyly, Matters Arising, Chordata, Nonvertebrate, Animals, lcsh:Science, Clade, History, Ancient, Phylogeny, Taxonomy, 030304 developmental biology, 0105 earth and related environmental sciences, Appendage, 0303 health sciences, Multidisciplinary, Deuterostome, Phylogenetic tree, biology, Fossils, Palaeontology, Geology, General Chemistry, 021001 nanoscience & nanotechnology, biology.organism_classification, Biological Evolution, Position (obstetrics), 030104 developmental biology, Taxon, Body plan, Echinoderm, Evolutionary biology, lcsh:Q, Geologi, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, 0210 nano-technology, Echinodermata
Abstract: Recently we documented a bilaterally symmetrical, solitary organism, Yanjiahella biscarpa from the early Cambrian (Fortunian) of China1. We interpreted that Y. biscarpa possessed an echinoderm-like plated theca, a muscular stalk similar to hemichordates and a pair of long, feeding appendages. Our interpretation and our phylogenetic analysis suggest that Y. biscarpa is a stem-echinoderm, which would confirm that echinoderms acquired plates before pentaradial symmetry and that their history is firmly rooted in bilateral forms. Zamora et al.2 however, have criticized our interpretation, arguing against an echinoderm affinity, instead suggesting that the phylogenetic placement of Y. biscarpa is dubious and its significance for understanding deuterostome evolution is uncertain. This criticism2 seems to stem from our interpretation of particular morphological features in Y. biscarpa1 and the perceived lack of echinoderm synapomorphies. Echinoderms possess a calcitic skeleton with a distinctive three-dimensional mesh-like microstructure called stereom, that is considered a major synapomorphy of the Echinodermata3. Zamora et al.2 highlighted the absence of stereom in Y. biscarpa, additionally stating that we had omitted appropriate methods, specifically latex casting, that may confirm the presence of stereom in our specimens. We concede that initially we did not latex cast any specimens of Y. biscarpa, predominantly due to the fragile nature and the associated risk of damaging the specimens in question. In lieu of latex casting we employed Scanning Electron Microscopy (SEM) to investigate the surface and the details of Y. biscarpa specimens. SEM has been extensively used in the past to study stereom microstructure4,5,6 and if such a microstructure was preserved in Y. biscarpa it would have been detected using this technique. Artikeln är ett refereegranskat svar på en publicerad kommentar på en tidigare artikel.
Published: 2020
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22. Global rise in emerging alien species results from increased accessibility of new source pools

Author: Stephanie L. Rorke, Shyama Pagad, Giuseppe Brundu, Tim M. Blackburn, Wayne Dawson, Alain Roques, Michael Ansong, Laura Celesti-Grapow, Silvia Rossinelli, Heinke Jäger, Alexander Mosena, Wolfgang Rabitsch, Franz Essl, Kateřina Štajerová, Helen E. Roy, Jonathan M. Jeschke, Hanno Seebens, John Kartesz, David Pearman, Julissa Rojas-Sandoval, Marc Kenis, Mark van Kleunen, Sven Bacher, Dietmar Moser, Riccardo Scalera, Margarita Arianoutsou, Eckehard G. Brockerhoff, Ingolf Kühn, Andrew M. Liebhold, Ellie E. Dyer, Bernd Lenzner, Piero Genovesi, Nicol Fuentes, Jan Pergl, Philip E. Hulme, Bernd Blasius, Kevin J. Walker, Evan P. Economo, Marten Winter, Stefan Dullinger, Darren F. Ward, Misako Nishino, Petr Pyšek, César Capinha, Stefan Schindler, Barbara Tokarska-Guzik, Benoit Guénard, Wolfgang Nentwig, Charlotte E. Causton, Takehiko Yamanaka, Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Goethe-Universität Frankfurt am Main-Senckenberg – Leibniz Institution for Biodiversity and Earth System Research - Senckenberg Gesellschaft für Naturforschung, Leibniz Association-Leibniz Association, University of Vienna [Vienna], Department of Genetics, Evolution and Environment, Centre for Biodiversity and Environment, Research, University College of London [London] (UCL), Institute of Zoology, Zoological Society of London, Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Institute for Environmental Protection and Research (ISPRA), International Union for Conservation of Nature, Bio-Protection Research Centre, Lincoln University, Leibniz-Institute of Freshwater Biology and Inland Fisheries, Freie Universität Berlin, Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), University of Auckland [Auckland], Institute of Botany, Department of Invasion Ecology, Czech Academy of Sciences [Prague] (CAS), Department of Ecology, Faculty of Science, Charles University [Prague] (CU), University of Konstanz, Taizhou University, Halle Jena Leipzig, German Centre for Integrative Biodiversity Research, Kwame Nkrumah University of Science and Technology [GHANA] (KNUST), Department of Ecology and Systematics, Faculty of Biology, National and Kapodistrian University of Athens (NKUA), Department of Biology, Northern Arizona University [Flagstaff], Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, New Zealand Forest Research Institute, SCION, Department of Agriculture, Università degli studi di Napoli Federico II, Universidade do Porto, Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Global Health and Tropical Medicine (GHTM), Charles Darwin Foundation, Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], School of Biological and Biomedical Sciences, Durham University, Okinawa Institute of Science and Technology Graduate University (OIST), Universidad de Concepción, University of Hong Kong, Biota of North America Program (BONAP), CABI Europe Switzerland, Department of Community Ecology, Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), Department of Geobotany and Botanical Garden, Martin-Luther-Universität Halle Wittenberg (MLU), Northern Research Station, Forest Research [Great Britain], Universität Bielefeld = Bielefeld University, Institute of Ecology and Evolution, Russian Academy of Sciences [Moscow] (RAS), Botanical Society of Britain and Ireland (BSBI), Environment Agency Austria, Smithsonian National Museum of Natural History (NMNH), Unité de recherche Zoologie Forestière (URZF), Institut National de la Recherche Agronomique (INRA), Natural Environment Research Council (NERC), University of Silesia, School of Biological Sciences, Manaaki Whenua – Landcare Research [Lincoln], Institute for Agro-Environmental Sciences, and National Agriculture and Food Research Organization (NARO)
Subjects: 0106 biological sciences, source species pools, Multidisciplinary, Environmental change, Ecology, 010604 marine biology & hydrobiology, [SDE.MCG]Environmental Sciences/Global Changes, Biosecurity, Alien, drivers, 15. Life on land, globalization, invasive species, time series, 010603 evolutionary biology, 01 natural sciences, Species pool, Taxon, Geography, 13. Climate action, ddc:570, source species pools, invasive species, drivers, time series, globalization, Alien species
Abstract: International audience; Our ability to predict the identity of future invasive alien species is largely based upon knowledge of prior invasion history. Emerging alien species-those never encountered as aliens before-therefore pose a significant challenge to biosecurity interventions worldwide. Understanding their temporal trends, origins, and the drivers of their spread is pivotal to improving prevention and risk assessment tools. Here, we use a database of 45,984 first records of 16,019 established alien species to investigate the temporal dynamics of occurrences of emerging alien species worldwide. Even after many centuries of invasions the rate of emergence of new alien species is still high: Onequarter of first records during 2000-2005 were of species that had not been previously recorded anywhere as alien, though with large variation across taxa. Model results show that the high proportion of emerging alien species cannot be solely explained by increases in well-known drivers such as the amount of imported commodities from historically important source regions. Instead, these dynamics reflect the incorporation of new regions into the pool of potential alien species, likely as a consequence of expanding trade networks and environmental change. This process compensates for the depletion of the historically important source species pool through successive invasions. We estimate that 1-16% of all species on Earth, depending on the taxonomic group, qualify as potential alien species. These results suggest that there remains a high proportion of emerging alien species we have yet to encounter, with future impacts that are difficult to predict.
Published: 2018
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23. Wonky whales: the evolution of cranial asymmetry in cetaceans

Author: Travis Park, Ellen J Coombs, Morgan Churchill, Julien Clavel, Anjali Goswami, Department of Genetics, Evolution and Environment, University College of London [London] (UCL), 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), The Natural History Museum [London] (NHM), and University of Wisconsin Oshkosh (UWO)
Subjects: 0106 biological sciences, Physiology, Toothed whale, Human echolocation, Plant Science, Late Miocene, 010603 evolutionary biology, 01 natural sciences, Monodontidae, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Hearing, Structural Biology, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Animals, 14. Life underwater, lcsh:QH301-705.5, Ecology, Evolution, Behavior and Systematics, Phylogeny, 030304 developmental biology, 0303 health sciences, Cetaceans, biology, Fossils, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Skull, Rostrum, Whales, Asymmetry, Cell Biology, Phylogenetic comparative methods, biology.organism_classification, Biological Evolution, Baleen, lcsh:Biology (General), Evolutionary biology, Trait evolution, Macroevolution, Female, Xenorophidae, General Agricultural and Biological Sciences, Morphometrics, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, Developmental Biology, Biotechnology, Beluga Whale, Research Article
Abstract: BackgroundUnlike most mammals, toothed whale (Odontoceti) skulls lack symmetry in the nasal and facial (nasofacial) region. This asymmetry is hypothesised to relate to echolocation, which may have evolved in the earliest diverging odontocetes. Early cetaceans (whales, dolphins, and porpoises) such as archaeocetes, namely the protocetids and basilosaurids, have asymmetric rostra, but it is unclear when nasofacial asymmetry evolved during the transition from archaeocetes to modern whales. We used three-dimensional geometric morphometrics and phylogenetic comparative methods to reconstruct the evolution of asymmetry in the skulls of 162 living and extinct cetaceans over 50 million years.ResultsIn archaeocetes, we found asymmetry is prevalent in the rostrum and also in the squamosal, jugal, and orbit, possibly reflecting preservational deformation. Asymmetry in odontocetes is predominant in the nasofacial region. Mysticetes (baleen whales) show symmetry similar to terrestrial artiodactyls such as bovines. The first significant shift in asymmetry occurred in the stem odontocete family Xenorophidae during the Early Oligocene. Further increases in asymmetry occur in the physeteroids in the Late Oligocene, Squalodelphinidae and Platanistidae in the Late Oligocene/Early Miocene, and in the Monodontidae in the Late Miocene/Early Pliocene. Additional episodes of rapid change in odontocete skull asymmetry were found in the Mid-Late Oligocene, a period of rapid evolution and diversification. No high-probability increases or jumps in asymmetry were found in mysticetes or archaeocetes. Unexpectedly, no increases in asymmetry were recovered within the highly asymmetric ziphiids, which may result from the extreme, asymmetric shape of premaxillary crests in these taxa not being captured by landmarks alone.ConclusionsEarly ancestors of living whales had little cranial asymmetry and likely were not able to echolocate. Archaeocetes display high levels of asymmetry in the rostrum, potentially related to directional hearing, which is lost in early neocetes—the taxon including the most recent common ancestor of living cetaceans. Nasofacial asymmetry becomes a significant feature of Odontoceti skulls in the Early Oligocene, reaching its highest levels in extant taxa. Separate evolutionary regimes are reconstructed for odontocetes living in acoustically complex environments, suggesting that these niches impose strong selective pressure on echolocation ability and thus increased cranial asymmetry.
Published: 2020
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24. Ecosystems monitoring powered by environmental genomics: a review of current strategies with an implementation roadmap

Author: Laura Alonso-Sáez, Agnès Bouchez, Xavier Pochon, Jan Pawlowski, Thorsten Stoeck, Larissa Frühe, Eva Aylagas, François Keck, Anders Lanzén, David A. Bohan, Olivier Laroche, Tristan Cordier, Simon Creer, Laure Apothéloz-Perret-Gentil, Florian Leese, Anthony A. Chariton, Nigel Keeley, Département de Génétique et Evolution, Université de Genève (UNIGE), Agroécologie [Dijon], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Universität Duisburg-Essen [Essen], Cawthron Institute, Dept of Ecology, University of Kaiserslautern, Department of genetics and evolution, University of Geneva [Switzerland], and ANR-17-CE32-0011,NGB,Biosurveillance Next-Gen des changements dans la structure et le fonctionnement des écosystèmes(2017)
Subjects: 0106 biological sciences, 0301 basic medicine, Biodiversity, Genomics, NOVEL APPROACHES TO MONITOR ECOSYSTEMS, Biology, 010603 evolutionary biology, 01 natural sciences, metabarcoding, 03 medical and health sciences, implementation strategy, Genetics, DNA Barcoding, Taxonomic, Ecosystem, Environmental DNA, Implementation, Environmental planning, Ecology, Evolution, Behavior and Systematics, biodiversity, ecosystem management, business.industry, Special Issue, 010604 marine biology & hydrobiology, Environmental resource management, Invited Review and Syntheses, environmental DNA, Toolbox, Ecological network, 030104 developmental biology, 13. Climate action, Metagenomics, Biomonitoring, [SDE]Environmental Sciences, Ecosystem management, Environmental science, Current (fluid), ecology, business, Biologie, Environmental Monitoring
Abstract: International audience; A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, technical limitations and conceptual issues still stand in the way of its broad application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception that the routine application of this methodology is premature or "in development", hence restraining regulators from binding these tools into legal frameworks. Here, we review recent implementations of environmental genomics-based methods, applied to the biomonitoring of ecosystems. By taking a general overview, without narrowing our perspective to particular habitats or groups of organisms, this paper aims to compare, review and discuss the strengths and limitations of four general implementation strategies of environmental genomics for monitoring: (A) Taxonomy-based analyses focused on identification of known bioindicators or described taxa; (B) De novo bioindicator analyses; (C) Structural community metrics including inferred ecological networks; and (D) Functional community metrics (metagenomics or metatranscriptomics). We emphasise the utility of the three latter strategies to integrate meiofauna and microorganisms that are not traditionally utilised in biomonitoring because of difficult taxonomic identification. Finally, we propose a roadmap for the implementation of environmental genomics into routine monitoring programs that leverage recent analytical advancements, while pointing out current limitations and future research needs.
Published: 2020
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25. Key questions for next-generation biomonitoring

Author: Andreas Makiola, Zacchaeus G. Compson, Donald J. Baird, Matthew A. Barnes, Sam P. Boerlijst, Agnès Bouchez, Georgina Brennan, Alex Bush, Elsa Canard, Tristan Cordier, Simon Creer, R. Allen Curry, Patrice David, Alex J. Dumbrell, Dominique Gravel, Mehrdad Hajibabaei, Brian Hayden, Berry van der Hoorn, Philippe Jarne, J. Iwan Jones, Battle Karimi, Francois Keck, Martyn Kelly, Ineke E. Knot, Louie Krol, Francois Massol, Wendy A. Monk, John Murphy, Jan Pawlowski, Timothée Poisot, Teresita M. Porter, Kate C. Randall, Emma Ransome, Virginie Ravigné, Alan Raybould, Stephane Robin, Maarten Schrama, Bertrand Schatz, Alireza Tamaddoni-Nezhad, Krijn B. Trimbos, Corinne Vacher, Valentin Vasselon, Susie Wood, Guy Woodward, David A. Bohan, Agroécologie [Dijon], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Environment and Climate Change Canada, University of New Brunswick (UNB), Texas Tech University [Lubbock] (TTU), Naturalis Biodiversity Center [Leiden], Leiden University, Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Bangor University, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-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), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-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 de Recherche pour le Développement (IRD [France-Sud]), Université de Sherbrooke (UdeS), Department of Integrative Biology & Biodiversity Institute of Ontario, University of Guelph, Simon Fraser University (SFU.ca), School of Biological and Chemical Sciences, Queen Mary University of London (QMUL), Bowburn Consultancy, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Google Inc., Department of genetics and evolution, University of Geneva [Switzerland], Université de Montréal (UdeM), Plymouth Marine Laboratory (PML), PML, 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), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Syngenta, Institut National Agronomique Paris-Grignon (INA P-G), Department of Computing, Imperial College London, Bio-Protection Research Centre, Lincoln University, Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de la Recherche Agronomique (INRA), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Biodiversité, Gènes et Communautés, Institut National de la Recherche Agronomique (INRA), Université de Sherbrooke [Sherbrooke], Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-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 la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Université de Montréal [Montréal], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Universiteit Leiden, Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paul-Valéry - Montpellier 3 (UPVM)-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 de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Genève = University of Geneva (UNIGE), Natural Environment Research Council (NERC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), INRAE UMR IGEPP RENNES FRA, Partenaires IRSTEA, and Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)
Subjects: 0106 biological sciences, Computer science, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, DIVERSITY, 01 natural sciences, Field (computer science), TEXT, Biomonitoring, 0502 Environmental Science and Management, lcsh:Environmental sciences, ComputingMilieux_MISCELLANEOUS, General Environmental Science, lcsh:GE1-350, 0303 health sciences, Biodiversity assessment, Suite, SCIENCE, METRICS, artificial intelligence, NETWORKS, biodiversity assessment, PARADIGM, [SDE]Environmental Sciences, Évaluation des ressources, P01 - Conservation de la nature et ressources foncières, Biodiversité, Environmental risk management, Life Sciences & Biomedicine, Écosystème, INDEXES, Environmental Sciences & Ecology, 010603 evolutionary biology, Surveillance de l’environnement, 03 medical and health sciences, QH301, ecological networks, PLANT, QH426, 030304 developmental biology, Science & Technology, Frame (networking), [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, 15. Life on land, Data science, Ecological network, MICROBIOME, metabarcoding, Key (cryptography), eDNA, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ENVIRONMENTAL DNA, Environmental Sciences, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; Classical biomonitoring techniques have focused primarily on measures linked to various biodiversity metrics and indicator species. Next-generation biomonitoring (NGB) describes a suite of tools and approaches that allow the examination of a broader spectrum of organizational levels-from genes to entire ecosystems. Here, we frame 10 key questions that we envisage will drive the field of NGB over the next decade. While not exhaustive, this list covers most of the key challenges facing NGB, and provides the basis of the next steps for research and implementation in this field. These questions have been grouped into current- and outlook-related categories, corresponding to the organization of this paper.
Published: 2020
Full Text: View/download PDF

26. Key questions for next-generation of biomonitoring

Author: Makiola, Andreas, Compson, Zacchaeus G., Baird, Donald J, Barnes, Matthew, Boerlijst, Sam P, Bouchez, Agnes, Brennan, Georgina, Bush, Alex, Canard, Elsa, Cordier, Tristan, Creer, Simon, Curry, Allen, Dumbrell, Alex J, Gravel, Dominique, Hajibabaei, Mehrdad, van Der Hoorn, Berry, Jarne, Philippe, Jones, J.Iwan, Karimi, Battle, Keck, François, Kelly, Martyn, Knot, Ineke, Krol, Louie, Massol, François, Monk, Wendy A., Murphy, John, Pawlowski, Jan, Poisot, Timothée, M. Porter, Teresita, C. Randall, Kate, Ransome, Emma, Ravigné, Virginie, Raybould, Alan, Robin, Stephane, Schrama, Maarten, Schatz, Bertrand, Tamaddoni- Nezhad, Alireza, Trimbos, Krijn B., Vacher, Corinne, Vasselon, Valentin, Wood, Susie, Woodward, Guy, Bohan, David, Agroécologie [Dijon], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Environment and Climate Change Canada @ Canadian Rivers Institute, Department of Biology, University of New Brunswick, NB, Canada, Centre for Environmental Genomics Applications, St. John’s, NL, Canada, Department of Natural Resources Management, Texas Tech University, Lubbock, TX, United States, Naturalis Biodiversity Center [Leiden], Institute of Environmental Sciences, Leiden University, Leiden, Netherlands, Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), School of Natural Sciences, Bangor University, Bangor, United Kingdom, Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), 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), Université de Genève = University of Geneva (UNIGE), Canadian Rivers Institute, Biology, Forestry and Environmental Management, University of New Brunswick, Fredericton, NB, Canada, School of Biological Sciences, University of Essex, Colchester, United Kingdom, Département de Médecine Nucléaire et Radiobiologie - Université de Sherbrooke - Canada, Université de Sherbrooke (UdeS), Centre for Biodiversity Genomics and Department of Integrative Biology, University of Guelph, Guelph, ON, Canada, 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)-Université de Montpellier (UM)-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 SupAgro, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom, Bowburn Consultancy, Durham, United Kingdom, Institute for Biodiversity and Ecosystem Dynamics, Department of Evolutionary and Population Biology, University of Amsterdam, Amsterdam The Netherlands, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB, Canada, Département de sciences biologiques, Université de Montréal, Montreal, QC, Canada, Great Lakes Forestry Centre, Canadian Forest Service, Natural Resources Canada, Sault Ste. Marie, ON, Canada, Imperial College London, 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), Syngenta Crop Protection AG, Basel, Switzerland, School of Social and Political Science, The University of Edinburgh, Edinburgh, United Kingdom, The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Global Academy of Agriculture and Food Security, Edinburgh, United Kingdom, Mathématiques et Informatique Appliquées (MIA Paris-Saclay), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Surrey (UNIS), Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Agence Française pour la Biodiversité, Pôle R&D ECLA, Évian-les-Bains, France, Cawthron Institute, Nelson, New Zealand, Naturalis Biodiversity Center, Leiden, Netherlands, CARRTEL, USMB, INRA, Thonon-les-Bains, France, Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Department of Genetics and Evolution, University of Geneva, Science III, Geneva, Switzerland, 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 de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Department of Life Sciences, Silwood Park Campus, Imperial College London, London, United Kingdom, Mathématiques et Informatique Appliquées (MIA-Paris), and BIOGECO, INRA, Univ. Bordeaux, Pessac, France
Subjects: metabarcoding, ecological networkseDNA, ecological networks, eDNA, artificial intelligence, biodiversity assessment, [SHS]Humanities and Social Sciences
Abstract: International audience; Classical biomonitoring techniques have focused primarily on measures linked tovarious biodiversity metrics and indicator species. Next-generation biomonitoring (NGB)describes a suite of tools and approaches that allow the examination of a broaderspectrum of organizational levels—from genes to entire ecosystems. Here, we frame10 key questions that we envisage will drive the field of NGB over the next decade. Whilenot exhaustive, this list covers most of the key challenges facing NGB, and provides thebasis of the next steps for research and implementation in this field. These questionshave been grouped into current- and outlook-related categories, corresponding to theorganization of this paper.
Published: 2020
Full Text: View/download PDF

27. Species Delimitation

Author: Rannala, Bruce, Yang, Ziheng, Department of Evolution and Ecology, UC Davis, Davis, United States of America, Department of Genetics, Evolution and Environment, University College of London [London] (UCL), Scornavacca, Celine, Delsuc, Frédéric, and Galtier, Nicolas
Subjects: urogenital system, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], food and beverages, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Abstract: International audience; Species delimitation is the process of determining which groups of individual organisms constitute different populations of a single species and which constitute different species. The problem goes back to the earliest days of taxonomy and formalized processes for describing new species exist and are widely used, although the methods are time-intensive and problematic for some species. Genomic data carries extensive information about the degree of genetic isolation among species and about ancient and recent introgression. For this reason, genomic data can play an important role in species delimitation under many existing species concepts. Here we review the history of molecular species delimitation leading up to the current genomic era. We then describe the most widely used computational methods for species delimitation using single-and multi-locus genomic data. Relative strengths and weaknesses of the approaches are discussed and a new method for delimiting species based on empirical criteria is proposed.
Published: 2020

28. Metamorphosis shapes cranial diversity and rate of evolution in salamanders

Author: Anjali Goswami, Julien Clavel, Jeffrey W. Streicher, Carla Bardua, Anne-Claire Fabre, Margot Bon, Jeanne Bonnel, David C. Blackburn, Ryan N. Felice, Edward L. Stanley, Department of Life Sciences, The Natural History Museum [London] (NHM), Department of Genetics, Evolution and Environment, Centre for Biodiversity and Environment, Research, University College of London [London] (UCL), 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), Centre for Integrative Anatomy, Department of Cell and Developmental Biology, University of Florida [Gainesville] (UF), University of Zurich, and Fabre, Anne-Claire
Subjects: 0106 biological sciences, 0301 basic medicine, Ontogeny, media_common.quotation_subject, Urodela, Morphology (biology), 10125 Paleontological Institute and Museum, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Phylogenetics, biology.animal, Animals, Metamorphosis, Evolutionary dynamics, Neoteny, Phylogeny, Ecology, Evolution, Behavior and Systematics, media_common, Life Cycle Stages, Ecology, biology, Skull, Metamorphosis, Biological, 15. Life on land, 030104 developmental biology, 1105 Ecology, Evolution, Behavior and Systematics, 560 Fossils & prehistoric life, Evolutionary biology, Salamander, Rate of evolution, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 2303 Ecology
Abstract: International audience; Metamorphosis is widespread across the animal kingdom and induces fundamental changes in the morphology, habitat and resources used by an organism during its lifetime. Metamorphic species are likely to experience more dynamic selective pres- sures through ontogeny compared with species with single-phase life cycles, which may drive divergent evolutionary dynamics. Here, we reconstruct the cranial evolution of the salamander using geometric morphometric data from 148 species spanning the order’s full phylogenetic, developmental and ecological diversity. We demonstrate that life cycle influences cranial shape diversity and rate of evolution. Shifts in the rate of cranial evolution are consistently associated with transitions from bipha- sic to either direct-developing or paedomorphic life cycle strategies. Direct-developers exhibit the slowest rates of evolution and the lowest disparity, and paedomorphic species the highest. Species undergoing complete metamorphosis (biphasic and direct-developing) exhibit greater cranial modularity (evolutionary independence among regions) than do paedomorphic species, which undergo differential metamorphosis. Biphasic and direct-developing species also display elevated disparity relative to the evolutionary rate for bones associated with feeding, whereas this is not the case for paedomorphic species. Metamorphosis has profoundly influenced salamander cranial evolution, requiring greater autonomy of cranial elements and facilitating the rapid evolution of regions that are remodelled through ontogeny. Rather than compounding functional con- straints on variation, metamorphosis seems to have promoted the morphological evolution of salamanders over 180 million years, which may explain the ubiquity of this complex life cycle strategy across disparate organisms.
Published: 2020
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29. High-throughput DNA barcoding of oligochaetes for abundance-based indices to assess the biological quality of sediments in streams and lakes

Author: Jan Pawlowski, Laure Apothéloz-Perret-Gentil, Benoît J.D. Ferrari, Régis Lionel Vivien, Inge Werner, Michel Lafont, Swiss Federal Insitute of Aquatic Science and Technology [Dübendorf] (EAWAG), Department of Genetics and Evolution, University of Geneva, University of Geneva, ID-GENE Ecodiagnostics, Institute of Oceanology, Polish Academy of Sciences (IO-PAN), Polska Akademia Nauk = Polish Academy of Sciences (PAN), 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), Swiss Centre for Applied Ecotoxicology Eawag-EPFL, Institute of Oceanology, Polish Academy of Sciences, and 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)
Subjects: 0106 biological sciences, 0301 basic medicine, Geologic Sediments, 010504 meteorology & atmospheric sciences, Molecular biology, lcsh:Medicine, 010501 environmental sciences, 01 natural sciences, DNA barcoding, ddc:590, Abundance (ecology), Biomonitoring, Molecular index, lcsh:Science, ComputingMilieux_MISCELLANEOUS, High-throughput sequencing, Multidisciplinary, Ecology, General Engineering, Streams, Identification (biology), Taxonomy (biology), Oligochaetes, Environmental Monitoring, STREAMS, Biology, 010603 evolutionary biology, DNA sequencing, Article, Sediments, 03 medical and health sciences, Species level, Rivers, Genetics, Animals, DNA Barcoding, Taxonomic, Ecosystem, Oligochaeta, Relative species abundance, 0105 earth and related environmental sciences, Biological quality, lcsh:R, Species diversity, Environmental sciences, Lakes, 030104 developmental biology, Sentinel Species, lcsh:Q, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Animal Distribution, Zoology
Abstract: Aquatic oligochaete communities are valuable indicators of the biological quality of sediments in streams and lakes, but identification of specimens to the species level based on morphological features requires solid expertise in taxonomy and is possible only for a fraction of specimens present in a sample. The identification of aquatic oligochaetes using DNA barcodes would facilitate their use in biomonitoring and allow a wider use of this taxonomic group for ecological diagnoses. Previous approaches based on DNA metabarcoding of samples composed of total sediments or pools of specimens have been proposed for assessing the biological quality of ecosystems, but such methods do not provide precise information on species abundance, which limits the value of resulting ecological diagnoses. Here, we tested how a DNA barcoding approach based on high-throughput sequencing of sorted and genetically tagged specimens performed to assess oligochaete species diversity and abundance and the biological quality of sediments in streams and lakes. We applied both molecular and morphological approaches at 13 sites in Swiss streams and at 7 sites in Lake Geneva. We genetically identified 33 or 66 specimens per site. For both approaches, we used the same index calculations. We found that the ecological diagnoses derived from the genetic approach matched well with those of the morphological approach and that the genetic identification of only 33 specimens per site provided enough ecological information for correctly estimating the biological quality of sediments in streams and lakes.
Published: 2019
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30. Alien versus native species as drivers of recent extinctions

Author: Tim M. Blackburn, Anthony Ricciardi, Céline Bellard, Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College of London [London] (UCL), Ecologie Systématique et Evolution (ESE), and AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, Ecology, Biodiversity, Introduced species, Alien, social sciences, 15. Life on land, Biology, Native plant, 010603 evolutionary biology, 01 natural sciences, humanities, 13. Climate action, [SDE]Environmental Sciences, IUCN Red List, Ecosystem, Alien species, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences
Abstract: International audience; Native plants and animals can rapidly become superabundant and dominate ecosystems, leading some people to claim that native species are no less likely than alien species to cause environmental damage such as biodiversity loss. We compared how frequently alien species and native species have been implicated as drivers of recent extinctions in a comprehensive global database, the 2017 IUCN Red List. Alien species were considered to be a contributing cause of 25% of plant extinctions and 33% of animal extinctions, whereas native species were implicated in less than 3% and 5% of animal and plant extinctions, respectively. When listed as a putative driver of recent extinctions, native species were more often associated with cooccurring drivers than were alien species. Our results add a new line of evidence that the biogeographic origin (evolutionary history) of a species is a determining factor of its potential to cause disruptive environmental impacts.
Published: 2019
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31. DNA metabarcoding—Need for robust experimental designs to draw sound ecological conclusions

Author: Inger Greve Alsos, Lucie Zinger, Gentile Francesco Ficetola, Aurélie Bonin, Frédéric Boyer, Marta De Barba, Simon N. Jarman, M. Thomas P. Gilbert, Ian A. Dickie, Leho Tedersoo, Anthony A. Chariton, Bruce E. Deagle, Philip Francis Thomsen, Johan Pansu, Alex J. Dumbrell, Ari Jumpponen, Håvard Kauserud, Holly M. Bik, Eske Willerslev, Pierre Taberlet, Luca Fumagalli, Simon Creer, Eric Coissac, Miklós Bálint, Jan Pawlowski, Ludovic Orlando, Noah Fierer, 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 [2016-2019] (UGA [2016-2019]), Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, New York University [New York] (NYU), NYU System (NYU), Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Australian Antarctic Division (AAD), Australian Government, Department of the Environment and Energy, emlyon business school, Politecnico di Milano [Milan] (POLIMI), University of Copenhagen = Københavns Universitet (KU), Microbial Evolution Research Group (MERG), Department of Biology [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO)-Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Department of Genetics and Evolution, Université de Genève (UNIGE), University of Tartu, JP was supported by the Marie Skłodowska-Curie actions (TEAM-Coast project, MSCA-GF 750570), Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - Faculté des Sciences et des Techniques, Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-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), Robotique Et Vivant (ReV), and Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - Faculté des Sciences et des Techniques
Subjects: 0106 biological sciences, replication, Ecology (disciplines), [SDV]Life Sciences [q-bio], experimental controls, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, Dna genetics, Replication (statistics), Genetics, DNA Barcoding, Taxonomic, data quality, Environmental DNA, Ecology, Evolution, Behavior and Systematics, Sound (geography), ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, geography, geography.geographical_feature_category, Ecology, Biodiversity, DNA, environmental DNA, chemistry, Evolutionary biology, [SDE]Environmental Sciences
Abstract: International audience
Published: 2019
Full Text: View/download PDF

32. Genetic components of human pain sensitivity: a protocol for a genome-wide association study of experimental pain in healthy volunteers

Author: Schmid, Annina B., Adhikari, Kaustubh, Ramirez-Aristeguieta, Luis Miguel, Chacón-Duque, Juan-Camilo, Poletti, Giovanni, Gallo, Carla, Rothhammer, Francisco, Bedoya, Gabriel, Ruiz-Linares, Andres, Bennett, David L, Dept of Genetics, Evolution and Environment [London] (UCL-GEE), University College of London [London] (UCL), Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), State Key Laboratory of Genetics Engineering & MOE Key Laboratory of Contemporary Anthropology, and Fudan University [Shanghai]-School of Life Sciences
Subjects: genome-wide association study, thermal pain, adult, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Hispanic, genetic analysis, Article, purl.org/pe-repo/ocde/ford#3.02.00 [https], human experiment, mechanical pain, experimental pain, genetics, pain, pain sensitivity, human, nociception, normal human, hyperalgesia
Abstract: IntroductionPain constitutes a major component of the global burden of diseases. Recent studies suggest a strong genetic contribution to pain susceptibility and severity. Whereas most of the available evidence relies on candidate gene association or linkage studies, research on the genetic basis of pain sensitivity using genome-wide association studies (GWAS) is still in its infancy. This protocol describes a proposed GWAS on genetic contributions to baseline pain sensitivity and nociceptive sensitisation in a sample of unrelated healthy individuals of mixed Latin American ancestry.Methods and analysisA GWAS on genetic contributions to pain sensitivity in the naïve state and following nociceptive sensitisation will be conducted in unrelated healthy individuals of mixed ancestry. Mechanical and thermal pain sensitivity will be evaluated with a battery of quantitative sensory tests evaluating pain thresholds. In addition, variation in mechanical and thermal sensitisation following topical application of mustard oil to the skin will be evaluated.Ethics and disseminationThis study received ethical approval from the University College London research ethics committee (3352/001) and from the bioethics committee of the Odontology Faculty at the University of Antioquia (CONCEPTO 01–2013). Findings will be disseminated to commissioners, clinicians and service users via papers and presentations at international conferences.
Published: 2019
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33. Genetic contributors to serum uric acid levels in Mexicans and their effect on premature coronary artery disease

Author: Carla Gallo, Paola León-Mimila, Luis Macías-Kauffer, Sofia Moran-Ramos, Andres Ruiz-Linares, Leonor Jacobo-Albavera, Christopher R. Stephens, Victor Acuña-Alonzo, Maria Cátira Bortolini, Francisco J. Flores-Murrieta, Sandra Romero-Hidalgo, Blanca E. Del-Rio-Navarro, Carlos A. Aguilar-Salinas, Teresa Villarreal-Molina, Hugo Villamil-Ramírez, Rolando González-José, Gabriel Bedoya, Carlos Posadas-Romero, Francisco Rothhammer, Rosalinda Posadas-Sánchez, Gilberto Vargas-Alarcón, Cecilia Fernández del Valle-Laisequilla, Samuel Canizales-Quinteros, Blanca E. López-Contreras, Miriam del Carmen Carrasco-Portugal, Rafael Velázquez-Cruz, Lina M. Barranco Garduño, Juan Gerardo Reyes-García, Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Dept of Genetics, Evolution and Environment [London] (UCL-GEE), University College of London [London] (UCL), Instituto Nacional de Cardiología, Molecular Genetics Laboratory, Escuela Nacional de Antropologia y Historia, Laboratorio de Genética Molecular, Universidad de Antioquia = University of Antioquia [Medellín, Colombia], Facultad de Medicina & Instituto de Alta Investigacion, Universidad de Tarapaca-Universidade de Chile, Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Universidad Nacional Autónoma de México (UNAM), Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán - National Institute of Medical Science and Nutrition Salvador Zubiran [Mexico], and Unit of Molecular Biology and Genomic Medicine
Subjects: Male, obesity, estimated glomerular filtration rate, ABCG2 gene, genotype, [SDV]Life Sciences [q-bio], [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Genome-wide association study, Coronary Artery Disease, 030204 cardiovascular system & hematology, Bioinformatics, Coronary artery disease, Genética y Herencia, 0302 clinical medicine, single nucleotide polymorphism, genetic variability, gender, purl.org/pe-repo/ocde/ford#3.02.04 [https], 030212 general & internal medicine, Child, ComputingMilieux_MISCELLANEOUS, Aged, 80 and over, child, biology, adult, Mexican, Mendelian Randomization Analysis, Middle Aged, cohort analysis, 3. Good health, aged, female, priority journal, breast cancer resistance protein, Female, Cardiology and Cardiovascular Medicine, CIENCIAS NATURALES Y EXACTAS, uric acid blood level, Adult, gene locus, Adolescent, GENETICS, Mendelian randomization analysis, Single-nucleotide polymorphism, Polymorphism, Single Nucleotide, Article, Ciencias Biológicas, 03 medical and health sciences, Young Adult, male, Mendelian randomization, medicine, SNP, Humans, controlled study, human, gene, Mexico, Aged, genome-wide association study, business.industry, medicine.disease, major clinical study, Uric Acid, URIC ACID, SLC2A9 gene, biology.protein, CORONARY ARTERY DISEASE, metabolic syndrome X, Metabolic syndrome, business, Biomarkers, SLC2A9, Genome-Wide Association Study
Abstract: Background: Serum uric acid (SUA) is a heritable trait associated with cardiovascular risk factors and coronary artery disease (CAD). Genome wide association studies (GWAS) have identified several genes associated with SUA, mainly in European populations. However, to date there are few GWAS in Latino populations, and the role of SUA-associated single nucleotide polymorphisms (SNPs) in cardiovascular disease has not been studied in the Mexican population. Methods: We performed genome-wide SUA association study in 2153 Mexican children and adults, evaluated whether genetic effects were modified by sex and obesity, and used a Mendelian randomization approach in an independent cohort to study the role of SUA modifying genetic variants in premature CAD. Results: Only two loci were associated with SUA levels: SLC2A9 (β = −0.47 mg/dl, P = 1.57 × 10−42 for lead SNP rs7678287) and ABCG2 (β = 0.23 mg/dl, P = 2.42 × 10−10 for lead SNP rs2231142). No significant interaction between SLC2A9 rs7678287 and ABCG2 rs2231142 genotypes and obesity was observed. However, a significant ABCG2 rs2231142 genotype*sex interaction (P = 0.001) was observed in adults but not in children. Although SUA levels were associated with premature CAD, metabolic syndrome and decreased glomerular filtration rate (eGFR), only ABCG2 rs2231142 was associated with decreased eGFR in the premature CAD group. Conclusions: SUA elevation was independently associated with premature CAD, metabolic syndrome and decreased eGFR in the Mexican population. However, a Mendelian randomization approach using the lead SUA-associated SNPs (SLC2A9 and ABCG2) did not support a causal role of elevated SUA levels for premature CAD. Fil: Macias Kauffer, Luis R.. Instituto Nacional de Medicina Genómica Mexico; México. Universidad Nacional Autónoma de México; México Fil: Villamil Ramírez, Hugo. Instituto Nacional de Medicina Genómica Mexico; México Fil: León Mimila, Paola. Instituto Nacional de Medicina Genómica Mexico; México Fil: Jacobo Albavera, Leonor. Inmegen; México Fil: Posadas Romero, Carlos. Instituto Nacional de Cardiologia Ignacio Chavez; México Fil: Posadas Sánchez, Rosalinda. Instituto Nacional de Cardiologia Ignacio Chavez; México Fil: López Contreras, Blanca E.. Instituto Nacional de Medicina Genómica Mexico; México Fil: Morán Ramos, Sofía. Instituto Nacional de Medicina Genómica Mexico; México Fil: Romero Hidalgo, Sandra. Inmegen; México Fil: Acuña Alonzo, Víctor. Colegio Universitario de Londres; Reino Unido Fil: del Río Navarro, Blanca E.. Hospital Infantil de Mexico Federico Gomez; México Fil: Bortolini, Maria Cátira. Universidade Federal do Rio Grande do Sul; Brasil Fil: Gallo, Carla. Universidad Peruana Cayetano Heredia; Perú Fil: Bedoya, Gabriel. Universidad de Antioquia; Colombia Fil: Rothhammer, Francisco. Universidad de Chile; Chile Fil: González José, Rolando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentina Fil: Ruiz-Linares, Andres. Fudan University; China. Anthropologie Bio-culturelle, Droit, Éthique & Fil: Stephens, Christopher R.. Universidad Nacional Autónoma de México. Instituto de Ciencias Nucleares; México Fil: Velazquez Cruz, Rafael. Instituto Nacional de Medicina Genómica Mexico; México Fil: Fernández del Valle Laisequilla, Cecilia. Productos Medix; México Fil: Reyes-García, Juan G.. INSTITUTO POLITÉCNICO NACIONAL (IPN); Fil: Barranco Garduño, Lina M.. Instituto Nacional de Enfermedades Respiratorias; México Fil: Carrasco-Portugal, Miriam del C.. Instituto Nacional de Enfermedades Respiratorias; México Fil: Flores-Murrieta, Francisco J.. Instituto Nacional de Enfermedades Respiratorias; México. INSTITUTO POLITÉCNICO NACIONAL (IPN); Fil: Vargas Alarcón, Gilberto. Instituto Nacional de Cardiologia Ignacio Chavez; México Fil: Aguilar Salinas, Carlos A.. Escuela de Medicina y Ciencias de la Salud Tecsalud; México. Instituto Nacional de la Nutrición Salvador Zubiran; México Fil: Villarreal Molina, Teresa. Inmegen; México Fil: Canizales Quinteros, Samuel. Instituto Nacional de Medicina Genómica Mexico; México
Published: 2019
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34. Variation in dental morphology and inference of continental ancestry in admixed Latin Americans

Author: Miguel A. Delgado, Luis Ramírez, Francisco Rothhammer, Samuel Canizales, Carla Gallo, Macarena Fuentes-Guajardo, Clément Zanolli, Andres Ruiz-Linares, Rolando González-José, Gabriel Bedoya, Maria Cátira Bortolini, Giovanni Poletti, Kaustubh Adhikari, Universitat Politècnica de Catalunya [Barcelona] (UPC), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Laboratorio de Genética Molecular, Universidad de Antioquia = University of Antioquia [Medellín, Colombia], Facultad de Medicina & Instituto de Alta Investigacion, Universidad de Tarapaca-Universidade de Chile, Dept of Genetics, Evolution and Environment [London] (UCL-GEE), University College of London [London] (UCL), Tecnológico de Monterrey (ITESM), Universidad de Tarapaca, De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB), Universidad Nacional Autónoma de México (UNAM), Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS), Universidad Peruana Cayetano Heredia (UPCH), Universidad de Chile = University of Chile [Santiago] (UCHILE), Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), and Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM)
Subjects: Male, 0106 biological sciences, purl.org/pe-repo/ocde/ford#5.04.03 [https], Latin Americans, [SDV]Life Sciences [q-bio], [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Inference, 01 natural sciences, Genética y Herencia, ANCESTRY INFERENCE, morphology, DENTAL MORPHOLOGY, 0601 history and archaeology, Statistic, education.field_of_study, Antropología, adult, article, Hispanic or Latino, differentiation, 06 humanities and the arts, ADMIXTURE, Colombian, female, Variation (linguistics), Photography, Dental, purl.org/pe-repo/ocde/ford#3.01.01 [https], American Indian, Trait, admixture, Female, Anatomy, CIENCIAS NATURALES Y EXACTAS, Adult, ancestry inference, Adolescent, Genetic genealogy, Population, education, Colombia, Biology, European, 010603 evolutionary biology, LATIN AMERICA, Anthropology, Physical, Ciencias Biológicas, Young Adult, male, Humans, human, genome, 060101 anthropology, dental morphology, Racial Groups, African, major clinical study, Genetic architecture, stomatognathic diseases, Genetics, Population, Latin America, validation process, Anthropology, Tooth, Demography
Abstract: Objectives: To investigate the variation in dental nonmetric traits and to evaluate the utility of this variation for inferring genetic ancestry proportions in a sample of admixed Latin Americans.; Materials and Methods: We characterized a sample from Colombia (N = 477) for 34 dental traits and obtained estimates of individual Native American, European, and African ancestry using genome‐wide SNP data. We tested for correlation between dental traits, genetic ancestry, age, and sex. We carried out a biodistance analysis between the Colombian sample and reference continental population samples using the mean measure of divergence statistic calculated from dental trait frequencies. We evaluated the inference of genetic ancestry from dental traits using a regression approach (with 10‐fold cross‐validation) as well as by testing the correlation between estimates of ancestry obtained from genetic and dental data.; Results: Latin Americans show intermediate dental trait frequencies when compared to Native Americans, Europeans, and Africans. Significant correlations were observed for several dental traits, genetic ancestry, age, and sex. The biodistance analysis displayed a closer relationship of Colombians to Europeans than to Native Americans and Africans. Mean ancestry estimates obtained from the dental data are similar to the genetic estimates (Native American: 32% vs. 28%, European: 59% vs. 63%, and African: 9% vs. 9%, respectively). However, dental features provided low predictive power for genetic ancestry of individuals in both approaches tested (R2, Facultad de Ciencias Naturales y Museo
Published: 2019
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35. Invasion Biology: Specific Problems and Possible Solutions

Author: Cleo Bertelsmeier, Jonathan M. Jeschke, Alice Fournier, Franck Courchamp, Elsa Bonnaud, Céline Bellard, James C. Russell, Ecologie Systématique et Evolution (ESE), Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Dept of Genetics, Evolution and Environment [London] (UCL-GEE), University College of London [London] (UCL), Département d'écologie et évolution [Lausanne] (DEE), Université de Lausanne (UNIL), Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Freie Universität Berlin, Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), University of Auckland [Auckland], BiodivERsA European Research Area (ERA-Net FFII grant), Agence Nationale de la Recherche (ANR), BNP Paribas (grant InvaCost), Deutsche Forschungsgemeinschaft (DFG) (grants JE 288/8-1, JE 288/9-1)., European Project: 266546,EC:FP7:ENV,FP7-ERANET-2010-RTD,BIODIVERSA2(2010), and Université de Lausanne = University of Lausanne (UNIL)
Subjects: 0106 biological sciences, engaging with the public, Ecology, 010604 marine biology & hydrobiology, Ecology (disciplines), biological invasions, Environmental ethics, Biodiversity, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, science communication, 010603 evolutionary biology, 01 natural sciences, decision making, Criticism, Science communication, citizen involvement, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Introduced Species, science–society interface, Alien species, Ecology, Evolution, Behavior and Systematics
Abstract: International audience; Biological invasions have been unambiguously shown to be one of the major global causes of biodiversity loss. Despite the magnitude of this threat and recent scientific advances, this field remains a regular target of criticism – from outright deniers of the threat to scientists questioning the utility of the discipline. This unique situation, combining internal strife and an unaware society, greatly hinders the progress of invasion biology. It is crucial to identify the specificities of this discipline that lead to such difficulties. We outline here 24 specificities and problems of this discipline and categorize them into four groups: understanding, alerting, supporting, and implementing the issues associated with invasive alien species, and we offer solutions to tackle these problems and push the field forward.
Published: 2017
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36. Genetic modification for disease resistance: a position paper

Author: Jean B. Ristaino, Lise Korsten, David Grzywacz, Serge Savary, Peter Scott, Richard N. Strange, Jennifer A. Thomson, Plant Pathology, Department of Molecular and Cell Biology, University of Cape Town, University of Greenwich, AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Department of Genetics, Evolution and Environment, University College of London [London] (UCL), North Carolina State University, Center for High Performance Simulation and Department of Chemical and Biomolecular Engineering, Department of Microbiology and Plant Pathology, and University of Pretoria [South Africa]
Subjects: 0106 biological sciences, 0301 basic medicine, S1, [SDV]Life Sciences [q-bio], Developing country, Development, 01 natural sciences, Plant breeding, Developing countries, [SHS]Humanities and Social Sciences, 03 medical and health sciences, Biosafety, Economics, 2. Zero hunger, Disease resistance, Food security, business.industry, food and beverages, Plant disease, Biotechnology, 030104 developmental biology, Risk analysis (engineering), Multinational corporation, Agriculture, Genetic modification, Genetic engineering, [SDE]Environmental Sciences, Objective approach, Position paper, business, Agronomy and Crop Science, 010606 plant biology & botany, Food Science
Abstract: This Position Paper was prepared by members of the Task Force on Global Food Security of the International Society for Plant Pathology. An objective approach is proposed to the assessment of the potential of genetic modification (GM) to reduce the impact of crop diseases. \ud \ud The addition of GM to the plant breeder’s conventional toolbox facilitates gene-by-gene introduction into breeding programmes of well defined characters, while also allowing access to genes from a greatly extended range of organisms. The current status of GM crops is outlined. GM could make an additional contribution to food security but its potential has been controversial, sometimes because of fixed views that GM is unnatural and risky. These have no factual basis: GM technology, where adopted, is widely regulated and no evidence has been reported of adverse consequences for human health. \ud \ud The potential benefits of GM could be particularly valuable for the developing world but there are numerous constraints. These include cost, inadequate seed supply systems, reluctance to adopt unfamiliar technology, concern about markets, inadequacy of local regulatory systems, mismatch between research and growers’ needs, and limited technical resources. The lower cost of new gene-editing methods should open the practice of GM beyond multinational corporations. As yet there are few examples of utilization of GM-based resistance to plant diseases.\ud \ud Two cases, papaya ringspot virus and banana xanthomonas wilt, are outlined. In the developing world there are many more potential cases whose progress is prevented by the absence of adequate biosafety regulation. \ud \ud It is concluded that there is untapped potential for using GM to introduce disease resistance. An objective approach to mobilizing this potential is recommended, to address the severe impact of plant disease on food security.
Published: 2016
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37. Do Developmental Constraints and High Integration Limit the Evolution of the Marsupial Oral Apparatus?

Author: P. David Polly, Anjali Goswami, Vera Weisbecker, Marcela Randau, Marcelo R. Sánchez-Villagra, C. Verity Bennett, Lionel Hautier, Department of Genetics, Evolution and Environment, Centre for Biodiversity and Environment, Research, University College of London [London] (UCL), Museum of Zoology, University of Cambridge, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), and University of Zurich
Subjects: 0106 biological sciences, 0301 basic medicine, Oral apparatus, [SDV]Life Sciences [q-bio], Ontogeny, Zoology, Plant Science, 10125 Paleontological Institute and Museum, A Bigger Picture: Organismal Function at the Nexus of Development, Ecology, and Evolution, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, 1110 Plant Science, medicine, Animals, [SDV.BDD]Life Sciences [q-bio]/Development Biology, ComputingMilieux_MISCELLANEOUS, Marsupial, Mouth, biology, biology.organism_classification, Biological Evolution, Altricial, Skull, Marsupialia, 030104 developmental biology, medicine.anatomical_structure, 560 Fossils & prehistoric life, Animal Science and Zoology, Trajectory analysis, 1103 Animal Science and Zoology, Forelimb, Pouch
Abstract: Developmental constraints can have significant influence on the magnitude and direction of evolutionary change, and many studies have demonstrated that these effects are manifested on macroevolutionary scales. Phenotypic integration, or the strong interactions among traits, has been similarly invoked as a major influence on morphological variation, and many studies have demonstrated that trait integration changes through ontogeny, in many cases decreasing with age. Here, we unify these perspectives in a case study of the ontogeny of the mammalian cranium, focusing on a comparison between marsupials and placentals. Marsupials are born at an extremely altricial state, requiring, in most cases, the use of the forelimbs to climb to the pouch, and, in all cases, an extended period of continuous suckling, during which most of their development occurs. Previous work has shown that marsupials are less disparate in adult cranial form than are placentals, particularly in the oral apparatus, and in forelimb ontogeny and adult morphology, presumably due to functional selection pressures on these two systems during early postnatal development. Using phenotypic trajectory analysis to quantify prenatal and early postnatal cranial ontogeny in 10 species of therian mammals, we demonstrate that this pattern of limited variation is also apparent in the development of the oral apparatus of marsupials, relative to placentals, but not in the skull more generally. Combined with the observation that marsupials show extremely high integration of the oral apparatus in early postnatal ontogeny, while other cranial regions show similar levels of integration to that observed in placentals, we suggest that high integration may compound the effects of the functional constraints for continuous suckling to ultimately limit the ontogenetic and adult disparity of the marsupial oral apparatus throughout their evolutionary history.
Published: 2016
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38. Selective zircon accumulation in a new benthic foraminifer,Psammophaga zirconia, sp. nov

Author: Enrico Dinelli, Pontus Lurcock, Roberta Galeazzi, Alessandra Negri, Anna Sabbatini, Omar Boudouma, Luca Massaccesi, Sergio Rocchi, Caterina Morigi, Fabio Florindo, Annachiara Bartolini, Jan Pawlowski, Maria Holzmann, Dpto Sc. Vita & Ambiente Ancona, Università Politecnica delle Marche [Ancona] (UNIVPM), Centre de recherche sur la Paléobiodiversité et les Paléoenvironnements (CR2P), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Dipartimento di Scienze della Terra [Pisa], University of Pisa - Università di Pisa, Institut des Sciences de la Terre de Paris (iSTeP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), Istituto Nazionale di Geofisica e Vulcanologia - Sezione di Bologna (INGV), Istituto Nazionale di Geofisica e Vulcanologia, Department of Genetics and Evolution, Université de Genève = University of Geneva (UNIGE), Istituto Nazionale di Geofisica e Vulcanologia - Sezione di Roma (INGV), Université de Genève (UNIGE), Sabbatini, A, Negri, A., Bartolini, A., Morigi, C., Boudouma, O., Dinelli, Enrico, Florindo, F., Galeazzi, R., Holzmann, M., Lurcock, P. C., Massaccesi, L., Pawlowski, J., and Rocchi, S.
Subjects: Cytoplasm, 010504 meteorology & atmospheric sciences, Foraminifera, zircon, 010502 geochemistry & geophysics, 01 natural sciences, early organisms, chemistry.chemical_compound, Cluster Analysis, Xenophyophora, Phylogeny, Eukaryota, Psammophaga, General Environmental Science, Magnetite, Minerals, Mineral, biology, heavy minerals, Rutile, Benthic zone, foraminifera, early organisms, zircon, heavy minerals, Earth and Planetary Sciences (all), Calcareous, RNA, Protozoan, Ilmenite, Geology, Zircon, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, Mineralogy, engineering.material, DNA, Ribosomal, Metals, Heavy, Mediterranean Sea, RNA, Ribosomal, 18S, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, Spectrometry, X-Ray Emission, Genes, rRNA, Sequence Analysis, DNA, DNA, Protozoan, biology.organism_classification, Ecology, Evolution, Behavior and Systematic, chemistry, Microscopy, Electron, Scanning, engineering, General Earth and Planetary Sciences, Zirconium
Abstract: International audience; Benthic foraminifera are single-celled eukaryotes that make a protective organic, agglutinated or calcareous test. Some agglutinated, single-chambered taxa, including Psammophaga Arnold, 1982, retain mineral particles in their cytoplasm, but the selective mechanism of accumulation is not clear. Here, we report the ability of a foraminiferal species to select and accumulate zircons and other heavy minerals in their cytoplasm. In particular, the use of Scanning Electron Microscope coupled with an Energy Dispersive X-ray microanalysis system (SEM–EDS) enabled a representative overview of the mineral diversity and showed that the analysed Psammophaga zirconia sp. nov. individuals contained dominantly crystals of zircon (51%), titanium oxides (27%), and ilmenite (11%) along with minor magnetite and other minerals. The studied specimens occur in the shallow central Adriatic Sea where the sediment has a content of zircon below 1% and of other heavy minerals below 4%. For that reason we hypothesize that: (i) P. zirconia may be able to chemically select minerals, specifically zircon and rutile; (ii) the chemical mechanism allowing the selection is based on electrostatic interaction, and it could work also for agglutinated foraminifera (whether for ingestion, like Xenophyophores, or incorporation in the test as in many other described taxa). In particular, this aptitude for high preferential uptake and differential ingestion or retention of zircon is reported here for the first time, together with the selection of other heavy minerals already described in members of the genus Psammophaga. They are generally counted among early foraminifera, constructing a morphologically simple test with a single chamber. Our molecular phylogenetic study confirms that P. zirconia is a new species, genetically distinctive from other Psammophaga, and occurs in the Adriatic as well as in the Black Sea.
Published: 2016
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39. A GWAS in Latin Americans highlights the convergent evolution of lighter skin pigmentation in Eurasia

Author: Adhikari, Kaustubh, Mendoza-Revilla, Javier, Sohail, Anood, Fuentes-Guajardo, Macarena, Lampert, Jodie, Chacón-Duque, Juan Camilo, Hurtado, Malena, Villegas, Valeria, Granja, Vanessa, Acuña-Alonzo, Victor, Jaramillo, Claudia, Arias, William, Lozano, Rodrigo Barquera, Everardo, Paola, Gómez-Valdés, Jorge, Villamil-Ramírez, Hugo, Silva de Cerqueira, Caio C., Hunemeier, Tábita, Ramallo, Virginia, Schuler-Faccini, Lavinia, Salzano, Francisco M., Gonzalez-José, Rolando, Bortolini, Maria-Cátira, Canizales-Quinteros, Samuel, Gallo, Carla, Poletti, Giovanni, Bedoya, Gabriel, Rothhammer, Francisco, Tobin, Desmond J., Fumagalli, Matteo, Balding, David, Ruiz-Linares, Andrés, Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Dept of Genetics, Evolution and Environment [London] (UCL-GEE), University College of London [London] (UCL), Molecular Genetics Laboratory, Escuela Nacional de Antropologia y Historia, Departamento de Genética, Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS)-Instituto de Biociencias, Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Unit of Molecular Biology and Genomic Medicine, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán - National Institute of Medical Science and Nutrition Salvador Zubiran [Mexico], Laboratorio de Genética Molecular, Universidad de Antioquia = University of Antioquia [Medellín, Colombia], Facultad de Medicina & Instituto de Alta Investigacion, Universidad de Tarapaca-Universidade de Chile, Center for Skin Sciences, and University of Bradford
Subjects: epistasis, Male, POSITIVE SELECTION, genetic association, EUROPEANS, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, LOCI, purl.org/pe-repo/ocde/ford#1.03.00 [https], Skin Pigmentation, chromosome 1q, human experiment, quantitative trait locus, Ethnicity, skin color, GWAS, Guanine Nucleotide Exchange Factors, genetics, lcsh:Science, ADAPTATION, POPULATION, ComputingMilieux_MISCELLANEOUS, transcription factor YY1, HERC2 protein, human, allele, Biological Evolution, chromosome 20q, Science & Technology - Other Topics, phenotype, Science, solar radiation, European Continental Ancestry Group, Quantitative Trait Loci, metabotropic receptor 5, White People, Article, medical photography, Ciencias Biológicas, Asian People, human genome, Humans, COLOR, human, normal human, GENOME-WIDE ASSOCIATION, convergent evolution, POLYMORPHISMS, Alleles, Science & Technology, binding site, human cell, Membrane Transport Proteins, Epistasis, Genetic, gene linkage disequilibrium, carrier protein, Genetics, Population, Latin America, hair root, lcsh:Q, GRM5 protein, human, melanocyte, [SDV]Life Sciences [q-bio], Gene Expression, purl.org/becyt/ford/1 [https], ethnic group, Genética y Herencia, Gene Frequency, single nucleotide polymorphism, guanine nucleotide exchange factor, membrane protein, exon, transcription factor EMX2, Eye Color, MFSD12 protein, human, OCA2 protein, human, phenotypic variation, melanin, ADMIXTURE, Multidisciplinary Sciences, female, immunohistochemistry, Female, CIENCIAS NATURALES Y EXACTAS, amino acid substitution, Asian Continental Ancestry Group, gene locus, intron, Ubiquitin-Protein Ligases, purl.org/pe-repo/ocde/ford#1.06.03 [https], Receptor, Metabotropic Glutamate 5, Ethnic Groups, ANCESTRY, Caucasian, Polymorphism, Single Nucleotide, South and Central America, MD Multidisciplinary, evolution, controlled study, purl.org/becyt/ford/1.6 [https], genome-wide association study, Genome, Human, population genetics, Membrane Proteins, human tissue, LATIN AMERICANS, chromosome 22q, Latin American medicine, purl.org/pe-repo/ocde/ford#1.04.00 [https], sense organs, MERCAPTOPYRUVATE SULFURTRANSFERASE, Genome-Wide Association Study
Abstract: We report a genome-wide association scan in >6,000 Latin Americans for pigmentation of skin and eyes. We found eighteen signals of association at twelve genomic regions. These include one novel locus for skin pigmentation (in 10q26) and three novel loci for eye pigmentation (in 1q32, 20q13 and 22q12). We demonstrate the presence of multiple independent signals of association in the 11q14 and 15q13 regions (comprising the GRM5/TYR and HERC2/OCA2 genes, respectively) and several epistatic interactions among independently associated alleles. Strongest association with skin pigmentation at 19p13 was observed for an Y182H missense variant (common only in East Asians and Native Americans) in MFSD12, a gene recently associated with skin pigmentation in Africans. We show that the frequency of the derived allele at Y182H is significantly correlated with lower solar radiation intensity in East Asia and infer that MFSD12 was under selection in East Asians, probably after their split from Europeans., Pigmentation variation in humans is influenced by complex genetic architecture in different populations. Here, the authors perform a genome-wide association analysis involving > 6,000 Latin Americans for pigmentation of skin and eyes, and identify known and novel genetic associations.
Published: 2019
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40. A geometric morphometric approach to the study of variation of shovel-shaped incisors

Author: Andres Ruiz-Linares, Jean Dumoncel, Paul Monsarrat, Macarena Fuentes-Guajardo, Lei Pan, Clément Zanolli, Frédéric Vaysse, Miguel A. Delgado, Anna Catherina Oettle, Rémi Esclassan, Benjamin Duployer, Frikkie de Beer, Christophe Tenailleau, Kaustubh Adhikari, Jakobus Hoffman, Richard Donat, José Braga, Delphine Carayon, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université Montpellier 1 (UM1), University College of London [London] (UCL), STROMALab, Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Etablissement Français du Sang-Institut National de la Santé et de la Recherche Médicale (INSERM), University of the Witwatersrand [Johannesburg] (WITS), Centre interuniversitaire de recherche et d'ingenierie des matériaux (CIRIMAT), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC), Universitat Politècnica de Catalunya [Barcelona] (UPC), Universidad de Tarapaca, South African Nuclear Energy Corporation [Pretoria] (NECSA), University of Pretoria [South Africa], Institut national de recherches archéologiques préventives (Inrap), Centre d'anthropologie et de génomique de Toulouse (CAGT), Nanjing Institute of Geology and Palaeontology (NIGPAS-CAS), Chinese Academy of Sciences [Nanjing Branch], Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences [Beijing] (CAS), State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Dept of Genetics, Evolution and Environment [London] (UCL-GEE), Fudan University [Shanghai], Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Etablissement Français du Sang-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées, Polytechnic University of Catalonia (UPC), Centre National de la Recherche Scientifique - CNRS (FRANCE), Centre Hospitalier Régional Universitaire de Montpellier - CHRU Montpellier (FRANCE), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Institute of Vertebrate Paleontology and Paleoanthropology - IVPP (CHINA), Nanjing Institute of Geology and Palaeontology (CHINA), University College of London - UCL (UNITED KINGDOM), Universidad Nacional de la Plata - UNLP (ARGENTINA), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), Universidad de Tarapacá (CHILE), Consejo Nacional de Investigaciones Científicas y Técnicas - CONICET (ARGENTINA), Centre Hospitalier Universitaire de Toulouse - CHU Toulouse (FRANCE), Institut National de Recherches Archéologiques Préventives - INRAP (FRANCE), South African Nuclear Energy Corporation - NECSA (SOUTH AFRICA), Shanghai University (CHINA), University of Pretoria (SOUTH AFRICA), University of the Witwatersrand - WITS (SOUTH AFRICA), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Etablissement Français du Sang-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), and Institut National Polytechnique de Toulouse - INPT (FRANCE)
Subjects: 0106 biological sciences, Computer science, Matériaux, [SDV]Life Sciences [q-bio], [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, ASUDAS, Virtual anthropology, 010603 evolutionary biology, 01 natural sciences, Anthropology, Physical, Dental anthropology, Imaging, Three-Dimensional, stomatognathic system, Shovel‐shape incisors, Visual scoring, Humans, Odontometry, 0601 history and archaeology, Maxillary central incisor, Shovel-shaped incisors, Virtual imaging, Orthodontics, Procrustes and non‐Procrustes superimpositions, 060101 anthropology, 06 humanities and the arts, Incisor, stomatognathic diseases, Anthropology, Standard protocol, Anatomy
Abstract: Objectives: The scoring and analysis of dental nonmetric traits are predominantly accomplished by using the Arizona State University Dental Anthropology System (ASUDAS), a standard protocol based on strict definitions and three‐dimensional dental plaques. However, visual scoring, even when controlled by strict definitions of features, visual reference, and the experience of the observer, includes an unavoidable part of subjectivity. In this methodological contribution, we propose a new quantitative geometric morphometric approach to quickly and efficiently assess the variation of shoveling in modern human maxillary central incisors (UI1).\ud \ud Materials and methods: We analyzed 87 modern human UI1s by means of virtual imaging and the ASU‐UI1 dental plaque grades using geometric morphometrics by placing semilandmarks on the labial crown aspect. The modern human sample was composed of individuals from Europe, Africa, and Asia and included representatives of all seven grades defined by the ASUDAS method.\ud \ud Results: Our results highlighted some limitations in the use of the current UI1 ASUDAS plaque, indicating that it did not necessarily represent an objective gradient of expression of a nonmetric tooth feature. Rating of shoveling tended to be more prone to intra‐ and interobserver bias for the highest grades. In addition, our analyses suggest that the observers were strongly influenced by the depth of the lingual crown aspect when assessing the shoveling.\ud \ud Discussion: In this context, our results provide a reliable and reproducible framework reinforced by statistical results supporting the fact that open scale numerical measurements can complement the ASUDAS method.
Published: 2019
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41. Development and implementation of eco-genomic tools for aquatic ecosystem biomonitoring: the SYNAQUA French-Swiss program

Author: Laura Crépin, Estelle Lefrancois, Alina Pawlowska, Dominique Trevisan, Jean-Christophe Hustache, Louis Jacas, Arielle Cordonier, Laure Apothéloz-Perret-Gentil, Samuel Botreau, Cécile Chardon, Jan Pawlowski, Tristan Cordier, Sonia Lacroix, Stéphan Jacquet, Pascal Perney, Frédéric Rimet, Isabelle Domaizon, Agnès Bouchez, Julie Guéguen, Philippe Blancher, Benoît J.D. Ferrari, Régis Lionel Vivien, Jean-François Rubin, Anne-Laurence Mazenq, Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Institut National de la Recherche Agronomique (INRA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Département de Génétique et Evolution, Université de Genève (UNIGE), Independent, Asters Conservatoire des Espaces Naturels de Haute-Savoie, Service cantonal de l'écologie de l'eau, Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), ID-GENE Ecodiagnostics, Department of genetics and evolution, University of Geneva [Switzerland], Ecole d'ingénieurs HES, HES, Swiss Federal Insitute of Aquatic Science and Technology [Dübendorf] (EAWAG), European Cross-Border Cooperation Program (Interreg France-Switzerland), Swiss cantons (Valais, Geneva, Vaud), European (European Regional Development Fund), Eco-in'Eau, Swiss Centre for Applied Ecotoxicology Eawag-EPFL, Maison de la Rivière, and Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, aquatic oligochaetes, Computer science, Health, Toxicology and Mutagenesis, [SDV]Life Sciences [q-bio], Fresh Water, water quality assessment, aquatic ecosystem, diatoms, aquatic oligochaetes, bioindication, 01 natural sciences, state, diatomées, Biomonitoring, Environmental monitoring, aquatic ecosystem, water quality assessment, Public awareness, bioindicateur, oligochaete communities, Environmental Biomarkers, Aquatic ecosystem, Environmental resource management, sediments, General Medicine, Pollution, quality, oligochète, [SDE]Environmental Sciences, France, Switzerland, Environmental Monitoring, biosurveillance, [SDE.MCG]Environmental Sciences/Global Changes, assemblages, 010603 evolutionary biology, diversity, recovery, biosurveillance, diatomées, oligochète, écosystème aquatique, metabarcoding, qualité écologique, bioindicateur, Environmental Chemistry, Animals, Oligochaeta, Ecosystem, Diatoms, business.industry, 010604 marine biology & hydrobiology, qualité écologique, bioindication, écosystème aquatique, 13. Climate action, metabarcoding, Metagenomics, business, Bioindicator
Abstract: International audience; The effectiveness of environmental protection measures is based on the early identification and diagnosis of anthropogenic pressures. Similarly, restoration actions require precise monitoring of changes in the ecological quality of ecosystems, in order to highlight their effectiveness. Monitoring the ecological quality relies on bioindicators, which are organisms revealing the pressures exerted on the environment through the composition of their communities. Their implementation, based on the morphological identification of species, is expensive because it requires time and experts in taxonomy. Recent genomic tools should provide access to reliable and high-throughput environmental monitoring by directly inferring the composition of bioindicators' communities from their DNA (metabarcoding). The French-Swiss program SYNAQUA (INTERREG France-Switzerland 2017-2019) proposes to use and validate the tools of environmental genomic for biomonitoring and aims ultimately at their implementation in the regulatory bio-surveillance. SYNAQUA will test the metabarcoding approach focusing on two bioindicators, diatoms, and aquatic oligochaetes, which are used in freshwater biomonitoring in France and Switzerland. To go towards the renewal of current biomonitoring practices, SYNAQUA will (1) bring together different actors: scientists, environmental managers, consulting firms, and biotechnological companies, (2) apply this approach on a large scale to demonstrate its relevance, (3) propose robust and reliable tools, and (4) raise public awareness and train the various actors likely to use these new tools. Biomonitoring approaches based on such environmental genomic tools should address the European need for reliable, higher-throughput monitoring to improve the protection of aquatic environments under multiple pressures, guide their restoration , and follow their evolution.
Published: 2018
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42. Diatom diversity through HTS-metabarcoding in coastal European seas

Author: Bente Edvardsen, Dominik Forster, Sarah Romac, Jean-Michel Claverie, Adriana Zingone, Marina Montresor, Fabrice Not, Jan Pawlowski, Hiroyuki Ogata, Micah Dunthorn, Wiebe H. C. F. Kooistra, Diana Sarno, Ramiro Logares, Ramon Massana, Johan Decelle, Roberta Piredda, Colomban de Vargas, Thorsten Stoeck, Wenche Eikrem, Stazione Zoologica Anton Dohrn (SZN), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Light Photosynthesis & Metabolism (Photosynthesis), Physiologie cellulaire et végétale (LPCV), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), 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)-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)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), University of Kaiserslautern [Kaiserslautern], Department of Biology [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), University of Oslo (UiO), Marine Botany, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Department of genetics and evolution, Université de Genève = University of Geneva (UNIGE), Dept of Ecology, University of Kaiserslautern, EU [2008-6530], Stazione Zoologica Anton Dohrn, Italian Ministry of Education, University and Research (MIUR) [RBAP10A2T4], Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), University of Geneva [Switzerland], Ministero dell'Istruzione, dell'Università e della Ricerca, European Commission, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Stazione Zoologica A. Dohrn, Consejo Superior de Investigaciones Científicas [Spain] (CSIC), Stazione Zoologica Napoli, Stazione Zoologica di Napoli (SZN), Stazione Zoologica di Napoli, and Zingone, Adriana
Subjects: 0301 basic medicine, taxonomie, Oceans and Seas, [SDV]Life Sciences [q-bio], lcsh:Medicine, Biotechnologies, diatomée, medicine.disease_cause, Article, 03 medical and health sciences, Water column, medicine, DNA Barcoding, Taxonomic, plancton, 14. Life underwater, milieu marin, lcsh:Science, Phylogeny, Diatoms, Multidisciplinary, biology, Ecology, Aquatic ecosystem, lcsh:R, fungi, Protist, Biodiversity, Plankton, DNA, Protozoan, biology.organism_classification, protiste, 030104 developmental biology, Diatom, Habitat, Benthic zone, RNA, Ribosomal, metabarcoding, Metagenome, Taxonomy (biology), lcsh:Q
Abstract: Piredda, Roberta ... et al.-- 12 pages, 5 figures, 1 table, supporting information https://doi.org/10.1038/s41598-018-36345-9, Diatoms constitute a diverse lineage of unicellular organisms abundant and ecologically important in aquatic ecosystems. Compared to other protists, their biology and taxonomy are well-studied, offering the opportunity to combine traditional approaches and new technologies. We examined a dataset of diatom 18S rRNA- and rDNA- (V4 region) reads from different plankton size-fractions and sediments from six European coastal marine sites, with the aim of identifying peculiarities and commonalities with respect to the whole protistan community. Almost all metabarcodes (99.6%) were assigned to known genera (121) and species (236), the most abundant of which were those already known from classic studies and coincided with those seen in light microscopy. rDNA and rRNA showed comparable patterns for the dominant taxa, but rRNA revealed a much higher diversity particularly in the sediment communities. Peculiar to diatoms is a tight bentho-pelagic coupling, with many benthic or planktonic species colonizing both water column and sediments and the dominance of planktonic species in both habitats. Overall metabarcoding results reflected the marked specificity of diatoms compared to other protistan groups in terms of morphological and ecological characteristics, at the same time confirming their great potential in the description of protist communities, Financial support to the project BioMarKs was provided by the EU (2008-6530, ERA-net BIODIVERSA, EU) and, for the Italian participation, by Stazione Zoologica Anton Dohrn and the projects FIRB Biodiversitalia-Approccio multitaxa allo studio delle risposte della biodiversità italiana al cambiamento climatico (RBAP10A2T4), funded by the Italian Ministry of Education, University and Research (MIUR), which also supported Roberta Piredda’s fellowship
Published: 2018
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43. Supervised machine learning outperforms taxonomy-based environmental DNA metabarcoding applied to biomonitoring

Author: Thorsten Stoeck, Catarina I. M. Martins, Tristan Cordier, Yoann Dufresne, Dominik Forster, Jan Pawlowski, Department of genetics and evolution, Université de Genève = University of Geneva (UNIGE), University of Kaiserslautern [Kaiserslautern], Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Swiss Network for International Studies. Grant Number: 316030_150817 Swiss National Science Foundation. Grant Number: 31003A_179125 Deutsche Forschungsgemeinschaft. Grant Number: STO414/15-1 Carl Zeiss Foundation NVIDIA GPU grant program, University of Geneva [Switzerland], and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, computer.software_genre, chemistry.chemical_compound, Molecular marker, Biomonitoring, Environmental DNA, supervised machine learning, Independent data, Eukaryota, Biodiversity, predictive models, MESH: Eukaryota, MESH: Supervised Machine Learning, Taxonomy (biology), MESH: Metagenomics, MESH: Environmental Monitoring, Biotechnology, Environmental Monitoring, Biology, Machine learning, MESH: Biodiversity, 03 medical and health sciences, MESH: Computer Simulation, Genetics, DNA Barcoding, Taxonomic, Computer Simulation, 14. Life underwater, MESH: DNA Barcoding, Taxonomic, Ecology, Evolution, Behavior and Systematics, Bacteria, business.industry, Marine aquaculture, Significant difference, biotic indices, environmental DNA, MESH: Bacteria, 030104 developmental biology, chemistry, RNA, Ribosomal, biomonitoring, MESH: Biomarkers, MESH: RNA, Ribosomal, Artificial intelligence, Metagenomics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, Bioindicator, computer, Biomarkers
Abstract: International audience; Biodiversity monitoring is the standard for environmental impact assessment of anthropogenic activities. Several recent studies showed that high-throughput amplicon sequencing of environmental DNA (eDNA metabarcoding) could overcome many limitations of the traditional morphotaxonomy-based bioassessment. Recently, we demonstrated that supervised machine learning (SML) can be used to predict accurate biotic indices values from eDNA metabarcoding data, regardless of the taxonomic affiliation of the sequences. However, it is unknown to which extent the accuracy of such models depends on taxonomic resolution of molecular markers or how SML compares with metabarcoding approaches targeting well-established bioindicator species. In this study, we address these issues by training predictive models upon five different ribosomal bacterial and eukaryotic markers and measuring their performance to assess the environmental impact of marine aquaculture on independent data sets. Our results show that all tested markers are yielding accurate predictive models and that they all outperform the assessment relying solely on taxonomically assigned sequences. Remarkably, we did not find any significant difference in the performance of the models built using universal eukaryotic or prokaryotic markers. Using any molecular marker with a taxonomic range broad enough to comprise different potential bioindicator taxa, SML approach can overcome the limits of taxonomy-based eDNA bioassessment.
Published: 2018
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44. Obesity, genomic ancestry, and socioeconomic variables in Latin American mestizos

Author: Ruderman, Anahí, Pérez, Luis, Adhikari, Kaustubh, Navarro, Pablo, Ramallo, Virginia, Gallo, Carla, Poletti, Giovanni, Bedoya, Gabriel, Bortolini, Maria, Acuña-Alonzo, Victor, Canizales-Quinteros, Samuel, Rothhammer, Francisco, Ruiz-Linares, Andrés, González-José, Rolando, Acuña‐Alonzo, Victor, Canizales‐Quinteros, Samuel, Ruiz‐Linares, Andres, González‐José, Rolando, Dept of Genetics, Evolution and Environment [London] (UCL-GEE), University College of London [London] (UCL), Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), State Key Laboratory of Genetics Engineering & MOE Key Laboratory of Contemporary Anthropology, Fudan University [Shanghai]-School of Life Sciences, Laboratorio de Genética Molecular, Universidad de Antioquia = University of Antioquia [Medellín, Colombia], Departamento de Genética, Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS)-Instituto de Biociencias, Molecular Genetics Laboratory, Escuela Nacional de Antropologia y Historia, Unit of Molecular Biology and Genomic Medicine, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán - National Institute of Medical Science and Nutrition Salvador Zubiran [Mexico], Facultad de Medicina & Instituto de Alta Investigacion, Universidad de Tarapaca-Universidade de Chile, and Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)
Subjects: Male, [SDV]Life Sciences [q-bio], [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Overweight, purl.org/becyt/ford/1 [https], 0302 clinical medicine, Waist–hip ratio, hemic and lymphatic diseases, Peru, Prevalence, 0601 history and archaeology, Chile, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, Waist-to-height ratio, education.field_of_study, 1. No poverty, Genomic ancestry, 06 humanities and the arts, Admixed populations, Middle Aged, population characteristics, Female, Anatomy, medicine.symptom, CIENCIAS NATURALES Y EXACTAS, Brazil, Adult, Waist, Otras Ciencias Biológicas, Population, education, 030209 endocrinology & metabolism, Colombia, Ciencias Biológicas, 03 medical and health sciences, Young Adult, Genetics, medicine, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Obesity, purl.org/becyt/ford/1.6 [https], neoplasms, Mexico, Ecology, Evolution, Behavior and Systematics, 060101 anthropology, business.industry, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Anthropometry, medicine.disease, eye diseases, Latin America, Social Class, Socioeconomic Factors, Anthropology, business, Body mass index, Demography
Abstract: Objectives: This article aims to assess the contribution of genomic ancestry and socioeconomic status to obesity in a sample of admixed Latin Americans. Methods: The study comprised 6776 adult volunteers from Brazil, Chile, Colombia, Mexico, and Peru. Each volunteer completed a questionnaire about socioeconomic variables. Anthropometric variables such as weight, height, waist, and hip circumference were measured to calculate body indices: body mass index, waist-to-hip ratio and waist-to-height ratio (WHtR). Genetic data were extracted from blood samples, and ancestry was estimated using chip genotypes. Multiple linear regression was used to evaluate the relationship between the indices and ancestry, educational level, and economic well-being. The body indices were dichotomized to obesity indices by using appropriate thresholds. Odds ratios were calculated for each obesity index. Results: The sample showed high percentages of obesity by all measurements. However, indices did not overlap consistently when classifying obesity. WHtR resulted in the highest prevalence of obesity. Overall, women with low education level and men with high economic wellness were more likely to be obese. American ancestry was statistically associated with obesity indices, although to a lesser extent than socioeconomic variables. Conclusions: The proportion of obesity was heavily dependent on the index and the population. Genomic ancestry has a significant influence on the anthropometric measurements, especially on central adiposity. As a whole, we detected a large interpopulation variation that suggests that better approaches to overweight and obesity phenotypes are needed in order to obtain more precise reference values. Fil: Ruderman, Anahí. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentina Fil: Perez, Luis Orlando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentina Fil: Adhikari, Kaustubh. Colegio Universitario de Londres; Reino Unido. Open University; Reino Unido Fil: Navarro, Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentina Fil: Ramallo, Virginia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentina Fil: Gallo, Carla. Universidad Peruana Cayetano Heredia; Perú Fil: Poletti, Giovanni. Universidad Peruana Cayetano Heredia; Perú Fil: Bedoya Berrío, Gabriel. Universidad de Antioquia; Colombia Fil: Bortolini, María Cátira. Universidade Federal do Rio Grande do Sul; Brasil Fil: Acuña Alonzo, Victor. Instituto Nacional de Antropología E Historia; México Fil: Canizales Quinteros, Samuel. Instituto Nacional de Medicina Genómica; México Fil: Rothhammer, Francisco. Universidad de Chile; Chile Fil: Ruiz-Linares, Andres. Colegio Universitario de Londres; Reino Unido. Fudan University; China Fil: González José, Rolando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentina
Published: 2018
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45. Genetic diversity of CHC22 clathrin impacts its function in glucose metabolism

Author: Agnel Praveen Joseph, Iain Mathieson, Peter Parham, Alice Burke, Laurent Abi-Rached, Stephane M Camus, Matteo Fumagalli, Mark G. Thomas, Andrea Benazzo, Frances M. Brodsky, Yoan Diekmann, Paul Norman, Maya Topf, Rita Rasteiro, Marine D. Camus, Dept of Genetics, Evolution and Environment [London] (UCL-GEE), University College of London [London] (UCL), Microbes évolution phylogénie et infections (MEPHI), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Department of Structural Biology [Stanford], Stanford Medicine, Stanford University-Stanford University, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Esko, Tõnu, and Wittkopp, Patricia J
Subjects: Life Sciences & Biomedicine - Other Topics, medicine.medical_treatment, RECOMBINATION, Adipose tissue, Negative selection, 0302 clinical medicine, cell biology, Gene duplication, PHYLOGENETIC ANALYSIS, Biology (General), ADAPTATION, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, Genetics, INSULIN-RESISTANCE, 0303 health sciences, education.field_of_study, General Neuroscience, GENOME SEQUENCE, General Medicine, cell biology, evolutionary biology, evolutionary selection, human, insulin response, membrane traffic, Clathrin Heavy Chains, alleles, diet, glucose, Clathrin Heavy Chains, Medicine, Life Sciences & Biomedicine, Research Article, Human, medicine.medical_specialty, BALANCING SELECTION, CLTCL1 Gene, QH301-705.5, Science, Population, Blood sugar, insulin response, membrane traffic, Carbohydrate metabolism, Biology, bcs, evolutionary selection, Clathrin, General Biochemistry, Genetics and Molecular Biology, NO, Evolution, Molecular, HEAVY-CHAIN ISOFORM, 03 medical and health sciences, Insulin resistance, Diabetes mellitus, Internal medicine, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], medicine, Humans, TRAFFICKING, human, Selection, Genetic, Sugar, education, Gene, Alleles, 030304 developmental biology, Evolutionary Biology, Science & Technology, General Immunology and Microbiology, Insulin, evolutionary biology, Glucose transporter, Genetic Variation, Cell Biology, PERFORMANCE, medicine.disease, POPULATION GENOMICS, Diet, Endocrinology, Glucose, biology.protein, CLTC, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], 030217 neurology & neurosurgery
Abstract: CHC22 clathrin plays a key role in intracellular membrane traffic of the insulin-responsive glucose transporter GLUT4 in humans. We performed population genetic and phylogenetic analyses of the CHC22-encoding CLTCL1 gene, revealing independent gene loss in at least two vertebrate lineages, after arising from gene duplication. All vertebrates retained the paralogous CLTC gene encoding CHC17 clathrin, which mediates endocytosis. For vertebrates retaining CLTCL1, strong evidence for purifying selection supports CHC22 functionality. All human populations maintained two high frequency CLTCL1 allelic variants, encoding either methionine or valine at position 1316. Functional studies indicated that CHC22-V1316, which is more frequent in farming populations than in hunter-gatherers, has different cellular dynamics than M1316-CHC22 and is less effective at controlling GLUT4 membrane traffic, altering its insulin-regulated response. These analyses suggest that ancestral human dietary change influenced selection of allotypes that affect CHC22’s role in metabolism and have potential to differentially influence the human insulin response., eLife digest When we eat carbohydrates, they are digested into sugars that circulate in the blood to provide energy for the brain and other parts of the body. But too much blood sugar can be poisonous. The body regulates blood sugar balance using the hormone insulin, which triggers the removal of sugar from the blood into muscle and fat cells. This removal process involves a pore in membranes at the surface of muscle and fat tissue, called a glucose transporter, through which the sugar molecules can pass. During fasting, the glucose transporter remains inside muscle and fat. But after a meal, insulin acts to release the transporter from its storage area to the surface of the tissue. How efficiently this process happens reflects how efficiently sugar can be removed from the blood. When this pathway breaks down, it can lead to diabetes. In humans, a protein called CHC22 is needed to deliver the glucose transporter to its storage area. In mice, CHC22 is absent. The question arises: do different animals' eating habits influence CHC22's role in controlling blood sugar? The evolutionary history of CHC22 in a number of different animals could reveal what is special about glucose transport after a meal in humans, and how it might fail in diabetes. By analyzing the genomes of several different species, Fumagalli et al. found that the gene encoding CHC22 first evolved around the time animals began developing a backbone and complex nervous systems. Afterwards, it was lost by some animals – including mice, sheep and pigs. Fumagalli et al. also discovered that CHC22 varies between individual people. A new form of CHC22, which first appeared in ancient humans, is less effective at holding the glucose transporter inside muscle and fat – leading to a tendency to reduce blood sugar levels. This new form became more common in humans over a period witnessing the introduction of cooking, and later farming; both of these technologies are associated with increased sugar in the diet. But not everyone has this new variant of the gene – both the old and newer variants are present in people today. The history of CHC22 suggests that it was useful for early humans to hold the glucose transporter inside muscle and fat, keeping blood sugar levels high, which contributed to the development of a large brain. But as humans became exposed to higher dietary levels of sugar the newer form of CHC22 allowed blood sugar to be lowered more readily. People with different forms of CHC22 are likely to differ in their ability to control blood sugar after a meal. In some cases, this could lead to heightened blood sugar levels, which in turn can lead to diabetes.
Published: 2018
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46. Evolutionary Origins of Rhizarian Parasites

Author: Jan Pawlowski, Christophe Klopp, Silvia J. Cañas-Duarte, Johan Fogelqvist, Roberto Sierra, Arne Schwelm, Claudio H. Slamovits, Gillian H. Gile, Silvia Restrepo, Fabien Burki, Laura Natalia González-García, Christina Dixelius, Isabelle Arzul, Department of Genetics and Evolution, Université de Genève (UNIGE), Universidad de Los Andes, Harvard University [Cambridge], Department of Botany, University of British Columbia (UBC), Department of Plant Biology, Swedish University of Agricultural Sciences (SLU), Dalhousie University, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), NSERC, Natural Sciences and Engineering Research Council of Canada [386345], BioSoM, Swedish University of Agricultural Sciences, SLU, and Swiss National Science Foundation [140766, 159709]
Subjects: 0301 basic medicine, Zoology, parasites, Biology, 03 medical and health sciences, Monophyly, Phylogenomics, Genetics, Animals, Parasites, [INFO]Computer Science [cs], [MATH]Mathematics [math], Clade, Molecular Biology, Phylogeny, Ecology, Evolution, Behavior and Systematics, Endomyxa, Obligate, Retaria, Ascetosporea, Rhizaria, Eukaryota, phylogenomics, Plants, biology.organism_classification, 030104 developmental biology, Sequence Alignment
Abstract: International audience; The SAR group (Stramenopila, Alveolata, Rhizaria) is one of the largest clades in the tree of eukaryotes and includes a great number of parasitic lineages. Rhizarian parasites are obligate and have devastating effects on commercially important plants and animals but despite this fact, our knowledge of their biology and evolution is limited. Here, we present rhizarian transcriptomes from all major parasitic lineages in order to elucidate their evolutionary relationships using a phylogenomic approach. Our results suggest that Ascetosporea, parasites of marine invertebrates, are sister to the novel clade Apofilosa. The phytomyxean plant parasites branch sister to the vampyrellid algal ectoparasites in the novel clade Phytorhiza. They also show that Ascetosporea + Apofilosa + Retaria + Filosa + Phytorhiza form a monophyletic clade, although the branching pattern within this clade is difficult to resolve and appears to be model-dependent. Our study does not support the monophyly of the rhizarian parasitic lineages (Endomyxa), suggesting independent origins for rhizarian animal and plant parasites.
Published: 2015
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47. virtualspecies, an R package to generate virtual species distributions

Author: Franck Courchamp, Christine N. Meynard, Céline Bellard, Boris Leroy, Ecologie Systématique et Evolution (ESE), Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-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), Virginia Institute of Marine Science (VIMS), Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College of London [London] (UCL), Department of Ecology and Evolutionary Biology, Center for Tropical Research, Institute of the Environment and Sustainability, University of California [Los Angeles] (UCLA), University of California-University of California, BL, CB and FC were funded under the FFII ERA-NET BiodivERsA project., Ecol Systemat & Evolut, UMR CNRS 8079, Centre National de la Recherche Scientifique (CNRS), Université Paris Sud (Paris 11), Université Paris-Saclay, AgroParisTech, Université Pierre et Marie Curie (Paris 6), Normandie Université (NU), Institut de Recherche pour le Développement (IRD [France-Ouest]), Sorbonne Universités, Dept Genet Evolut & Environm, Ctr Biodivers & Environm Res, University College London (UCL), Dept Ecol & Evolutionary Biol, FFII ERA-NET BiodivERsA project, and University of California (UC)-University of California (UC)
Subjects: 0106 biological sciences, numerical models, distribution virtuelle, Ecology, espèce virtuelle, [SDV]Life Sciences [q-bio], 010604 marine biology & hydrobiology, media_common.quotation_subject, Ecology (disciplines), Species distribution, Probabilistic logic, Sampling (statistics), Biology, modèle, 010603 evolutionary biology, 01 natural sciences, Set (abstract data type), R package, Biological dispersal, ComputingMethodologies_GENERAL, Function (engineering), Ecology, Evolution, Behavior and Systematics, media_common
Abstract: virtualspecies is a freely available package for R designed to generate virtual species distributions, a procedure increasingly used in ecology to improve species distribution models. This package combines the existing methodological approaches with the objective of generating virtual species distributions with increased ecological realism. The package includes 1) generating the probability of occurrence of a virtual species from a spatial set of environmental conditions (i.e. environmental suitability), with two different approaches; 2) converting the environmental suitability into presence-absence with a probabilistic approach; 3) introducing dispersal limitations in the realised virtual species distributions and 4) sampling occurrences with different biases in the sampling procedure. The package was designed to be extremely flexible, to allow users to simulate their own defined species-environment relationships, as well as to provide a fine control over every simulation parameter. The package also includes a function to generate random virtual species distributions. We provide a simple example in this paper showing how increasing ecological realism of the virtual species impacts the predictive performance of species distribution models. We expect that this new package will be valuable to researchers willing to test techniques and protocols of species distribution models as well as various biogeographical hypotheses.
Published: 2015
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48. Meta-analysis of genome-wide association studies identifies 8 novel loci involved in shape variation of human head hair

Author: Francisco Rothhammer, Giovanni Poletti, Fuduan Peng, Victor Acuña-Alonzo, Samuel Canizales-Quinteros, Charanya Muralidharan, Nicholas G. Martin, Rolando González-José, Pirro G. Hysi, Krystal Breslin, Li Jin, Susan Walsh, Gu Zhu, Maria C. Bortolini, Wojciech Branicki, Andres Ruiz-Linares, Tamar Nijsten, Kaustubh Adhikari, Ewelina Pośpiech, Sarah E. Medland, Changqing Zeng, M. Arfan Ikram, Shuhua Xu, Carla Gallo, Sijia Wang, Cornelia M. van Duijn, Manfred Kayser, André G. Uitterlinden, Tim D. Spector, Gabriel Bedoya, Merel A. Hamer, Fan Liu, Sijie Wu, Yan Chen, Department of Physics, National University of Singapore (NUS), King‘s College London, Central South University [Changsha], Molecular Genetics Laboratory, Escuela Nacional de Antropologia y Historia, Unit of Molecular Biology and Genomic Medicine, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán - National Institute of Medical Science and Nutrition Salvador Zubiran [Mexico], Laboratorio de Genética Molecular, Universidad de Antioquia = University of Antioquia [Medellín, Colombia], Facultad de Medicina & Instituto de Alta Investigacion, Universidad de Tarapaca-Universidade de Chile, Departamento de Genética, Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS)-Instituto de Biociencias, Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), University of Chinese Academy of Sciences [Beijing] (UCAS), State Key Laboratory of Genetics Engineering & MOE Key Laboratory of Contemporary Anthropology, Fudan University [Shanghai]-School of Life Sciences, Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands, Department of Twin Research and Genetic Epidemiology, King's College London, London, Queensland Institute of Medical Research, Forensic Molecular Biology, ErasmusMC, Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Dept of Genetics, Evolution and Environment [London] (UCL-GEE), University College of London [London] (UCL), Genetic Identification, Dermatology, Epidemiology, and Internal Medicine
Subjects: 0301 basic medicine, Otras Ciencias Biológicas, [SDV]Life Sciences [q-bio], Population, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Single-nucleotide polymorphism, Genome-wide association study, Biology, Genome, Polymorphism, Single Nucleotide, purl.org/becyt/ford/1 [https], Ciencias Biológicas, 03 medical and health sciences, Polymorphism (computer science), Native Americans, Genetics, Journal Article, Humans, Genetic Predisposition to Disease, purl.org/becyt/ford/1.6 [https], education, Molecular Biology, Genetics (clinical), ComputingMilieux_MISCELLANEOUS, Genetic association, education.field_of_study, Asian, Association Studies Articles, Regression analysis, General Medicine, 3. Good health, purl.org/pe-repo/ocde/ford#3.01.02 [https], 030104 developmental biology, Genes, Evolutionary biology, Meta-analysis, Single Nucleotide Polymorphism, native, CIENCIAS NATURALES Y EXACTAS, americans, Genome-Wide Association Study, Hair
Abstract: Shape variation of human head hair shows striking variation within and between human populations, while its genetic basis is far from being understood. We performed a series of genome-wide association studies (GWASs) and replication studies in a total of 28 964 subjects from 9 cohorts from multiple geographic origins. A meta-analysis of three European GWASs identified 8 novel loci (1p36.23 ERRFI1/SLC45A1, 1p36.22 PEX14, 1p36.13 PADI3, 2p13.3 TGFA, 11p14.1 LGR4, 12q13.13 HOXC13, 17q21.2 KRTAP, and 20q13.33 PTK6), and confirmed 4 previously known ones (1q21.3 TCHH/TCHHL1/LCE3E, 2q35 WNT10A, 4q21.21 FRAS1, and 10p14 LINC00708/GATA3), all showing genome-wide significant association with hair shape (P
Published: 2018
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49. Latin Americans show wide-spread Converso ancestry and imprint of local Native ancestry on physical appearance

Author: Juan C. Chacon-Duque, Hugo Villamil-Ramírez, Giovanni Poletti, Samuel Canizales-Quinteros, Mirsha Quinto-Sánchez, Maria Cátira Bortolini, Maria-Laura Parolin, Macarena Fuentes-Guajardo, Francisco Rothhammer, Rolando González-José, Valeria Villegas, Francisco Mauro Salzano, Javier Mendoza-Revilla, Verónica Gomes, Caio Cesar Silva de Cerqueira, Cheryl A. Winkler, José R. Sandoval, Carla Gallo, Elena Llop, Rosenda I. Peñaloza-Espinosa, Vanessa Granja, Daniel Corach, Lavinia Schuler-Faccini, Yali Xue, Garrett Hellenthal, Mercedes Villena, Virginia Ramallo, Victor Acuña-Alonzo, Gabriel Bedoya, Paola Everardo Martínez, Karla Sandoval, Andres Ruiz-Linares, David J. Balding, Claudio M. Bravi, Pedro Moral, Jean-Michel Dugoujon, Tábita Hünemeier, António Amorim, Malena Hurtado, Kaustubh Adhikari, René Vasquez, Julio Molina, Leonor Gusmão, Ramiro Barrantes, Carlos Resende, Jorge Gómez-Valdés, Alberto Salazar-Granara, Héctor Rangel-Villalobos, William Klitz, Rodrigo Barquera, Molecular Genetics Laboratory, Escuela Nacional de Antropologia y Historia, Departamento de Genética, Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS)-Instituto de Biociencias, Instituto Boliviano de Biologıa de la Altura, Universidad Autonoma Tomas Frias, Facultad de Medicina & Instituto de Alta Investigacion, Universidad de Tarapaca-Universidade de Chile, School of Human Evolution and Social Change, Arizona State University [Tempe] (ASU), Instituto Multidisciplinario de Biología Celular [La Plata] (IMBICE), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Universidad Nacional de la Plata [Argentine] (UNLP)-Comisión de Investigaciones Científicas [Buenos Aires] (CIC), Centro de Investigaciones Biomédicas de Guatemala, Servicio de Huellas Digitales Genéticas [Buenos Aires], Facultad de Farmacia y Bioquímica [Buenos Aires] (FFYB), Universidad de Buenos Aires [Buenos Aires] (UBA)-Universidad de Buenos Aires [Buenos Aires] (UBA), Escuela de Biologia, Universidad Nacional de Costa Rica, Population Genetics, Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Universidade de Lisboa (ULISBOA), Human Evolution, The Wellcome Trust Sanger Institute [Cambridge], Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), University of Barcelona, Unit of Molecular Biology and Genomic Medicine, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán - National Institute of Medical Science and Nutrition Salvador Zubiran [Mexico], Laboratorio de Genética Molecular, Universidad de Antioquia = University of Antioquia [Medellín, Colombia], University College of London [London] (UCL), Dept of Genetics, Evolution and Environment [London] (UCL-GEE), Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Instituto de Investigação e Inovação em Saúde, Universidade de Lisboa = University of Lisbon (ULISBOA), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: haplotype, Latin Americans, Biología, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, purl.org/pe-repo/ocde/ford#1.03.00 [https], Human physical appearance, Colonialism, migration, CONVERSO JEWS, purl.org/becyt/ford/1 [https], Genética y Herencia, 0302 clinical medicine, genetics, Nose / anatomy & histology, East mediterranean, lcsh:Science, 0303 health sciences, Genealogy, Geography, Indians, South American / genetics, American Indian, Genetic structure, CIENCIAS NATURALES Y EXACTAS, Latin americans, Science, purl.org/pe-repo/ocde/ford#1.06.03 [https], Human Migration, Nose, Article, Ciencias Biológicas, 03 medical and health sciences, Indians, North American / genetics, parasitic diseases, Humans, human, purl.org/becyt/ford/1.6 [https], Mexico, Historical record, 030304 developmental biology, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Indians, South American, ANCESTRY INFORMATIVE, Environmental adaptation, South America, Converso jews, LATIN AMERICANS, Haplotypes, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Ancestry informative, purl.org/pe-repo/ocde/ford#1.04.00 [https], Indians, North American, lcsh:Q, 030217 neurology & neurosurgery, anatomy and histology
Abstract: Historical records and genetic analyses indicate that Latin Americans trace their ancestry mainly to the intermixing (admixture) of Native Americans, Europeans and Sub-Saharan Africans. Using novel haplotype-based methods, here we infer sub-continental ancestry in over 6,500 Latin Americans and evaluate the impact of regional ancestry variation on physical appearance. We find that Native American ancestry components in Latin Americans correspond geographically to the present-day genetic structure of Native groups, and that sources of non-Native ancestry, and admixture timings, match documented migratory flows. We also detect South/East Mediterranean ancestry across Latin America, probably stemming mostly from the clandestine colonial migration of Christian converts of non-European origin (Conversos). Furthermore, we find that ancestry related to highland (Central Andean) versus lowland (Mapuche) Natives is associated with variation in facial features, particularly nose morphology, and detect significant differences in allele frequencies between these groups at loci previously associated with nose morphology in this sample., Latin Americans trace their ancestry to the admixture of Native Americans, Europeans and Sub-Saharan Africans. Here, the authors develop a novel haplotype-based approach and analyse over 6,500 Latin Americans to infer the geographically-detailed genetic structure of this population.
Published: 2018
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50. Developmental pathways inferred from modularity, morphological integration and fuctuating asymmetry patterns in the human face

Author: Virginia Ramallo, Andres Ruiz-Linares, Williams Arias, Francisco Rothhammer, Rolando González-José, Javier Rosique, Carolina Paschetta, Paola Everardo, Victor Acuña-Alonzo, Soledad de Azevedo, Jorge Gómez-Valdés, Samuel Canizales-Quinteros, Mirsha Quinto-Sánchez, Francesc Muñoz-Muñoz, Francisco de Avila, G. Poletti, Pablo E. Navarro, Claudia Jaramillo, Caio Cesar Silva de Cerqueira, Celia Cintas, Kaustubh Adhikari, Macarena Fuentes-Guajardo, Gabriel Bedoya, Maria Cátira Bortolini, Carla Gallo, Tábita Hünemeier, Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Dept of Genetics, Evolution and Environment [London] (UCL-GEE), University College of London [London] (UCL), State Key Laboratory of Genetics Engineering & MOE Key Laboratory of Contemporary Anthropology, Fudan University [Shanghai]-School of Life Sciences, Molecular Genetics Laboratory, Escuela Nacional de Antropologia y Historia, Departamento de Genética, Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS)-Instituto de Biociencias, Laboratorio de Genética Molecular, Universidad de Antioquia = University of Antioquia [Medellín, Colombia], Unit of Molecular Biology and Genomic Medicine, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán - National Institute of Medical Science and Nutrition Salvador Zubiran [Mexico], Facultad de Medicina & Instituto de Alta Investigacion, Universidad de Tarapaca-Universidade de Chile, and Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)
Subjects: Male, 0301 basic medicine, Developmental noise, [SDV]Life Sciences [q-bio], Biological anthropology, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, lcsh:Medicine, Genome-wide association study, Evolutionary biology, Fluctuating asymmetry, HUMAN FACE, purl.org/becyt/ford/1 [https], 0302 clinical medicine, FLUCTUATING ASYMMETRY, lcsh:Science, Maxillofacial Development, purl.org/pe-repo/ocde/ford#1.06.15 [https], ComputingMilieux_MISCELLANEOUS, Multidisciplinary, Middle Aged, Phenotype, Female, CIENCIAS NATURALES Y EXACTAS, GEOMETRIC MORPHOMETRIC, Adult, Rostro humano, Adolescent, Otras Ciencias Biológicas, Biology, GENOMAS, Article, Ciencias Biológicas, Young Adult, 03 medical and health sciences, Humans, Set (psychology), purl.org/becyt/ford/1.6 [https], Modularity (networks), Modularidad, lcsh:R, Quantitative genetics, Antropología biológica, Genetic architecture, LATIN AMERICANS, Latin America, 030104 developmental biology, Face, Evolutionary developmental biology, lcsh:Q, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract: Facial asymmetries are usually measured and interpreted as proxies to developmental noise. However, analyses focused on its developmental and genetic architecture are scarce. To advance on this topic, studies based on a comprehensive and simultaneous analysis of modularity, morphological integration and facial asymmetries including both phenotypic and genomic information are needed. Here we explore several modularity hypotheses on a sample of Latin American mestizos, in order to test if modularity and integration patterns differ across several genomic ancestry backgrounds. To do so, 4104 individuals were analyzed using 3D photogrammetry reconstructions and a set of 34 facial landmarks placed on each individual. We found a pattern of modularity and integration that is conserved across sub-samples differing in their genomic ancestry background. Specifically, a signal of modularity based on functional demands and organization of the face is regularly observed across the whole sample. Our results shed more light on previous evidence obtained from Genome Wide Association Studies performed on the same samples, indicating the action of different genomic regions contributing to the expression of the nose and mouth facial phenotypes. Our results also indicate that large samples including phenotypic and genomic metadata enable a better understanding of the developmental and genetic architecture of craniofacial phenotypes. Fil: Quinto Sanchez, Mirsha Emmanuel. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Muñoz-Muñoz, Francesc. Universidad Nacional Autónoma de México; México Fil: Gomez-Valdes, Jorge. Universitat Autònoma de Barcelona; España Fil: Cintas, Celia. Instituto Nacional de Antropologia E Historia, Mexico; México Fil: Navarro, Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentina Fil: Cerqueira, Caio Cesar Silva De. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Paschetta, Carolina Andrea. Equipe de Perícias Criminalísticas de Ourinhos; Fil: de Azevedo, Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentina Fil: Ramallo, Virginia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentina Fil: Acuña-Alonzo, Victor. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Adhikari, Kaustubh. Colegio Universitario de Londres; Reino Unido Fil: Fuentes-Guajardo, MacArena. Instituto Nacional de Antropologia E Historia, Mexico; México Fil: Hünemeier, Tábita. Colegio Universitario de Londres; Reino Unido Fil: Everardo, Paola. Universidad de Tarapaca de Arica; Chile Fil: De Avila, Francisco. Colegio Universitario de Londres; Reino Unido Fil: Jaramillo, Claudia. Universidade de Sao Paulo; Brasil Fil: Arias, Williams. Instituto Nacional de Antropologia E Historia, Mexico; México Fil: Gallo, Carla. Universidad Nacional Autónoma de México; México Fil: Poletti, Giovani. Instituto Nacional de Antropologia E Historia, Mexico; México Fil: Bedoya Berrío, Gabriel. Universidad de Antioquia; Colombia Fil: Bortolini, Maria Catira. Universidad de Antioquia; Colombia Fil: Canizales-Quinteros, Samuel. Universidad Peruana Cayetano Heredia; Perú Fil: Rothhammer, Francisco. Universidad Peruana Cayetano Heredia; Perú Fil: Rosique, Javier. Universidad de Antioquia; Colombia Fil: Ruiz-Linares, Andres. Universidade Federal do Rio Grande do Sul; Brasil Fil: González José, Rolando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentina
Published: 2018
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