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Clarke JG, Smith AC, Cullingham CI. Genetic rescue often leads to higher fitness as a result of increased heterozygosity across animal taxa. Mol Ecol 2024; 33:e17532. [PMID: 39279498 DOI: 10.1111/mec.17532] [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: 03/13/2024] [Revised: 08/28/2024] [Accepted: 09/03/2024] [Indexed: 09/18/2024]
Abstract
Biodiversity loss has reached critical levels partly due to anthropogenic habitat loss and degradation. These landscape changes are damaging as they can fragment species distributions into small, isolated populations, resulting in limited gene flow, population declines and reduced adaptive potential. Genetic rescue, the translocation of individuals to increase genetic diversity and ultimately fitness, has produced promising results for fragmented populations but remains underutilized due to a lack of long-term data and monitoring. To promote a better understanding of genetic rescue and its potential risks and benefits over the short-term, we reviewed and analysed published genetic rescue attempts to identify whether genetic diversity increases following translocation, and if this change is associated with increased fitness. Our review identified 19 studies that provided genetic and fitness data from before and after the translocation; the majority of these were on mammals, and included experimental, natural and conservation-motivated translocations. Using a Bayesian meta-analytical approach, we found that on average, genetic diversity and fitness increased in populations post translocations, although there were some exceptions to this trend. Overall, genetic diversity was a positive predictor of population fitness, and in some cases this relationship extended three generations post-rescue. These data suggest a single translocation can have lasting fitness benefits, and support translocation as another tool to facilitate conservation success. Given the limited number of studies with long-term data, we echo the need for genetic monitoring of populations post-translocation to understand whether genetic rescue can also limit the loss of adaptive potential in the long-term.
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Affiliation(s)
- Julia G Clarke
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Adam C Smith
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
- National Wildlife Research Centre, Environment and Climate Change Canada, Ottawa, Ontario, Canada
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2
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Quinn CB, Preckler-Quisquater S, Buchalski MR, Sacks BN. Whole Genomes Inform Genetic Rescue Strategy for Montane Red Foxes in North America. Mol Biol Evol 2024; 41:msae193. [PMID: 39288165 PMCID: PMC11424165 DOI: 10.1093/molbev/msae193] [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: 03/12/2024] [Revised: 08/07/2024] [Accepted: 09/03/2024] [Indexed: 09/19/2024] Open
Abstract
A few iconic examples have proven the value of facilitated gene flow for counteracting inbreeding depression and staving off extinction; yet, the practice is often not implemented for fear of causing outbreeding depression. Using genomic sequencing, climatic niche modeling, and demographic reconstruction, we sought to assess the risks and benefits of using translocations as a tool for recovery of endangered montane red fox (Vulpes vulpes) populations in the western United States. We demonstrated elevated inbreeding and homozygosity of deleterious alleles across all populations, but especially those isolated in the Cascade and Sierra Nevada ranges. Consequently, translocations would be expected to increase population growth by masking deleterious recessive alleles. Demographic reconstructions further indicated shallow divergences of less than a few thousand years among montane populations, suggesting low risk of outbreeding depression. These genomic-guided findings set the stage for future management, the documentation of which will provide a roadmap for recovery of other data-deficient taxa.
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Affiliation(s)
- Cate B Quinn
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
- California Department of Fish and Wildlife, Wildlife Genetics Research Unit, Wildlife Health Laboratory, Sacramento, CA, USA
- National Genomics Center for Wildlife and Fish Conservation, USDA Forest Service, Rocky Mountain Research Station, Missoula, MT, USA
| | - Sophie Preckler-Quisquater
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Michael R Buchalski
- California Department of Fish and Wildlife, Wildlife Genetics Research Unit, Wildlife Health Laboratory, Sacramento, CA, USA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
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3
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Rando HM, Alexander EP, Preckler-Quisquater S, Quinn CB, Stutchman JT, Johnson JL, Bastounes ER, Horecka B, Black KL, Robson MP, Shepeleva DV, Herbeck YE, Kharlamova AV, Trut LN, Pauli JN, Sacks BN, Kukekova AV. Missing history of a modern domesticate: Historical demographics and genetic diversity in farm-bred red fox populations. J Hered 2024; 115:411-423. [PMID: 38624218 PMCID: PMC11235124 DOI: 10.1093/jhered/esae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 02/09/2024] [Accepted: 04/09/2024] [Indexed: 04/17/2024] Open
Abstract
The first record of captive-bred red foxes (Vulpes vulpes) dates to 1896 when a breeding enterprise emerged in the provinces of Atlantic Canada. Because its domestication happened during recent history, the red fox offers a unique opportunity to examine the genetic diversity of an emerging domesticated species in the context of documented historical and economic influences. In particular, the historical record suggests that North American and Eurasian farm-bred populations likely experienced different demographic trajectories. Here, we focus on the likely impacts of founder effects and genetic drift given historical trends in fox farming on North American and Eurasian farms. A total of 15 mitochondrial haplotypes were identified in 369 foxes from 10 farm populations that we genotyped (n = 161) or that were previously published. All haplotypes are endemic to North America. Although most haplotypes were consistent with eastern Canadian ancestry, a small number of foxes carried haplotypes typically found in Alaska and other regions of western North America. The presence of these haplotypes supports historical reports of wild foxes outside of Atlantic Canada being introduced into the breeding stock. These putative Alaskan and Western haplotypes were more frequently identified in Eurasian farms compared to North American farms, consistent with historical documentation suggesting that Eurasian economic and breeding practices were likely to maintain low-frequency haplotypes more effectively than in North America. Contextualizing inter- vs. intra-farm genetic diversity alongside the historical record is critical to understanding the origins of this emerging domesticate and the relationships between wild and farm-bred fox populations.
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Affiliation(s)
- Halie M Rando
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
- Department of Computer Science, Smith College, Northampton, MA 01063, United States
| | - Emmarie P Alexander
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Sophie Preckler-Quisquater
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616, United States
| | - Cate B Quinn
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616, United States
- National Genomics Center for Wildlife and Fish Conservation, USDA Forest Service, Rocky Mountain Research Station, Missoula, MT, United States
| | - Jeremy T Stutchman
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Jennifer L Johnson
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Estelle R Bastounes
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Beata Horecka
- Faculty of Animal Sciences and Bioeconomy, Institute of Biological Basis of Animal Production, University of Life Sciences in Lublin, Lublin, Poland
| | - Kristina L Black
- Department of Forestry and Wildlife Ecology, University of Wisconsin, Madison, WI 53706, United States
| | - Michael P Robson
- Department of Computer Science, Smith College, Northampton, MA 01063, United States
| | - Darya V Shepeleva
- Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Yury E Herbeck
- Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk 630090, Russia
- Koret School of Veterinary Medicine, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Anastasiya V Kharlamova
- Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Lyudmila N Trut
- Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Jonathan N Pauli
- Department of Forestry and Wildlife Ecology, University of Wisconsin, Madison, WI 53706, United States
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616, United States
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, United States
| | - Anna V Kukekova
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
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4
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Preckler-Quisquater S, Quinn CB, Sacks BN. Maintenance of a narrow hybrid zone between native and introduced red foxes (Vulpes vulpes) despite conspecificity and high dispersal capabilities. Mol Ecol 2024; 33:e17418. [PMID: 38847182 DOI: 10.1111/mec.17418] [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: 01/30/2024] [Revised: 05/04/2024] [Accepted: 05/13/2024] [Indexed: 06/27/2024]
Abstract
Human-facilitated introductions of nonnative populations can lead to secondary contact between allopatric lineages, resulting in lineage homogenisation or the formation of stable hybrid zones maintained by reproductive barriers. We investigated patterns of gene flow between the native Sacramento Valley red fox (Vulpes vulpes patwin) and introduced conspecifics of captive-bred origin in California's Central Valley. Considering their recent divergence (20-70 kya), we hypothesised that any observed barriers to gene flow were primarily driven by pre-zygotic (e.g. behavioural differences) rather than post-zygotic (e.g. reduced hybrid fitness) barriers. We also explored whether nonnative genes could confer higher fitness in the human-dominated landscape resulting in selective introgression into the native population. Genetic analysis of red foxes (n = 682) at both mitochondrial (cytochrome b + D-loop) and nuclear (19,051 SNPs) loci revealed narrower cline widths than expected under a simulated model of unrestricted gene flow, consistent with the existence of reproductive barriers. We identified several loci with reduced introgression that were previously linked to behavioural divergence in captive-bred and domestic canids, supporting pre-zygotic, yet possibly hereditary, barriers as a mechanism driving the narrowness and stability of the hybrid zone. Several loci with elevated gene flow from the nonnative into the native population were linked to genes associated with domestication and adaptation to human-dominated landscapes. This study contributes to our understanding of hybridisation dynamics in vertebrates, particularly in the context of species introductions and landscape changes, underscoring the importance of considering how multiple mechanisms may be maintaining lineages at the species and subspecies level.
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Affiliation(s)
- Sophie Preckler-Quisquater
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Cate B Quinn
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California, USA
- USDA Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, Missoula, Montana, USA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
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Balestrieri A, Gigliotti S, Caniglia R, Velli E, Zambuto F, De Giorgi E, Mucci N, Tremolada P, Gazzola A. Nutritional ecology of a prototypical generalist predator, the red fox (Vulpes vulpes). Sci Rep 2024; 14:7918. [PMID: 38575633 PMCID: PMC10995161 DOI: 10.1038/s41598-024-58711-6] [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: 01/23/2024] [Accepted: 04/02/2024] [Indexed: 04/06/2024] Open
Abstract
Generalist species, which exploit a wide range of food resources, are expected to be able to combine available resources as to attain their specific macronutrient ratio (percentage of caloric intake of protein, lipids and carbohydrates). Among mammalian predators, the red fox Vulpes vulpes is a widespread, opportunistic forager: its diet has been largely studied, outlining wide variation according to geographic and climatic factors. We aimed to check if, throughout the species' European range, diets vary widely in macronutrient composition or foxes can combine complementary foods to gain the same nutrient intake. First, we assessed fox's intake target in the framework of nutritional geometry. Secondly, we aimed to highlight the effects of unbalanced diets on fox density, which was assumed as a proxy for Darwinian fitness, as assessed in five areas of the western Italian Alps. Unexpectedly, the target macronutrient ratio of the fox (52.4% protein-, 38.7% lipid- and 8.9% carbohydrate energy) was consistent with that of hypercarnivores, such as wolves and felids, except for carbohydrate intakes in urban and rural habitats. The inverse relation between density and the deviation of observed macronutrient ratios from the intake target suggests that fox capability of surviving in a wide range of habitats may not be exempt from fitness costs and that nutrient availability should be regarded among the biotic factors affecting animal abundance and distribution.
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Affiliation(s)
- A Balestrieri
- Dipartimento di Scienze e Politiche Ambientali, Università di Milano, via Celoria 26, 20133, Milan, Italy.
| | - S Gigliotti
- Dipartimento di Biologia, Università di Padova, via Ugo Bassi 58/B, 35131, Padua, Italy
- Dipartimento di Scienze della Terra e dell'Ambiente, Università di Pavia, 27100, Pavia, Italy
| | - R Caniglia
- Area per la Genetica della Conservazione, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), via Ca' Fornacetta 9, Ozzano Emilia, 40064, Bologna, Italy
| | - E Velli
- Area per la Genetica della Conservazione, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), via Ca' Fornacetta 9, Ozzano Emilia, 40064, Bologna, Italy
| | - F Zambuto
- IRCCS Ospedale Galeazzi-Sant'Ambrogio, via C. Belgioioso 173, 20161, Milano, Italy
| | - E De Giorgi
- Dipartimento di Scienze della Terra e dell'Ambiente, Università di Pavia, 27100, Pavia, Italy
| | - N Mucci
- Area per la Genetica della Conservazione, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), via Ca' Fornacetta 9, Ozzano Emilia, 40064, Bologna, Italy
| | - P Tremolada
- Dipartimento di Scienze e Politiche Ambientali, Università di Milano, via Celoria 26, 20133, Milan, Italy
| | - A Gazzola
- Dipartimento di Scienze della Terra e dell'Ambiente, Università di Pavia, 27100, Pavia, Italy
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Green DS, Martin ME, Matthews SM, Akins JR, Carlson J, Figura P, Hatfield BE, Perrine JD, Quinn CB, Sacks BN, Stephenson TR, Stock SL, Tucker JM. A hierarchical modeling approach to predict the distribution and density of Sierra Nevada Red Fox ( Vulpes vulpes necator). J Mammal 2023; 104:820-832. [PMID: 37545667 PMCID: PMC10399920 DOI: 10.1093/jmammal/gyad026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/08/2023] [Indexed: 08/08/2023] Open
Abstract
Carnivores play critical roles in ecosystems, yet many species are declining worldwide. The Sierra Nevada Red Fox (Vulpes vulpes necator; SNRF) is a rare and endangered subspecies of red fox limited to upper montane forests, subalpine, and alpine environments of California and Oregon, United States. Having experienced significant distribution contractions and population declines in the last century, the subspecies is listed as at-risk by relevant federal and state agencies. Updated information on its contemporary distribution and density is needed to guide and evaluate conservation and management actions. We combined 12 years (2009-2020) of detection and nondetection data collected throughout California and Oregon to model the potential distribution and density of SNRFs throughout their historical and contemporary ranges. We used an integrated species distribution and density modeling approach, which predicted SNRF density in sampled locations based on observed relationships between environmental covariates and detection frequencies, and then projected those predictions to unsampled locations based on the estimated correlations with environmental covariates. This approach provided predictions that serve as density estimates in sampled regions and projections in unsampled areas. Our model predicted a density of 1.06 (95% credible interval = 0.8-1.36) foxes per 100 km2 distributed throughout 22,926 km2 in three distinct regions of California and Oregon-Sierra Nevada, Lassen Peak, and Oregon Cascades. SNRFs were most likely to be found in areas with low minimum temperatures and high snow water equivalent. Our results provide a contemporary baseline to inform the development and evaluation of conservation and management actions, and guide future survey efforts.
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Affiliation(s)
- David S Green
- Institute for Natural Resources, Oregon State University, Corvallis, Oregon 97331, USA
| | - Marie E Martin
- Institute for Natural Resources, Oregon State University, Corvallis, Oregon 97331, USA
| | | | - Jocelyn R Akins
- Cascades Carnivore Project, 505 17th Street, Hood River, Oregon 97031, USA
| | - Jennifer Carlson
- California Department of Fish and Wildlife, 601 Locust Street, Redding, California 96001, USA
| | - Pete Figura
- California Department of Fish and Wildlife, 601 Locust Street, Redding, California 96001, USA
| | - Brian E Hatfield
- California Department of Fish and Wildlife, 787 North Main Street, Suite 220, Bishop, California 93514, USA
| | - John D Perrine
- Biological Sciences Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, USA
| | - Cate B Quinn
- Mammalian Ecology and Conservation Unit, Veterinary Genetics laboratory, University of California, Davis, 1 Shields Avenue, Davis, California 95616, USA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics laboratory, University of California, Davis, 1 Shields Avenue, Davis, California 95616, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, 1 Shields Avenue, Davis, California 95616, USA
| | - Thomas R Stephenson
- Sierra Nevada Bighorn Sheep Recovery Program, California Department of Fish and Wildlife, 787 North Main St., Suite 220, Bishop, California 93514, USA
| | - Sarah L Stock
- Resources Management and Science Division, Yosemite National Park, El Portal, California 95318, USA
| | - Jody M Tucker
- Present address: USDA Forest Service, Rocky Mountain Research Station, 800 E. Beckwith Avenue, Missoula, Montana 59801, USA
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Wallén J, Norén K, Angerbjörn A, Eide NE, Landa A, Flagstad Ø. Context‐dependent demographic and genetic effects of translocation from a captive breeding project. Anim Conserv 2022. [DOI: 10.1111/acv.12831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- J. Wallén
- Department of Zoology Stockholm University Stockholm Sweden
| | - K. Norén
- Department of Zoology Stockholm University Stockholm Sweden
| | - A. Angerbjörn
- Department of Zoology Stockholm University Stockholm Sweden
| | - N. E. Eide
- Norwegian Institute for Nature Research Trondheim Norway
| | - A. Landa
- Norwegian Institute for Nature Research Bergen Norway
| | - Ø. Flagstad
- Norwegian Institute for Nature Research Trondheim Norway
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8
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Aylward CM, Grahn RA, Barthman-Thompson LM, Kelt DA, Sacks BN, Statham MJ. A novel noninvasive genetic survey technique for small mammals. J Mammal 2022. [DOI: 10.1093/jmammal/gyac070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Noninvasive genetic surveys, often conducted by collecting fecal samples, have become a popular tool for surveying wildlife, but have primarily been applied to species with large and conspicuous scat. Although many small mammals are threatened, endangered, or data deficient, noninvasive genetic surveys have rarely been applied due to the challenges of detecting their inconspicuous fecal pellets. As part of a broader study of the endangered salt marsh harvest mouse (Reithrodontomys raviventris), we developed a noninvasive genetic survey technique for the community of small mammals in their putative range. We designed bait stations to passively collect fecal samples from rodents, and developed a multiplex primer set that amplified unique fragment sizes for salt marsh harvest mice and four other sympatric species. We tested the primer set on positive controls and on fecal pellets collected from bait stations at two regularly monitored field sites known to have very different densities of salt marsh harvest mice. The multiplex amplified DNA from all five species, even when all five species were present in a single sample. A positive species identification was made for all field-collected samples, and 43% of these field-collected samples had multispecies detections. The combination of bait stations and genetic species identification proved to be an effective means of noninvasively surveying small mammals in potential salt marsh harvest mouse habitat. The sampling technique should be applicable to a wide variety of small mammals in other systems.
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Affiliation(s)
- Cody M Aylward
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis , Davis, California 95616 , USA
- Department of Wildlife, Fish and Conservation Biology, University of California, Davis , Davis, California 95616 , USA
| | - Robert A Grahn
- Veterinary Genetics Laboratory, University of California, Davis , Davis, California 95616 , USA
| | - Laureen M Barthman-Thompson
- California Department of Fish and Wildlife, Region 3 , 2109 Arch Airport Road, Stockton, California 95206 , USA
| | - Douglas A Kelt
- Department of Wildlife, Fish and Conservation Biology, University of California, Davis , Davis, California 95616 , USA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis , Davis, California 95616 , USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis , Davis, California 95616 , USA
| | - Mark J Statham
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis , Davis, California 95616 , USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis , Davis, California 95616 , USA
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Shimozuru M, Jimbo M, Adachi K, Kawamura K, Shirane Y, Umemura Y, Ishinazaka T, Nakanishi M, Kiyonari M, Yamanaka M, Amagai Y, Ijuin A, Sakiyama T, Kasai S, Nose T, Shirayanagi M, Tsuruga H, Mano T, Tsubota T, Fukasawa K, Uno H. Estimation of breeding population size using DNA-based pedigree reconstruction in brown bears. Ecol Evol 2022; 12:e9246. [PMID: 36091344 PMCID: PMC9448969 DOI: 10.1002/ece3.9246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/18/2022] [Accepted: 07/27/2022] [Indexed: 11/11/2022] Open
Abstract
Robust estimates of demographic parameters are critical for effective wildlife conservation and management but are difficult to obtain for elusive species. We estimated the breeding and adult population sizes, as well as the minimum population size, in a high-density brown bear population on the Shiretoko Peninsula, in Hokkaido, Japan, using DNA-based pedigree reconstruction. A total of 1288 individuals, collected in and around the Shiretoko Peninsula between 1998 and 2020, were genotyped at 21 microsatellite loci. Among them, 499 individuals were identified by intensive genetic sampling conducted in two consecutive years (2019 and 2020) mainly by noninvasive methods (e.g., hair and fecal DNA). Among them, both parents were assigned for 330 bears, and either maternity or paternity was assigned to 47 and 76 individuals, respectively. The subsequent pedigree reconstruction indicated a range of breeding and adult (≥4 years old) population sizes: 128-173 for female breeders and 66-91 male breeders, and 155-200 for female adults and 84-109 male adults. The minimum population size was estimated to be 449 (252 females and 197 males) in 2019. Long-term continuous genetic sampling prior to a short-term intensive survey would enable parentage to be identified in a population with a high probability, thus enabling reliable estimates of breeding population size for elusive species.
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Affiliation(s)
- Michito Shimozuru
- Laboratory of Wildlife Biology and Medicine, Faculty of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Mina Jimbo
- Laboratory of Wildlife Biology and Medicine, Faculty of Veterinary MedicineHokkaido UniversitySapporoJapan
- Hokkaido Research OrganizationSapporoJapan
| | - Keisuke Adachi
- Laboratory of Wildlife Biology and Medicine, Faculty of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Kei Kawamura
- Laboratory of Wildlife Biology and Medicine, Faculty of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Yuri Shirane
- Laboratory of Wildlife Biology and Medicine, Faculty of Veterinary MedicineHokkaido UniversitySapporoJapan
- Hokkaido Research OrganizationSapporoJapan
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Toshio Tsubota
- Laboratory of Wildlife Biology and Medicine, Faculty of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Keita Fukasawa
- Center for Environmental Biology and Ecosystem StudiesNational Institute for Environmental StudiesTsukubaJapan
| | - Hiroyuki Uno
- Faculty of AgricultureTokyo University of Agriculture and TechnologyTokyoJapan
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10
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Contrasting genetic trajectories of endangered and expanding red fox populations in the western U.S. Heredity (Edinb) 2022; 129:123-136. [PMID: 35314789 PMCID: PMC9338314 DOI: 10.1038/s41437-022-00522-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 12/04/2022] Open
Abstract
As anthropogenic disturbances continue to drive habitat loss and range contractions, the maintenance of evolutionary processes will increasingly require targeting measures to the population level, even for common and widespread species. Doing so requires detailed knowledge of population genetic structure, both to identify populations of conservation need and value, as well as to evaluate suitability of potential donor populations. We conducted a range-wide analysis of the genetic structure of red foxes in the contiguous western U.S., including a federally endangered distinct population segment of the Sierra Nevada subspecies, with the objectives of contextualizing field observations of relative scarcity in the Pacific mountains and increasing abundance in the cold desert basins of the Intermountain West. Using 31 autosomal microsatellites, along with mitochondrial and Y-chromosome markers, we found that populations of the Pacific mountains were isolated from one another and genetically depauperate (e.g., estimated Ne range = 3–9). In contrast, red foxes in the Intermountain regions showed relatively high connectivity and genetic diversity. Although most Intermountain red foxes carried indigenous western matrilines (78%) and patrilines (85%), the presence of nonindigenous haplotypes at lower elevations indicated admixture with fur-farm foxes and possibly expanding midcontinent populations as well. Our findings suggest that some Pacific mountain populations could likely benefit from increased connectivity (i.e., genetic rescue) but that nonnative admixture makes expanding populations in the Intermountain basins a non-ideal source. However, our results also suggest contact between Pacific mountain and Intermountain basin populations is likely to increase regardless, warranting consideration of risks and benefits of proactive measures to mitigate against unwanted effects of Intermountain gene flow.
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11
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Hayward KM, Clemente-Carvalho RBG, Jensen EL, de Groot PVC, Branigan M, Dyck M, Tschritter C, Sun Z, Lougheed SC. Genotyping-in-thousands by sequencing (GT-seq) of non-invasive fecal and degraded samples: a new panel to enable ongoing monitoring of Canadian polar bear populations. Mol Ecol Resour 2022; 22:1906-1918. [PMID: 35007402 PMCID: PMC9305793 DOI: 10.1111/1755-0998.13583] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 11/25/2021] [Accepted: 12/07/2021] [Indexed: 11/26/2022]
Abstract
Genetic monitoring using noninvasive samples provides a complement or alternative to traditional population monitoring methods. However, next‐generation sequencing approaches to monitoring typically require high quality DNA and the use of noninvasive samples (e.g., scat) is often challenged by poor DNA quality and contamination by nontarget species. One promising solution is a highly multiplexed sequencing approach called genotyping‐in‐thousands by sequencing (GT‐seq), which can enable cost‐efficient genomics‐based monitoring for populations based on noninvasively collected samples. Here, we develop and validate a GT‐seq panel of 324 single nucleotide polymorphisms (SNPs) optimized for genotyping of polar bears based on DNA from noninvasively collected faecal samples. We demonstrate (1) successful GT‐seq genotyping of DNA from a range of sample sources, including successful genotyping (>50% loci) of 62.9% of noninvasively collected faecal samples determined to contain polar bear DNA; and (2) that we can reliably differentiate individuals, ascertain sex, assess relatedness, and resolve population structure of Canadian polar bear subpopulations based on a GT‐seq panel of 324 SNPs. Our GT‐seq data reveal spatial‐genetic patterns similar to previous polar bear studies but at lesser cost per sample and through use of noninvasively collected samples, indicating the potential of this approach for population monitoring. This GT‐seq panel provides the foundation for a noninvasive toolkit for polar bear monitoring and can contribute to community‐based programmes – a framework which may serve as a model for wildlife conservation and management for species worldwide.
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Affiliation(s)
- Kristen M Hayward
- Department of Biology, Queen's University, Kingston, Ontario, Canada
| | | | - Evelyn L Jensen
- School of Natural and Environmental Sciences, Newcastle University, Newcastle, United Kingdom
| | | | - Marsha Branigan
- Department of Environment and Natural Resources, Government of the Northwest Territories, Inuvik, Northwest Territories, Canada
| | - Markus Dyck
- Department of Environment, Government of Nunavut, Igloolik, Nunavut, Canada
| | | | - Zhengxin Sun
- Department of Biology, Queen's University, Kingston, Ontario, Canada
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McLellan ML, McLellan BN, Sollmann R, Wittmer HU. Vital rates of two small populations of brown bears in Canada and range-wide relationship between population size and trend. Ecol Evol 2021; 11:3422-3434. [PMID: 33841794 PMCID: PMC8019027 DOI: 10.1002/ece3.7301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 01/20/2021] [Accepted: 01/26/2021] [Indexed: 11/11/2022] Open
Abstract
Identifying mechanisms of population change is fundamental for conserving small and declining populations and determining effective management strategies. Few studies, however, have measured the demographic components of population change for small populations of mammals (<50 individuals). We estimated vital rates and trends in two adjacent but genetically distinct, threatened brown bear (Ursus arctos) populations in British Columbia, Canada, following the cessation of hunting. One population had approximately 45 resident bears but had some genetic and geographic connectivity to neighboring populations, while the other population had <25 individuals and was isolated. We estimated population-specific vital rates by monitoring survival and reproduction of telemetered female bears and their dependent offspring from 2005 to 2018. In the larger, connected population, independent female survival was 1.00 (95% CI: 0.96-1.00) and the survival of cubs in their first year was 0.85 (95% CI: 0.62-0.95). In the smaller, isolated population, independent female survival was 0.81 (95% CI: 0.64-0.93) and first-year cub survival was 0.33 (95% CI: 0.11-0.67). Reproductive rates did not differ between populations. The large differences in age-specific survival estimates resulted in a projected population increase in the larger population (λ = 1.09; 95% CI: 1.04-1.13) and population decrease in the smaller population (λ = 0.84; 95% CI: 0.72-0.95). Low female survival in the smaller population was the result of both continued human-caused mortality and an unusually high rate of natural mortality. Low cub survival may have been due to inbreeding and the loss of genetic diversity common in small populations, or to limited resources. In a systematic literature review, we compared our population trend estimates with those reported for other small populations (<300 individuals) of brown bears. Results suggest that once brown bear populations become small and isolated, populations rarely increase and, even with intensive management, recovery remains challenging.
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Affiliation(s)
- Michelle L. McLellan
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | | | - Rahel Sollmann
- Department of Wildlife, Fish, and Conservation BiologyUniversity of California DavisDavisCAUSA
| | - Heiko U. Wittmer
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
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Walton Z, Hagenlund M, Østbye K, Samelius G, Odden M, Norman A, Willebrand T, Spong G. Moving far, staying close: red fox dispersal patterns revealed by SNP genotyping. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01332-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
AbstractThe genetic structure of a population can provide important insights into animal movements at varying geographical scales. Individual and social behaviors, such as philopatry and dispersal, affect patterns of relatedness, age and sex structure, shaping the local genetic structure of populations. However, these fine scale patterns may not be detected within broader population genetic structure. Using SNP genotyping for pairwise relatedness estimates, we investigated the spatial and genetic structuring of 141 red foxes within south-central Sweden at two scales. First, we looked at broad scale population structuring among red foxes at the regional level. We then estimated pairwise relatedness values to evaluate the spatial and genetic structure of male, female and mixed sex pairs for patterns of philopatry and dispersal at a more localized scale. We found limited genetic differentiation at the regional scale. However, local investigations revealed patterns of female philopatry and male biased dispersal. There were significant differences in pairwise geographic distances between highly related same sex pairs with the average distance between related males, 37.8 km, being six times farther than that of related females, averaging 6.3 km. In summary, the low levels of genetic differentiation found in this study illustrates the mobility and dispersal ability of red foxes across scales. However, relatedness plays a strong role in the spatial organization of red foxes locally, ultimately contributing to male biased dispersal patterns.
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Multiscale landscape genetics of American marten at their southern range periphery. Heredity (Edinb) 2020; 124:550-561. [PMID: 31992842 PMCID: PMC7080830 DOI: 10.1038/s41437-020-0295-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 11/10/2019] [Accepted: 11/11/2019] [Indexed: 11/08/2022] Open
Abstract
American marten (Martes americana) are a conservation priority in many forested regions of North America. Populations are fragmented at the southern edge of their distribution due to suboptimal habitat conditions. Facilitating gene flow may improve population resilience through genetic and demographic rescue. We used a multiscale approach to estimate the relationship between genetic connectivity and landscape characteristics among individuals at three scales in the northeastern United States: regional, subregional, and local. We integrated multiple modeling techniques and identified top models based on consensus. Top models were used to parameterize resistance surfaces at each scale, and circuit theory was used to identify potential movement corridors. Regional gene flow was affected by forest cover, elevation, developed land cover, and slope. At subregional and local scales, the effects were site specific and included subsets of temperature, elevation, developed land cover, and slope. Developed land cover significantly affected gene flow at each scale. At finer scales, lack of variance in forest cover may have limited the ability to detect a relationship with gene flow. The effect of slope on gene flow was positive or negative, depending on the site examined. Occupancy probability was a relatively poor predictor, and we caution its use as a proxy for landscape resistance. Our results underscore the importance of replication and multiscale approaches in landscape genetics. Climate warming and landscape conversion may reduce the genetic connectivity of marten populations in the northeastern United States, and represent the primary challenges to marten conservation at the southern periphery of their range.
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