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Stoffel MA, Johnston SE, Pilkington JG, Pemberton JM. Genetic architecture and lifetime dynamics of inbreeding depression in a wild mammal. Nat Commun 2021; 12:2972. [PMID: 34016997 PMCID: PMC8138023 DOI: 10.1038/s41467-021-23222-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 03/29/2021] [Indexed: 02/03/2023] Open
Abstract
Inbreeding depression is ubiquitous, but we still know little about its genetic architecture and precise effects in wild populations. Here, we combine long-term life-history data with 417 K imputed SNP genotypes for 5952 wild Soay sheep to explore inbreeding depression on a key fitness component, annual survival. Inbreeding manifests in long runs of homozygosity (ROH), which make up nearly half of the genome in the most inbred individuals. The ROH landscape varies widely across the genome, with islands where up to 87% and deserts where only 4% of individuals have ROH. The fitness consequences of inbreeding are severe; a 10% increase in individual inbreeding FROH is associated with a 60% reduction in the odds of survival in lambs, though inbreeding depression decreases with age. Finally, a genome-wide association scan on ROH shows that many loci with small effects and five loci with larger effects contribute to inbreeding depression in survival.
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Affiliation(s)
- M A Stoffel
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
| | - S E Johnston
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - J G Pilkington
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - J M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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Stoffel MA, Humble E, Paijmans AJ, Acevedo-Whitehouse K, Chilvers BL, Dickerson B, Galimberti F, Gemmell NJ, Goldsworthy SD, Nichols HJ, Krüger O, Negro S, Osborne A, Pastor T, Robertson BC, Sanvito S, Schultz JK, Shafer ABA, Wolf JBW, Hoffman JI. Demographic histories and genetic diversity across pinnipeds are shaped by human exploitation, ecology and life-history. Nat Commun 2018; 9:4836. [PMID: 30446730 PMCID: PMC6240053 DOI: 10.1038/s41467-018-06695-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 09/18/2018] [Indexed: 12/22/2022] Open
Abstract
A central paradigm in conservation biology is that population bottlenecks reduce genetic diversity and population viability. In an era of biodiversity loss and climate change, understanding the determinants and consequences of bottlenecks is therefore an important challenge. However, as most studies focus on single species, the multitude of potential drivers and the consequences of bottlenecks remain elusive. Here, we combined genetic data from over 11,000 individuals of 30 pinniped species with demographic, ecological and life history data to evaluate the consequences of commercial exploitation by 18th and 19th century sealers. We show that around one third of these species exhibit strong signatures of recent population declines. Bottleneck strength is associated with breeding habitat and mating system variation, and together with global abundance explains much of the variation in genetic diversity across species. Overall, bottleneck intensity is unrelated to IUCN status, although the three most heavily bottlenecked species are endangered. Our study reveals an unforeseen interplay between human exploitation, animal biology, demographic declines and genetic diversity. Historical hunting has caused documented declines in pinnipeds, but the extent to which hunting caused genetic bottlenecks among species was unknown. Here, the authors show evidence of severe bottlenecks in several pinniped species, particularly those that breed on land.
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Affiliation(s)
- M A Stoffel
- Department of Animal Behaviour, Bielefeld University, Postfach 100131, 33501, Bielefeld, Germany.,School of Natural Sciences and Psychology, Faculty of Science, Liverpool John Moores University, Liverpool, L3 3AF, UK
| | - E Humble
- Department of Animal Behaviour, Bielefeld University, Postfach 100131, 33501, Bielefeld, Germany.,British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK
| | - A J Paijmans
- Department of Animal Behaviour, Bielefeld University, Postfach 100131, 33501, Bielefeld, Germany
| | - K Acevedo-Whitehouse
- Unit for Basic and Applied Microbiology, School of Natural Sciences, Autonomous University of Queretaro, Avenida de las Ciencias S/N, Queretaro, 76230, Mexico
| | - B L Chilvers
- Wildbase, Institute of Veterinary, Animal and Biomedical Science, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand
| | - B Dickerson
- National Marine Mammal Laboratory, Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, 98115, WA, USA
| | - F Galimberti
- Elephant Seal Research Group, Sea Lion Island, FIQQ 1ZZ, Falkland Islands
| | - N J Gemmell
- Department of Anatomy, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - S D Goldsworthy
- South Australian Research and Development Institute, West Beach, SA, 5024, Australia
| | - H J Nichols
- School of Natural Sciences and Psychology, Faculty of Science, Liverpool John Moores University, Liverpool, L3 3AF, UK.,Department of Animal Behaviour Bielefeld University, Postfach 100131 33501, Bielefeld, Germany.,Department of Biosciences, Swansea University, Swansea, SA2 8PP, UK
| | - O Krüger
- Department of Animal Behaviour, Bielefeld University, Postfach 100131, 33501, Bielefeld, Germany
| | - S Negro
- UMR de Génétique Quantitative et Évolution - Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, 91190, France.,GIGA-R, Medical Genomics - BIO3, Université of Liège, Liège, 4000, Belgium
| | - A Osborne
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand, 8140
| | - T Pastor
- EUROPARC Federation, Carretera de l'Església, 92, 08017, Barcelona, Spain
| | - B C Robertson
- Department of Zoology, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - S Sanvito
- Elephant Seal Research Group, Sea Lion Island, FIQQ 1ZZ, Falkland Islands
| | - J K Schultz
- National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 1315 East West Highway, Silver Spring, MD, 20910, USA
| | - A B A Shafer
- Forensic Science & Environmental Life Sciences, Trent University, Peterborough, ON, Canada, K9J 7B8
| | - J B W Wolf
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinstried, Munich, 82152, Germany.,Science of Life Laboratory and Department of Evolutionary Biology, Uppsala University, Uppsala, 752 36, Sweden
| | - J I Hoffman
- Department of Animal Behaviour, Bielefeld University, Postfach 100131, 33501, Bielefeld, Germany. .,British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK.
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