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Hanski E, Joseph S, Raulo A, Wanelik KM, O'Toole Á, Knowles SCL, Little TJ. Epigenetic age estimation of wild mice using faecal samples. Mol Ecol 2024; 33:e17330. [PMID: 38561950 DOI: 10.1111/mec.17330] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/19/2024] [Accepted: 03/01/2024] [Indexed: 04/04/2024]
Abstract
Age is a key parameter in population ecology, with a myriad of biological processes changing with age as organisms develop in early life then later senesce. As age is often hard to accurately measure with non-lethal methods, epigenetic methods of age estimation (epigenetic clocks) have become a popular tool in animal ecology and are often developed or calibrated using captive animals of known age. However, studies typically rely on invasive blood or tissue samples, which limit their application in more sensitive or elusive species. Moreover, few studies have directly assessed how methylation patterns and epigenetic age estimates compare across environmental contexts (e.g. captive or laboratory-based vs. wild animals). Here, we built a targeted epigenetic clock from laboratory house mice (strain C57BL/6, Mus musculus) using DNA from non-invasive faecal samples, and then used it to estimate age in a population of wild mice (Mus musculus domesticus) of unknown age. This laboratory mouse-derived epigenetic clock accurately predicted adult wild mice to be older than juveniles and showed that wild mice typically increased in epigenetic age over time, but with wide variation in epigenetic ageing rate among individuals. Our results also suggested that, for a given body mass, wild mice had higher methylation across targeted CpG sites than laboratory mice (and consistently higher epigenetic age estimates as a result), even among the smallest, juvenile mice. This suggests wild and laboratory mice may display different CpG methylation levels from very early in life and indicates caution is needed when developing epigenetic clocks on laboratory animals and applying them in the wild.
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Affiliation(s)
- Eveliina Hanski
- University of Oxford, Oxford, UK
- University of Helsinki, Helsinki, Finland
| | | | - Aura Raulo
- University of Oxford, Oxford, UK
- University of Turku, Turku, Finland
| | - Klara M Wanelik
- University of Oxford, Oxford, UK
- University of Surrey, Guildford, UK
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Goldman SL, Sanders JG, Yan W, Denice A, Cornwall M, Ivey KN, Taylor EN, Gunderson AR, Sheehan MJ, Mjungu D, Lonsdorf EV, Pusey AE, Hahn BH, Moeller AH. Culture-enriched community profiling improves resolution of the vertebrate gut microbiota. Mol Ecol Resour 2022; 22:122-136. [PMID: 34174174 PMCID: PMC8688194 DOI: 10.1111/1755-0998.13456] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 06/13/2021] [Accepted: 06/17/2021] [Indexed: 01/03/2023]
Abstract
Vertebrates harbour gut microbial communities containing hundreds of bacterial species, most of which have never been cultivated or isolated in the laboratory. The lack of cultured representatives from vertebrate gut microbiotas limits the description and experimental interrogation of these communities. Here, we show that representatives from >50% of the bacterial genera detected by culture-independent sequencing in the gut microbiotas of fence lizards, house mice, chimpanzees, and humans were recovered in mixed cultures from frozen faecal samples plated on a panel of nine media under a single growth condition. In addition, culturing captured >100 rare bacterial genera overlooked by culture-independent sequencing, more than doubling the total number of bacterial sequence variants detected. Our approach recovered representatives from 23 previously uncultured candidate bacterial genera, 12 of which were not detected by culture-independent sequencing. Results identified strategies for both indiscriminate and selective culturing of the gut microbiota that were reproducible across vertebrate species. Isolation followed by whole-genome sequencing of 161 bacterial colonies from wild chimpanzees enabled the discovery of candidate novel species closely related to the opportunistic pathogens of humans Clostridium difficile and Hungatella hathewayi. This study establishes culturing methods that improve inventories and facilitate isolation of gut microbiota constituents from a wide diversity of vertebrate species.
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Affiliation(s)
- Samantha L. Goldman
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
| | - Jon G. Sanders
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY 14850, USA
| | - Weiwei Yan
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
| | - Anthony Denice
- Project Chimps, Morganton, GA 30560, USA
- Present address: Chimpanzee Sanctuary Northwest, Cle Elum, WA 98922, USA
| | - Margaret Cornwall
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Kathleen N. Ivey
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA 93407, USA
- Present address: Department of Biology, University of Texas, Arlington, TX 76019, USA
| | - Emily N. Taylor
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Alex R. Gunderson
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118, USA
| | - Michael J. Sheehan
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14850, USA
| | | | - Elizabeth V. Lonsdorf
- Department of Psychology and Biological Foundations of Behavior Program, LSP 261B, Franklin and Marshall College, Lancaster, PA 17603, USA
| | - Anne E. Pusey
- Department of Evolutionary Anthropology, 101 Biological Sciences Building, Duke University, Durham, NC 27708, USA
| | - Beatrice H. Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew H. Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
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McClelland GTW, Altwegg R, van Aarde RJ, Ferreira S, Burger AE, Chown SL. Climate change leads to increasing population density and impacts of a key island invader. Ecol Appl 2018; 28:212-224. [PMID: 29055070 DOI: 10.1002/eap.1642] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 10/02/2017] [Indexed: 06/07/2023]
Abstract
The considerable threats of invasive rodents to island biodiversity are likely to be compounded by climate change. Forecasts for such interactions have been most pronounced for the Southern Ocean islands where ameliorating conditions are expected to decrease thermal and resource restrictions on rodents. Firm evidence for changing rodent populations in response to climate change, and demonstrations of associated impacts on the terrestrial environment, are nonetheless entirely absent for the region. Using data collected over three decades on sub-Antarctic Marion Island, we tested empirically whether mouse populations have changed through time and whether these changes can be associated significantly with changing abiotic conditions. Changes in invertebrate populations, which have previously been attributed to mouse predation, but with little explicit demographic analysis, were also examined to determine whether they can be associated with changing mouse populations. The total number of mice on the island at annual peak density increased by 430.0% between 1979-1980 and 2008-2011. This increase was due to an advanced breeding season, which was robustly related to the number of precipitation-free days during the non-breeding season. Mice directly reduced invertebrate densities, with biomass losses of up to two orders of magnitude in some habitats. Such invertebrate declines are expected to have significant consequences for ecosystem processes over the long term. Our results demonstrate that as climate change continues to create ameliorating conditions for invasive rodents on sub-Antarctic islands, the severity of their impacts will increase. They also emphasize the importance of rodent eradication for the restoration of invaded islands.
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Affiliation(s)
- Gregory T W McClelland
- Department of Botany and Zoology, Centre for Invasion Biology, Stellenbosch University, Matieland, South Africa
| | - Res Altwegg
- Department of Statistical Sciences, Centre for Statistics in Ecology, Environment and Conservation, University of Cape Town, Private Bag X3, Rondebosch, 7701, South Africa
- African Climate and Development Initiative, University of Cape Town, Private Bag X3, Rondebosch, 7701, South Africa
| | - Rudi J van Aarde
- Conservation Ecology Research Unit, Department of Zoology and Entomology, University of Pretoria, Hatfield, Pretoria, 0083, South Africa
| | - Sam Ferreira
- Conservation Ecology Research Unit, Department of Zoology and Entomology, University of Pretoria, Hatfield, Pretoria, 0083, South Africa
- Scientific Services, SANParks, Kruger National Park, South Africa
| | - Alan E Burger
- Department of Biology, University of Victoria, Victoria, British Columbia, V8W 3N5, Canada
| | - Steven L Chown
- School of Biological Sciences, Monash University, Victoria, 3800, Australia
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