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Walter WD, Fameli A, Russo‐Petrick K, Edson JE, Rosenberry CS, Schuler KL, Tonkovich MJ. Large-scale assessment of genetic structure to assess risk of populations of a large herbivore to disease. Ecol Evol 2024; 14:e11347. [PMID: 38774134 PMCID: PMC11106048 DOI: 10.1002/ece3.11347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 03/28/2024] [Accepted: 04/12/2024] [Indexed: 05/24/2024] Open
Abstract
Chronic wasting disease (CWD) can spread among cervids by direct and indirect transmission, the former being more likely in emerging areas. Identifying subpopulations allows the delineation of focal areas to target for intervention. We aimed to assess the population structure of white-tailed deer (Odocoileus virginianus) in the northeastern United States at a regional scale to inform managers regarding gene flow throughout the region. We genotyped 10 microsatellites in 5701 wild deer samples from Maryland, New York, Ohio, Pennsylvania, and Virginia. We evaluated the distribution of genetic variability through spatial principal component analysis and inferred genetic structure using non-spatial and spatial Bayesian clustering algorithms (BCAs). We simulated populations representing each inferred wild cluster, wild deer in each state and each physiographic province, total wild population, and a captive population. We conducted genetic assignment tests using these potential sources, calculating the probability of samples being correctly assigned to their origin. Non-spatial BCA identified two clusters across the region, while spatial BCA suggested a maximum of nine clusters. Assignment tests correctly placed deer into captive or wild origin in most cases (94%), as previously reported, but performance varied when assigning wild deer to more specific origins. Assignments to clusters inferred via non-spatial BCA performed well, but efficiency was greatly reduced when assigning samples to clusters inferred via spatial BCA. Differences between spatial BCA clusters are not strong enough to make assignment tests a reliable method for inferring the geographic origin of deer using 10 microsatellites. However, the genetic distinction between clusters may indicate natural and anthropogenic barriers of interest for management.
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Affiliation(s)
- W. David Walter
- U.S. Geological Survey, Pennsylvania Cooperative Fish and Wildlife Research UnitThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Alberto Fameli
- Pennsylvania Cooperative Fish and Wildlife Research UnitThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Kelly Russo‐Petrick
- Pennsylvania Cooperative Fish and Wildlife Research UnitThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Jessie E. Edson
- Pennsylvania Cooperative Fish and Wildlife Research UnitThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | | | - Krysten L. Schuler
- Cornell Wildlife Health Lab, New York State Wildlife Health ProgramIthacaNew YorkUSA
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Pereira JC, Gonçalves-Anjo N, Orge L, Pires MA, Rocha S, Figueira L, Matos AC, Silva J, Mendonça P, Carvalho P, Tavares P, Lima C, Alves A, Esteves A, Pinto ML, Pires I, Gama A, Sargo R, Silva F, Seixas F, Vieira-Pinto M, Bastos E. Estimating sequence diversity of prion protein gene ( PRNP) in Portuguese populations of two cervid species: red deer and fallow deer. Prion 2023; 17:75-81. [PMID: 36945178 PMCID: PMC10038017 DOI: 10.1080/19336896.2023.2191540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
Among the transmissible spongiform encephalopathies (TSEs), chronic wasting disease (CWD) in cervids is now a rising concern in wildlife within Europe, after the detection of the first case in Norway in 2016, in a wild reindeer and until June 2022 a total of 34 cases were described in Norway, Sweden and Finland. The definite diagnosis is post-mortem, performed in target areas of the brain and lymph nodes. Samples are first screened using a rapid test and, if positive, confirmed by immunohistochemistry and Western immunoblotting. The study of the genetics of the prion protein gene, PRNP, has been proved to be a valuable tool for determining the relative susceptibility to TSEs. In the present study, the exon 3 of PRNP gene of 143 samples from red deer (Cervus elaphus) and fallow deer (Dama dama) of Portugal was analysed. Three single nucleotide polymorphisms (SNPs) were found in red deer - codon A136A, codon T98A, codon Q226E - and no sequence variation was detected in fallow deer. The low genetic diversity found in our samples is compatible with previous studies in Europe. The comparison with results from North America suggests that the free-ranging deer from our study may present susceptibility to CWD, although lack of experimental data and the necessity of continuous survey are necessary to evaluate these populations.
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Affiliation(s)
- Jorge C Pereira
- Animal and Veterinary Research Centre (CECAV), Vila Real, Portugal
| | - Nuno Gonçalves-Anjo
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
| | - Leonor Orge
- Animal and Veterinary Research Centre (CECAV), Vila Real, Portugal
- Pathology Laboratory, UEISPSA, National Institute for Agricultural and Veterinary Research (INIAV), I.P, Oeiras, Portugal
| | - Maria A Pires
- Animal and Veterinary Research Centre (CECAV), Vila Real, Portugal
| | - Sara Rocha
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
| | - Luís Figueira
- Polytechnic Institute of Castelo Branco (IPCB), Castelo Branco, Portugal
| | - Ana C Matos
- Polytechnic Institute of Castelo Branco (IPCB), Castelo Branco, Portugal
| | - João Silva
- Pathology Laboratory, UEISPSA, National Institute for Agricultural and Veterinary Research (INIAV), I.P, Oeiras, Portugal
| | - Paula Mendonça
- Pathology Laboratory, UEISPSA, National Institute for Agricultural and Veterinary Research (INIAV), I.P, Oeiras, Portugal
| | - Paulo Carvalho
- Pathology Laboratory, UEISPSA, National Institute for Agricultural and Veterinary Research (INIAV), I.P, Oeiras, Portugal
| | - Paula Tavares
- Pathology Laboratory, UEISPSA, National Institute for Agricultural and Veterinary Research (INIAV), I.P, Oeiras, Portugal
| | - Carla Lima
- Pathology Laboratory, UEISPSA, National Institute for Agricultural and Veterinary Research (INIAV), I.P, Oeiras, Portugal
| | - Anabela Alves
- Animal and Veterinary Research Centre (CECAV), Vila Real, Portugal
| | | | - Maria L Pinto
- Animal and Veterinary Research Centre (CECAV), Vila Real, Portugal
| | - Isabel Pires
- Animal and Veterinary Research Centre (CECAV), Vila Real, Portugal
| | - Adelina Gama
- Animal and Veterinary Research Centre (CECAV), Vila Real, Portugal
| | - Roberto Sargo
- Animal and Veterinary Research Centre (CECAV), Vila Real, Portugal
| | - Filipe Silva
- Animal and Veterinary Research Centre (CECAV), Vila Real, Portugal
| | - Fernanda Seixas
- Animal and Veterinary Research Centre (CECAV), Vila Real, Portugal
| | | | - Estela Bastos
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
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Wootton E, Robert C, Taillon J, Côté SD, Shafer ABA. Genomic health is dependent on long-term population demographic history. Mol Ecol 2023; 32:1943-1954. [PMID: 36704858 DOI: 10.1111/mec.16863] [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: 09/15/2022] [Revised: 01/08/2023] [Accepted: 01/13/2023] [Indexed: 01/28/2023]
Abstract
Current genetic methods of population assessment in conservation biology have been challenged by genome-scale analyses due to their quantitatively novel insights. These analyses include assessments of runs-of-homozygosity (ROH), genomic evolutionary rate profiling (GERP), and mutational load. Here, we aim to elucidate the relationships between these measures using three divergent ungulates: white-tailed deer, caribou, and mountain goat. The white-tailed deer is currently expanding, while caribou are in the midst of a significant decline. Mountain goats remain stable, having suffered a large historical bottleneck. We assessed genome-wide signatures of inbreeding using the inbreeding coefficient F and %ROH (FROH ) and identified evolutionarily constrained regions with GERP. Mutational load was estimated by identifying mutations in highly constrained elements (CEs) and sorting intolerant from tolerant (SIFT) mutations. Our results showed that F and FROH are higher in mountain goats than in caribou and white-tailed deer. Given the extended bottleneck and low Ne of the mountain goat, this supports the idea that the genome-wide effects of demographic change take time to accrue. Similarly, we found that mountain goats possess more highly constrained CEs and the lowest dN/dS values, both of which are indicative of greater purifying selection; this is also reflected by fewer mutations in CEs and deleterious mutations identified by SIFT. In contrast, white-tailed deer presented the highest mutational load with both metrics, in addition to dN/dS, while caribou were intermediate. Our results demonstrate that extended bottlenecks may lead to reduced diversity and increased FROH in ungulates, but not necessarily an increase in mutational load, probably due to the purging of deleterious alleles in small populations.
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Affiliation(s)
- Eric Wootton
- Biochemistry and Molecular Biology, Trent University, Peterborough, Ontario, Canada
| | - Claude Robert
- Département des Sciences Animales, Université Laval, Québec, Québec, Canada
| | - Joëlle Taillon
- Direction de l'Expertise sur la Faune Terrestre, l'Herpétofaune et l'Avifaune, Ministère des Forêts, de la Faune et des Parcs, Gouvernement du Québec, Québec, Québec, Canada
| | - Steeve D Côté
- Département de Biologie, Caribou Ungava and Centre d'Études Nordiques, Université Laval, Québec, Québec, Canada
| | - Aaron B A Shafer
- Environmental and Life Sciences Graduate Programme, Trent University, Peterborough, Ontario, Canada
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Anderson SJ, Côté SD, Richard JH, Shafer ABA. Genomic architecture of phenotypic extremes in a wild cervid. BMC Genomics 2022; 23:126. [PMID: 35151275 PMCID: PMC8841092 DOI: 10.1186/s12864-022-08333-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/24/2022] [Indexed: 12/30/2022] Open
Abstract
Identifying the genes underlying fitness-related traits such as body size and male ornamentation can provide tools for conservation and management and are often subject to various selective pressures. Here we performed high-depth whole genome re-sequencing of pools of individuals representing the phenotypic extremes for antler and body size in white-tailed deer (Odocoileus virginianus). Samples were selected from a tissue repository containing phenotypic data for 4,466 male white-tailed deer from Anticosti Island, Quebec, with four pools representing the extreme phenotypes for antler and body size after controlling for age. Our results revealed a largely homogenous population but detected highly divergent windows between pools for both traits, with the mean allele frequency difference of 14% for and 13% for antler and body SNPs in outlier windows, respectively. Genes in outlier antler windows were enriched for pathways associated with cell death and protein metabolism and some of the most differentiated windows included genes associated with oncogenic pathways and reproduction, processes consistent with antler evolution and growth. Genes associated with body size were more nuanced, suggestive of a highly complex trait. Overall, this study revealed the complex genomic make-up of both antler morphology and body size in free-ranging white-tailed deer and identified target loci for additional analyses.
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Ketz AC, Robinson SJ, Johnson CJ, Samuel MD. Pathogen‐mediated selection and management implications for white‐tailed deer exposed to chronic wasting disease. J Appl Ecol 2022. [DOI: 10.1111/1365-2664.14109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Alison C. Ketz
- Wisconsin Cooperative Research Unit Department of Forest and Wildlife Ecology University of Wisconsin Madison WI USA
| | - Stacie J. Robinson
- NOAA Hawaiian Monk Seal Research Program Pacific Islands Fisheries Science Center Honolulu HI USA
| | - Chad J. Johnson
- Medical Microbiology and Immunology University of Wisconsin Madison WI USA
| | - Michael D. Samuel
- Department of Forest and Wildlife Ecology University of Wisconsin Madison WI USA
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