Significance

A small and relict population of brown bears lives in complete isolation in the Italian Apennine Mountains, providing a unique opportunity to study the impact of drift and selection on the genomes of a large endangered mammal and reconstruct the phenotypic consequences and the conservation implications of such evolutionary processes. The Apennine bear is highly inbred and harbors very low genomic variation. Several deleterious mutations have been accumulated by drift. We found evidence that this is a consequence of habitat fragmentation in the Neolithic, when human expansion and land clearance shrank its habitat, and that retention of variation at immune system and olfactory receptor genes as well as changes in diet and behavior prevented the extinction of the Apennine bear.

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.

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Data Availability

Data deposition: The sequences reported in this paper have been deposited in GenBank's sequence read archive (accession nos. PRJNA395974 and MF593957–MF593987).

Acknowledgments

We thank coworkers at the State Nature Conservancy of Slovakia for tissue samples from legally culled brown bears. We also thank Anna Mazzarella for revising the manuscript. We thank the regional governments of Asturias and Castilla y León in Spain for providing tissue samples of Cantabrian bears. We thank the genotoul bioinformatics platform Toulouse Midi-Pyrenees (Bioinfo Genotoul) for providing computing resources. We also thank the Abruzzo Lazio and Molise National Park for permissions and assistance with logistics and the Istituto di Ecologia Applicata for financial support of genomic analyses. Apennine bear samples were obtained during a live-trapping and telemetry project funded by a US private citizen through the Wildlife Conservation Society. The samples were exported from Greece with Convention on International Trade in Endangered Species (CITES) Permit 86731. 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.

Supporting Information

Appendix (PDF)

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Information & Authors

Information

Published in

Go to Proceedings of the National Academy of Sciences
Go to Proceedings of the National Academy of Sciences
Proceedings of the National Academy of Sciences
Vol. 114 | No. 45
November 7, 2017
PubMed: 29078308

Classifications

Data Availability

Data deposition: The sequences reported in this paper have been deposited in GenBank's sequence read archive (accession nos. PRJNA395974 and MF593957–MF593987).

Submission history

Published online: October 24, 2017
Published in issue: November 7, 2017

Keywords

  1. balancing selection
  2. genetic drift
  3. genetic load
  4. Ursus arctos
  5. Neolithic impact

Acknowledgments

We thank coworkers at the State Nature Conservancy of Slovakia for tissue samples from legally culled brown bears. We also thank Anna Mazzarella for revising the manuscript. We thank the regional governments of Asturias and Castilla y León in Spain for providing tissue samples of Cantabrian bears. We thank the genotoul bioinformatics platform Toulouse Midi-Pyrenees (Bioinfo Genotoul) for providing computing resources. We also thank the Abruzzo Lazio and Molise National Park for permissions and assistance with logistics and the Istituto di Ecologia Applicata for financial support of genomic analyses. Apennine bear samples were obtained during a live-trapping and telemetry project funded by a US private citizen through the Wildlife Conservation Society. The samples were exported from Greece with Convention on International Trade in Endangered Species (CITES) Permit 86731. 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.

Notes

This article is a PNAS Direct Submission.

Authors

Affiliations

Andrea Benazzo1
Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy;
Emiliano Trucchi1
Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy;
Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo 1066, Norway;
James A. Cahill
Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064;
Pierpaolo Maisano Delser
Institute de Systematics, Evolution, Biodiversite, UMR 7205-CNRS, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, École Pratique des Hautes Études (EPHE), CP39, 75005 Paris, France;
EPHE, Paris Sciences & Lettres Research University, 75005 Paris, France;
Smurfit Institute of Genetics, Trinity College, University of Dublin, Dublin 2, Ireland;
Stefano Mona
Institute de Systematics, Evolution, Biodiversite, UMR 7205-CNRS, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, École Pratique des Hautes Études (EPHE), CP39, 75005 Paris, France;
EPHE, Paris Sciences & Lettres Research University, 75005 Paris, France;
Matteo Fumagalli
Department of Life Sciences, Imperial College London, Ascot SL5 7PY, United Kingdom;
Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom;
Biological and Environmental Sciences, University of Stirling, Stirling FK9 4LA, United Kingdom;
Luca Cornetti
Zoological Institute, University of Basel, 4051 Basel, Switzerland;
Silvia Ghirotto
Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy;
Matteo Girardi
Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy;
Lino Ometto
Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy;
Independent Researcher, 38016 Mezzocorona, Italy;
Alex Panziera
Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy;
Omar Rota-Stabelli
Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy;
Enrico Zanetti
Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy;
Alexandros Karamanlidis
Protection and Management of Wildlife and the Natural Environment, ARCTUROS, 53075 Aetos, Florina, Greece;
Claudio Groff
Forest and Wildlife Service, Provincia Autonoma di Trento, 38100 Trento, Italy;
Ladislav Paule
Department of Phytology, Faculty of Forestry, Technical University, 96053 Zvolen, Slovakia;
Leonardo Gentile
Veterinary Service, National Park of Abruzzo Lazio and Molise, 67032 Pescasseroli, Italy;
Department of Integrative Ecology, Doñana Biological Station, Consejo Superior de Investigaciones Científicas, 4102 Seville, Spain;
Saverio Vicario
Institute of Atmospheric Pollution Research and Technologies, National Research Council, 70126 Bari, Italy;
Luigi Boitani
Department of Biology and Biotechnologies “Charles Darwin,” University of Rome La Sapienza, 00185 Rome, Italy;
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 K Copenhagen, Denmark
Silvia Fuselli
Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy;
Cristiano Vernesi
Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy;
Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064;
Department of Biology and Biotechnologies “Charles Darwin,” University of Rome La Sapienza, 00185 Rome, Italy;
Giorgio Bertorelle2 [email protected]
Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy;

Notes

2
To whom correspondence should be addressed. Email: [email protected].
Author contributions: A.B., E.T., L. Boitani, P.C., and G.B. designed research; J.A.C., M.G., A.K., C.G., L.P., L.G., C. Vilà, S.F., C. Vernesi, and G.B. performed research; A.B., E.T., J.A.C., P.M.D., S.M., M.F., L. Bunnefeld, L.C., S.G., L. Ometto, A.P., O.R.-S., E.Z., S.V., L. Orlando, S.F., and G.B. analyzed data; A.K., C.G., L.P., L.G., and C. Vilà provided samples; and E.T., B.S., P.C., and G.B. wrote the paper.
1
A.B. and E.T. contributed equally to this work.

Competing Interests

The authors declare no conflict of interest.

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    Survival and divergence in a small group: The extraordinary genomic history of the endangered Apennine brown bear stragglers
    Proceedings of the National Academy of Sciences
    • Vol. 114
    • No. 45
    • pp. 11799-E9754

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