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Ning Y, Liu D, Gu J, Zhang Y, Roberts NJ, Guskov VY, Sun J, Liu D, Gong M, Qi J, He Z, Shi C, Jiang G. The genetic status and rescue measure for a geographically isolated population of Amur tigers. Sci Rep 2024; 14:8088. [PMID: 38582794 PMCID: PMC10998829 DOI: 10.1038/s41598-024-58746-9] [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: 08/18/2023] [Accepted: 04/02/2024] [Indexed: 04/08/2024] Open
Abstract
The Amur tiger is currently confronted with challenges of anthropogenic development, leading to its population becoming fragmented into two geographically isolated groups: smaller and larger ones. Small and isolated populations frequently face a greater extinction risk, yet the small tiger population's genetic status and survival potential have not been assessed. Here, a total of 210 samples of suspected Amur tiger feces were collected from this small population, and the genetic background and population survival potentials were assessed by using 14 microsatellite loci. Our results demonstrated that the mean number of alleles in all loci was 3.7 and expected heterozygosity was 0.6, indicating a comparatively lower level of population genetic diversity compared to previously reported studies on other subspecies. The genetic estimates of effective population size (Ne) and the Ne/N ratio were merely 7.6 and 0.152, respectively, representing lower values in comparison to the Amur tiger population in Sikhote-Alin (the larger group). However, multiple methods have indicated the possibility of genetic divergence within our isolated population under study. Meanwhile, the maximum kinship recorded was 0.441, and the mean inbreeding coefficient stood at 0.0868, both of which are higher than those observed in other endangered species, such as the African lion and the grey wolf. Additionally, we have identified a significant risk of future extinction if the lethal equivalents were to reach 6.26, which is higher than that of other large carnivores. Further, our simulation results indicated that an increase in the number of breeding females would enhance the prospects of this population. In summary, our findings provide a critical theoretical basis for further bailout strategies concerning Amur tigers.
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Affiliation(s)
- Yao Ning
- College of Life Science, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Dongqi Liu
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Jiayin Gu
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Yifei Zhang
- College of Life Science, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Nathan James Roberts
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Valentin Yu Guskov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of Russian Academy of Sciences (FSCEATB FEB RAS), Vladivostok, Russian Federation
| | - Jiale Sun
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Dan Liu
- Siberian Tiger Park, Harbin, 150028, Heilongjiang, China
| | - Ming Gong
- Siberian Tiger Park, Harbin, 150028, Heilongjiang, China
| | - Jinzhe Qi
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Zhijian He
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Chunmei Shi
- College of Mathematics and Computer Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Guangshun Jiang
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China.
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Khatun D, Tanaka T, Aranishi F. Population structure and demographic history for year cohort dynamics of landlocked ayu Plecoglossus altivelis altivelis in dam reservoir of Japan. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:10896-10910. [PMID: 38214853 DOI: 10.1007/s11356-023-31743-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 12/22/2023] [Indexed: 01/13/2024]
Abstract
Ayu Plecoglossus altivelis altivelis is a valuable osmeroid species for inland fishery in Japan. It is classified into two ecological forms of amphidromous migrating between rivers and sea and landlocked migrating between rivers and lakes or dam reservoirs. The number of dams and their reservoirs has remarkably increased in the twenty-first century under climate change, because of their respective roles in hydropower generation with negligible carbon emissions and in flood control. Dam reservoirs therefore become increasingly important as inland nursery grounds of ayu. In this study, we investigated the reproduction status of landlocked ayu migrating in the Haidzuka Dam reservoir and the Tabusa River in western Japan by molecular phylogenetic analysis based on population structure and demographic history for year cohort dynamics. A total of 849 individuals were collected monthly from October 2018 to September 2021 according to an annual life cycle of ayu. Nucleotide sequences of the partial mitochondrial DNA control region yielded 31 haplotypes, consisting of 4 shared haplotypes among the 2019, 2020 and 2021 cohorts and 27 unique haplotypes. The overall haplotype diversity and nucleotide diversity were calculated to be relatively low at 0.3503 ± 0.0206 and 0.0077 ± 0.0045, respectively, suggesting a founder event by dominant haplotypes. Star-shaped radiational haplotypes from dominant shared haplotypes on the median-joining network likely support a founder event. Although pairwise ФST values were determined to be very low among the year cohorts, only the 2019 cohort was found to have a significant difference from the 2020 and 2021 cohorts, for both of which Tajima's D values were also statistically significant. For the overall population, multimodal mismatch distribution and negative Tajima's D and Fu's Fs values in the neutrality test suggested population expansion or population subdivision. The native riverine population in the Tabusa River suffered habitat fragmentation and population bottleneck from dam construction, and therefore severe founder effect remained behind the artificially landlocked population with a low level of genetic diversity in the Haidzuka Dam reservoir.
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Affiliation(s)
- Dalia Khatun
- The United Graduate School of Agricultural Sciences, Tottori University, Tottori, 6808553, Japan
| | - Tomomi Tanaka
- Fisheries Ecosystem Project Center, Shimane University, Matsue, 6908504, Japan
| | - Futoshi Aranishi
- The United Graduate School of Agricultural Sciences, Tottori University, Tottori, 6808553, Japan.
- Fisheries Ecosystem Project Center, Shimane University, Matsue, 6908504, Japan.
- Institute of Agricultural and Life Sciences, Shimane University, Matsue, 6908504, Japan.
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Klingler KB, Nichols LB, Hekkala ER, Stewart JAE, Peacock MM. Life on the edge-a changing genetic landscape within an iconic American pika metapopulation over the last half century. PeerJ 2023; 11:e15962. [PMID: 37790628 PMCID: PMC10542391 DOI: 10.7717/peerj.15962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 08/03/2023] [Indexed: 10/05/2023] Open
Abstract
Declines and extirpations of American pika (Ochotona princeps) populations at historically occupied sites started being documented in the literature during the early 2000s. Commensurate with global climate change, many of these losses at peripheral and lower elevation sites have been associated with changes in ambient air temperature and precipitation regimes. Here, we report on a decline in available genetic resources for an iconic American pika metapopulation, located at the southwestern edge of the species distribution in the Bodie Hills of eastern California, USA. Composed of highly fragmented habitat created by hard rock mining, the ore dumps at this site were likely colonized by pikas around the end of the 19th century from nearby natural talus outcrops. Genetic data extracted from both contemporary samples and archived natural history collections allowed us to track population and patch-level genetic diversity for Bodie pikas across three distinct sampling points during the last half- century (1948-1949, 1988-1991, 2013-2015). Reductions in within-population allelic diversity and expected heterozygosity were observed across the full time period. More extensive sampling of extant patches during the 1988-1991 and 2013-2015 periods revealed an increase in population structure and a reduction in effective population size. Furthermore, census records from the last 51 years as well as archived museum samples collected in 1947 from a nearby pika population in the Wassuk range (Nevada, USA) provide further support of the increasing isolation and genetic coalescence occurring in this region. This study highlights the importance of museum samples and long-term monitoring in contextualizing our understanding of population viability.
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Affiliation(s)
- Kelly B. Klingler
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, Massachusetts, United States
| | - Lyle B. Nichols
- Department of Life Sciences, Santa Monica College, Santa Monica, California, United States
| | - Evon R. Hekkala
- Department of Biological Sciences, Fordham University, Bronx, New York, United States
| | - Joseph A. E. Stewart
- Department of Plant Sciences, University of California, Davis, Davis, California, United States
| | - Mary M. Peacock
- Department of Biology, University of Nevada, Reno, Reno, Nevada, United States
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4
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Stoner DC, McDonald Z, Coon CAC. Stepping stones to extirpation: Puma patch occupancy thresholds in an urban-wildland matrix. Ecol Evol 2023; 13:e10381. [PMID: 37546565 PMCID: PMC10401668 DOI: 10.1002/ece3.10381] [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: 11/29/2022] [Revised: 07/04/2023] [Accepted: 07/19/2023] [Indexed: 08/08/2023] Open
Abstract
Habitat loss and fragmentation are the leading causes of species range contraction and extirpation, worldwide. Factors that predict sensitivity to fragmentation include high trophic level, large body size, and extensive spatial requirements. Pumas (Puma concolor) exemplify these qualities, making them particularly susceptible to fragmentation and subsequent reductions in demographic connectivity. The chaparral-dominated ecosystems surrounding the greater San Francisco Bay Area encompass over 10,000 km2 of suitable puma habitat, but inland waterways, croplands, urban land uses, and extensive transportation infrastructure have resulted in widespread habitat fragmentation. Pumas in this region now exist as a metapopulation marked by loss of genetic diversity, collisions with vehicles, and extensive human-puma conflict. Given these trends, we conducted a photo survey from 2017 to 2021 across 19 patches of predicted habitat and compiled a dataset of >6584 puma images. We used a logistic regression analytical framework to evaluate the hypothesis that puma patch occupancy would exhibit a threshold response explained by patch size, isolation, and habitat quality. Contrary to predictions, only variables related to patch size demonstrated any power to explain occupancy. On average, occupied patches were 18× larger than those where they were not detected (825 ± 1238 vs. 46 ± 101 km2). Although we observed pumas in patches as small as 1 km2, logistic regression models indicated a threshold occupancy probability between 300 and 400 km2, which is remarkably close to the mean male puma home range size in coastal California (~381 km2). Puma populations dependent on habitats below this value may be susceptible to inbreeding depression and human-wildlife conflict, and therefore vulnerable to extirpation. For species conservation, we suggest conflicts might be ameliorated by identifying the largest, isolated patches for public education campaigns with respect to management of domestic animals, and remaining connective parcels be identified, mapped, and prioritized for targeted mitigation.
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Affiliation(s)
- David C. Stoner
- Department of Wildland ResourcesUtah State UniversityLoganUtahUSA
- Felidae Conservation FundMill ValleyCaliforniaUSA
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Feline Leukemia Virus Frequently Spills Over from Domestic Cats to North American Pumas. J Virol 2022; 96:e0120122. [PMID: 36374109 PMCID: PMC9749473 DOI: 10.1128/jvi.01201-22] [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: 11/16/2022] Open
Abstract
Feline leukemia virus (FeLV) is a gammaretrovirus with horizontally transmitted and endogenous forms. Domestic cats are the primary reservoir species, but FeLV outbreaks in endangered Florida panthers and Iberian lynxes have resulted in mortalities. To assess prevalence and interspecific/intraspecific transmission, we conducted an extensive survey and phylogenetic analysis of FeLV infection in free-ranging pumas (n = 641) and bobcats (n = 212) and shelter domestic cats (n = 304). Samples were collected from coincident habitats across the United States between 1985 and 2018. FeLV infection was detected in 3.12% of the puma samples, 0.47% of the bobcat samples, and 6.25% of the domestic cat samples analyzed. Puma prevalence varied by location, with Florida having the highest rate of infection. FeLV env sequences revealed variation among isolates, and we identified two distinct clades. Both progressive and regressive infections were identified in cats and pumas. Based on the time and location of sampling and phylogenetic analysis, we inferred 3 spillover events between domestic cats and pumas; 3 puma-to-puma transmissions in Florida were inferred. An additional 14 infections in pumas likely represented spillover events following contact with reservoir host domestic cat populations. Our data provide evidence that FeLV transmission from domestic cats to pumas occurs widely across the United States, and puma-to-puma transmission may occur in genetically and geographically constrained populations. IMPORTANCE Feline leukemia virus (FeLV) is a retrovirus that primarily affects domestic cats. Close interactions with domestic cats, including predation, can lead to the interspecific transmission of the virus to pumas, bobcats, or other feline species. Some infected individuals develop progressive infections, which are associated with clinical signs of disease and can result in mortality. Therefore, outbreaks of FeLV in wildlife, including the North American puma and the endangered Florida panther, are of high conservation concern. This work provides a greater understanding of the dynamics of the transmission of FeLV between domestic cats and wild felids and presents evidence of multiple spillover events and infections in all sampled populations. These findings highlight the concern for pathogen spillover from domestic animals to wildlife but also identify an opportunity to understand viral evolution following cross-species transmissions more broadly.
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6
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Pratzer M, Nill L, Kuemmerle T, Zurell D, Fandos G. Large carnivore range expansion in Iberia in relation to different scenarios of permeability of human‐dominated landscapes. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Marie Pratzer
- Geography Department Humboldt‐Universität zu Berlin Berlin Germany
| | - Leon Nill
- Geography Department Humboldt‐Universität zu Berlin Berlin Germany
| | - Tobias Kuemmerle
- Geography Department Humboldt‐Universität zu Berlin Berlin Germany
| | - Damaris Zurell
- Geography Department Humboldt‐Universität zu Berlin Berlin Germany
- Institute for Biochemistry and Biology University of Potsdam Potsdam Germany
| | - Guillermo Fandos
- Geography Department Humboldt‐Universität zu Berlin Berlin Germany
- Institute for Biochemistry and Biology University of Potsdam Potsdam Germany
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Wang D, Accatino F, Smith JLD, Wang T. Contributions of distemper control and habitat expansion to the Amur leopard viability. Commun Biol 2022; 5:1153. [PMID: 36310335 PMCID: PMC9618572 DOI: 10.1038/s42003-022-04127-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022] Open
Abstract
The Amur leopard (Panthera pardus orientalis) is a critically endangered top predator that struggles on the brink of extinction due to threats such as canine distemper virus (CDV), habitat loss, and inbreeding depression. Here we develop a viability analysis metamodel that combines a traditional individual-based demographic model with an epidemiological model to assess the benefits of alternative population management actions in response to multiple distinct threats. Our results showed an extinction risk of 10.3%-99.9% if no management actions were taken over 100 years under different levels of inbreeding depression. Reducing the risk of CDV infection in Amur leopards through the low-coverage vaccination of leopards and the management of sympatric domestic dogs could effectively improve the survival probability of the leopard population, and with habitat expansion added to these management measures, the population expanded further. Our findings highlight that protecting the Amur leopard necessitates a multifaceted synergistic effort, and controlling multiple threats together may significantly escalate overall viability of a species, especially for small-isolated threatened population. More broadly, our modeling framework could offer critical perspectives and scientific support for conservation planning, as well as specific adaptive management actions for endangered species around the world. In the absence of management strategies, canine distemper virus threatens the future existence of the endangered Amur leopard.
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8
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Vandergast AG, Kus BE, Smith JG, Mitelberg A. Recent declines in genetic diversity with limited dispersal among coastal cactus wren populations in San Diego County, California. CONSERVATION SCIENCE AND PRACTICE 2022. [DOI: 10.1111/csp2.12780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Amy G. Vandergast
- Western Ecological Research Center U.S. Geological Survey San Diego California USA
| | - Barbara E. Kus
- Western Ecological Research Center U.S. Geological Survey San Diego California USA
| | - Julia G. Smith
- Western Ecological Research Center U.S. Geological Survey San Diego California USA
| | - Anna Mitelberg
- Western Ecological Research Center U.S. Geological Survey San Diego California USA
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9
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The effect of urbanization on spatiotemporal interactions between gray foxes and coyotes. Ecosphere 2022. [DOI: 10.1002/ecs2.3993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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10
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LaBarge LR, Evans MJ, Miller JRB, Cannataro G, Hunt C, Elbroch LM. Pumas
Puma concolor
as ecological brokers: a review of their biotic relationships. Mamm Rev 2022. [DOI: 10.1111/mam.12281] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Laura R. LaBarge
- Program in Evolution, Ecology and Behavior, Department of Environment and Sustainability, The State University of New York University at Buffalo Amherst NY14260USA
- Center for Conservation Innovation Defenders of Wildlife Washington DC20036USA
- Max Planck Institute of Animal Behavior Bücklestraße 5 Konstanz DE78467Germany
| | - Michael J. Evans
- Center for Conservation Innovation Defenders of Wildlife Washington DC20036USA
- Department of Environmental Science and Policy George Mason University 4400 University Dr Fairfax VA22030USA
| | - Jennifer R. B. Miller
- Center for Conservation Innovation Defenders of Wildlife Washington DC20036USA
- Department of Environmental Science and Policy George Mason University 4400 University Dr Fairfax VA22030USA
| | - Gillian Cannataro
- Center for Conservation Innovation Defenders of Wildlife Washington DC20036USA
- Conservation, Management and Welfare Sciences Association of Zoos and Aquariums 8403 Colesville Rd., Suite 710 Silver Spring MD20910‐3314USA
| | - Christian Hunt
- Field Conservation Defenders of Wildlife Washington DC20036USA
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11
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Huffmeyer AA, Sikich JA, Vickers TW, Riley SPD, Wayne RK. First reproductive signs of inbreeding depression in Southern California male mountain lions (Puma concolor). Theriogenology 2022; 177:157-164. [PMID: 34710647 DOI: 10.1016/j.theriogenology.2021.10.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/14/2021] [Accepted: 10/16/2021] [Indexed: 11/18/2022]
Abstract
Long-term studies of mountain lions (Puma concolor) in Southern California have documented persistent small population sizes and the lowest genetic variation of any mountain lion population, except for the Federally endangered mountain lion subspecies, the Florida panther (Puma concolor coryi). There is overwhelming molecular evidence supporting inbreeding and low genetic diversity in these Southern California populations but there is a lack of phenotypical evidence of inbreeding depression. The primary goal of this study was to assess male mountain lions, in Southern California, for teratospermia (>60% abnormal sperm production), one of the first signs of inbreeding depression in mountain lions that are associated with decreased reproduction and population decline. From December 2019 to December 2020, we surveyed mountain lions during live captures, after mortality events, and in images collected from camera traps in the following populations: Santa Monica Mountains, Santa Susana Mountains, Santa Ana Mountains, and the Eastern Peninsular Range. Mountain lions were sampled for known physical abnormalities associated with inbreeding depression such as teratospermia, cryptorchidism, and distal tail kinks. For teratospermia, we extracted testes from five males post-mortem to assess sperm morphology. Epididymal sperm evaluations revealed all males were teratospermic. Across all samples, on average, 93% of observed spermatozoa were abnormal. We physically examined 32 mountain lions (males and females) for distal tail kinks, and we observed one individual affected. We examined 15 male mountain lions for cryptorchidism, and we observed one unilaterally cryptorchid male and one male with testes that differed significantly in size, likely reflecting asynchronous migration of the testes during puberty. Further, we identified three other animals in camera-trap images that had distal tail kinks, for a total of four. In conclusion, from December 2019 to December 2020, we identified nine individuals exhibiting physical signs of inbreeding depression. These reproductive and physical signs of inbreeding depression in Southern California mountain lions increase the urgency of conservation efforts in the region.
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Affiliation(s)
- Audra A Huffmeyer
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA.
| | - Jeff A Sikich
- Santa Monica Mountains National Recreation Area, National Park Service, 401 West Hillcrest Drive, Thousand Oaks, CA, 91360, USA
| | - T Winston Vickers
- Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Seth P D Riley
- Santa Monica Mountains National Recreation Area, National Park Service, 401 West Hillcrest Drive, Thousand Oaks, CA, 91360, USA; Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
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12
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Gustafson KD, Gagne RB, Buchalski MR, Vickers TW, Riley SP, Sikich JA, Rudd JL, Dellinger JA, LaCava ME, Ernest HB. Multi‐population puma connectivity could restore genomic diversity to at‐risk coastal populations in California. Evol Appl 2021; 15:286-299. [PMID: 35233248 PMCID: PMC8867711 DOI: 10.1111/eva.13341] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 12/25/2021] [Indexed: 12/01/2022] Open
Abstract
Urbanization is decreasing wildlife habitat and connectivity worldwide, including for apex predators, such as the puma (Puma concolor). Puma populations along California's central and southern coastal habitats have experienced rapid fragmentation from development, leading to calls for demographic and genetic management. To address urgent conservation genomic concerns, we used double‐digest restriction‐site associated DNA (ddRAD) sequencing to analyze 16,285 genome‐wide single‐nucleotide polymorphisms (SNPs) from 401 pumas sampled broadly across the state. Our analyses indicated support for 4–10 geographically nested, broad‐ to fine‐scale genetic clusters. At the broadest scale, the four genetic clusters had high genetic diversity and exhibited low linkage disequilibrium, indicating that pumas have retained genomic diversity statewide. However, multiple lines of evidence indicated substructure, including 10 finer‐scale genetic clusters, some of which exhibited fixed alleles and linkage disequilibrium. Fragmented populations along the Southern Coast and Central Coast had particularly low genetic diversity and strong linkage disequilibrium, indicating genetic drift and close inbreeding. Our results demonstrate that genetically at risk populations are typically nested within a broader‐scale group of interconnected populations that collectively retain high genetic diversity and heterogenous fixations. Thus, extant variation at the broader scale has potential to restore diversity to local populations if management actions can enhance vital gene flow and recombine locally sequestered genetic diversity. These state‐ and genome‐wide results are critically important for science‐based conservation and management practices. Our nested population genomic analysis highlights the information that can be gained from population genomic studies aiming to provide guidance for the conservation of fragmented populations.
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Affiliation(s)
- Kyle D. Gustafson
- Arkansas State University Department of Biological Sciences Jonesboro 72401
| | - Roderick B. Gagne
- University of Pennsylvania School of Veterinary Medicine Department of Pathobiology Kennett Square Wildlife Futures Program PA USA
| | | | - T. Winston Vickers
- University of California ‐ Davis School of Veterinary Medicine Karen C. Drayer Wildlife Health Center Davis 95616
| | - Seth P.D. Riley
- National Park Service Santa Monica Mountains National Recreation Area 401 W. Hillcrest Dr Thousand Oaks 91360
| | - Jeff A. Sikich
- National Park Service Santa Monica Mountains National Recreation Area 401 W. Hillcrest Dr Thousand Oaks 91360
| | - Jaime L. Rudd
- California Department of Fish and Wildlife Rancho Cordova 95670
| | | | - Melanie E.F. LaCava
- Wildlife Genomics and Disease Ecology Laboratory Department of Veterinary Sciences University of Wyoming Laramie 82071
| | - Holly B. Ernest
- Wildlife Genomics and Disease Ecology Laboratory Department of Veterinary Sciences University of Wyoming Laramie 82071
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13
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Kertson BN, Keren IN. Cougar use of residential areas and interactions with people in periods of population stability and growth. J Mammal 2021. [DOI: 10.1093/jmammal/gyab145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
The presence of large carnivores close to people poses unique challenges for wildlife managers working to maintain fully functioning ecosystems while simultaneously minimizing potential risks to public safety and private property. In western North America, cougar (Puma concolor) use of residential areas is relatively commonplace and has contributed to undesirable interactions with people. A common assumption is that cougar population growth translates into greater proximity to people and more interactions, but to our knowledge, direct evaluation of this assumption has not occurred. We used GPS telemetry locations and confirmed cougar–human interaction reports to construct single-sex Leslie matrices, utilization distributions, and a two-stage hurdle model within a Bayesian framework to investigate the effects of population trajectory on cougar use of residential areas and interactions with people in the wildland–urban interface of western Washington. We collected data during two time periods with different expected population growth rates, anticipating greater cougar use of residential areas and interaction levels during the period of increased growth. Contrary to our initial expectations, we did not detect meaningful differences in cougar presence in residential areas or number of interactions with humans between study periods. Instead, we documented consistent space use patterns by all demographic classes that seemed to be governed by different life-history strategies. Interactions with humans were largely a function of individual cougar behaviors during both study periods. The consistent presence of abundant, well-connected wildlands coupled with cougar dispersal likely mitigated the potential effects of population trajectory as the increased expected growth rate in Period 2 manifested primarily as subadult emigration via wildlands. We found that a source population does not necessarily translate into greater proximity to people and more interactions. Cougar management in wildland–urban environments would benefit from the application of strategies that address the complex interplay of biological and anthropogenic factors that contribute to cougar presence in residential areas and their likelihood of interacting with people.
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Affiliation(s)
- Brian N Kertson
- Washington Department of Fish and Wildlife, 7007 Curtis DR SE, Snoqualmie, WA, USA
| | - Ilai N Keren
- Washington Department of Fish and Wildlife, 1111 Washington Street SE, Olympia, WA, USA
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RILEY SETHPD, SIKICH JEFFA, BENSON JOHNF. Big Cats in the Big City: Spatial Ecology of Mountain Lions in Greater Los Angeles. J Wildl Manage 2021. [DOI: 10.1002/jwmg.22127] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- SETH P. D. RILEY
- Santa Monica Mountains National Recreation Area National Park Service 401 W. Hillcrest Drive Thousand Oaks CA 91360 USA
| | - JEFF A. SIKICH
- Santa Monica Mountains National Recreation Area National Park Service 401 W. Hillcrest Drive Thousand Oaks CA 91360 USA
| | - JOHN F. BENSON
- School of Natural Resources University of Nebraska Lincoln, 3310 Holdrege St—Hardin Hall Lincoln NE 68583 USA
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15
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Shilling F, Nguyen T, Saleh M, Kyaw MK, Tapia K, Trujillo G, Bejarano M, Waetjen D, Peterson J, Kalisz G, Sejour R, Croston S, Ham E. A Reprieve from US wildlife mortality on roads during the COVID-19 pandemic. BIOLOGICAL CONSERVATION 2021; 256:109013. [PMID: 34580543 PMCID: PMC8457620 DOI: 10.1016/j.biocon.2021.109013] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/24/2021] [Accepted: 02/09/2021] [Indexed: 05/02/2023]
Abstract
High traffic volume is one of the main contributors to wildlife-vehicle collision (WVC) and wildlife mortality on roads. Government shelter-in-place (SIP) orders have been used to help mitigate the spread of COVID-19, resulting in unprecedented reductions in global traffic volumes. Using traffic and collision data from four US states (California, Idaho, Maine, and Washington), we investigated changes in total WVC, following the state and local SIP orders. From mid-March to mid-April 2020, these orders have resulted in up to 71%, 63%, 73%, and 72% reduction in driving, as measured by vehicle miles traveled (VMT), in CA, ID, ME, and WA respectively. The daily WVC rates from the 4 weeks prior to SIP orders going into effect, to the 4 weeks after, declined 34%, with 21, 36, 44, and 33% declines for CA, ID, ME, and WA, respectively. For mountain lions (Puma concolor) in CA, there was a 58% decline in mortality during the traffic reduction. The changes in WVC from 1 month pre-SIP orders to 1 month post-order only occurred in 2020 and not 2015, 2016, 2017, 2018, or 2019, suggesting that the reductions were associated with the reductions in traffic. The measured declines in WVC reversed in ME and WA during May, June and July 2020, paralleling reversals in traffic volumes. A 34% reduction in WVC would potentially equate to 10s of millions fewer vertebrates killed on US roadways during one month of traffic reduction, representing an unintentional conservation action unprecedented in modern times.
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Affiliation(s)
- Fraser Shilling
- Department of Environmental Science and Policy, University of California, Davis, CA 95616, USA
| | - Tricia Nguyen
- Department of Environmental Science and Policy, University of California, Davis, CA 95616, USA
| | - Malak Saleh
- Department of Environmental Science and Policy, University of California, Davis, CA 95616, USA
| | - Min Khant Kyaw
- Department of Environmental Science and Policy, University of California, Davis, CA 95616, USA
| | - Karla Tapia
- Department of Environmental Science and Policy, University of California, Davis, CA 95616, USA
| | - Gabrielle Trujillo
- Department of Environmental Science and Policy, University of California, Davis, CA 95616, USA
| | - Mireya Bejarano
- Department of Environmental Science and Policy, University of California, Davis, CA 95616, USA
| | - Dave Waetjen
- Department of Environmental Science and Policy, University of California, Davis, CA 95616, USA
| | - Jon Peterson
- Washington Department of Transportation, Olympia, WA 98504, USA
| | - Glen Kalisz
- Washington Department of Transportation, Olympia, WA 98504, USA
| | - Raquel Sejour
- Washington Department of Transportation, Olympia, WA 98504, USA
| | - Sarah Croston
- Washington Department of Transportation, Olympia, WA 98504, USA
| | - Eric Ham
- Maine Department of Transportation, Augusta, ME 04333, USA
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Non-Invasive Molecular Survey of Sarcoptic Mange in Wildlife: Diagnostic Performance in Wolf Faecal Samples Evaluated by Multi-Event Capture-Recapture Models. Pathogens 2021; 10:pathogens10020243. [PMID: 33672583 PMCID: PMC7924033 DOI: 10.3390/pathogens10020243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/12/2021] [Accepted: 02/17/2021] [Indexed: 11/16/2022] Open
Abstract
Sarcoptic mange is globally enzootic, and non-invasive methods with high diagnostic specificity for its surveillance in wildlife are lacking. We describe the molecular detection of Sarcoptes scabiei in non-invasively collected faecal samples, targeting the 16S rDNA gene. We applied this method to 843 Iberian wolf Canis lupus signatus faecal samples collected in north-western Portugal (2006-2018). We further integrated this with serological data (61 samples from wolf and 20 from red fox Vulpes vulpes, 1997-2019) in multi-event capture-recapture models. The mean predicted prevalence by the molecular analysis of wolf faecal samples from 2006-2018 was 7.2% (CI95 5.0-9.4%; range: 2.6-11.7%), highest in 2009. The mean predicted seroprevalence in wolves was 24.5% (CI95 18.5-30.6%; range: 13.0-55.0%), peaking in 2006-2009. Multi-event capture-recapture models estimated 100% diagnostic specificity and moderate diagnostic sensitivity (30.0%, CI95 14.0-53.0%) for the molecular method. Mange-infected individually identified wolves showed a tendency for higher mortality versus uninfected wolves (ΔMortality 0.150, CI95 -0.165-0.458). Long-term serology data highlights the endemicity of sarcoptic mange in wild canids but uncovers multi-year epidemics. This study developed and evaluated a novel method for surveying sarcoptic mange in wildlife populations by the molecular detection of S. scabiei in faecal samples, which stands out for its high specificity and non-invasive character.
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17
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Abstract
Ecological corridors are one of the best, and possibly only viable, management tools to maintain biodiversity at large scales and to allow species, and ecological processes, to track climate change. This document has been assembled as a summary of the best available information about managing these systems. Our aim with this paper is to provide managers with a convenient guidance document and tool to assist in applying scientific management principles to management of corridors. We do not cover issues related to corridor design or political buy in, but focus on how a corridor should be managed once it has been established. The first part of our paper outlines the history and value of ecological corridors. We next describe our methodologies for developing this guidance document. We then summarize the information about the impacts of linear features on corridors and strategies for dealing with them—specifically, we focus on the effects of roads, canals, security fences, and transmission lines. Following the description of effects, we provide a summary of the best practices for managing the impacts of linear barriers. Globally, many corridors are established in the flood plains of stream and rivers and occur in riparian areas associated with surface waters. Therefore, we next provide guidance on how to manage corridors that occur in riparian areas. We then segue into corridors and the urban/suburban environment, and summarize strategies for dealing with urban development within corridors. The final major anthropic land use that may affect corridor management is cultivation and grazing agriculture. We end this review by identifying gaps in knowledge pertaining to how best to manage corridors.
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18
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Vardi R, Berger-Tal O, Roll U. iNaturalist insights illuminate COVID-19 effects on large mammals in urban centers. BIOLOGICAL CONSERVATION 2021; 254:108953. [PMID: 33424027 PMCID: PMC7784545 DOI: 10.1016/j.biocon.2021.108953] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/13/2020] [Accepted: 12/22/2020] [Indexed: 05/22/2023]
Abstract
Restricted human activity during the COVID-19 pandemic raised global attention to the presence of wildlife in cities. Here, we analyzed iNaturalist observations of prominent wildlife species around North-American urban centers, before and during the COVID-19 pandemic outbreak. We suggest that the popular notion of 'wildlife reclaiming cities' may have been exaggerated. We found that while pumas ventured deeper into urban habitats during the COVID-19 pandemic, bears, bobcats, coyotes, and moose did not. Species differential behavioral responses may highlight their evolutionary history cohabiting human habitats. Nevertheless, our results highlight the importance of urban nature for people during the pandemic. Our insights could help manage urban wildlife, better plan greenspaces, and promote positive nature engagements.
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Affiliation(s)
- Reut Vardi
- The Albert Katz International School for Desert Studies, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion 8499000, Israel
| | - Oded Berger-Tal
- Mitrani Department of Desert Ecology, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion 8499000, Israel
| | - Uri Roll
- Mitrani Department of Desert Ecology, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion 8499000, Israel
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19
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Nabutanyi P, Wittmann MJ. Models for Eco-Evolutionary Extinction Vortices under Balancing Selection. Am Nat 2021; 197:336-350. [PMID: 33625964 DOI: 10.1086/712805] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractThe smaller a population is, the faster it loses genetic diversity as a result of genetic drift. Loss of genetic diversity can reduce population growth rate, making populations even smaller and more vulnerable to loss of genetic diversity. Ultimately, the population can be driven to extinction by this "eco-evolutionary extinction vortex." While there are already quantitative models for extinction vortices resulting from inbreeding depression and mutation accumulation, to date extinction vortices resulting from loss of genetic diversity at loci under various forms of balancing selection have been mainly described verbally. To understand better when such extinction vortices arise and to develop methods for detecting them, we propose quantitative eco-evolutionary models, both stochastic individual-based simulations and deterministic approximations, linking loss of genetic diversity and population decline. Using mathematical analysis and simulations, we identify parameter combinations that exhibit strong interactions between population size and genetic diversity and match our definition of an eco-evolutionary vortex (i.e., per capita population decline rates and per-locus fixation rates increase with decreasing population size and number of polymorphic loci). We further highlight cues that may be exhibited by such populations but find that classical early-warning signals are of limited use in detecting populations undergoing an eco-evolutionary extinction vortex.
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20
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Dellinger JA, Gustafson KD, Gammons DJ, Ernest HB, Torres SG. Minimum habitat thresholds required for conserving mountain lion genetic diversity. Ecol Evol 2020; 10:10687-10696. [PMID: 33072289 PMCID: PMC7548186 DOI: 10.1002/ece3.6723] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 07/31/2020] [Accepted: 08/05/2020] [Indexed: 11/24/2022] Open
Abstract
Jointly considering the ecology (e.g., habitat use) and genetics (e.g., population genetic structure and diversity) of a species can increase understanding of current conservation status and inform future management practices. Previous analyses indicate that mountain lion (Puma concolor) populations in California are genetically structured and exhibit extreme variation in population genetic diversity. Although human development may have fragmented gene flow, we hypothesized the quantity and quality of remaining habitat available would affect the genetic viability of each population. Our results indicate that area of suitable habitat, determined via a resource selection function derived using 843,500 location fixes from 263 radio‐collared mountain lions, is strongly and positively associated with population genetic diversity and viability metrics, particularly with effective population size. Our results suggested that contiguous habitat of ≥10,000 km2 may be sufficient to alleviate the negative effects of genetic drift and inbreeding, allowing mountain lion populations to maintain suitable effective population sizes. Areas occupied by five of the nine geographic–genetic mountain lion populations in California fell below this habitat threshold, and two (Santa Monica Area and Santa Ana) of those five populations lack connectivity to nearby populations. Enhancing ecological conditions by protection of greater areas of suitable habitat and facilitating positive evolutionary processes by increasing connectivity (e.g., road‐crossing structures) might promote persistence of small or isolated populations. The conservation status of suitable habitat also appeared to influence genetic diversity of populations. Thus, our results demonstrate that both the area and status (i.e., protected or unprotected) of suitable habitat influence the genetic viability of mountain lion populations.
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Affiliation(s)
| | - Kyle D Gustafson
- Department of Biological Sciences Arkansas State University Jonesboro Arkansas USA.,Wildlife Genomics and Disease Ecology Laboratory University of Wyoming Laramie Wyoming USA
| | - Daniel J Gammons
- California Department of Fish and Wildlife Sacramento California USA
| | - Holly B Ernest
- Wildlife Genomics and Disease Ecology Laboratory University of Wyoming Laramie Wyoming USA
| | - Steven G Torres
- California Department of Fish and Wildlife Sacramento California USA
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21
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Genetic diversity and structure of the round-tailed paradise fish (Macropodus ocellatus): Implications for population management. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2019.e00876] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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22
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Bleich VC. Mountain lions, minimum viable populations, and intact ecosystems: a cautionary note. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2020; 30:e01990. [PMID: 31400180 DOI: 10.1002/eap.1990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 07/16/2019] [Indexed: 06/10/2023]
Affiliation(s)
- Vernon C Bleich
- Department of Natural Resources and Environmental Science, University of Nevada Reno, 1664 N. Virginia Street, Mail Stop 186, Reno, Nevada, 89557, USA
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23
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Benson JF, Mahoney PJ, Vickers TW, Sikich JA, Beier P, Riley SPD, Ernest HB, Boyce WM. Conserving ecological roles of top predators in isolated mountains. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2020; 30:e02029. [PMID: 31675131 DOI: 10.1002/eap.2029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 09/26/2019] [Indexed: 06/10/2023]
Affiliation(s)
- John F Benson
- School of Natural Resources, University of Nebraska, Lincoln, Nebraska, 68583, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, California, 90095, USA
| | - Peter J Mahoney
- School of Natural Resources, University of Nebraska, Lincoln, Nebraska, 68583, USA
| | - T Winston Vickers
- Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, California, 95616, USA
| | - Jeff A Sikich
- National Park Service, Santa Monica Mountains National Recreation Area, Thousand Oaks, California, 91360, USA
| | - Paul Beier
- School of Forestry, Northern Arizona University, Flagstaff, Arizona, 86011, USA
| | - Seth P D Riley
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, California, 90095, USA
- National Park Service, Santa Monica Mountains National Recreation Area, Thousand Oaks, California, 91360, USA
| | - Holly B Ernest
- Department of Veterinary Sciences, University of Wyoming, Laramie, Wyoming, 82070, USA
| | - Walter M Boyce
- Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, California, 95616, USA
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