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Vendrami DLJ, Gossmann TI, Chakarov N, Paijmans AJ, Eyre-Walker A, Forcada J, Hoffman JI. Signatures of selection on mitonuclear integrated genes uncover hidden mitogenomic variation in fur seals. Genome Biol Evol 2022; 14:6637498. [PMID: 35809042 PMCID: PMC9338431 DOI: 10.1093/gbe/evac104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2022] [Indexed: 11/13/2022] Open
Abstract
Nuclear copies of mitochondrial genes (numts) are commonplace in vertebrate genomes and have been characterized in many species. However, relatively little attention has been paid to understanding their evolutionary origins and to disentangling alternative sources of insertions. Numts containing genes with intact mitochondrial reading frames represent good candidates for this purpose. The sequences of the genes they contain can be compared to their mitochondrial homologs to characterize synonymous to non-synonymous substitution rates, which can shed light on the selection pressures these genes have been subjected to. Here, we characterise 25 numts in the Antarctic fur seal (Arctocephalus gazella) genome. Among those containing genes with intact mitochondrial reading frames, three carry multiple substitutions in comparison to their mitochondrial homologs. Our analyses reveal that one represents a historic insertion subjected to strong purifying selection since it colonized the Otarioidea in a genomic region enriched in retrotransposons. By contrast, the other two numts appear to be more recent and their large number of substitutions can be attributed to non-canonical insertions, either the integration of heteroplasmic mtDNA or hybridization. Our study sheds new light on the evolutionary history of pinniped numts and uncovers the presence of hidden sources of mitonuclear variation.
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Affiliation(s)
- David L J Vendrami
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany
| | - Toni I Gossmann
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany
| | - Nayden Chakarov
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany
| | - Anneke J Paijmans
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany
| | - Adam Eyre-Walker
- School of Life Science, University of Sussex, Brighton, BN1 9QG, UK
| | - Jaume Forcada
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK
| | - Joseph I Hoffman
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany.,British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK
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2
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Nagel R, Kaiser S, Stainfield C, Toscani C, Fox‐Clarke C, Paijmans AJ, Costa Castro C, Vendrami DLJ, Forcada J, Hoffman JI. Low heritability and high phenotypic plasticity of salivary cortisol in response to environmental heterogeneity in a wild pinniped. Ecol Evol 2022; 12:e8757. [PMID: 35356576 PMCID: PMC8956859 DOI: 10.1002/ece3.8757] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 12/15/2021] [Revised: 02/24/2022] [Accepted: 03/07/2022] [Indexed: 11/18/2022] Open
Abstract
Individuals are unique in how they interact with and respond to their environment. Correspondingly, unpredictable challenges or environmental stressors often produce an individualized response of the hypothalamic‐pituitary‐adrenal (HPA) axis and its downstream effector cortisol. We used a fully crossed, repeated measures design to investigate the factors shaping individual variation in baseline cortisol in Antarctic fur seal pups and their mothers. Saliva samples were collected from focal individuals at two breeding colonies, one with low and the other with high density, during two consecutive years of contrasting food availability. Mothers and pups were sampled concurrently at birth and shortly before weaning, while pups were additionally sampled every 20 days. We found that heritability was low for baseline cortisol, while within‐individual repeatability and among‐individual variability were high. A substantial proportion of the variation in baseline cortisol could be explained in pups and mothers by a combination of intrinsic and extrinsic factors including sex, weight, day, season, and colony of birth. Our findings provide detailed insights into the individualization of endocrine phenotypes and their genetic and environmental drivers in a wild pinniped. Furthermore, the strong associations between cortisol and life history traits that we report in fur seals could have important implications for understanding the population dynamics of species impacted by environmental change.
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Affiliation(s)
- Rebecca Nagel
- Department of Animal Behaviour Bielefeld University Bielefeld Germany
| | - Sylvia Kaiser
- Department of Behavioural Biology University of Münster Münster Germany
| | | | | | | | | | | | | | | | - Joseph I. Hoffman
- Department of Animal Behaviour Bielefeld University Bielefeld Germany
- British Antarctic Survey Cambridge UK
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Paijmans AJ, Stoffel MA, Bester MN, Cleary AC, De Bruyn PJN, Forcada J, Goebel ME, Goldsworthy SD, Guinet C, Lydersen C, Kovacs KM, Lowther A, Hoffman JI. The genetic legacy of extreme exploitation in a polar vertebrate. Sci Rep 2020; 10:5089. [PMID: 32198403 PMCID: PMC7083876 DOI: 10.1038/s41598-020-61560-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 10/17/2019] [Accepted: 01/24/2020] [Indexed: 12/12/2022] Open
Abstract
Understanding the effects of human exploitation on the genetic composition of wild populations is important for predicting species persistence and adaptive potential. We therefore investigated the genetic legacy of large-scale commercial harvesting by reconstructing, on a global scale, the recent demographic history of the Antarctic fur seal (Arctocephalus gazella), a species that was hunted to the brink of extinction by 18th and 19th century sealers. Molecular genetic data from over 2,000 individuals sampled from all eight major breeding locations across the species' circumpolar geographic distribution, show that at least four relict populations around Antarctica survived commercial hunting. Coalescent simulations suggest that all of these populations experienced severe bottlenecks down to effective population sizes of around 150-200. Nevertheless, comparably high levels of neutral genetic variability were retained as these declines are unlikely to have been strong enough to deplete allelic richness by more than around 15%. These findings suggest that even dramatic short-term declines need not necessarily result in major losses of diversity, and explain the apparent contradiction between the high genetic diversity of this species and its extreme exploitation history.
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Affiliation(s)
- Anneke J Paijmans
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany.
| | - Martin A Stoffel
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, United Kingdom
| | - Marthán N Bester
- Department of Zoology and Entomology, Mammal Research Institute, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Alison C Cleary
- Norwegian Polar Institute, Fram Centre, 9296, Tromsø, Norway
- Department of Natural Sciences, University of Agder, 4630, Kristiansand, Norway
| | - P J Nico De Bruyn
- Department of Zoology and Entomology, Mammal Research Institute, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Jaume Forcada
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK
| | - Michael E Goebel
- Antarctic Ecosystem Research Division, Southwest Fisheries Science Center, National Marine Fisheries, National Oceanographic and Atmospheric Administration, 8901 La Jolla Shores Drive, La Jolla, CA, 92037, USA
- Institute of Marine Science, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Simon D Goldsworthy
- South Australian Research and Development Institute, 2 Hamra Avenue, West Beach, South Australia, 5024, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Christophe Guinet
- Centre d'Etudes Biologiques de Chizé (CEBC), CNRS and Université de La Rochelle - UMR 7372, 79360, Villiers en Bois, France
| | | | - Kit M Kovacs
- Norwegian Polar Institute, Fram Centre, 9296, Tromsø, Norway
| | - Andrew Lowther
- Norwegian Polar Institute, Fram Centre, 9296, Tromsø, Norway
| | - Joseph I Hoffman
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany.
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK.
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5
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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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