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Caruso G, Alaimo Di Loro P, Mingione M, Tardella L, Pace DS, Jona Lasinio G. Finite mixtures in capture-recapture surveys for modeling residency patterns in marine wildlife populations. Biom J 2024; 66:e2200350. [PMID: 38285406 DOI: 10.1002/bimj.202200350] [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: 12/14/2022] [Revised: 09/13/2023] [Accepted: 09/25/2023] [Indexed: 01/30/2024]
Abstract
This work aims to show how prior knowledge about the structure of a heterogeneous animal population can be leveraged to improve the abundance estimation from capture-recapture survey data. We combine the Open Jolly-Seber model with finite mixtures and propose a parsimonious specification tailored to the residency patterns of the common bottlenose dolphin. We employ a Bayesian framework for our inference, discussing the appropriate choice of priors to mitigate label-switching and nonidentifiability issues, commonly associated with finite mixture models. We conduct a series of simulation experiments to illustrate the competitive advantage of our proposal over less specific alternatives. The proposed approach is applied to data collected on the common bottlenose dolphin population inhabiting the Tiber River estuary (Mediterranean Sea). Our results provide novel insights into this population's size and structure, shedding light on some of the ecological processes governing its dynamics.
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Affiliation(s)
- Gianmarco Caruso
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
- Department of Statistical Sciences, Sapienza University of Rome, Rome, Italy
| | | | - Marco Mingione
- Department of Political Sciences, University of Roma Tre, Rome, Italy
| | - Luca Tardella
- Department of Statistical Sciences, Sapienza University of Rome, Rome, Italy
| | - Daniela Silvia Pace
- Department of of Environmental Biology, Sapienza University of Rome, Rome, Italy
- Institute for the Study of Anthropogenic Impacts and Sustainability in the Marine Environment, CNR, Trapani, Italy
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2
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Theng M, Milleret C, Bracis C, Cassey P, Delean S. Confronting spatial capture-recapture models with realistic animal movement simulations. Ecology 2022; 103:e3676. [PMID: 35253209 DOI: 10.1002/ecy.3676] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/26/2021] [Accepted: 09/14/2021] [Indexed: 12/13/2022]
Abstract
Spatial capture-recapture (SCR) models have emerged as a robust method to estimate the population density of mobile animals. However, model evaluation has generally been based on data simulated from simplified representations of animal space use. Here, we generated data from animal movement simulated from a mechanistic individual-based model, in which movement emerges from the individual's response to a changing environment (i.e., from the bottom-up), driven by key ecological processes (e.g., resource memory and territoriality). We drew individual detection data from simulated movement trajectories and fitted detection data sets to a basic, resource selection and transience SCR model, as well as their variants accounting for resource-driven heterogeneity in density and detectability. Across all SCR models, abundance estimates were robust to multiple, but low-degree violations of the specified movement processes (e.g., resource selection). SCR models also successfully captured the positive effect of resource quality on density. However, covariate models failed to capture the finer scale effect of resource quality on detectability and space use, which may be a consequence of the low temporal resolution of SCR data sets and/or model misspecification. We show that home-range size is challenging to infer from the scale parameter alone, compounded by reliance on conventional measures of "true" home-range size that are highly sensitive to sampling regime. Additionally, we found the transience model challenging to fit, probably due to data sparsity and violation of the assumption of normally distributed inter-occasion movement of activity centers, suggesting that further development of the model is required for general applicability. Our results showed that further integration of complex movement into SCR models may not be necessary for population estimates of abundance when the level of individual heterogeneity induced by the underlying movement process is low, but appears warranted in terms of accurately revealing finer scale patterns of ecological and movement processes. Further investigation into whether this holds true in populations with other types of realistic movement characteristics is merited. Our study provides a framework to generate realistic SCR data sets to develop and evaluate more complex movement processes in SCR models.
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Affiliation(s)
- Meryl Theng
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Cyril Milleret
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway
| | - Chloe Bracis
- TIMC / MAGE, Université Grenoble Alpes, Grenoble, France
| | - Phillip Cassey
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Steven Delean
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
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3
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De R, Nigam P, Williams AC, Goyal SP. Beyond consensus genotyping: a case study on the Asian elephant Elephas maximus. CONSERV GENET RESOUR 2022. [DOI: 10.1007/s12686-022-01287-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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4
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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 Medicine Hokkaido University Sapporo Japan
| | - Mina Jimbo
- Laboratory of Wildlife Biology and Medicine, Faculty of Veterinary Medicine Hokkaido University Sapporo Japan.,Hokkaido Research Organization Sapporo Japan
| | - Keisuke Adachi
- Laboratory of Wildlife Biology and Medicine, Faculty of Veterinary Medicine Hokkaido University Sapporo Japan
| | - Kei Kawamura
- Laboratory of Wildlife Biology and Medicine, Faculty of Veterinary Medicine Hokkaido University Sapporo Japan
| | - Yuri Shirane
- Laboratory of Wildlife Biology and Medicine, Faculty of Veterinary Medicine Hokkaido University Sapporo Japan.,Hokkaido Research Organization Sapporo Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Toshio Tsubota
- Laboratory of Wildlife Biology and Medicine, Faculty of Veterinary Medicine Hokkaido University Sapporo Japan
| | - Keita Fukasawa
- Center for Environmental Biology and Ecosystem Studies National Institute for Environmental Studies Tsukuba Japan
| | - Hiroyuki Uno
- Faculty of Agriculture Tokyo University of Agriculture and Technology Tokyo Japan
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5
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Hinton JW, Chamberlain MJ. Evidence of reduced abundance, density, and survival of coyotes under federal management for red wolf recovery. Ecosphere 2022. [DOI: 10.1002/ecs2.4216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
| | - Michael J. Chamberlain
- Warnell School of Forestry and Natural Resources University of Georgia Athens Georgia USA
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6
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Cowen S, Smith M, McArthur S, Rayner K, Jackson C, Anderson G, Ottewell K. Novel microsatellites and investigation of faecal DNA as a non-invasive population monitoring tool for the banded hare-wallaby (. AUST J ZOOL 2022. [DOI: 10.1071/zo21015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Monitoring programs for populations of small or medium-sized animals often use live-capture or photo-monitoring trapping methods to estimate population size. The banded hare-wallaby (Lagostrophus fasciatus), a small macropodiform marsupial, does not readily enter traps or have individually unique distinguishing physical features and is consequently difficult to monitor using these methods. Isolating DNA from faecal material to obtain individual genotypes is a promising monitoring technique and may present an alternative approach for this species. We developed novel species-specific microsatellite markers and undertook trials to assess faecal DNA degradation in ambient environmental conditions at two locations where this species has been translocated. The quality of DNA yielded from faecal pellets was evaluated through amplification failure and genotyping error rates of microsatellite markers. Error rates were compared for different treatments and exposure duration across multiple individuals. DNA was successfully obtained from all samples and error rates increased with exposure duration, peaking after 14–30 days depending on the site and treatment. The level of solar exposure was the most significant factor affecting degradation rate but both this and exposure duration had significant effects on amplification failure. Analysing DNA obtained from faecal pellets may represent a practical non-invasive method of deriving population estimates for this species and warrants further development.
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7
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Lindsø LK, Dupont P, Rød-Eriksen L, Andersskog IPØ, Ulvund KR, Flagstad Ø, Bischof R, Eide NE. Estimating red fox density using non-invasive genetic sampling and spatial capture-recapture modelling. Oecologia 2021; 198:139-151. [PMID: 34859281 PMCID: PMC8803778 DOI: 10.1007/s00442-021-05087-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 11/20/2021] [Indexed: 11/28/2022]
Abstract
Spatial capture–recapture modelling (SCR) is a powerful tool for estimating density, population size, and space use of elusive animals. Here, we applied SCR modelling to non-invasive genetic sampling (NGS) data to estimate red fox (Vulpes vulpes) densities in two areas of boreal forest in central (2016–2018) and southern Norway (2017–2018). Estimated densities were overall lower in the central study area (mean = 0.04 foxes per km2 in 2016, 0.10 in 2017, and 0.06 in 2018) compared to the southern study area (0.16 in 2017 and 0.09 in 2018). We found a positive effect of forest cover on density in the central, but not the southern study area. The absence of an effect in the southern area may reflect a paucity of evidence caused by low variation in forest cover. Estimated mean home-range size in the central study area was 45 km2 [95%CI 34–60] for females and 88 km2 [69–113] for males. Mean home-range sizes were smaller in the southern study area (26 km2 [16–42] for females and 56 km2 [35–91] for males). In both study areas, detection probability was session-dependent and affected by sampling effort. This study highlights how SCR modelling in combination with NGS can be used to efficiently monitor red fox populations, and simultaneously incorporate ecological factors and estimate their effects on population density and space use.
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Affiliation(s)
- Lars K Lindsø
- Norwegian Institute for Nature Research, Høgskoleringen 9, 7034, Trondheim, Norway. .,Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Universitetstunet 3, 1430, Ås, Norway. .,Centre for Ecological and Evolutionary Synthesis (CEES), The Department of Biosciences, University of Oslo, Blindernveien 31, 0371, Oslo, Norway.
| | - Pierre Dupont
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Universitetstunet 3, 1430, Ås, Norway
| | - Lars Rød-Eriksen
- Norwegian Institute for Nature Research, Høgskoleringen 9, 7034, Trondheim, Norway
| | | | | | - Øystein Flagstad
- Norwegian Institute for Nature Research, Høgskoleringen 9, 7034, Trondheim, Norway
| | - Richard Bischof
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Universitetstunet 3, 1430, Ås, Norway
| | - Nina E Eide
- Norwegian Institute for Nature Research, Høgskoleringen 9, 7034, Trondheim, Norway
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8
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De R, Sharma R, Davidar P, Arumugam N, Sedhupathy A, Puyravaud JP, Selvan KM, Rahim PA, Udayraj S, Parida J, Digal DK, Kanagaraj R, Kakati K, Nigam P, Williams AC, Habib B, Goyal SP. Pan-India population genetics signifies the importance of habitat connectivity for wild Asian elephant conservation. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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9
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Parker LD, Campana MG, Quinta JD, Cypher B, Rivera I, Fleischer RC, Ralls K, Wilbert TR, Boarman R, Boarman WI, Maldonado JE. An efficient method for simultaneous species, individual, and sex identification via in-solution single nucleotide polymorphism capture from low-quality scat samples. Mol Ecol Resour 2021; 22:1345-1361. [PMID: 34779133 DOI: 10.1111/1755-0998.13552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/24/2021] [Accepted: 10/27/2021] [Indexed: 12/01/2022]
Abstract
Understanding predator population dynamics is important for conservation management because of the critical roles predators play within ecosystems. Noninvasive genetic sampling methods are useful for the study of predators like canids that can be difficult to capture or directly observe. Here, we introduce the FAECES* method (Fast and Accurate Enrichment of Canid Excrement for Species* and other analyses) which expands the toolbox for canid researchers and conservationists by using in-solution hybridization sequence capture to produce single nucleotide polymorphism (SNP) genotypes for multiple canid species from scat-derived DNA using a single enrichment. We designed a set of hybridization probes to genotype both coyotes (Canis latrans) and kit foxes (Vulpes macrotis) at hundreds of polymorphic SNP loci and we tested the probes on both tissues and field-collected scat samples. We enriched and genotyped by sequencing 52 coyote and 70 kit fox scats collected in and around a conservation easement in the Nevada Mojave Desert. We demonstrate that the FAECES* method produces genotypes capable of differentiating coyotes and kit foxes, identifying individuals and their sex, and estimating genetic diversity and effective population sizes, even using highly degraded, low-quantity DNA extracted from scat. We found that the study area harbours a large and diverse population of kit foxes and a relatively smaller population of coyotes. By replicating our methods in the future, conservationists can assess the impacts of management decisions on canid populations. The method can also be adapted and applied more broadly to enrich and sequence multiple loci from any species of interest using scat or other noninvasive genetic samples.
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Affiliation(s)
- Lillian D Parker
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA.,School of Systems Biology, George Mason University, Fairfax, Virginia, USA
| | - Michael G Campana
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA.,School of Systems Biology, George Mason University, Fairfax, Virginia, USA.,Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
| | - Jessica D Quinta
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA
| | - Brian Cypher
- Endangered Species Recovery Program, California State University, Turlock, California, USA
| | - Isabel Rivera
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA
| | - Katherine Ralls
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA
| | - Tammy R Wilbert
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA
| | - Ryan Boarman
- Conservation Science Research and Consultation, Spring Valley, California, USA
| | - William I Boarman
- Conservation Science Research and Consultation, Spring Valley, California, USA
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute and National Zoological Park, Washington, District of Columbia, USA.,School of Systems Biology, George Mason University, Fairfax, Virginia, USA.,Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
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10
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Murphy SM, Adams JR, Waits LP, Cox JJ. Evaluating otter reintroduction outcomes using genetic spatial capture-recapture modified for dendritic networks. Ecol Evol 2021; 11:15047-15061. [PMID: 34765159 PMCID: PMC8571598 DOI: 10.1002/ece3.8187] [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: 06/25/2021] [Revised: 09/06/2021] [Accepted: 09/10/2021] [Indexed: 11/23/2022] Open
Abstract
Monitoring the demographics and genetics of reintroduced populations is critical to evaluating reintroduction success, but species ecology and the landscapes that they inhabit often present challenges for accurate assessments. If suitable habitats are restricted to hierarchical dendritic networks, such as river systems, animal movements are typically constrained and may violate assumptions of methods commonly used to estimate demographic parameters. Using genetic detection data collected via fecal sampling at latrines, we demonstrate applicability of the spatial capture-recapture (SCR) network distance function for estimating the size and density of a recently reintroduced North American river otter (Lontra canadensis) population in the Upper Rio Grande River dendritic network in the southwestern United States, and we also evaluated the genetic outcomes of using a small founder group (n = 33 otters) for reintroduction. Estimated population density was 0.23-0.28 otter/km, or 1 otter/3.57-4.35 km, with weak evidence of density increasing with northerly latitude (β = 0.33). Estimated population size was 83-104 total otters in 359 km of riverine dendritic network, which corresponded to average annual exponential population growth of 1.12-1.15/year since reintroduction. Growth was ≥40% lower than most reintroduced river otter populations and strong evidence of a founder effect existed 8-10 years post-reintroduction, including 13-21% genetic diversity loss, 84%-87% genetic effective population size decline, and rapid divergence from the source population (F ST accumulation = 0.06/generation). Consequently, genetic restoration via translocation of additional otters from other populations may be necessary to mitigate deleterious genetic effects in this small, isolated population. Combined with non-invasive genetic sampling, the SCR network distance approach is likely widely applicable to demogenetic assessments of both reintroduced and established populations of multiple mustelid species that inhabit aquatic dendritic networks, many of which are regionally or globally imperiled and may warrant reintroduction or augmentation efforts.
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Affiliation(s)
- Sean M. Murphy
- Wildlife Management DivisionNew Mexico Department of Game & FishSanta FeNew MexicoUSA
| | - Jennifer R. Adams
- Department of Fish and Wildlife SciencesUniversity of IdahoMoscowIdahoUSA
| | - Lisette P. Waits
- Department of Fish and Wildlife SciencesUniversity of IdahoMoscowIdahoUSA
| | - John J. Cox
- Department of Forestry and Natural ResourcesUniversity of KentuckyLexingtonKentuckyUSA
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11
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Ruprecht JS, Eriksson CE, Forrester TD, Clark DA, Wisdom MJ, Rowland MM, Johnson BK, Levi T. Evaluating and integrating spatial capture-recapture models with data of variable individual identifiability. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2021; 31:e02405. [PMID: 34245619 PMCID: PMC9286611 DOI: 10.1002/eap.2405] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/17/2021] [Accepted: 02/22/2021] [Indexed: 05/05/2023]
Abstract
Spatial capture-recapture (SCR) models have become the preferred tool for estimating densities of carnivores. Within this family of models are variants requiring identification of all individuals in each encounter (SCR), a subset of individuals only (generalized spatial mark-resight, gSMR), or no individual identification (spatial count or spatial presence-absence). Although each technique has been shown through simulation to yield unbiased results, the consistency and relative precision of estimates across methods in real-world settings are seldom considered. We tested a suite of models ranging from those only requiring detections of unmarked individuals to others that integrate remote camera, physical capture, genetic, and global positioning system (GPS) data into a hybrid model, to estimate population densities of black bears, bobcats, cougars, and coyotes. For each species, we genotyped fecal DNA collected with detection dogs during a 20-d period. A subset of individuals from each species was affixed with GPS collars bearing unique markings and resighted by remote cameras over 140 d contemporaneous with scat collection. Camera-based gSMR models produced density estimates that differed by <10% from genetic SCR for bears, cougars, and coyotes once important sources of variation (sex or behavioral status) were controlled for. For bobcats, SCR estimates were 33% higher than gSMR. The cause of the discrepancies in estimates was likely attributable to challenges designing a study compatible for species with disparate home range sizes and the difficulty of collecting sufficient data in a timeframe in which demographic closure could be assumed. Unmarked models estimated densities that varied greatly from SCR, but estimates became more consistent in models wherein more individuals were identifiable. Hybrid models containing all data sources exhibited the most precise estimates for all species. For studies in which only sparse data can be obtained and the strictest model assumptions are unlikely to be met, we suggest researchers use caution making inference from models lacking individual identity. For best results, we further recommend the use of methods requiring at least a subset of the population is marked and that multiple data sets are incorporated when possible.
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Affiliation(s)
- Joel S. Ruprecht
- Department of Fisheries and WildlifeOregon State University104 Nash HallCorvallisOregon97331USA
| | - Charlotte E. Eriksson
- Department of Fisheries and WildlifeOregon State University104 Nash HallCorvallisOregon97331USA
| | - Tavis D. Forrester
- Oregon Department of Fish and Wildlife1401 Gekeler LaneLa GrandeOregon97850USA
| | - Darren A. Clark
- Oregon Department of Fish and Wildlife1401 Gekeler LaneLa GrandeOregon97850USA
| | - Michael J. Wisdom
- Pacific Northwest Research StationUSDA Forest Service1401 Gekeler LaneLa GrandeOregon97850USA
| | - Mary M. Rowland
- Pacific Northwest Research StationUSDA Forest Service1401 Gekeler LaneLa GrandeOregon97850USA
| | - Bruce K. Johnson
- Oregon Department of Fish and Wildlife1401 Gekeler LaneLa GrandeOregon97850USA
| | - Taal Levi
- Department of Fisheries and WildlifeOregon State University104 Nash HallCorvallisOregon97331USA
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12
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Sadhukhan S, Root-Gutteridge H, Habib B. Identifying unknown Indian wolves by their distinctive howls: its potential as a non-invasive survey method. Sci Rep 2021; 11:7309. [PMID: 33790346 PMCID: PMC8012383 DOI: 10.1038/s41598-021-86718-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 03/19/2021] [Indexed: 02/01/2023] Open
Abstract
Previous studies have posited the use of acoustics-based surveys to monitor population size and estimate their density. However, decreasing the bias in population estimations, such as by using Capture-Mark-Recapture, requires the identification of individuals using supervised classification methods, especially for sparsely populated species like the wolf which may otherwise be counted repeatedly. The cryptic behaviour of Indian wolf (Canis lupus pallipes) poses serious challenges to survey efforts, and thus, there is no reliable estimate of their population despite a prominent role in the ecosystem. Like other wolves, Indian wolves produce howls that can be detected over distances of more than 6 km, making them ideal candidates for acoustic surveys. Here, we explore the use of a supervised classifier to identify unknown individuals. We trained a supervised Agglomerative Nesting hierarchical clustering (AGNES) model using 49 howls from five Indian wolves and achieved 98% individual identification accuracy. We tested our model's predictive power using 20 novel howls from a further four individuals (test dataset) and resulted in 75% accuracy in classifying howls to individuals. The model can reduce bias in population estimations using Capture-Mark-Recapture and track individual wolves non-invasively by their howls. This has potential for studies of wolves' territory use, pack composition, and reproductive behaviour. Our method can potentially be adapted for other species with individually distinctive vocalisations, representing an advanced tool for individual-level monitoring.
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Affiliation(s)
- Sougata Sadhukhan
- grid.452923.b0000 0004 1767 4167Animal Ecology and Conservation Biology, Wildlife Institute of India, Dehradun, 248001 India
| | - Holly Root-Gutteridge
- grid.36511.300000 0004 0420 4262Animal Behaviour, Cognition and Welfare Group, University of Lincoln, Lincoln, UK ,grid.12082.390000 0004 1936 7590Reby Lab, School of Psychology, University of Sussex, Brighton, UK
| | - Bilal Habib
- grid.452923.b0000 0004 1767 4167Animal Ecology and Conservation Biology, Wildlife Institute of India, Dehradun, 248001 India
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13
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McNitt DC, Alonso RS, Cherry MJ, Fies ML, Kelly MJ. Sex-specific effects of reproductive season on bobcat space use, movement, and resource selection in the Appalachian Mountains of Virginia. PLoS One 2020; 15:e0225355. [PMID: 32750055 PMCID: PMC7402482 DOI: 10.1371/journal.pone.0225355] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 07/08/2020] [Indexed: 11/18/2022] Open
Abstract
Across taxa, sex-specific demands vary temporally in accordance with reproductive investments. In solitary carnivores, females must provision and protect young independently while meeting increased energetic demands. Males seek to monopolize access to females by maintaining large territories and defending them from other males. For many species, it is poorly understood how these demands relate to broad-scale animal movements. To investigate predictions surrounding the reproductive strategies of solitary carnivores and effects of local conditions on bobcat (Lynx rufus) spatial ecology, we examined the effects of sex and reproductive season on home range size, movement rate, and resource selection of bobcats in the central Appalachian Mountains. Male seasonal home ranges were approximately 3 times larger than those of females (33.9 ± 2.6 vs. 12.1 ± 2.4 km2, x±SE), and male movement rates were 1.4 times greater than females (212.6 ± 3.6 vs. 155 ± 8.2 m/hr), likely reflecting male efforts to maximize access to females. Both sexes appear to maintain relatively stable seasonal home ranges despite temporally varying reproductive investments, instead adjusting movements within home ranges. Males increased movements during the dispersal period, potentially reflecting increased territoriality prior to breeding. Females increased movements during the kitten-rearing period, when foraging more intensively, and frequently returning to den sites. Both sexes selected home ranges at higher elevations. However, females selected deciduous forest and avoided fields, whereas males selected fields and avoided deciduous forest, perhaps explained by male pressure to access multiple females across several mountain ridges and higher risk tolerance. Seasonal changes in home range selection likely reflect changes in home range shape. Increased female avoidance of fields during kitten rearing may indicate female avoidance of presumably resource rich, yet risky, fields at the time when kittens are most vulnerable. Our results indicate that while reproductive chronology influences the spatial ecology of solitary carnivores, effects may be constrained by territoriality.
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Affiliation(s)
- David C. McNitt
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, Virginia, United State of America
- * E-mail:
| | - Robert S. Alonso
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, Virginia, United State of America
| | - Michael J. Cherry
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, Virginia, United State of America
| | - Michael L. Fies
- Virginia Department of Game and Inland Fisheries, Verona, Virginia, United States of America
| | - Marcella J. Kelly
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, Virginia, United State of America
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14
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Quinn CB, Alden PB, Sacks BN. Noninvasive Sampling Reveals Short-Term Genetic Rescue in an Insular Red Fox Population. J Hered 2020; 110:559-576. [PMID: 31002340 DOI: 10.1093/jhered/esz024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 04/15/2019] [Indexed: 11/12/2022] Open
Abstract
Genetic factors in the decline of small populations are extremely difficult to study in nature. We leveraged a natural experiment to investigate evidence of inbreeding depression and genetic rescue in a remnant population of subalpine-specialized Sierra Nevada red foxes (Vulpes vulpes necator) using noninvasive genetic monitoring during 2010-2017. Only 7 individuals were detected in the first 2 years. These individuals assigned genetically to the historical population and exhibited genetic hallmarks of inbreeding and no evidence of reproduction. Two years into the study, we detected 2 first-generation immigrant males from a recently expanding population of red foxes in the Great Basin Desert. Through annual resampling of individuals (634 red fox DNA samples, 41 individuals) and molecular reconstruction of pedigrees, we documented 1-3 litters/year for 5 years, all descended directly or indirectly from matings involving immigrant foxes. The observed heterozygosity and allelic richness of the population nearly doubled in 2 years. Abundance increased, indicative of a rapidly expanding population. Throughout the study, adult survival was high. Restoration of gene flow apparently improved the demographic trajectory of this population in the short term. Whether these benefits continue in the longer term could depend on numerous factors, such as maintenance of any locally adapted alleles. This study highlights the value of noninvasive genetic monitoring to assess rapidly shifting conditions in small populations. Uncertainties about the longer-term trajectory of this population underscore the need to continue monitoring and to research potential for both negative and positive aspects of continued genetic infusion.
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Affiliation(s)
- Cate B Quinn
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, Davis, CA
| | - Preston B Alden
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, Davis, CA.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, Davis, CA.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA
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15
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Piaggio AJ, Shriner SA, Young JK, Griffin DL, Callahan P, Wostenberg DJ, Gese EM, Hopken MW. DNA persistence in predator saliva from multiple species and methods for optimal recovery from depredated carcasses. J Mammal 2019. [DOI: 10.1093/jmammal/gyz156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
AbstractMolecular forensics is an important component of wildlife research and management. Using DNA from noninvasive samples collected at predation sites, we can identify predator species and obtain individual genotypes, improving our understanding of predator–prey dynamics and impacts of predators on livestock and endangered species. To improve sample collection strategies, we tested two sample collection methods and estimated degradation rates of predator DNA on the carcasses of multiple prey species. We fed carcasses of calves (Bos taurus) and lambs (Ovis aires) to three captive predator species: wolves (Canis lupus), coyotes (C. latrans), and mountain lions (Puma concolor). We swabbed the carcass in the field, as well as removed a piece of hide from the carcasses and then swabbed it in the laboratory. We swabbed all tissue samples through time and attempted to identify the predator involved in the depredation using salivary DNA. We found the most successful approach for yielding viable salivary DNA was removing hide from the prey and swabbing it in the laboratory. As expected, genotyping error increased through time and our ability to obtain complete genotypes decreased over time, the latter falling below 50% after 24 h. We provide guidelines for sampling salivary DNA from tissues of depredated carcasses for maximum probability of detection.
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Affiliation(s)
- Antoinette J Piaggio
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO, USA
| | - Susan A Shriner
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO, USA
| | - Julie K Young
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center-Predator Research Facility, Utah State University, Logan, UT,USA
| | - Doreen L Griffin
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO, USA
| | | | - Darren J Wostenberg
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO, USA
| | - Eric M Gese
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center-Predator Research Facility, Utah State University, Logan, UT,USA
| | - Matthew W Hopken
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO, USA
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16
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Morin DJ, Higdon SD, Lonsinger RC, Gosselin EN, Kelly MJ, Waits LP. Comparing methods of estimating carnivore diets with uncertainty and imperfect detection. WILDLIFE SOC B 2019. [DOI: 10.1002/wsb.1021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Dana J. Morin
- Department of Wildlife, Fisheries and AquacultureMississippi State University Box 9680 Mississippi State MS 39762 USA
| | - Summer D. Higdon
- School of Natural ResourcesUniversity of Missouri 302 Anheuser‐Busch Natural Resources Building Columbia MO 65211 USA
| | - Robert C. Lonsinger
- Department of Natural Resource ManagementSouth Dakota State University 1390 College Avenue Brookings SD 57007 USA
| | - Elyce N. Gosselin
- College of Natural ResourcesUniversity of Idaho 875 Perimeter Drive Moscow ID 83844 USA
| | - Marcella J. Kelly
- Department of Fish and Wildlife Conservation 100 Cheatham Hall, Virginia Tech Blacksburg VA 24061 USA
| | - Lisette P. Waits
- College of Natural ResourcesUniversity of Idaho 875 Perimeter Drive Moscow ID 83844 USA
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17
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Mastro LL, Morin DJ, Gese EM. Home Range and Habitat Use of West Virginia Canis latrans (Coyote). Northeast Nat (Steuben) 2019. [DOI: 10.1656/045.026.0318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Lauren L. Mastro
- US Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, 105B Ponderosa Drive, Christiansburg, VA 24073
| | - Dana J. Morin
- Cooperative Wildlife Research Laboratory, Southern Illinois University, 1125 Lincoln Drive, Carbondale, IL 62901
| | - Eric M. Gese
- US Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Utah State University, Logan, UT 84322
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18
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Skrbinšek T, Luštrik R, Majić-Skrbinšek A, Potočnik H, Kljun F, Jelenčič M, Kos I, Trontelj P. From science to practice: genetic estimate of brown bear population size in Slovenia and how it influenced bear management. EUR J WILDLIFE RES 2019. [DOI: 10.1007/s10344-019-1265-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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19
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Roffler GH, Waite JN, Pilgrim KL, Zarn KE, Schwartz MK. Estimating abundance of a cryptic social carnivore using spatially explicit capture–recapture. WILDLIFE SOC B 2019. [DOI: 10.1002/wsb.953] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Gretchen H. Roffler
- Alaska Department of Fish and GameDivision of Wildlife Conservation802 3rd StreetDouglasAK99824USA
| | - Jason N. Waite
- Alaska Department of Fish and GameDivision of Wildlife Conservation802 3rd StreetDouglasAK99824USA
| | - Kristine L. Pilgrim
- National Genomics Center for Wildlife and Fish ConservationRocky Mountain Research StationU.S. Department of Agriculture Forest Service800 E BeckwithMissoulaMT59801USA
| | - Katherine E. Zarn
- National Genomics Center for Wildlife and Fish ConservationRocky Mountain Research StationU.S. Department of Agriculture Forest Service800 E BeckwithMissoulaMT59801USA
| | - Michael K. Schwartz
- National Genomics Center for Wildlife and Fish ConservationRocky Mountain Research StationU.S. Department of Agriculture Forest Service800 E BeckwithMissoulaMT59801USA
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20
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Murphy SM, Augustine BC, Adams JR, Waits LP, Cox JJ. Integrating multiple genetic detection methods to estimate population density of social and territorial carnivores. Ecosphere 2018. [DOI: 10.1002/ecs2.2479] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Sean M. Murphy
- Louisiana Department of Wildlife and Fisheries; Large Carnivore Program; Lafayette Louisiana 70506 USA
| | - Ben C. Augustine
- Department of Fish and Wildlife Conservation; Virginia Polytechnic Institute and State University; Blacksburg Virginia 24061 USA
| | - Jennifer R. Adams
- Laboratory for Ecological, Evolutionary and Conservation Genetics; Department of Fish and Wildlife Sciences; University of Idaho; Moscow Idaho 83844 USA
| | - Lisette P. Waits
- Laboratory for Ecological, Evolutionary and Conservation Genetics; Department of Fish and Wildlife Sciences; University of Idaho; Moscow Idaho 83844 USA
| | - John J. Cox
- Department of Forestry and Natural Resources; University of Kentucky; Lexington Kentucky 40546 USA
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21
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Lonsinger R, Lukacs P, Gese E, Knight R, Waits L. Estimating densities for sympatric kit foxes (Vulpes macrotis) and coyotes (Canis latrans) using noninvasive genetic sampling. CAN J ZOOL 2018. [DOI: 10.1139/cjz-2017-0332] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Kit fox (Vulpes macrotis Merriam, 1888) populations in the Great Basin Desert have declined and are of increasing concern for managers. Increasing coyote (Canis latrans Say, 1823) abundance and subsequent intraguild interactions may be one cause for this decline. Concurrent monitoring of carnivores is challenging and therefore rarely conducted. One possible solution for monitoring elusive carnivores is using noninvasive genetic sampling. We used noninvasive genetic sampling to collect fecal DNA from kit foxes and coyotes and estimate their densities from 2013–2014 in Utah, USA. We identified individuals based on microsatellite genotypes and estimated density with multisession spatially explicit capture–recapture models. Mean kit fox density was 0.02 foxes·km−2, while coyote densities were up to four times greater (0.07–0.08 coyotes·km−2). Kit fox densities were significantly lower than densities in the 1950s but were comparable with estimates from the late 1990s, suggesting that populations may be stabilizing after a precipitous decline. Our kit fox density estimates were among the lowest documented for the species. Our coyote density estimate was the first reported in our region and revealed that despite seemingly high abundance, densities are low compared with other regions. Our results suggested that kit foxes may be able to coexist with coyotes.
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Affiliation(s)
- R.C. Lonsinger
- Department of Natural Resource Management, South Dakota State University, Brookings, SD 57007, U.S.A
| | - P.M. Lukacs
- University of Montana, Wildlife Biology Program, Department of Ecosystems and Conservation Sciences, W.A. Franke College of Forestry and Conservation, Missoula, MT 59812, U.S.A
| | - E.M. Gese
- United States Department of Agriculture, Wildlife Services, National Wildlife Research Center, Department of Wildland Resources, Utah State University, Logan, UT 84322, U.S.A
| | - R.N. Knight
- United States Army Dugway Proving Ground, Natural Resource Program, Dugway, UT 84022, U.S.A
| | - L.P. Waits
- University of Idaho, Department of Fish and Wildlife Sciences, Moscow, ID 83844, U.S.A
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22
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Aylward ML, Sullivan AP, Perry GH, Johnson SE, Louis EE. An environmental DNA sampling method for aye-ayes from their feeding traces. Ecol Evol 2018; 8:9229-9240. [PMID: 30377496 PMCID: PMC6194247 DOI: 10.1002/ece3.4341] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/08/2018] [Accepted: 06/12/2018] [Indexed: 01/05/2023] Open
Abstract
Noninvasive sampling is an important development in population genetic monitoring of wild animals. Particularly, the collection of environmental DNA (eDNA) which can be collected without needing to encounter the target animal facilitates the genetic analysis of endangered species. One method that has been applied to these sample types is target capture and enrichment which overcomes the issue of high proportions of exogenous (nonhost) DNA from these lower quality samples. We tested whether target capture of mitochondrial DNA from sampled feeding traces of the aye-aye, an endangered lemur species would yield mitochondrial DNA sequences for population genetic monitoring. We sampled gnawed wood where aye-ayes excavate wood-boring insect larvae from trees. We designed RNA probes complementary to the aye-aye's mitochondrial genome and used these to isolate aye-aye DNA from other nontarget DNA in these samples. We successfully retrieved six near-complete mitochondrial genomes from two sites within the aye-aye's geographic range that had not been sampled previously. Our method demonstrates the application of next-generation molecular techniques to species of conservation concern. This method can likely be applied to alternative foraged remains to sample endangered species other than aye-ayes.
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Affiliation(s)
- Megan L. Aylward
- Department of Anthropology and ArchaeologyUniversity of CalgaryCalgaryABCanada
| | - Alexis P. Sullivan
- Department of BiologyPennsylvania State UniversityState CollegePennsylvania
| | - George H. Perry
- Department of BiologyPennsylvania State UniversityState CollegePennsylvania
- Department of AnthropologyPennsylvania State UniversityState CollegePennsylvania
| | - Steig E. Johnson
- Department of Anthropology and ArchaeologyUniversity of CalgaryCalgaryABCanada
| | - Edward E. Louis
- Grewcock Center for Conservation and ResearchOmaha's Henry Doorly Zoo and AquariumOmahaNebraska
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23
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Modave E, MacDonald AJ, Sarre SD. A single mini-barcode test to screen for Australian mammalian predators from environmental samples. Gigascience 2018; 6:1-13. [PMID: 28810700 PMCID: PMC5545080 DOI: 10.1093/gigascience/gix052] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 06/27/2017] [Indexed: 01/25/2023] Open
Abstract
Identification of species from trace samples is now possible through the comparison of diagnostic DNA fragments against reference DNA sequence databases. DNA detection of animals from non-invasive samples, such as predator faeces (scats) that contain traces of DNA from their species of origin, has proved to be a valuable tool for the management of elusive wildlife. However, application of this approach can be limited by the availability of appropriate genetic markers. Scat DNA is often degraded, meaning that longer DNA sequences, including standard DNA barcoding markers, are difficult to recover. Instead, targeted short diagnostic markers are required to serve as diagnostic mini-barcodes. The mitochondrial genome is a useful source of such trace DNA markers because it provides good resolution at the species level and occurs in high copy numbers per cell. We developed a mini-barcode based on a short (178 bp) fragment of the conserved 12S ribosomal ribonucleic acid mitochondrial gene sequence, with the goal of discriminating amongst the scats of large mammalian predators of Australia. We tested the sensitivity and specificity of our primers and can accurately detect and discriminate amongst quolls, cats, dogs, foxes, and devils from trace DNA samples. Our approach provides a cost-effective, time-efficient, and non-invasive tool that enables identification of all 8 medium-large mammal predators in Australia, including native and introduced species, using a single test. With modification, this approach is likely to be of broad applicability elsewhere.
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Affiliation(s)
- Elodie Modave
- Institute for Applied Ecology, University of Canberra, ACT, 2601, Canberra, Australia
| | - Anna J MacDonald
- Institute for Applied Ecology, University of Canberra, ACT, 2601, Canberra, Australia
| | - Stephen D Sarre
- Institute for Applied Ecology, University of Canberra, ACT, 2601, Canberra, Australia
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24
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Morin DJ, Waits LP, McNitt DC, Kelly MJ. Efficient single-survey estimation of carnivore density using fecal DNA and spatial capture-recapture: a bobcat case study. POPUL ECOL 2018. [DOI: 10.1007/s10144-018-0606-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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25
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Piggott MP, Hansen B, Soderquist T, Eldridge MDB, Taylor AC. Population monitoring of small and declining brush-tailed rock wallaby (Petrogale penicillata) colonies at the extreme of their range using faecal DNA sampling. AUSTRALIAN MAMMALOGY 2018. [DOI: 10.1071/am16056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Obtaining much-needed information on population parameters such as abundance and genetic diversity can be difficult for small and declining populations. The brush-tailed rock-wallaby (Petrogale penicillata) is an endangered and cryptic species with many colonies in decline. The Warrumbungle National Park (NP) in New South Wales contains a declining metapopulation of P. penicillata at the western (inland) extreme of the species’ current range. Loss of these colonies would cause substantial range contraction and probable loss of regional genetic diversity in the Central Evolutionary Significance Unit (ESU). We used non-invasive genetic methods to identify individuals from faecal DNA from five colonies in the Warrumbungle NP. We identified a minimum of 21 individuals, with the largest colony containing seven individuals. The Warrumbungle NP colonies showed significant intercolony structuring and we were able to detect a single dispersal event. Comparison of genetic diversity to other Central ESU colonies shows that loss of the Warrumbungle NP population will result in loss of unique diversity from this region. The minimum number of animals and genetic diversity information obtained in this study was used to support management actions of herbivore control and translocation in the Warrumbungle NP population.
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26
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Non-invasively determined multi-site variation in pine marten Martes martes density, a recovering carnivore in Europe. EUR J WILDLIFE RES 2017. [DOI: 10.1007/s10344-017-1108-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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27
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Morin DJ, Kelly MJ. The dynamic nature of territoriality, transience and biding in an exploited coyote population. WILDLIFE BIOLOGY 2017. [DOI: 10.2981/wlb.00335] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Dana J. Morin
- D. J. Morin and M. J. Kelly, Dept of Fish and Wildlife Conservation, 106 Cheatham Hall, Virginia Tech, Blacksburg, VA 24061, USA
| | - Marcella J. Kelly
- D. J. Morin and M. J. Kelly, Dept of Fish and Wildlife Conservation, 106 Cheatham Hall, Virginia Tech, Blacksburg, VA 24061, USA
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28
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Morin DJ, Higdon SD, Holub JL, Montague DM, Fies ML, Waits LP, Kelly MJ. Bias in carnivore diet analysis resulting from misclassification of predator scats based on field identification. WILDLIFE SOC B 2016. [DOI: 10.1002/wsb.723] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Dana J. Morin
- Department of Fish and Wildlife Conservation; Virginia Tech; Blacksburg VA 24061 USA
| | - Summer D. Higdon
- Department of Fish and Wildlife Conservation; Virginia Tech; Blacksburg VA 24061 USA
| | - Jennifer L. Holub
- Department of Fish and Wildlife Conservation; Virginia Tech; Blacksburg VA 24061 USA
| | - David M. Montague
- Department of Fish and Wildlife Conservation; Virginia Tech; Blacksburg VA 24061 USA
| | - Michael L. Fies
- Virginia Department of Game and Inland Fisheries; Verona VA 24482 USA
| | - Lisette P. Waits
- Department of Fish and Wildlife Science; University of Idaho; Moscow ID 83844 USA
| | - Marcella J. Kelly
- Department of Fish and Wildlife Conservation; Virginia Tech; Blacksburg VA 24061 USA
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29
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Gulsby WD, Killmaster CH, Bowers JW, Laufenberg JS, Sacks BN, Statham MJ, Miller KV. Efficacy and precision of fecal genotyping to estimate coyote abundance. WILDLIFE SOC B 2016. [DOI: 10.1002/wsb.712] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- William D. Gulsby
- School of Forestry and Wildlife Sciences; Auburn University; Auburn AL 36849 USA
| | - Charlie H. Killmaster
- Georgia Department of Natural Resources; Wildlife Resources Division; 2070 United States Highway 278 SE, Social Circle GA 30025 USA
| | - John W. Bowers
- Georgia Department of Natural Resources; Wildlife Resources Division; 2070 United States Highway 278 SE, Social Circle GA 30025 USA
| | - Jared S. Laufenberg
- Department of Fish, Wildlife, and Conservation Biology; Colorado State University; 1474 Campus Delivery Fort Collins CO 80523 USA
| | - Benjamin N. Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, Department of Population Health and Reproduction; University of California; Davis, One Shields Avenue/Old Davis Road Davis CA 95616 USA
| | - Mark J. Statham
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory; University of California; Davis, One Shields Avenue/Old Davis Road Davis CA 95616 USA
| | - Karl V. Miller
- Warnell School of Forestry and Natural Resources; University of Georgia; Athens GA 30602 USA
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30
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Cherry MJ, Howell PE, Seagraves CD, Warren RJ, Conner LM. Effects of land cover on coyote abundance. WILDLIFE RESEARCH 2016. [DOI: 10.1071/wr16052] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Context
Throughout the world, declines in large mammalian carnivores have led to the release of smaller meso-mammalian predators. Coyotes (Canis latrans) have increased in abundance, distribution and ecological influence following the extirpation of apex predators in North America. Coyotes have had substantial influence on many ecosystems in recently colonised portions of their range, but those influences can vary across land cover types. Thus, understanding the relationship between coyote abundance and land cover may enhance our ability to predict spatial variation in the ecological effects of coyotes.
Aims
Our objective was to examine the influence of landscape attributes on eastern coyote abundance to ultimately facilitate predictions of spatial variation in the effects of coyotes on prey populations, ecological communities and human interests.
Methods
We collected count data from repeated visits to 24 sites by eliciting howl responses from coyotes. We fit abundance models to howl-response data to examine the effects of landscape composition and configuration on coyote abundance in a mixed forest/agricultural ecosystem in south-western Georgia, USA.
Key results
Our investigation revealed that coyote abundance was positively associated with grasslands that were predominantly used for livestock production, and negatively associated with patch diversity.
Conclusions
Our results supported the prediction that coyotes would be positively associated with open habitats and that they are well adapted for areas structurally similar to the plains of central North America, where the species originated. In addition, these results suggest that aspects of fragmentation, such as patch diversity, can negatively affect coyote abundance. Our results highlight the importance of patch type and landscape juxtaposition on the abundance of coyotes in complex heterogeneous landscapes.
Implications
Our results further our understanding of the spatial variation in coyote abundances across a recently colonised portion of the species range. Combining howl-response surveys with abundance modelling is a promising approach for studying the associations between population dynamics of vocal canids and landscape structure over large spatial scales.
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