1. Andrea Benazzo, Emiliano Trucchi, James A. Cahill, Pierpaolo Maisano Delser, Stefano Mona, Matteo Fumagalli, View ORCID ProfileLynsey Bunnefeld, Luca Cornetti, Silvia Ghirotto, Matteo Girardi, Lino Ometto, Alex Panziera, Omar Rota-Stabelli, Enrico Zanetti, Alexandros Karamanlidis, Claudio Groff, Ladislav Paule, Leonardo Gentile, View ORCID ProfileCarles Vilà, Saverio Vicario, Luigi Boitani, View ORCID ProfileLudovic Orlando, Silvia Fuselli, Cristiano Vernesi, View ORCID ProfileBeth Shapiro, View ORCID ProfilePaolo Ciucci, and Giorgio Bertorelle
- Author
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Giorgio Bertorelle, Lynsey Bunnefeld, Lino Ometto, Alexandros A. Karamanlidis, Pierpaolo Maisano Delser, Enrico Zanetti, Omar Rota-Stabelli, Ludovic Orlando, Cristiano Vernesi, Stefano Mona, Matteo Fumagalli, Leonardo Gentile, James A. Cahill, Luca Cornetti, Silvia Ghirotto, Andrea Benazzo, Claudio Groff, Emiliano Trucchi, Paolo Ciucci, Silvia Fuselli, Beth Shapiro, Carles Vilà, Alex Panziera, Ladislav Paule, Luigi Boitani, Saverio Vicario, Matteo Girardi, Vodafone, Università degli Studi di Ferrara, Agence Nationale de la Recherche (France), Department of Life Sciences and Biotechnology, Università degli Studi di Ferrara = University of Ferrara (UniFE), Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences [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), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), 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), Fondazione Edmund Mach - Functional genomics, Fondazione Edmund Mach - Edmund Mach Foundation [Italie] (FEM), Biology and Evolution, University of Ferrara, Dipartimento di Biologia e Biotecnologie 'Lazzaro Spallanzani' = Department of Biology and Biotechnology [Univ di Pavia] (DBB UNIPV), Università degli Studi di Pavia = University of Pavia (UNIPV), Dipartimento di Biologia ed Evoluzione, University of Milano, Czech University of Life Science, and National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR)
- Subjects
balancing selection, genetic drift, genetic load, ursus arctos, neolithic impact ,0106 biological sciences ,0301 basic medicine ,Rome ,Genetic load ,Balancing selection ,BIASED DISPERSAL ,01 natural sciences ,Inbreeding depression ,Amino Acids ,Phylogeny ,Extinction vortex ,Neolithic impact ,education.field_of_study ,Genome ,Multidisciplinary ,Ecology ,Population size ,Genomics ,Mitochondrial ,Ursus arctos ,Aggression ,Multidisciplinary Sciences ,Fixation (population genetics) ,PNAS Plus ,Science & Technology - Other Topics ,Sequence Analysis ,Ursidae ,GENETIC RESCUE ,INBREEDING DEPRESSION ,Life on Land ,POPULATION-SIZE ,Settore BIO/18 - GENETICA ,Population ,COPY-NUMBER VARIATION ,Biology ,SPATIAL-PATTERNS ,010603 evolutionary biology ,NO ,03 medical and health sciences ,Genetic drift ,EXTINCTION VORTEX ,MD Multidisciplinary ,Genetics ,Animals ,education ,Alleles ,Population Density ,LAND-COVER CHANGE ,balancing selection, genetic drift, genetic load,Ursus arctos, Neolithic impact ,Science & Technology ,Human Genome ,Genetic Variation ,URSUS-ARCTOS ,Small population size ,balance selection ,Sequence Analysis, DNA ,DNA ,030104 developmental biology ,Evolutionary biology ,NATAL DISPERSAL ,Genome, Mitochondrial ,genetic drift ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology - Abstract
About 100 km east of Rome, in the central Apennine Mountains, a critically endangered population of ∼50 brown bears live in complete isolation. Mating outside this population is prevented by several 100 km of bear-free territories. We exploited this natural experiment to better understand the gene and genomic consequences of surviving at extremely small population size. We found that brown bear populations in Europe lost connectivity since Neolithic times, when farming communities expanded and forest burning was used for land clearance. In central Italy, this resulted in a 40-fold population decline. The overall genomic impact of this decline included the complete loss of variation in the mitochondrial genome and along long stretches of the nuclear genome. Several private and deleterious amino acid changes were fixed by random drift; predicted effects include energy deficit, muscle weakness, anomalies in cranial and skeletal development, and reduced aggressiveness. Despite this extreme loss of diversity, Apennine bear genomes show nonrandom peaks of high variation, possibly maintained by balancing selection, at genomic regions significantly enriched for genes associated with immune and olfactory systems. Challenging the paradigm of increased extinction risk in small populations, we suggest that random fixation of deleterious alleles (i) can be an important driver of divergence in isolation, (ii) can be tolerated when balancing selection prevents random loss of variation at important genes, and (iii) is followed by or results directly in favorable behavioral changes., Financial support for the collection of the samples was provided by Vodafone Greece and the Vodafone Group Foundation. Fondo Ateneo Ricerca (FAR) grants from the University of Ferrara supported the study. P.M.D. was funded by Agence Nationale de la Recherche Demochips Grant ANR-12-BSV7-0012.
- Published
- 2017
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