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Jiménez J, Del Río L, Ferreras P, Godinho R. Low signs of territorial behavior in the Eurasian otter during low-water conditions in a Mediterranean river. Sci Rep 2024; 14:11478. [PMID: 38769409 PMCID: PMC11106847 DOI: 10.1038/s41598-024-62432-1] [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: 12/08/2023] [Accepted: 05/16/2024] [Indexed: 05/22/2024] Open
Abstract
The Eurasian otter Lutra lutra is a territorial semi-aquatic carnivore usually found at low densities in rivers, coastal areas, and wetlands. Its diet is based on prey associated with aquatic environments. Mediterranean rivers are highly seasonal, and suffer reduced flow during the summer, resulting in isolated river sections (pools) that sometimes can be left with a minimal amount of water, leading to concentrations of food for otters. To our knowledge, this process, which was known to field naturalists, has not been accurately described, nor have otter densities been estimated under these conditions. In this study, we describe the population size and movements of an aggregation of otters in an isolated pool in the Guadiana River in the Tablas de Daimiel National Park (central Spain), which progressively dried out during the spring-summer of 2022, in a context of low connectivity due to the absence of circulating water in the Guadiana and Gigüela rivers. Using non-invasive genetic sampling of 120 spraints collected along 79.4 km of sampling transects and spatial capture-recapture methods, we estimated the otter density at 1.71 individuals/km of river channel length (4.21 individuals/km2) in a progressively drying river pool, up to five times higher than previously described in the Iberian Peninsula. The movement patterns obtained with the spatial capture-recapture model are not quite different from those described in low density, which seems to indicate a wide home range overlap, with low signs of territoriality.
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Affiliation(s)
- José Jiménez
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC-UCLM-JCCM), Ronda de Toledo 12, 13071, Ciudad Real, Spain.
| | - Lucía Del Río
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC-UCLM-JCCM), Ronda de Toledo 12, 13071, Ciudad Real, Spain
| | - Pablo Ferreras
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC-UCLM-JCCM), Ronda de Toledo 12, 13071, Ciudad Real, Spain
| | - Raquel Godinho
- Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, CIBIO, Universidade Do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade Do Porto, 4169-007, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
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2
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van Dam-Bates P, Papathomas M, Stevenson BC, Fewster RM, Turek D, Stewart FEC, Borchers DL. A flexible framework for spatial capture-recapture with unknown identities. Biometrics 2024; 80:ujad019. [PMID: 38372400 DOI: 10.1093/biomtc/ujad019] [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: 11/18/2022] [Revised: 10/30/2023] [Accepted: 11/22/2023] [Indexed: 02/20/2024]
Abstract
Camera traps or acoustic recorders are often used to sample wildlife populations. When animals can be individually identified, these data can be used with spatial capture-recapture (SCR) methods to assess populations. However, obtaining animal identities is often labor-intensive and not always possible for all detected animals. To address this problem, we formulate SCR, including acoustic SCR, as a marked Poisson process, comprising a single counting process for the detections of all animals and a mark distribution for what is observed (eg, animal identity, detector location). The counting process applies equally when it is animals appearing in front of camera traps and when vocalizations are captured by microphones, although the definition of a mark changes. When animals cannot be uniquely identified, the observed marks arise from a mixture of mark distributions defined by the animal activity centers and additional characteristics. Our method generalizes existing latent identity SCR models and provides an integrated framework that includes acoustic SCR. We apply our method to estimate density from a camera trap study of fisher (Pekania pennanti) and an acoustic survey of Cape Peninsula moss frog (Arthroleptella lightfooti). We also test it through simulation. We find latent identity SCR with additional marks such as sex or time of arrival to be a reliable method for estimating animal density.
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Affiliation(s)
- Paul van Dam-Bates
- School of Mathematics and Statistics, University of St Andrews, St Andrews, Fife, KY16 9LZ, United Kingdom
| | - Michail Papathomas
- School of Mathematics and Statistics, University of St Andrews, St Andrews, Fife, KY16 9LZ, United Kingdom
| | - Ben C Stevenson
- Department of Statistics, University of Auckland, Auckland, 1010, New Zealand
| | - Rachel M Fewster
- Department of Statistics, University of Auckland, Auckland, 1010, New Zealand
| | - Daniel Turek
- Department of Mathematics and Statistics, Williams College, Williamstown, 01267, United States
| | - Frances E C Stewart
- Department of Biology, Wilfrid Laurier University, Waterloo, N2L 3C5, Canada
| | - David L Borchers
- School of Mathematics and Statistics, University of St Andrews, St Andrews, Fife, KY16 9LZ, United Kingdom
- Centre for Statistics in Ecology, Environment and Conservation, Department of Statistical Sciences, University of Cape Town, Private Bag 7700, Rondebosch, South Africa
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3
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Wildlife Population Assessment: Changing Priorities Driven by Technological Advances. JOURNAL OF STATISTICAL THEORY AND PRACTICE 2023. [DOI: 10.1007/s42519-023-00319-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
AbstractAdvances in technology are having a large effect on the priorities for innovation in statistical ecology. Collaborations between statisticians and ecologists have always been important in driving methodological development, but increasingly, expertise from computer scientists and engineers is also needed. We discuss changes that are occurring and that may occur in the future in surveys for estimating animal abundance. As technology advances, we expect classical distance sampling and capture-recapture to decrease in importance, as camera (still and video) survey, acoustic survey, spatial capture-recapture and genetic methods continue to develop and find new applications. We explore how these changes are impacting the work of the statistical ecologist.
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4
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Efford MG. ipsecr: An R package for awkward spatial capture–recapture data. Methods Ecol Evol 2023. [DOI: 10.1111/2041-210x.14088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Affiliation(s)
- Murray G. Efford
- Department of Mathematics and Statistics University of Otago Dunedin New Zealand
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5
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Cove MV, Herrmann V, Herrera DJ, Augustine BC, Flockhart DTT, McShea WJ. Counting the Capital's cats: Estimating drivers of abundance of free-roaming cats with a novel hierarchical model. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2023; 33:e2790. [PMID: 36482050 DOI: 10.1002/eap.2790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 07/11/2022] [Accepted: 08/23/2022] [Indexed: 06/17/2023]
Abstract
Free-roaming cats are a conservation concern in many areas but identifying their impacts and developing mitigation strategies requires a robust understanding of their distribution and density patterns. Urban and residential areas may be especially relevant in this process because free-roaming cats are abundant in these anthropogenic landscapes. Here, we estimate the occupancy and density of free-roaming cats in Washington D.C. and relate these metrics to known landscape and social factors. We conducted an extended camera trap survey of public and private spaces across D.C. and analyzed data collected from 1483 camera deployments from 2018 to 2020. We estimated citywide cat distribution by fitting hierarchical occupancy models and further estimated cat abundance using a novel random thinning spatial capture-recapture model that allows for the use of photos that can and cannot be identified to individual. Within this model, we utilized individual covariates that provided identity exclusions between photos of unidentifiable cats with inconsistent coat patterns, thus increasing the precision of abundance estimates. This combined model also allowed for unbiased estimation of density when animals cannot be identified to individual at the same rate as for free-roaming cats whose identifiability depended on their coat characteristics. Cat occupancy and abundance declined with increasing distance from residential areas, an effect that was more pronounced in wealthier neighborhoods. There was noteworthy absence of cats detected in larger public spaces and forests. Realized densities ranged from 0.02 to 1.75 cats/ha in sampled areas, resulting in a district-wide estimate of ~7296 free-roaming cats. Ninety percent of cat detections lacked collars and nearly 35% of known individuals were ear-tipped, indicative of district Trap-Neuter-Return (TNR) programs. These results suggest that we mainly sampled and estimated the unowned cat subpopulation, such that indoor/outdoor housecats were not well represented. The precise estimation of cat population densities is difficult due to the varied behavior of subpopulations within free-roaming cat populations (housecats, stray and feral cats), but our methods provide a first step in establishing citywide baselines to inform data-driven management plans for free-roaming cats in urban environments.
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Affiliation(s)
- Michael V Cove
- North Carolina Museum of Natural Sciences, Raleigh, North Carolina, USA
- Smithsonian Conservation Biology Institute, Front Royal, Virginia, USA
| | | | - Daniel J Herrera
- Department of Environmental Science and Policy, College of Science, George Mason University, Fairfax, Virginia, USA
| | - Ben C Augustine
- Department of Natural Resources, Cornell University, Ithaca, New York, USA
| | - D T Tyler Flockhart
- Appalachian Laboratory - University of Maryland Center for Environmental Science, Frostburg, Maryland, USA
| | - William J McShea
- Smithsonian Conservation Biology Institute, Front Royal, Virginia, USA
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6
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Applications of non-intrusive methods to study the sand cat: a field study in the Sahara Desert. EUR J WILDLIFE RES 2023. [DOI: 10.1007/s10344-023-01645-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
AbstractSurveys based on indirect signs and camera trapping are two non-invasive methods extensively used for monitoring elusive mammals. Both approaches can be useful to obtain key information on wildlife in remote areas, since they may allow for the logistically viable design of optimal field frameworks. The sand cat (Felis margarita) is a feline that inhabits the Sahara Desert, the Arabian Peninsula, and western Asian deserts. Its basic ecology is poorly known and the status and impacts of threats are difficult to assess. Some local population declines have been detected, and more research is needed. Based on field surveys carried out in the Atlantic Sahara, we have evaluated the applications of both methods to study this species. Our results show that (a) camera trapping provided reliable data on several key aspects of its ecology, (b) walking surveys to collect feces for molecular data failed completely, and (c) for footprints, identification problems and the marked effects of the absence of optimal substrates and the prevalence of wind are relevant handicaps. Beyond this evaluation, we provide for the first time some key aspects of the ecology of sand cats in the Sahara Desert, including habitat selection, density, diel activity, and predator–prey relationships.
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Lauret V, Labach H, Turek D, Laran S, Gimenez O. Integrated spatial models foster complementarity between monitoring programmes in producing large‐scale bottlenose dolphin indicators. Anim Conserv 2022. [DOI: 10.1111/acv.12815] [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]
Affiliation(s)
- V. Lauret
- CEFE, Université Montpellier, CNRS, EPHE, IRD Montpellier France
| | - H. Labach
- CEFE, Université Montpellier, CNRS, EPHE, IRD Montpellier France
- MIRACETI, Connaissance et conservation des cétacés Place des traceurs de pierres La Couronne France
| | - D. Turek
- Department of Mathematics and Statistics Williams College Williamstown MA USA
| | - S. Laran
- Observatoire PELAGIS UMS 3462 CNRS‐La Rochelle Université La Rochelle France
| | - O. Gimenez
- CEFE, Université Montpellier, CNRS, EPHE, IRD Montpellier France
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Jiménez J, Díaz‐Ruiz F, Monterroso P, Tobajas J, Ferreras P. Occupancy data improves parameter precision in spatial capture-recapture models. Ecol Evol 2022; 12:e9250. [PMID: 36052294 PMCID: PMC9412271 DOI: 10.1002/ece3.9250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/22/2022] [Accepted: 08/05/2022] [Indexed: 11/17/2022] Open
Abstract
Population size is one of the basic demographic parameters for species management and conservation. Among different estimation methods, spatially explicit capture-recapture (SCR) models allow the estimation of population density in a framework that has been greatly developed in recent years. The use of automated detection devices, such as camera traps, has impressively extended SCR studies for individually identifiable species. However, its application to unmarked/partially marked species remains challenging, and no specific method has been widely used. We fitted an SCR-integrated model (SCR-IM) to stone marten Martes foina data, a species for which only some individuals are individually recognizable by natural marks, and estimate population size based on integration of three submodels: (1) individual capture histories from live capture and transponder tagging; (2) detection/nondetection or "occupancy" data using camera traps in a bigger area to extend the geographic scope of capture-recapture data; and (3) telemetry data from a set of tagged individuals. We estimated a stone marten density of 0.352 (SD: 0.081) individuals/km2. We simulated four dilution scenarios of occupancy data to study the variation in the coefficient of variation in population size estimates. We also used simulations with similar characteristics as the stone marten case study, comparing the accuracy and precision obtained from SCR-IM and SCR, to understand how submodels' integration affects the posterior distributions of estimated parameters. Based on our simulations, we found that population size estimates using SCR-IM are more accurate and precise. In our stone marten case study, the SCR-IM density estimation increased the precision by 37% when compared to the standard SCR model as regards to the coefficient of variation. This model has high potential to be used for species in which individual recognition by natural markings is not possible, therefore limiting the need to rely on invasive sampling procedures.
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Affiliation(s)
- José Jiménez
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC‐UCLM‐JCCM)Ciudad RealSpain
| | - Francisco Díaz‐Ruiz
- Departamento de Biología Animal, Facultad de CienciasUniversidad de MálagaMálagaSpain
| | - Pedro Monterroso
- CIBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, InBIO Laboratório AssociadoUniversidade do PortoVairãoPortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land PlanningCIBIOVairãoPortugal
| | - Jorge Tobajas
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC‐UCLM‐JCCM)Ciudad RealSpain
- Departamento de Botánica, Ecología y Fisiología VegetalUniversidad de CórdobaCórdobaSpain
| | - Pablo Ferreras
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC‐UCLM‐JCCM)Ciudad RealSpain
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9
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Comparison of methods for estimating density and population trends for low-density Asian bears. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02058] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
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10
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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 2022; 198:139-151. [PMID: 34859281 PMCID: PMC8803778 DOI: 10.1007/s00442-021-05087-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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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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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12
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Chutipong W, Steinmetz R, Gale GA. Spatial capture–recapture reveals high densities of large Indian civet, an omnivorous small carnivore in Southeast Asia. Mamm Biol 2021. [DOI: 10.1007/s42991-021-00172-9] [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]
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