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Merchant HN, Ivanova A, Hart DW, García C, Bennett NC, Portugal SJ, Faulkes CG. Patterns of Genetic Diversity and Gene Flow Associated With an Aridity Gradient in Populations of Common Mole-rats, Cryptomys hottentotus hottentotus. Genome Biol Evol 2024; 16:evae144. [PMID: 38953183 PMCID: PMC11258414 DOI: 10.1093/gbe/evae144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 05/30/2024] [Accepted: 06/25/2024] [Indexed: 07/03/2024] Open
Abstract
Genetic adaptation is the change of a population toward a phenotype that best fits the present ecological conditions of the environment it inhabits. As environmental conditions change, allele frequencies shift, resulting in different populations of the same species possessing genetic variation and divergent phenotypes. Cooperatively breeding common mole-rats (Cryptomys hottentotus hottentotus) inhabit environments along an aridity gradient in South Africa, which provides an opportunity for local genetic adaptations to occur. Using one mitochondrial gene (cytochrome b) and 3,540 SNP loci across the whole genome, we determined the phylogenetic relationship, population structure and genetic diversity of five populations of C. h. hottentotus located along an aridity gradient. Mitochondrial data identified population-specific clades that were less distinct in the two mesic populations, potentially indicating historical or recent gene flow, or the retention of ancestral haplotypes. Arid and semi-arid populations formed a distinct cluster from the non-arid populations. Genetic diversity and gene flow were higher in arid-dwelling individuals, suggesting greater connectivity and interactions between colonies in arid regions in comparison to mesic ones. Using an Aridity Index, we determined that isolation by environment, rather than isolation by geographical distance, best explains the genetic distance between the populations. Further analyses using target loci may determine if there are differing underlying genetic adaptations among populations of C. h. hottentotus. These analyses could help unravel population differences in response to environmental factors within a subspecies of bathyergid mole-rat and determine the adaptive capacity of this small nonmigratory subterranean rodent species in response to aridification in the face of climate change.
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Affiliation(s)
- Hana N Merchant
- Department of Biological Sciences, School of Life and Environmental Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Anastasia Ivanova
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Daniel W Hart
- Department of Zoology and Entomology, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Cristina García
- Department of Biological Sciences, School of Life and Environmental Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Nigel C Bennett
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Steven J Portugal
- Department of Biological Sciences, School of Life and Environmental Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
| | - Chris G Faulkes
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
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Clough J, Schwab S, Mikac K. Gut Microbiome Profiling of the Endangered Southern Greater Glider ( Petauroides volans) after the 2019-2020 Australian Megafire. Animals (Basel) 2023; 13:3583. [PMID: 38003202 PMCID: PMC10668662 DOI: 10.3390/ani13223583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
Studying the gut microbiome can provide valuable insights into animal health and inform the conservation management of threatened wildlife. Gut microbiota play important roles in regulating mammalian host physiology, including digestion, energy metabolism and immunity. Dysbiosis can impair such physiological processes and compromise host health, so it is essential that the gut microbiome be considered in conservation planning. The southern greater glider (Petauroides volans) is an endangered arboreal marsupial that faced widespread habitat fragmentation and population declines following the 2019-2020 Australian bushfire season. This study details baseline data on the gut microbiome of this species. The V3-V4 region of the 16S rRNA gene was amplified from scats collected from individuals inhabiting burnt and unburnt sites across southeastern Australia and sequenced to determine bacterial community composition. Southern greater glider gut microbiomes were characterised by high relative abundances of Firmicutes and Bacteroidota, which is consistent with that reported for other marsupial herbivores. Significant differences in gut microbial diversity and community structure were detected among individuals from different geographic locations. Certain microbiota and functional orthologues were also found to be significantly differentially abundant between locations. The role of wildfire in shaping southern greater glider gut microbiomes was shown, with some significant differences in the diversity and abundance of microbiota detected between burnt and unburnt sites. Overall, this study details the first data on greater glider (Petauroides) gut microbiomes, laying the foundation for future studies to further explore relationships between microbial community structure, environmental stressors and host health.
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Affiliation(s)
- Jordyn Clough
- School of Earth, Atmospheric and Life Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia;
| | - Sibylle Schwab
- School of Medical, Indigenous and Health Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Katarina Mikac
- School of Earth, Atmospheric and Life Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia;
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Jones GM, Goldberg JF, Wilcox TM, Buckley LB, Parr CL, Linck EB, Fountain ED, Schwartz MK. Fire-driven animal evolution in the Pyrocene. Trends Ecol Evol 2023; 38:1072-1084. [PMID: 37479555 DOI: 10.1016/j.tree.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 06/02/2023] [Accepted: 06/06/2023] [Indexed: 07/23/2023]
Abstract
Fire regimes are a major agent of evolution in terrestrial animals. Changing fire regimes and the capacity for rapid evolution in wild animal populations suggests the potential for rapid, fire-driven adaptive animal evolution in the Pyrocene. Fire drives multiple modes of evolutionary change, including stabilizing, directional, disruptive, and fluctuating selection, and can strongly influence gene flow and genetic drift. Ongoing and future research in fire-driven animal evolution will benefit from further development of generalizable hypotheses, studies conducted in highly responsive taxa, and linking fire-adapted phenotypes to their underlying genetic basis. A better understanding of evolutionary responses to fire has the potential to positively influence conservation strategies that embrace evolutionary resilience to fire in the Pyrocene.
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Affiliation(s)
- Gavin M Jones
- USDA Forest Service, Rocky Mountain Research Station, Albuquerque, NM 87102, USA.
| | - Joshua F Goldberg
- USDA Forest Service, Rocky Mountain Research Station, Albuquerque, NM 87102, USA
| | - Taylor M Wilcox
- National Genomics Center for Fish and Wildlife Conservation, USDA Forest Service, Rocky Mountain Research Station, Missoula, MT 59801, USA
| | - Lauren B Buckley
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Catherine L Parr
- Department of Earth, Ocean and Ecological Sciences, University of Liverpool, Liverpool, L3 5TR, UK; Department of Zoology and Entomology, University of Pretoria, Pretoria 0028, South Africa; School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Wits 2050, South Africa
| | - Ethan B Linck
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
| | - Emily D Fountain
- Department of Forest and Wildlife Ecology, University of Wisconsin, Madison, WI 53706, USA
| | - Michael K Schwartz
- National Genomics Center for Fish and Wildlife Conservation, USDA Forest Service, Rocky Mountain Research Station, Missoula, MT 59801, USA
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Informing Wildlife Corridor Creation through Population Genetics of an Arboreal Marsupial in a Fragmented Landscape. Genes (Basel) 2023; 14:genes14020349. [PMID: 36833276 PMCID: PMC9957349 DOI: 10.3390/genes14020349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/31/2023] Open
Abstract
Habitat loss and fragmentation contribute significantly to the decline of arboreal mammal populations. As populations become fragmented and isolated, a reduction in gene flow can result in a loss of genetic diversity and have an overall impact upon long-term persistence. Creating wildlife corridors can mitigate such effects by increasing the movement and dispersal of animals, thus acting to reduce population isolation. To evaluate the success of a corridor, a before-after experimental research framework can be used. Here, we report the genetic diversity and structure of sugar glider (Petaurus breviceps) sampling locations within a fragmented landscape prior to the implementation of a wildlife corridor. This study used 5999 genome-wide SNPs from 94 sugar gliders caught from 8 locations in a fragmented landscape in south-eastern New South Wales, Australia. Overall genetic structure was limited, and gene flow was detected across the landscape. Our findings indicate that the study area contains one large population. A major highway dissecting the landscape did not act as a significant barrier to dispersal, though this may be because of its relatively new presence in the landscape (completed in 2018). Future studies may yet indicate its long-term impact as a barrier to gene flow. Future work should aim to repeat the methods of this study to examine the medium-to-long-term impacts of the wildlife corridor on sugar gliders, as well as examine the genetic structure of other native, specialist species in the landscape.
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