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Cars BS, Kessler C, Hoffman EA, Côté SD, Koelsch D, Shafer ABA. Island demographics and trait associations in white-tailed deer. Heredity (Edinb) 2024; 133:1-10. [PMID: 38802598 PMCID: PMC11222433 DOI: 10.1038/s41437-024-00685-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/29/2024] Open
Abstract
When a population is isolated and composed of few individuals, genetic drift is the paramount evolutionary force and results in the loss of genetic diversity. Inbreeding might also occur, resulting in genomic regions that are identical by descent, manifesting as runs of homozygosity (ROHs) and the expression of recessive traits. Likewise, the genes underlying traits of interest can be revealed by comparing fixed SNPs and divergent haplotypes between affected and unaffected individuals. Populations of white-tailed deer (Odocoileus virginianus) on islands of Saint Pierre and Miquelon (SPM, France) have high incidences of leucism and malocclusions, both considered genetic defects; on the Florida Keys islands (USA) deer exhibit smaller body sizes, a polygenic trait. Here we aimed to reconstruct island demography and identify the genes associated with these traits in a pseudo case-control design. The two island populations showed reduced levels of genomic diversity and a build-up of deleterious mutations compared to mainland deer; there was also significant genome-wide divergence in Key deer. Key deer showed higher inbreeding levels, but not longer ROHs, consistent with long-term isolation. We identified multiple trait-related genes in ROHs including LAMTOR2 which has links to pigmentation changes, and NPVF which is linked to craniofacial abnormalities. Our mixed approach of linking ROHs, fixed SNPs and haplotypes matched a high number (~50) of a-priori body size candidate genes in Key deer. This suite of biomarkers and candidate genes should prove useful for population monitoring, noting all three phenotypes show patterns consistent with a complex trait and non-Mendelian inheritance.
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Affiliation(s)
- Brooklyn S Cars
- Environmental and Life Sciences Graduate Program, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada
- Department of Forensics, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada
| | - Camille Kessler
- Environmental and Life Sciences Graduate Program, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada
| | - Eric A Hoffman
- Department of Biology, University of Central Florida, 4000, Central Florida Blvd, Orlando, FL, USA
| | - Steeve D Côté
- Département de Biologie and Centre d'Études Nordiques, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Daniel Koelsch
- Fédération des chasseurs de Saint-Pierre et Miquelon, Saint-Pierre et Miquelon, France
- Direction des Territoires de l'Alimentation et de la Mer, service Biodiversité, Saint-Pierre et Miquelon, France
| | - Aaron B A Shafer
- Environmental and Life Sciences Graduate Program, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada.
- Department of Forensics, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada.
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Lettoof DC, Thomson VA, Cornelis J, Bateman PW, Aubret F, Gagnon MM, von Takach B. Bioindicator snake shows genomic signatures of natural and anthropogenic barriers to gene flow. PLoS One 2021; 16:e0259124. [PMID: 34714831 PMCID: PMC8555784 DOI: 10.1371/journal.pone.0259124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/12/2021] [Indexed: 11/18/2022] Open
Abstract
Urbanisation alters landscapes, introduces wildlife to novel stressors, and fragments habitats into remnant 'islands'. Within these islands, isolated wildlife populations can experience genetic drift and subsequently suffer from inbreeding depression and reduced adaptive potential. The Western tiger snake (Notechis scutatus occidentalis) is a predator of wetlands in the Swan Coastal Plain, a unique bioregion that has suffered substantial degradation through the development of the city of Perth, Western Australia. Within the urban matrix, tiger snakes now only persist in a handful of wetlands where they are known to bioaccumulate a suite of contaminants, and have recently been suggested as a relevant bioindicator of ecosystem health. Here, we used genome-wide single nucleotide polymorphism (SNP) data to explore the contemporary population genomics of seven tiger snake populations across the urban matrix. Specifically, we used population genomic structure and diversity, effective population sizes (Ne), and heterozygosity-fitness correlations to assess fitness of each population with respect to urbanisation. We found that population genomic structure was strongest across the northern and southern sides of a major river system, with the northern cluster of populations exhibiting lower heterozygosities than the southern cluster, likely due to a lack of historical gene flow. We also observed an increasing signal of inbreeding and genetic drift with increasing geographic isolation due to urbanisation. Effective population sizes (Ne) at most sites were small (< 100), with Ne appearing to reflect the area of available habitat rather than the degree of adjacent urbanisation. This suggests that ecosystem management and restoration may be the best method to buffer the further loss of genetic diversity in urban wetlands. If tiger snake populations continue to decline in urban areas, our results provide a baseline measure of genomic diversity, as well as highlighting which 'islands' of habitat are most in need of management and protection.
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Affiliation(s)
- Damian C. Lettoof
- Behavioural Ecology Lab, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Vicki A. Thomson
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Jari Cornelis
- Behavioural Ecology Lab, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Philip W. Bateman
- Behavioural Ecology Lab, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Fabien Aubret
- Station d’Ecologie Théorique et Expérimentale, CNRS, Moulis, France
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Marthe M. Gagnon
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Brenton von Takach
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
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