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Li Y, Devenish C, Tosa MI, Luo M, Bell DM, Lesmeister DB, Greenfield P, Pichler M, Levi T, Yu DW. Combining environmental DNA and remote sensing for efficient, fine-scale mapping of arthropod biodiversity. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230123. [PMID: 38705177 PMCID: PMC11070265 DOI: 10.1098/rstb.2023.0123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 01/31/2024] [Indexed: 05/07/2024] Open
Abstract
Arthropods contribute importantly to ecosystem functioning but remain understudied. This undermines the validity of conservation decisions. Modern methods are now making arthropods easier to study, since arthropods can be mass-trapped, mass-identified, and semi-mass-quantified into 'many-row (observation), many-column (species)' datasets, with homogeneous error, high resolution, and copious environmental-covariate information. These 'novel community datasets' let us efficiently generate information on arthropod species distributions, conservation values, uncertainty, and the magnitude and direction of human impacts. We use a DNA-based method (barcode mapping) to produce an arthropod-community dataset from 121 Malaise-trap samples, and combine it with 29 remote-imagery layers using a deep neural net in a joint species distribution model. With this approach, we generate distribution maps for 76 arthropod species across a 225 km2 temperate-zone forested landscape. We combine the maps to visualize the fine-scale spatial distributions of species richness, community composition, and site irreplaceability. Old-growth forests show distinct community composition and higher species richness, and stream courses have the highest site-irreplaceability values. With this 'sideways biodiversity modelling' method, we demonstrate the feasibility of biodiversity mapping at sufficient spatial resolution to inform local management choices, while also being efficient enough to scale up to thousands of square kilometres. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.
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Affiliation(s)
- Yuanheng Li
- Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, State Key Laboratory of Genetic Resources and Evolution, Chinese Academy of Sciences, Kunming, Yunnan 650223, People’s Republic of China
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, People’s Republic of China
- Faculty of Biology, University of Duisburg-Essen, Essen 45141, Germany
| | - Christian Devenish
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR47TJ, UK
| | - Marie I. Tosa
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Mingjie Luo
- Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, State Key Laboratory of Genetic Resources and Evolution, Chinese Academy of Sciences, Kunming, Yunnan 650223, People’s Republic of China
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, People’s Republic of China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, People’s Republic of China
| | - David M. Bell
- Pacific Northwest Research Station, U.S. Department of Agriculture Forest Service, Corvallis, OR 97331, USA
| | - Damon B. Lesmeister
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, OR 97331, USA
- Pacific Northwest Research Station, U.S. Department of Agriculture Forest Service, Corvallis, OR 97331, USA
| | - Paul Greenfield
- CSIRO Energy, Lindfield, New South Wales, Australia
- School of Biological Sciences, Macquarie University, Sydney, Australia
| | | | - Taal Levi
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Douglas W. Yu
- Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, State Key Laboratory of Genetic Resources and Evolution, Chinese Academy of Sciences, Kunming, Yunnan 650223, People’s Republic of China
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, People’s Republic of China
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR47TJ, UK
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming Yunnan 650223, People’s Republic of China
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Eriksson CE, Roffler GH, Allen JM, Lewis A, Levi T. The origin, connectivity, and individual specialization of island wolves after deer extirpation. Ecol Evol 2024; 14:e11266. [PMID: 38633525 PMCID: PMC11021858 DOI: 10.1002/ece3.11266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/28/2024] [Accepted: 03/30/2024] [Indexed: 04/19/2024] Open
Abstract
Wolves are assumed to be ungulate obligates, however, a recently described pack on Pleasant Island, Alaska USA, is persisting on sea otters and other marine resources without ungulate prey, violating this long-held assumption. We address questions about these wolves regarding their origin and fate, degree of isolation, risk of inbreeding depression, and diet specialization by individual and sex. We applied DNA metabarcoding and genotyping by amplicon sequencing using 957 scats collected from 2016 to 2022, and reduced representation sequencing of tissue samples to establish a detailed understanding of Pleasant Island wolf ecology and compare them with adjacent mainland wolves. Dietary overlap was higher among individual wolves on Pleasant Island (Pianka's index mean 0.95 ± 0.03) compared to mainland wolves (0.70 ± 0.21). The individual diets of island wolves were dominated by sea otter, ranging from 40.6% to 63.2% weighted percent of occurrence (wPOO) (mean 55.5 ± 8.7). In contrast, individual mainland wolves primarily fed on ungulates (42.2 ± 21.3) or voles during a population outbreak (31.2 ± 23.2). We traced the origin of the Pleasant Island pack to a mainland pair that colonized around 2013 and produced several litters. After this breeding pair was killed, their female offspring and an immigrant male became the new breeders in 2019. We detected 20 individuals of which 8 (40%) were trapped and killed while two died of natural causes during the 6-year study. Except for the new breeding male, the pedigree analysis and genotype results showed no additional movement to or from the island, indicating limited dispersal but no evidence of inbreeding. Our findings suggest wolves exhibit more flexible foraging behavior than previously believed, and hunting strategies can substantially differ between individuals within or between packs. Nevertheless, anthropogenic and natural mortality combined with limited connectivity to the mainland may inhibit the continued persistence of Pleasant Island wolves.
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Affiliation(s)
- Charlotte E. Eriksson
- Department of Fisheries, Wildlife, and Conservation SciencesOregon State UniversityCorvallisOregonUSA
| | - Gretchen H. Roffler
- Alaska Department of Fish and GameDivision of Wildlife ConservationDouglasAlaskaUSA
| | - Jennifer M. Allen
- Department of Fisheries, Wildlife, and Conservation SciencesOregon State UniversityCorvallisOregonUSA
| | - Alex Lewis
- Alaska Department of Fish and GameDivision of Wildlife ConservationDouglasAlaskaUSA
| | - Taal Levi
- Department of Fisheries, Wildlife, and Conservation SciencesOregon State UniversityCorvallisOregonUSA
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Adams MS, Levi T, Bourbonnais M, Service CN, Artelle K, Bryan H, Paquet P, Nelson T, Darimont CT. Human disturbance in riparian areas disrupts predator-prey interactions between grizzly bears and salmon. Ecol Evol 2024; 14:e11058. [PMID: 38505181 PMCID: PMC10950355 DOI: 10.1002/ece3.11058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 03/21/2024] Open
Abstract
Wildlife must increasingly balance trade-offs between the need to access important foods and the mortality risks associated with human-dominated landscapes. Human disturbance can profoundly influence wildlife behavior, but managers know little about the relationship between disturbance-behavior dynamics and associated consequences for foraging. We address this gap by empirically investigating the consequences of human activity on a keystone predator-prey interaction in a region with limited but varied industrial disturbance. Using stable isotope data from 226 hair samples of grizzly bears (Ursus arctos horribilis) collected from 1995 to 2014 across 22 salmon-bearing watersheds (88,000 km2) in British Columbia, Canada, we examined how human activity influenced their consumption of spawning salmon (Oncorhynchus spp.), a fitness-related food. Accounting for the abundance of salmon and other foods, salmon consumption strongly decreased (up to 59% for females) with increasing human disturbance (as measured by the human footprint index) in riparian zones of salmon-bearing rivers. Declines in salmon consumption occurred with disturbance even in watersheds with low footprints. In a region currently among the least influenced by industrial activity, intensification of disturbance in river valleys is predicted to increasingly decouple bears from salmon, possibly driving associated reductions in population productivity and provisioning of salmon nutrients to terrestrial ecosystems. Accordingly, we draw on our results to make landscape-scale and access-related management recommendations beyond current streamside protection buffers. This work illustrates the interaction between habitat modification and food security for wildlife, highlighting the potential for unacknowledged interactions and cumulative effects in increasingly modified landscapes.
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Affiliation(s)
- Megan S. Adams
- Department of GeographyUniversity of VictoriaVictoriaBritish ColumbiaCanada
- Raincoast Conservation FoundationSidneyBritish ColumbiaCanada
- Hakai InstituteCampbell RiverBritish ColumbiaCanada
- Central Coast Indigenous Resource AllianceCampbell RiverBritish ColumbiaCanada
| | - Taal Levi
- Department of Fisheries and WildlifeOregon State UniversityCorvallisOregonUSA
| | - Mathieu Bourbonnais
- Department of Earth, Environmental and Geographic SciencesUniversity of British Columbia OkanaganKelownaBritish ColumbiaCanada
| | - Christina N. Service
- Department of GeographyUniversity of VictoriaVictoriaBritish ColumbiaCanada
- Kitasoo Xai'xais Stewardship Authority, Kitasoo Xai'xais First NationKlemtuBritish ColumbiaCanada
- School of Environmental StudiesUniversity of VictoriaVictoriaBritish ColumbiaCanada
| | - Kyle Artelle
- Department of GeographyUniversity of VictoriaVictoriaBritish ColumbiaCanada
- Raincoast Conservation FoundationSidneyBritish ColumbiaCanada
- Department of Earth, Environmental and Geographic SciencesUniversity of British Columbia OkanaganKelownaBritish ColumbiaCanada
- Department of Environmental Biology, and Center for Native Peoples and the EnvironmentState University of New York, College of Environmental Science and ForestrySyracuseNew YorkUSA
| | - Heather Bryan
- Department of GeographyUniversity of VictoriaVictoriaBritish ColumbiaCanada
- Raincoast Conservation FoundationSidneyBritish ColumbiaCanada
- Hakai InstituteCampbell RiverBritish ColumbiaCanada
- Department of Ecosystem Science and ManagementUniversity of Northern British ColumbiaPrince GeorgeBritish ColumbiaCanada
| | - Paul Paquet
- Department of GeographyUniversity of VictoriaVictoriaBritish ColumbiaCanada
- Raincoast Conservation FoundationSidneyBritish ColumbiaCanada
| | - Trisalyn Nelson
- Department of GeographyUniversity of California Santa BarbaraSanta BarbaraCaliforniaUSA
| | - Chris T. Darimont
- Department of GeographyUniversity of VictoriaVictoriaBritish ColumbiaCanada
- Raincoast Conservation FoundationSidneyBritish ColumbiaCanada
- Hakai InstituteCampbell RiverBritish ColumbiaCanada
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Dziedzic E, Sidlauskas B, Cronn R, Anthony J, Cornwell T, Friesen TA, Konstantinidis P, Penaluna BE, Stein S, Levi T. Creating, curating and evaluating a mitogenomic reference database to improve regional species identification using environmental DNA. Mol Ecol Resour 2023; 23:1880-1904. [PMID: 37602732 DOI: 10.1111/1755-0998.13855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/11/2023] [Accepted: 08/02/2023] [Indexed: 08/22/2023]
Abstract
Species detection using eDNA is revolutionizing global capacity to monitor biodiversity. However, the lack of regional, vouchered, genomic sequence information-especially sequence information that includes intraspecific variation-creates a bottleneck for management agencies wanting to harness the complete power of eDNA to monitor taxa and implement eDNA analyses. eDNA studies depend upon regional databases of mitogenomic sequence information to evaluate the effectiveness of such data to detect and identify taxa. We created the Oregon Biodiversity Genome Project to create a database of complete, nearly error-free mitogenomic sequences for all of Oregon's fishes. We have successfully assembled the complete mitogenomes of 313 specimens of freshwater, anadromous and estuarine fishes representing 24 families, 55 genera and 129 species and lineages. Comparative analyses of these sequences illustrate that many regions of the mitogenome are taxonomically informative, that the short (~150 bp) mitochondrial 'barcode' regions typically used for eDNA assays do not consistently diagnose for species and that complete single or multiple genes of the mitogenome are preferable for identifying Oregon's fishes. This project provides a blueprint for other researchers to follow as they build regional databases, illustrates the taxonomic value and limits of complete mitogenomic sequences and offers clues as to how current eDNA assays and environmental genomics methods of the future can best leverage this information.
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Affiliation(s)
- Emily Dziedzic
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Brian Sidlauskas
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Richard Cronn
- Pacific Northwest Research Station, US Department of Agriculture Forest Service, Corvallis, Oregon, USA
| | - James Anthony
- Oregon Department of Fish and Wildlife, Corvallis Research Laboratory, Corvallis, Oregon, USA
| | - Trevan Cornwell
- Oregon Department of Fish and Wildlife, Corvallis Research Laboratory, Corvallis, Oregon, USA
| | - Thomas A Friesen
- Oregon Department of Fish and Wildlife, Corvallis Research Laboratory, Corvallis, Oregon, USA
| | - Peter Konstantinidis
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Brooke E Penaluna
- Pacific Northwest Research Station, US Department of Agriculture Forest Service, Corvallis, Oregon, USA
| | - Staci Stein
- Oregon Department of Fish and Wildlife, Corvallis Research Laboratory, Corvallis, Oregon, USA
| | - Taal Levi
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
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5
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Ruprecht J, Wisdom MJ, Clark DA, Rowland MM, Levi T. Density-dependent changes in elk resource selection over successional time scales following forest disturbance. Ecol Appl 2023; 33:e2891. [PMID: 37232432 DOI: 10.1002/eap.2891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/07/2023] [Accepted: 04/14/2023] [Indexed: 05/27/2023]
Abstract
There is an increasing need to understand how animals respond to modifications of their habitat following landscape-scale disturbances such as wildfire or timber harvest. Such disturbances can promote increased use by herbivores due to changes in plant community structure that improve forage conditions, but can also cause avoidance if other habitat functions provided by cover are substantially reduced or eliminated. Quantifying the total effects of these disturbances, however, is challenging because they may not fully be apparent unless observed at successional timescales. Further, the effects of disturbances that improve habitat quality may be density dependent, such that the benefits are (1) less valuable to high-density populations because the per-capita benefits are reduced when shared among more users or, alternatively, (2) more valuable to animals living in high densities because resources may be more depleted from the greater intraspecific competition. We used 30 years of telemetry data on elk occurring at two distinct population densities to quantify changes in space use at diel, monthly, and successional timescales following timber harvest. Elk selected logged areas at night only, with selection strongest during midsummer, and peak selection occurring 14 years post harvest, but persisting for 26-33 years. This pattern of increased selection at night following a reduction in overhead canopy cover is consistent with elk exploiting improved nutritional conditions for foraging. The magnitude of selection for logged areas was 73% higher for elk at low population density, consistent with predictions from the ideal free distribution. Yet elk avoided these same areas during daytime for up to 28 years post logging and instead selected untreated forest, suggesting a role for cover to meet other life history requirements. Our results demonstrate that while landscape-scale disturbances can lead to increased selection by large herbivores and suggest that the improvement in foraging conditions can persist over short-term successional timescales, the magnitude of the benefits may not be equal across population densities. Further, the enduring avoidance of logging treatments during the daytime indicates a need for structurally intact forests and suggests that a mosaic of forest patches of varying successional stages and structural completeness is likely to be the most beneficial to large herbivores.
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Affiliation(s)
- Joel Ruprecht
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Michael J Wisdom
- USDA Pacific Northwest Research Station, US Forest Service, La Grande, Oregon, USA
| | - Darren A Clark
- Oregon Department of Fish and Wildlife, La Grande, Oregon, USA
| | - Mary M Rowland
- USDA Pacific Northwest Research Station, US Forest Service, La Grande, Oregon, USA
| | - Taal Levi
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
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6
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Di Florio M, Care M, Beaubois R, Cota VR, Barban F, Levi T, Chiappalone M. Design of an experimental setup for delivering intracortical microstimulation in vivo via Spiking Neural Network. Annu Int Conf IEEE Eng Med Biol Soc 2023; 2023:1-4. [PMID: 38083051 DOI: 10.1109/embc40787.2023.10340907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Electroceutical approaches for the treatment of neurological disorders, such as stroke, can take advantage of neuromorphic engineering, to develop devices able to achieve a seamless interaction with the neural system. This paper illustrates the development and test of a hardware-based Spiking Neural Network (SNN) to deliver neural-like stimulation patterns in an open-loop fashion. Neurons in the SNN have been designed by following the Hodgkin-Huxley formalism, with parameters taken from neuroscientific literature. We then built the set-up to deliver the SNN-driven stimulation in vivo. We used deeply anesthetized healthy rats to test the potential effect of the SNN-driven stimulation. We analyzed the neuronal firing activity pre- and post-stimulation in both the primary somatosensory and the rostral forelimb area. Our results showed that the SNN-based neurostimulation was able increase the spontaneous level of neuronal firing at both monitored locations, as found in the literature only for closed-loop stimulation. This study represents the first step towards translating the use of neuromorphic-based devices into clinical applications.Clinical Relevance- Stroke represents one of the leading causes of long-term disability and death worldwide. Intracortical microstimulation is an effective approach for restoring lost sensory motor integration by promoting plasticity among the affected brain areas. Stimulation delivered via neuromorphic-based open-loop systems (i.e. neuromorphic prostheses) can pave the way to novel electroceutical strategies for brain repair.
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7
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Darimont CT, Cooke R, Bourbonnais ML, Bryan HM, Carlson SM, Estes JA, Galetti M, Levi T, MacLean JL, McKechnie I, Paquet PC, Worm B. Humanity's diverse predatory niche and its ecological consequences. Commun Biol 2023; 6:609. [PMID: 37386144 PMCID: PMC10310721 DOI: 10.1038/s42003-023-04940-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 05/15/2023] [Indexed: 07/01/2023] Open
Abstract
Although humans have long been predators with enduring nutritive and cultural relationships with their prey, seldom have conservation ecologists considered the divergent predatory behavior of contemporary, industrialized humans. Recognizing that the number, strength and diversity of predator-prey relationships can profoundly influence biodiversity, here we analyze humanity's modern day predatory interactions with vertebrates and estimate their ecological consequences. Analysing IUCN 'use and trade' data for ~47,000 species, we show that fishers, hunters and other animal collectors prey on more than a third (~15,000 species) of Earth's vertebrates. Assessed over equivalent ranges, humans exploit up to 300 times more species than comparable non-human predators. Exploitation for the pet trade, medicine, and other uses now affects almost as many species as those targeted for food consumption, and almost 40% of exploited species are threatened by human use. Trait space analyses show that birds and mammals threatened by exploitation occupy a disproportionally large and unique region of ecological trait space, now at risk of loss. These patterns suggest far more species are subject to human-imposed ecological (e.g., landscapes of fear) and evolutionary (e.g., harvest selection) processes than previously considered. Moreover, continued overexploitation will likely bear profound consequences for biodiversity and ecosystem function.
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Affiliation(s)
- Chris T Darimont
- Department of Geography, University of Victoria, Victoria, BC, Canada.
- Raincoast Conservation Foundation, Sidney, BC, Canada.
| | - Rob Cooke
- UK Centre for Ecology & Hydrology, Wallingford, UK.
| | - Mathieu L Bourbonnais
- Department of Earth, Environmental, and Geographic Sciences, University of British Columbia Okanagan, Kelowna, BC, Canada
| | - Heather M Bryan
- Raincoast Conservation Foundation, Sidney, BC, Canada
- Department of Ecosystem Science and Management, University of Northern British Columbia, Prince George, BC, Canada
| | - Stephanie M Carlson
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - James A Estes
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Mauro Galetti
- São Paulo State University (UNESP), Department of Biodiversity, Rio Claro, São Paulo, Brazil
- Kimberly Green Latin American and Caribbean Center, Florida International University (FIU), Miami, FL, USA
| | - Taal Levi
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, OR, USA
| | - Jessica L MacLean
- Department of Geography, University of Victoria, Victoria, BC, Canada
- Raincoast Conservation Foundation, Sidney, BC, Canada
| | - Iain McKechnie
- Department of Anthropology, University of Victoria, Victoria, BC, Canada
- Hakai Institute, Heriot Bay, Quadra Island, BC, Canada
| | - Paul C Paquet
- Department of Geography, University of Victoria, Victoria, BC, Canada
- Raincoast Conservation Foundation, Sidney, BC, Canada
| | - Boris Worm
- Department of Biology, Dalhousie University, Halifax, NS, Canada
- Ocean Frontier Institute, Dalhousie University, Halifax, NS, Canada
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Levi T, Massey AL. Teasing apart the dilution effect by combining DNA metabarcoding and statistical modelling. Mol Ecol 2023; 32:1814-1816. [PMID: 36846962 DOI: 10.1111/mec.16906] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 03/01/2023]
Affiliation(s)
- Taal Levi
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Aimee L Massey
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
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Appel CL, Lesmeister DB, Duarte A, Davis RJ, Weldy MJ, Levi T. Using passive acoustic monitoring to estimate northern spotted owl landscape use and pair occupancy. Ecosphere 2023. [DOI: 10.1002/ecs2.4421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023] Open
Affiliation(s)
- Cara L. Appel
- Pacific Northwest Research Station USDA Forest Service Corvallis Oregon USA
- Department of Fisheries, Wildlife, and Conservation Sciences Oregon State University Corvallis Oregon USA
- Oak Ridge Institute for Science and Education Oak Ridge Tennessee USA
| | - Damon B. Lesmeister
- Pacific Northwest Research Station USDA Forest Service Corvallis Oregon USA
- Department of Fisheries, Wildlife, and Conservation Sciences Oregon State University Corvallis Oregon USA
| | - Adam Duarte
- Department of Fisheries, Wildlife, and Conservation Sciences Oregon State University Corvallis Oregon USA
- Pacific Northwest Research Station USDA Forest Service Olympia Washington USA
| | - Raymond J. Davis
- Pacific Northwest Region USDA Forest Service Corvallis Oregon USA
| | - Matthew J. Weldy
- Pacific Northwest Research Station USDA Forest Service Corvallis Oregon USA
- Oak Ridge Institute for Science and Education Oak Ridge Tennessee USA
- Department of Forest Ecosystems and Society Oregon State University Corvallis Oregon USA
| | - Taal Levi
- Department of Fisheries, Wildlife, and Conservation Sciences Oregon State University Corvallis Oregon USA
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Roffler GH, Pilgrim KL, Zarn KE, Schwartz MK, Levi T. Variation in adult and pup wolf diets at natal den sites is influenced by forest composition and configuration. Ecol Evol 2023; 13:e9648. [PMID: 36644699 PMCID: PMC9834010 DOI: 10.1002/ece3.9648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 11/26/2022] [Accepted: 12/01/2022] [Indexed: 01/13/2023] Open
Abstract
Although wolves are wide-ranging generalist carnivores throughout their life cycle, during the pup-rearing season wolf activity is focused on natal den sites where pup survival depends upon pack members provisioning food. Because prey availability is influenced by habitat quality within the home range, we investigated the relative importance of prey species for adults and pups and further examined the relationship between habitat characteristics, wolf diet, and litter size on Prince of Wales Island (POW) in Southeast Alaska. During 2012-2020, we detected 13 active den sites within the home ranges of nine wolf packs. We estimated minimum pup counts using motion-detecting cameras and individual genotypes from noninvasive samples (hair: n = 322; scat: n = 227) and quantified wolf diet composition using fecal DNA metabarcoding (n = 538). We assessed habitat composition, configuration, and connectivity within denning and annual home ranges estimated using wolf GPS-collar data. Contrary to expectations, wolves had a more constricted diet during denning season (April 15-July 31), and within this season pups had a narrower dietary niche (species richness [S] = 4) focused more on deer (relative frequency of occurrence [O/I] = 0.924) than adults (S = 15; deer O/I = 0.591). Litter size had a positive relationship with the relative frequency of deer in a wolf pack's diet. Wolf consumption of deer was positively associated with the proportion of young-growth forest (≤25 years old) within denning and annual home ranges. High levels of vegetation patch interspersion, and the density of closed logging roads were also important predictors, suggesting these habitat qualities were influential for increasing the availability of deer to wolves. Our results contrast with previous research indicating wolf pup diets included more alternate prey (i.e., beaver) than adults and emphasize the importance of deer to wolf viability on POW, especially during denning season.
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Affiliation(s)
- Gretchen H. Roffler
- Division of Wildlife ConservationAlaska Department of Fish and GameDouglasAlaskaUSA
| | - Kristine L. Pilgrim
- National Genomics Center for Wildlife and Fish ConservationRocky Mountain Research Station, USDA Forest ServiceMissoulaMontanaUSA
| | - Katherine E. Zarn
- National Genomics Center for Wildlife and Fish ConservationRocky Mountain Research Station, USDA Forest ServiceMissoulaMontanaUSA
- Present address:
National Technology and Development ProgramUSDA Forest ServiceFlagstaffArizonaUSA
| | - Michael K. Schwartz
- National Genomics Center for Wildlife and Fish ConservationRocky Mountain Research Station, USDA Forest ServiceMissoulaMontanaUSA
| | - Taal Levi
- Department of Fisheries and WildlifeOregon State UniversityCorvallisOregonUSA
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11
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Tosa MI, Lesmeister DB, Allen JM, Levi T. Multi‐locus
DNA
metabarcoding reveals seasonality of foraging ecology of western spotted skunks in the Pacific Northwest. Ecosphere 2023. [DOI: 10.1002/ecs2.4386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Marie I. Tosa
- Department of Fisheries, Wildlife, and Conservation Sciences Oregon State University Corvallis Oregon USA
| | - Damon B. Lesmeister
- Department of Fisheries, Wildlife, and Conservation Sciences Oregon State University Corvallis Oregon USA
- Pacific Northwest Research Station U.S. Department of Agriculture Forest Service Corvallis Oregon USA
| | - Jennifer M. Allen
- Department of Fisheries, Wildlife, and Conservation Sciences Oregon State University Corvallis Oregon USA
| | - Taal Levi
- Department of Fisheries, Wildlife, and Conservation Sciences Oregon State University Corvallis Oregon USA
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Ruprecht J, Forrester TD, Jackson NJ, Clark DA, Wisdom MJ, Rowland MM, Smith JB, Stewart KM, Levi T. A seasonal pulse of ungulate neonates influences space use by carnivores in a multi-predator, multi-prey system. Ecol Evol 2022; 12:e9389. [PMID: 36254298 PMCID: PMC9558345 DOI: 10.1002/ece3.9389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 07/27/2022] [Accepted: 08/28/2022] [Indexed: 11/08/2022] Open
Abstract
The behavioral mechanisms by which predators encounter prey are poorly resolved. In particular, the extent to which predators engage in active search for prey versus incidentally encountering them has not been well studied in many systems and particularly not for neonate prey during the birth pulse. Parturition of many large herbivores occurs during a short and predictable temporal window in which young are highly vulnerable to predation. Our study aims to determine how a suite of carnivores responds to the seasonal pulse of newborn ungulates using contemporaneous global positioning system (GPS) locations of four species of predators and two species of prey. We used step‐selection functions to assess whether coyotes, cougars, black bears, and bobcats encountered parturient adult female ungulates more often than expected by chance in a low‐density population of mule deer and a high‐density population of elk. We then assessed whether the carnivore species that encountered parturient prey more often than expected by chance did so by shifting their habitat use toward areas with a high probability of encountering neonates. None of the four carnivore species encountered GPS‐collared parturient mule deer more often than expected by chance. By contrast, we determined that cougar and male bear movements positioned them in the proximity of GPS‐collared parturient elk more often than expected by chance which may provide evidence of searching behavior. Although both male bears and cougars exhibited behavior consistent with active search for neonates, only male bears used elk parturition habitat in a way that dynamically tracked the phenology of the elk birth pulse suggesting that maximizing encounters with juvenile elk was a motivation when selecting resources. Our results suggest that there is high interspecific and intersexual variability in foraging strategies among large mammalian predators and their prey.
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Affiliation(s)
- Joel Ruprecht
- Department of Fisheries, Wildlife, and Conservation SciencesOregon State UniversityCorvallisOregonUSA
| | | | - Nathan J. Jackson
- Department of Natural Resources and Environmental ScienceUniversity of Nevada, RenoRenoNevadaUSA
| | | | - Michael J. Wisdom
- US Department of Agriculture Forest Service Pacific Northwest Research StationLa GrandeOregonUSA
| | - Mary M. Rowland
- US Department of Agriculture Forest Service Pacific Northwest Research StationLa GrandeOregonUSA
| | | | - Kelley M. Stewart
- Department of Natural Resources and Environmental ScienceUniversity of Nevada, RenoRenoNevadaUSA
| | - Taal Levi
- Department of Fisheries, Wildlife, and Conservation SciencesOregon State UniversityCorvallisOregonUSA
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13
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Lennox RJ, Brownscombe JW, Darimont C, Horodysky A, Levi T, Raby GD, Cooke SJ. The roles of humans and apex predators in sustaining ecosystem structure and function: Contrast, complementarity and coexistence. People and Nature 2022. [DOI: 10.1002/pan3.10385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Robert J. Lennox
- Laboratory for Freshwater Ecology and Inland Fisheries at NORCE Norwegian Research Center Bergen Norway
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology Carleton University Ottawa Ontario Canada
- Norwegian Institute for Nature Research (NINA) Trondheim Norway
| | - Jacob W. Brownscombe
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology Carleton University Ottawa Ontario Canada
- Great Lakes Laboratory for Fisheries and Aquatic Sciences Fisheries and Oceans Canada Burlington Ontario Canada
| | | | - Andrij Horodysky
- Department of Marine and Environmental Science Hampton University Hampton Virginia USA
| | - Taal Levi
- Department of Fisheries and Wildlife Oregon State University Corvallis Oregon USA
| | - Graham D. Raby
- Department of Biology Trent University Peterborough Ontario Canada
| | - Steven J. Cooke
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology Carleton University Ottawa Ontario Canada
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14
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Thorson JT, Arimitsu ML, Levi T, Roffler GH. Diet analysis using generalized linear models derived from foraging processes using R package
mvtweedie. Ecology 2022; 103:e3637. [PMID: 35060624 PMCID: PMC9286827 DOI: 10.1002/ecy.3637] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 10/19/2021] [Accepted: 10/27/2021] [Indexed: 11/09/2022]
Abstract
Diet analysis integrates a wide variety of visual, chemical, and biological identification of prey. Samples are often treated as compositional data, where each prey is analyzed as a continuous percentage of the total. However, analyzing compositional data results in analytical challenges, for example, highly parameterized models or prior transformation of data. Here, we present a novel approximation involving a Tweedie generalized linear model (GLM). We first review how this approximation emerges from considering predator foraging as a thinned and marked point process (with marks representing prey species and individual prey size). This derivation can motivate future theoretical and applied developments. We then provide a practical tutorial for the Tweedie GLM using new package mvtweedie that extends capabilities of widely used packages in R (mgcv and ggplot2) by transforming output to calculate prey compositions. We demonstrate this approach and software using two examples. Tufted Puffins (Fratercula cirrhata) provisioning their chicks on a colony in the northern Gulf of Alaska show decadal prey switching among sand lance and prowfish (1980–2000) and then Pacific herring and capelin (2000–2020), while wolves (Canis lupus ligoni) in southeast Alaska forage on mountain goats and marmots in northern uplands and marine mammals in seaward island coastlines.
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Affiliation(s)
| | - Mayumi L. Arimitsu
- U.S. Geological Survey Alaska Science Center, 250 Egan Dr. Juneau Alaska USA
| | - Taal Levi
- Department of Forest Ecosystems and Society OSU Corvallis Oregon USA
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15
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Barry BR, Moriarty K, Green D, Hutchinson RA, Levi T. Integrating multi‐method surveys and recovery trajectories into occupancy models. Ecosphere 2021. [DOI: 10.1002/ecs2.3886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Brent R. Barry
- Department of Fisheries and Wildlife Oregon State University Corvallis Oregon 97331 USA
| | - Katie Moriarty
- Pacific Northwest Research Station USDA Forest Service Corvallis Oregon 97331 USA
| | - David Green
- Institute of Natural Resources Oregon State University Portland Oregon 97207 USA
| | - Rebecca A. Hutchinson
- Department of Fisheries and Wildlife Oregon State University Corvallis Oregon 97331 USA
- School of Electrical Engineering and Computer Science Oregon State University Corvallis Oregon 97331 USA
| | - Taal Levi
- Department of Fisheries and Wildlife Oregon State University Corvallis Oregon 97331 USA
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16
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Parker‐Shames P, Choi C, Butsic V, Green D, Barry B, Moriarty K, Levi T, Brashares JS. The spatial overlap of small‐scale cannabis farms with aquatic and terrestrial biodiversity. Conservat Sci and Prac 2021. [DOI: 10.1111/csp2.602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Phoebe Parker‐Shames
- Department of Environmental Science, Policy & Management University of California Berkeley Berkeley California USA
- Cannabis Research Center at Berkeley University of California Berkeley Berkeley California USA
| | - Christopher Choi
- NASA DEVELOP National Program NASA Langley Research Center Hampton Virginia USA
| | - Van Butsic
- Department of Environmental Science, Policy & Management University of California Berkeley Berkeley California USA
- Cannabis Research Center at Berkeley University of California Berkeley Berkeley California USA
| | - David Green
- Institute for Natural Resources Oregon State University Corvallis Oregon USA
| | - Brent Barry
- Confederated Tribes of the Grande Ronde Grande Ronde Oregon USA
| | - Katie Moriarty
- National Council for Air and Stream Improvement, Inc (NCASI) Cary North Carolina USA
| | - Taal Levi
- Department of Fisheries and Wildlife Oregon State University Corvallis Oregon USA
| | - Justin S. Brashares
- Department of Environmental Science, Policy & Management University of California Berkeley Berkeley California USA
- Cannabis Research Center at Berkeley University of California Berkeley Berkeley California USA
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17
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Eriksson CE, Kantek DLZ, Miyazaki SS, Morato RG, Dos Santos-Filho M, Ruprecht JS, Peres CA, Levi T. Extensive aquatic subsidies lead to territorial breakdown and high density of an apex predator. Ecology 2021; 103:e03543. [PMID: 34841521 DOI: 10.1002/ecy.3543] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/27/2021] [Accepted: 09/22/2021] [Indexed: 01/25/2023]
Abstract
Energetic subsidies between terrestrial and aquatic ecosystems can strongly influence food webs and population dynamics. Our objective was to study how aquatic subsidies affected jaguar (Panthera onca) diet, sociality, and population density in a seasonally flooded protected area in the Brazilian Pantanal. The diet (n = 138 scats) was dominated by fish (46%) and aquatic reptiles (55%), representing the first jaguar population known to feed extensively on fish and to minimally consume mammals (11%). These aquatic subsidies supported the highest jaguar population density estimate to date (12.4 jaguars/100 km²) derived from camera traps (8,065 trap nights) and GPS collars (n = 13). Contrary to their mostly solitary behavior elsewhere, we documented social interactions previously unobserved between same-sex adults including cooperative fishing, co-traveling, and play. Our study demonstrates that aquatic subsidies, frequently described in omnivores, can also transform the ecology and behavior of obligate carnivores.
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Affiliation(s)
- Charlotte E Eriksson
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Daniel L Z Kantek
- Instituto Chico Mendes de Conservação da Biodiversidade (ICMBIO), Estação Ecológica de Taiamã (EET), Cáceres, Mato Grosso, Brazil
| | - Selma S Miyazaki
- Instituto Chico Mendes de Conservação da Biodiversidade (ICMBIO), Estação Ecológica de Taiamã (EET), Cáceres, Mato Grosso, Brazil
| | - Ronaldo G Morato
- Instituto Chico Mendes de Conservação da Biodiversidade (ICMBIO), Centro Nacional de Pesquisa e Conservação de Mamíferos Carnívoros (CENAP), Atibaia, São Paulo, Brazil
| | - Manoel Dos Santos-Filho
- Departamento de Ciências Biológicas, Universidade do Estado de Mato Grosso (UNEMAT), Cáceres, Mato Grosso, Brazil
| | - Joel S Ruprecht
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Carlos A Peres
- Centre for Ecology, Evolution and Conservation, School of Environmental Sciences, University of East Anglia, Norfolk, Norwich, NR4 7TJ, UK.,Instituto Juruá, Rua das Papoulas 97, Manaus, Brazil
| | - Taal Levi
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon, 97331, USA
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18
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Massey AL, Bronzoni RVDM, da Silva DJF, Allen JM, de Lázari PR, Dos Santos-Filho M, Canale GR, Bernardo CSS, Peres CA, Levi T. Invertebrates for vertebrate biodiversity monitoring: Comparisons using three insect taxa as iDNA samplers. Mol Ecol Resour 2021; 22:962-977. [PMID: 34601818 DOI: 10.1111/1755-0998.13525] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 09/17/2021] [Accepted: 09/29/2021] [Indexed: 11/30/2022]
Abstract
Metabarcoding of environmental DNA (eDNA) is now widely used to build diversity profiles from DNA that has been shed by species into the environment. There is substantial interest in the expansion of eDNA approaches for improved detection of terrestrial vertebrates using invertebrate-derived DNA (iDNA) in which hematophagous, sarcophagous, and coprophagous invertebrates sample vertebrate blood, carrion, or faeces. Here, we used metabarcoding and multiple iDNA samplers (carrion flies, sandflies, and mosquitos) collected from 39 forested sites in the southern Amazon to profile gamma and alpha diversity. Our main objectives were to (1) compare diversity found with iDNA to camera trapping, which is the conventional method of vertebrate diversity surveillance; and (2) compare each of the iDNA samplers to assess the effectiveness, efficiency, and potential biases associated with each sampler. In total, we collected and analysed 1759 carrion flies, 48,686 sandflies, and 4776 mosquitos. Carrion flies revealed the greatest total vertebrate species richness at the landscape level, despite the least amount of sampling effort and the fewest number of individuals captured for metabarcoding, followed by sandflies. Camera traps had the highest median species richness at the site-level but showed strong bias towards carnivore and ungulate species and missed much of the diversity described by iDNA methods. Mosquitos showed a strong feeding preference for humans as did sandflies for armadillos, thus presenting potential utility to further study related to host-vector interactions.
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Affiliation(s)
- Aimee L Massey
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | | | | | - Jennifer M Allen
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Patrick Ricardo de Lázari
- Centro de Estudos de Limnologia e Biodiversidade e Etnobiologia do Pantanal, Universidade do Estado de Mato Grosso, Cáceres, Brazil
| | - Manoel Dos Santos-Filho
- Centro de Estudos de Limnologia e Biodiversidade e Etnobiologia do Pantanal, Universidade do Estado de Mato Grosso, Cáceres, Brazil
| | - Gustavo Rodrigues Canale
- Instituto de Ciências Naturais, Humanas e Sociais, Universidade Federal de Mato Grosso, Sinop, Brazil
| | | | - Carlos Augusto Peres
- School of Environmental Sciences, University of East Anglia, Norwich, UK.,Instituto Juruá, Manaus, Brazil
| | - Taal Levi
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
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19
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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. Ecol Appl 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] [What about the content of this article? (0)] [Affiliation(s)] [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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20
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Abstract
Abstract
Understanding the mechanisms by which alien species become invasive can assure successful control programs and mitigate alien species’ impacts. The distribution of invasive wild pigs (Sus scrofa) has been sharply expanding throughout all regions of Brazil in the last few years. Here we demonstrate that large monocultural plantations provide the primary resource subsidies to invasive wild pigs in Brazil. We analyzed 106 stomach contents and carbon stable isotopes (δ13C) of 50 hair samples of wild pigs from a population immersed in a landscape dominated by sugar cane agriculture. Stomach contents were dominated by corn (41%), sugarcane (28.5%), vegetal matter (all other vegetation besides crops, 27%), and animal matter (vertebrates and invertebrates, 4%). Bayesian mixing model analysis of δ13C showed that food sources from C4 photosynthetic pathway (represented by corn and sugarcane) accounted for 94% of the long-term diet, while C3 food sources for only 6.2%. Our results indicate that corn and sugar cane are subsidizing the diet of wild pigs and can facilitate the population growth of this invasive species. Given that Brazil is a major agricultural producer and a hotspot of biodiversity, it is extremely concerning that extensive agriculture may accelerate the expansion of this invasive species, resulting in economic losses and cascading effects on natural habitats.
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Affiliation(s)
- Felipe Pedrosa
- Departamento de Biodiversidade, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro, SP, Brazil
- Mão na Mata – Manejo e Soluções Ambientais, São Paulo, SP, Brazil
| | - William Bercê
- Departamento de Biodiversidade, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro, SP, Brazil
| | - Vladimir Eliodoro Costa
- Centro de Isótopos Estáveis, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil
| | - Taal Levi
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA
| | - Mauro Galetti
- Departamento de Biodiversidade, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro, SP, Brazil
- Department of Biology, University of Miami, Coral Gables, FL, USA
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21
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Moriarty KM, Thompson J, Delheimer M, Barry BR, Linnell M, Levi T, Hamm K, Early D, Gamblin H, Szykman Gunther M, Ellison J, Prevéy JS, Hartman J, Davis R. Predicted distribution of a rare and understudied forest carnivore: Humboldt marten ( Martes caurina humboldtensis). PeerJ 2021; 9:e11670. [PMID: 34434640 PMCID: PMC8354145 DOI: 10.7717/peerj.11670] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 06/03/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Many mammalian species have experienced range contractions. Following a reduction in distribution that has resulted in apparently small and disjunct populations, the Humboldt marten (Martes caurina humboldtensis) was recently designated as federally Threatened and state Endangered. This subspecies of Pacific marten occurring in coastal Oregon and northern California, also known as coastal martens, appear unlike martens that occur in snow-associated regions in that vegetation associations appear to differ widely between Humboldt marten populations. We expected current distributions represent realized niches, but estimating factors associated with long-term occurrence was challenging for this rare and little-known species. Here, we assessed the predicted contemporary distribution of Humboldt martens and interpret our findings as hypotheses correlated with the subspecies' niche to inform strategic conservation actions. METHODS We modeled Humboldt marten distribution using a maximum entropy (Maxent) approach. We spatially-thinned 10,229 marten locations collected from 1996-2020 by applying a minimum distance of 500-m between locations, resulting in 384 locations used to assess correlations of marten occurrence with biotic and abiotic variables. We independently optimized the spatial scale of each variable and focused development of model variables on biotic associations (e.g., hypothesized relationships with forest conditions), given that abiotic factors such as precipitation are largely static and not alterable within a management context. RESULTS Humboldt marten locations were positively associated with increased shrub cover (salal (Gautheria shallon)), mast producing trees (e.g., tanoak, Notholithocarpus densiflorus), increased pine (Pinus sp.) proportion of total basal area, annual precipitation at home-range spatial scales, low and high amounts of canopy cover and slope, and cooler August temperatures. Unlike other recent literature, we found little evidence that Humboldt martens were associated with old-growth structural indices. This case study provides an example of how limited information on rare or lesser-known species can lead to differing interpretations, emphasizing the need for study-level replication in ecology. Humboldt marten conservation would benefit from continued survey effort to clarify range extent, population sizes, and fine-scale habitat use.
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Affiliation(s)
- Katie M. Moriarty
- Western Sustainable Forestry, National Council for Air and Stream Improvement, Inc., Corvallis, OR, United States of America
| | - Joel Thompson
- Pacific Northwest Region Data Resources Management, USDA Forest Service, Joseph, OR, United States of America
| | - Matthew Delheimer
- Pacific Southwest Research Station, USDA Forest Service, Placerville, CA, United States of America
| | - Brent R. Barry
- Confederated Tribes of the Grand Ronde, Grand Ronde, OR, United States of America
| | - Mark Linnell
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, OR, United States of America
| | - Taal Levi
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, United States of America
| | - Keith Hamm
- Green Diamond Resource Company, Korbel, CA, United States of America
| | - Desiree Early
- Green Diamond Resource Company, Korbel, CA, United States of America
| | - Holly Gamblin
- Department of Wildlife, Humboldt State University, Arcata, CA, United States of America
| | | | - Jordan Ellison
- Western Sustainable Forestry, National Council for Air and Stream Improvement, Inc., Corvallis, OR, United States of America
| | - Janet S. Prevéy
- Fort Collins Science Center, US Geological Survey, Fort Collins, CO, United States of America
| | | | - Raymond Davis
- Pacific Northwest Region, USDA Forest Service, Corvallis, OR, United States of America
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22
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Tosa MI, Dziedzic EH, Appel CL, Urbina J, Massey A, Ruprecht J, Eriksson CE, Dolliver JE, Lesmeister DB, Betts MG, Peres CA, Levi T. The Rapid Rise of Next-Generation Natural History. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.698131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Many ecologists have lamented the demise of natural history and have attributed this decline to a misguided view that natural history is outdated and unscientific. Although there is a perception that the focus in ecology and conservation have shifted away from descriptive natural history research and training toward hypothetico-deductive research, we argue that natural history has entered a new phase that we call “next-generation natural history.” This renaissance of natural history is characterized by technological and statistical advances that aid in collecting detailed observations systematically over broad spatial and temporal extents. The technological advances that have increased exponentially in the last decade include electronic sensors such as camera-traps and acoustic recorders, aircraft- and satellite-based remote sensing, animal-borne biologgers, genetics and genomics methods, and community science programs. Advances in statistics and computation have aided in analyzing a growing quantity of observations to reveal patterns in nature. These robust next-generation natural history datasets have transformed the anecdotal perception of natural history observations into systematically collected observations that collectively constitute the foundation for hypothetico-deductive research and can be leveraged and applied to conservation and management. These advances are encouraging scientists to conduct and embrace detailed descriptions of nature that remain a critically important component of the scientific endeavor. Finally, these next-generation natural history observations are engaging scientists and non-scientists alike with new documentations of the wonders of nature. Thus, we celebrate next-generation natural history for encouraging people to experience nature directly.
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23
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Massey AL, Roffler GH, Vermeul T, Allen JM, Levi T. Comparison of mechanical sorting and DNA metabarcoding for diet analysis with fresh and degraded wolf scats. Ecosphere 2021. [DOI: 10.1002/ecs2.3557] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Aimee L. Massey
- Department of Fisheries and Wildlife Oregon State University Corvallis Oregon97331USA
| | - Gretchen H. Roffler
- Alaska Department of Fish and Game Division of Wildlife Conservation P.O. Box 110024 Juneau Alaska99811USA
| | - Tessa Vermeul
- Department of Fisheries and Wildlife Oregon State University Corvallis Oregon97331USA
| | - Jennifer M. Allen
- Department of Fisheries and Wildlife Oregon State University Corvallis Oregon97331USA
| | - Taal Levi
- Department of Fisheries and Wildlife Oregon State University Corvallis Oregon97331USA
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24
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da Silva Pessoa Vieira CJ, Steiner São Bernardo C, Ferreira da Silva DJ, Rigotti Kubiszeski J, Serpa Barreto E, de Oliveira Monteiro HA, Canale GR, Peres CA, Massey AL, Levi T, Vieira de Morais Bronzoni R. Land-use effects on mosquito biodiversity and potential arbovirus emergence in the Southern Amazon, Brazil. Transbound Emerg Dis 2021; 69:1770-1781. [PMID: 33993650 DOI: 10.1111/tbed.14154] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/10/2021] [Indexed: 01/02/2023]
Abstract
The Amazon rainforest is considered the largest reservoir of culicids and arboviruses in the world. It has been under intense human-driven alteration, especially in the so-called 'Arc of Deforestation', located in the eastern and southern regions. The emergence and transmission of infectious diseases are increasing, potentially due to land-use change. We used landscape-scale mosquito surveillance across a forest fragmentation gradient in the southern Amazon to evaluate the relationship between forest disturbance and the composition and structure of mosquito communities with a particular focus on the potential for arbovirus emergence in the region. Generalized linear models and logistic regression were used to associate the degree of landscape disturbance with arbovirus vectors' richness and abundance. A total of 1,960 culicids, belonging to 50 species, were collected from 2015 to 2016. Among these species, 20 have been associated with the transmission of arboviruses. Our results show an association of land use, more specifically small size of forest remnants with more irregular shape and higher edge density, with the increase of arbovirus vectors' richness and abundance. Six species of mosquito vectors exhibited a higher probability of occurrence in landscapes with medium or high degrees of disturbance. Our results indicate that land-use change influences mosquito communities with potential implications for the emergence of arboviruses.
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Affiliation(s)
| | | | | | | | - Eriana Serpa Barreto
- Instituto de Ciências da Saúde, Universidade Federal de Mato Grosso, Sinop, Brazil
| | | | - Gustavo Rodrigues Canale
- Instituto de Ciências Naturais, Humanas e Sociais, Universidade Federal de Mato Grosso, Sinop, Brazil
| | | | - Aimee Leigh Massey
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA
| | - Taal Levi
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA
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25
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Affiliation(s)
- Lance Waller
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Taal Levi
- Quantitative Wildlife Ecology, Conservation, and Environmental Genetics Lab, Department of Fisheries Wildlife and Conservation Sciences, College of Agricultural Science, Oregon State University, Corvallis, Oregon, United States of America
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26
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Rodriguez JT, Lesmeister DB, Levi T. Mesocarnivore landscape use along a gradient of urban, rural, and forest cover. PeerJ 2021; 9:e11083. [PMID: 33868809 PMCID: PMC8034353 DOI: 10.7717/peerj.11083] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 02/17/2021] [Indexed: 11/23/2022] Open
Abstract
Mesocarnivores fill a vital role in ecosystems through effects on community health and structure. Anthropogenic-altered landscapes can benefit some species and adversely affect others. For some carnivores, prey availability increases with urbanization, but landscape use can be complicated by interactions among carnivores as well as differing human tolerance of some species. We used camera traps to survey along a gradient of urban, rural, and forest cover to quantify how carnivore landscape use varies among guild members and determine if a species was a human exploiter, adapter, or avoider. Our study was conducted in and around Corvallis, Oregon from April 2018 to February 2019 (11,914 trap nights) using 47 camera trap locations on a gradient from urban to rural. Our focal species were bobcat (Lynx rufus), coyote (Canis latrans), gray fox (Urocyon cinereoargenteus), opossum (Didelphis virginiana), raccoon (Procyon lotor), and striped skunk (Mephitis mephitis). Raccoon and opossum were human exploiters with low use of forest cover and positive association with urban and rural developed areas likely due to human-derived resources as well as some refugia from larger predators. Coyote and gray fox were human adapters with high use of natural habitats while the effects of urbanization ranged from weak to indiscernible. Bobcat and striped skunk appeared to be human avoiders with negative relationship with urban cover and higher landscape use of forest cover. We conducted a diel temporal activity analysis and found mostly nocturnal activity within the guild, but more diurnal activity by larger-bodied predators compared to the smaller species. Although these species coexist as a community in human-dominated landscapes throughout much of North America, the effects of urbanization were not equal across species. Our results, especially for gray fox and striped skunk, are counter to research in other regions, suggesting that mesopredator use of urbanized landscapes can vary depending on the environmental conditions of the study area and management actions are likely to be most effective when decisions are based on locally derived data.
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Affiliation(s)
- Jordan T. Rodriguez
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, OR, United States of America
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, United States of America
| | - Damon B. Lesmeister
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, OR, United States of America
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, United States of America
| | - Taal Levi
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, United States of America
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27
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Wolf C, Levi T, Ripple WJ, Zárrate-Charry DA, Betts MG. A forest loss report card for the world's protected areas. Nat Ecol Evol 2021; 5:520-529. [PMID: 33574606 DOI: 10.1038/s41559-021-01389-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 01/08/2021] [Indexed: 01/30/2023]
Abstract
Protected areas are a key tool in the conservation of global biodiversity and carbon stores. We conducted a global test of the degree to which more than 18,000 terrestrial protected areas (totalling 5,293,217 km2) reduce deforestation in relation to unprotected areas. We also derived indices that quantify how well countries' forests are protected, both in terms of forested area protected and effectiveness of protected areas at reducing deforestation, in relation to vertebrate species richness, aboveground forest carbon biomass and background deforestation rates. Overall, protected areas did not eliminate deforestation, but reduced deforestation rates by 41%. Protected area deforestation rates were lowest in small reserves with low background deforestation rates. Critically, we found that after adjusting for effectiveness, only 6.5%-rather than 15.7%-of the world's forests are protected, well below the Aichi Convention on Biological Diversity's 2020 Target of 17%. We propose that global targets for protected areas should include quantitative goals for effectiveness in addition to spatial extent.
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Affiliation(s)
- Christopher Wolf
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA.
| | - Taal Levi
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA
| | - William J Ripple
- Global Trophic Cascades Program, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Diego A Zárrate-Charry
- Forest Biodiversity Research Network, Oregon State University, Corvallis, OR, USA.,Proyecto de Conservación de Aguas y Tierras, Bogotá, Colombia
| | - Matthew G Betts
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA.,Forest Biodiversity Research Network, Oregon State University, Corvallis, OR, USA
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28
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White KS, Levi T, Breen J, Britt M, Meröndun J, Martchenko D, Shakeri YN, Porter B, Shafer ABA. Integrating Genetic Data and Demographic Modeling to Facilitate Conservation of Small, Isolated Mountain Goat Populations. J Wildl Manage 2021. [DOI: 10.1002/jwmg.21978] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kevin S. White
- Division of Wildlife Conservation Alaska Department of Fish and Game Juneau AK 99811 USA
| | - Taal Levi
- Department of Fish and Wildlife Oregon State University Corvallis OR 97331 USA
| | - Jessica Breen
- Forensics Program, Trent University Peterborough ON K9J 7B8 Canada
| | - Meghan Britt
- Forensics Program, Trent University Peterborough ON K9J 7B8 Canada
| | - Justin Meröndun
- Environmental and Life Sciences Graduate Program Trent University Peterborough ON K9J 7B8 Canada
| | - Daria Martchenko
- Environmental and Life Sciences Graduate Program Trent University Peterborough ON K9J 7B8 Canada
| | - Yasaman N. Shakeri
- Division of Wildlife Conservation Alaska Department of Fish and Game Juneau AK 99811 USA
| | - Boyd Porter
- Division of Wildlife Conservation Alaska Department of Fish and Game Juneau AK 99811 USA
| | - Aaron B. A. Shafer
- Forensic Science Program and Environmental and Life Sciences Graduate Program Trent University Peterborough ON K9J 7B8 Canada
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29
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Penaluna BE, Allen JM, Arismendi I, Levi T, Garcia TS, Walter JK. Better boundaries: identifying the upper extent of fish distributions in forested streams using eDNA and electrofishing. Ecosphere 2021. [DOI: 10.1002/ecs2.3332] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Brooke E. Penaluna
- Pacific Northwest Research Station U.S. Department of Agriculture, Forest Service 3200 SW Jefferson Way Corvallis Oregon97331USA
| | - Jennifer M. Allen
- Department of Fisheries and Wildlife Oregon State University 104 Nash Hall Corvallis Oregon97331USA
| | - Ivan Arismendi
- Department of Fisheries and Wildlife Oregon State University 104 Nash Hall Corvallis Oregon97331USA
| | - Taal Levi
- Department of Fisheries and Wildlife Oregon State University 104 Nash Hall Corvallis Oregon97331USA
| | - Tiffany S. Garcia
- Department of Fisheries and Wildlife Oregon State University 104 Nash Hall Corvallis Oregon97331USA
| | - Jason K. Walter
- Weyerhaeuser Centralia Research Center 505 North Pearl Street Centralia Washington98531USA
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Roffler GH, Allen JM, Massey A, Levi T. Metabarcoding of fecal DNA shows dietary diversification in wolves substitutes for ungulates in an island archipelago. Ecosphere 2021. [DOI: 10.1002/ecs2.3297] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Gretchen H. Roffler
- Alaska Department of Fish and Game Division of Wildlife Conservation 802 3rd Street Douglas Alaska99824USA
| | - Jennifer M. Allen
- Department of Fisheries and Wildlife Oregon State University Corvallis Oregon97331USA
| | - Aimee Massey
- Department of Fisheries and Wildlife Oregon State University Corvallis Oregon97331USA
| | - Taal Levi
- Department of Fisheries and Wildlife Oregon State University Corvallis Oregon97331USA
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31
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Abstract
Understanding how a pathogen can grow on different substrates and how this growth impacts its dispersal are critical to understanding the risks and control of emerging infectious diseases. Pseudogymnoascus destructans (Pd) causes white-nose syndrome (WNS) in many bat species and can persist in, and transmit from, the environment. We experimentally evaluated Pd growth on common substrates to better understand mechanisms of pathogen persistence, transmission and viability. We inoculated autoclaved guano, fresh guano, soil, and wood with live Pd fungus and evaluated (1) whether Pd grows or persists on each (2) if spores of the fungus remain viable 4 months after inoculation on each substrate, and (3) whether detection and quantitation of Pd on swabs is sensitive to the choice to two commonly used DNA extraction kits. After inoculating each substrate with 460,000 Pd spores, we collected ~ 0.20 g of guano and soil, and swabs from wood every 16 days for 64 days to quantify pathogen load through time using real-time qPCR. We detected Pd on all substrates over the course of the experiment. We observed a tenfold increase in pathogen loads on autoclaved guano and persistence but not growth in fresh guano. Pathogen loads increased marginally on wood but declined ~ 60-fold in soil. After four months, apparently viable spores were harvested from all substrates but germination did not occur from fresh guano. We additionally found that detection and quantitation of Pd from swabs of wood surfaces is sensitive to the DNA extraction method. The commonly used PrepMan Ultra Reagent protocol yielded substantially less DNA than did the QIAGEN DNeasy Blood and Tissue Kit. Notably the PrepMan Ultra Reagent failed to detect Pd in many wood swabs that were detected by QIAGEN and were subsequently found to contain substantial live conidia. Our results indicate that Pd can persist or even grow on common environmental substrates with results dependent on whether microbial competitors have been eliminated. Although we observed clear rapid declines in Pd on soil, viable spores were harvested four months after inoculation. These results suggest that environmental substrates and guano can in general serve as infectious environmental reservoirs due to long-term persistence, and even growth, of live Pd. This should inform management interventions to sanitize or modify structures to reduce transmission risk as well early detection rapid response (EDRR) planning.
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Affiliation(s)
- Jenny Urbina
- Department of Fisheries and Wildlife, Oregon State University, 2820 SW Campus Way, Nash Hall, Corvallis, OR, 97331, USA.
| | - Tara Chestnut
- National Park Service, Mount Rainier National Park, Ashford, WA, USA
| | - Jennifer M Allen
- Department of Fisheries and Wildlife, Oregon State University, 2820 SW Campus Way, Nash Hall, Corvallis, OR, 97331, USA
| | - Taal Levi
- Department of Fisheries and Wildlife, Oregon State University, 2820 SW Campus Way, Nash Hall, Corvallis, OR, 97331, USA
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Levi T, Hilderbrand GV, Hocking MD, Quinn TP, White KS, Adams MS, Armstrong JB, Crupi AP, Darimont CT, Deacy W, Gilbert SL, Ripple WJ, Shakeri YN, Wheat RE, Wilmers CC. Community Ecology and Conservation of Bear-Salmon Ecosystems. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.513304] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Apex predators play keystone roles in ecosystems through top-down control, but the effects of apex omnivores on ecosystems could be more varied because changes in the resource base alter their densities and reverberate through ecosystems in complex ways. In coastal temperate ecosystems throughout much of the Northern Hemisphere, anadromous salmon once supported abundant bear populations, but both taxa have declined or been extirpated from large parts of their former ranges with limited research on the consequences of diminished or absent interactions among species. Here we review the biogeography of bear-salmon interactions and the role of salmon-subsidized bears in (1) resource provisioning to plants and scavengers through the distribution of salmon carcasses, (2) competition among bears and other large carnivores, (3) predation of ungulate neonates, (4) seed dispersal, and (5) resource subsidies to rodents with seed-filled scats. In addition to our review of the literature, we present original data to demonstrate two community-level patterns that are currently unexplained. First, deer densities appear to be consistently higher on islands with abundant brown bears than adjacent islands with black bears and wolves, and moose calf survival is higher at low bear densities (<∼25 bears per 100 km2) but is constant across the vast majority of bear densities found in the wild (i.e., ∼>25 bears per 100 km2). Our review and empirical data highlight key knowledge gaps and research opportunities to understand the complex ecosystem effects related to bear-salmon interactions.
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33
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Vieira CJDSP, Andrade CDD, Kubiszeski JR, Silva DJFD, Barreto ES, Massey AL, Canale GR, Bernardo CSS, Levi T, Peres CA, Bronzoni RVDM. Detection of Ilheus virus in mosquitoes from southeast Amazon, Brazil. Trans R Soc Trop Med Hyg 2020; 113:424-427. [PMID: 31050765 DOI: 10.1093/trstmh/trz031] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/28/2019] [Accepted: 04/01/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Arbovirus surveillance in field-collected mosquitoes is essential in monitoring virus activity to avoid emergence and outbreaks of arboviruses. METHODS We used reverse transcription polymerase chain reaction methods to search for arbovirus in mosquitoes collected in Brazil's southeast Amazon forest remnants during 2015-2016. RESULTS We detected Iheus virus (ILHV) RNA in Culex declarator, Culex (Melanoconion) and Ochlerotatus serratus mosquitoes. CONCLUSIONS These results indicate ILHV circulation in the studied area, highlighting its potential emergence in human population. More studies are necessary to confirm the roles of these three species in ILHV maintenance.
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Affiliation(s)
| | - Camila Decol de Andrade
- Instituto de Ciências da Saúde, Universidade Federal de Mato Grosso, 1200 Avenida Alexandre Ferronato, Sinop, Brazil
| | - Janaína Rigotti Kubiszeski
- Instituto de Ciências da Saúde, Universidade Federal de Mato Grosso, 1200 Avenida Alexandre Ferronato, Sinop, Brazil
| | - David José Ferreira da Silva
- Instituto de Ciências da Saúde, Universidade Federal de Mato Grosso, 1200 Avenida Alexandre Ferronato, Sinop, Brazil
| | - Eriana Serpa Barreto
- Instituto de Ciências da Saúde, Universidade Federal de Mato Grosso, 1200 Avenida Alexandre Ferronato, Sinop, Brazil
| | - Aimee Leigh Massey
- College of Agricultural Sciences, Oregon State University, Nash Hall, 2820 SW Campus Way, Corvallis, USA
| | - Gustavo Rodrigues Canale
- Instituto de Ciências Naturais, Humanas e Sociais, Universidade Federal de Mato Grosso, 1200 Avenida Alexandre Ferronato, Sinop, Brazil
| | - Christine Steiner São Bernardo
- Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Rua José Moreira Sobrinho, Jequié, Brazil
| | - Taal Levi
- College of Agricultural Sciences, Oregon State University, Nash Hall, 2820 SW Campus Way, Corvallis, USA
| | - Carlos Augusto Peres
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, England
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34
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Eriksson CE, Ruprecht J, Levi T. More affordable and effective noninvasive single nucleotide polymorphism genotyping using high‐throughput amplicon sequencing. Mol Ecol Resour 2020; 20:1505-1516. [DOI: 10.1111/1755-0998.13208] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 12/26/2022]
Affiliation(s)
| | - Joel Ruprecht
- Department of Fisheries and Wildlife Oregon State University Corvallis OR USA
| | - Taal Levi
- Department of Fisheries and Wildlife Oregon State University Corvallis OR USA
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35
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Merems JL, Shipley LA, Levi T, Ruprecht J, Clark DA, Wisdom MJ, Jackson NJ, Stewart KM, Long RA. Nutritional-Landscape Models Link Habitat Use to Condition of Mule Deer (Odocoileus hemionus). Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00098] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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36
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Urbina J, Chestnut T, Schwalm D, Allen J, Levi T. Experimental evaluation of genomic DNA degradation rates for the pathogen Pseudogymnoascus destructans (Pd) in bat guano. PeerJ 2020; 8:e8141. [PMID: 31998550 PMCID: PMC6977466 DOI: 10.7717/peerj.8141] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 11/01/2019] [Indexed: 11/30/2022] Open
Abstract
Pseudogymnoascus destructans (Pd), the causative agent of white-nose syndrome in bats (WNS), has led to dramatic declines of bat populations in eastern North America. In the spring of 2016, WNS was first detected at several locations in Washington State, USA, which has prompted the need for large scale surveillance efforts to monitor the spread of Pd. Pd is typically detected in bats using invasive methods requiring capturing and swabbing individual bats. However, Pd can also be detected in guano, which may provide an efficient, affordable, and noninvasive means to monitor Pd in bats across North America. The widespread implementation of Pd surveillance in guano is hindered by substantial uncertainty about the probability of detecting Pd when present, and how this probability is influenced by the time since defecation, local environmental conditions, the amount of guano sampled, and the original concentration of DNA shed in the guano. In addition, the expected degradation rate of Pd DNA depends on whether the Pd DNA found in guano represents extracellular DNA fragments, intracellular DNA from dead Pd fungal cells, or from intracellular and viable Pd cells. While this is currently unknown, it has been posited that most environmental DNA, such as Pd found in guano long after defecation, is fragmented extracellular DNA. Using non-viable isolated DNA at precise quantities, we experimentally characterized the degradation rates of Pd DNA in guano samples. We spiked 450 guano samples with Pd gDNA in a 10-fold dilution series from 1 million to 1,000 fg and placed them in variable environmental conditions at five sites at Mount Rainier National Park in Washington State, which is a priority location for Pd surveillance. We evaluated DNA degradation over 70 days by quantifying the amount of DNA in samples collected every 14 days using real-time quantitative PCR (qPCR). Our sampling period was from July 10th to September 17th 2018 which overlaps with bat movement between summer roosts as well as movement from maternity colonies fall swarms. We detected Pd DNA in guano 56 and 70 days after inoculation with 1 million and 100,000 fg respectively, while the lowest quantity (1,000 fg) was detected until 42 days. Detection probability was variable among sites and lower where samples were left exposed without overhead cover. If Pd is shed as extracellular DNA in guano at quantities above 1,000 fg, then guano collection is likely to provide an effective tool for environmental screening of Pd that can be employed in an early detection and rapid response framework throughout Washington and other regions where this disease is rapidly emerging.
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Affiliation(s)
- Jenny Urbina
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, United States of America
| | - Tara Chestnut
- Mount Rainier National Park, National Park Service, Ashford, WA, United States of America
| | - Donelle Schwalm
- Department of Biology, University of Maine-Farmington, Farmington, ME, United States of America
| | - Jenn Allen
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, United States of America
| | - Taal Levi
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, United States of America
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37
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Pochardt M, Allen JM, Hart T, Miller SDL, Yu DW, Levi T. Environmental DNA facilitates accurate, inexpensive, and multiyear population estimates of millions of anadromous fish. Mol Ecol Resour 2019; 20:457-467. [DOI: 10.1111/1755-0998.13123] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 12/02/2019] [Accepted: 12/02/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Meredith Pochardt
- Department of Fisheries and Wildlife Oregon State University Corvallis OR USA
- Chilkoot Indian Association Haines AK USA
- Takshanuk Watershed Council Haines AK USA
| | - Jennifer M. Allen
- Department of Fisheries and Wildlife Oregon State University Corvallis OR USA
| | - Ted Hart
- Chilkoot Indian Association Haines AK USA
| | - Sophie D. L. Miller
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
- School of Biological Sciences University of East Anglia Norwich UK
| | - Taal Levi
- Department of Fisheries and Wildlife Oregon State University Corvallis OR USA
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38
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Sabino-Santos G, Ferreira FF, da Silva DJF, Machado DM, da Silva SG, São Bernardo CS, Dos Santos Filho M, Levi T, Figueiredo LTM, Peres CA, de Morais Bronzoni RV, Canale GR. Hantavirus antibodies among phyllostomid bats from the arc of deforestation in Southern Amazonia, Brazil. Transbound Emerg Dis 2019; 67:1045-1051. [PMID: 31793244 DOI: 10.1111/tbed.13442] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/19/2019] [Accepted: 11/25/2019] [Indexed: 12/15/2022]
Abstract
In order to determine whether southern Amazonian bats could harbour hantaviruses we, serologically and molecularly, screened blood, saliva, excreta and organ tissues of 47 bats captured from September to December 2015. We found that only phyllostomid bats presented antibodies against hantavirus. The seropositive bats belonged to two species of Phyllostomid bats: the greater spear-nosed bat Phyllostomus hastatus (omnivorous) and the gnome fruit-eating bat Dermanura gnoma. The overall seroprevalence was of 4.2%. Therefore, we show here that hantaviruses are circulating among phyllostomid bats in the Amazonian arc of deforestation.
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Affiliation(s)
- Gilberto Sabino-Santos
- Center for Virology Research, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto-SP, Brazil.,Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Francimeire Fernandes Ferreira
- Biological Collection of Southern Amazon, Federal University of Mato Grosso, Sinop-MT, Brazil.,Graduate Program of Environmental Sciences, Department of Biological Sciences, State University of Mato Grosso, Caceres-MT, Brazil
| | - David José Ferreira da Silva
- Laboratory of Immunology and Virology, Veterinary Medicine Hospital, Federal University of Mato Grosso, Sinop-MT, Brazil
| | - Danilo Melo Machado
- Center for Virology Research, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto-SP, Brazil
| | - Sergio Gomes da Silva
- Laboratory of Biological and Ecological Sciences, Federal Institute of Sciences, Education and Technologies of Mato Grosso State, Pontes e Lacerda-MT, Brazil
| | | | - Manoel Dos Santos Filho
- Laboratory of Mammalogy, Department of Biological Sciences, State University of Mato Grosso, Caceres-MT, Brazil
| | - Taal Levi
- Laboratory of Quantitative Wildlife Ecology, Conservation, and Environmental Genetics, Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA
| | | | - Carlos A Peres
- School of Environmental Sciences, University of East Anglia, Norwich, UK
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Betts MG, Wolf C, Pfeifer M, Banks-Leite C, Arroyo-Rodríguez V, Ribeiro DB, Barlow J, Eigenbrod F, Faria D, Fletcher RJ, Hadley AS, Hawes JE, Holt RD, Klingbeil B, Kormann U, Lens L, Levi T, Medina-Rangel GF, Melles SL, Mezger D, Morante-Filho JC, Orme CDL, Peres CA, Phalan BT, Pidgeon A, Possingham H, Ripple WJ, Slade EM, Somarriba E, Tobias JA, Tylianakis JM, Urbina-Cardona JN, Valente JJ, Watling JI, Wells K, Wearn OR, Wood E, Young R, Ewers RM. Extinction filters mediate the global effects of habitat fragmentation on animals. Science 2019; 366:1236-1239. [DOI: 10.1126/science.aax9387] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 10/23/2019] [Indexed: 12/16/2022]
Abstract
Habitat loss is the primary driver of biodiversity decline worldwide, but the effects of fragmentation (the spatial arrangement of remaining habitat) are debated. We tested the hypothesis that forest fragmentation sensitivity—affected by avoidance of habitat edges—should be driven by historical exposure to, and therefore species’ evolutionary responses to disturbance. Using a database containing 73 datasets collected worldwide (encompassing 4489 animal species), we found that the proportion of fragmentation-sensitive species was nearly three times as high in regions with low rates of historical disturbance compared with regions with high rates of disturbance (i.e., fires, glaciation, hurricanes, and deforestation). These disturbances coincide with a latitudinal gradient in which sensitivity increases sixfold at low versus high latitudes. We conclude that conservation efforts to limit edges created by fragmentation will be most important in the world’s tropical forests.
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Affiliation(s)
- Matthew G. Betts
- Forest Biodiversity Research Network, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331, USA
| | - Christopher Wolf
- Forest Biodiversity Research Network, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331, USA
| | - Marion Pfeifer
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, UK
| | | | - Víctor Arroyo-Rodríguez
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México (UNAM), Campus Morelia, Antigua Carretera Patzcuaro no. 8701, Ex-Hacienda de San José de la Huerta, 58190 Morelia, Michoacán, Mexico
| | - Danilo Bandini Ribeiro
- Instituo de Biociências, Universidade Federal de Mato Grosso do Sul, Caixa Postal 549, 79070-900 Campo Grande, Brazil
| | - Jos Barlow
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
- Setor Ecologia, Departamento de Biologia, Universidade Federal de Lavras, 37200-000, Lavras, MG, Brazil
| | - Felix Eigenbrod
- Geography and Environmental Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Deborah Faria
- Applied Conservation Ecology Lab, Programa de Pós-graduação em Ecologia e Conservação, da Biodiversidade, Universidade Estadual de Santa Cruz, Rodovia Ilhéus-Itabuna, km 16, Salobrinho, 45662-000 Ilhéus, Bahia, Brazil
| | - Robert J. Fletcher
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611, USA
| | - Adam S. Hadley
- Forest Biodiversity Research Network, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331, USA
| | - Joseph E. Hawes
- Applied Ecology Research Group, School of Life Sciences, Anglia Ruskin University, Cambridge CB1 1PT, UK
| | - Robert D. Holt
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Brian Klingbeil
- School of Forestry and Wildlife Sciences, Auburn University, Auburn, AL 36849, USA
| | - Urs Kormann
- Forest Biodiversity Research Network, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331, USA
- Swiss Ornithological Institute, Sempach, Switzerland
- Division of Forest Sciences, School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Zollikofen, Switzerland
| | - Luc Lens
- Ghent University, Department of Biology, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Taal Levi
- Forest Biodiversity Research Network, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331, USA
| | - Guido F. Medina-Rangel
- Groupo de Biodiversidad y Conservación, Reptiles, Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Ciudad Universitaria, Edificio 425, Bogotá, Distrito Capital, Colombia
| | - Stephanie L. Melles
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada
| | - Dirk Mezger
- Department of Science and Education, Field Museum of Natural History, Chicago, IL 60605, USA
| | - José Carlos Morante-Filho
- Applied Conservation Ecology Lab, Programa de Pós-graduação em Ecologia e Conservação, da Biodiversidade, Universidade Estadual de Santa Cruz, Rodovia Ilhéus-Itabuna, km 16, Salobrinho, 45662-000 Ilhéus, Bahia, Brazil
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Avenida Transnordestina, s/n - Novo Horizonte, 44036-900 Feira de Santana, Bahia, Brazil
| | - C. David L. Orme
- Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot SL5 7PY, UK
| | - Carlos A. Peres
- Centre for Ecology, Evolution and Conservation, School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Benjamin T. Phalan
- Instituto de Biologia, Universidade Federal da Bahia, Salvador, 40170-115 Bahia, Brazil
| | - Anna Pidgeon
- Department of Forest and Wildlife Ecology, University of Wisconsin–Madison, 1630 Linden Drive, Madison, WI 53706, USA
| | - Hugh Possingham
- School of Biological Sciences, University of Queensland, St Lucia, Queensland, Australia
- The Nature Conservancy, Arlington, VA 22203, USA
| | - William J. Ripple
- Forest Biodiversity Research Network, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331, USA
| | - Eleanor M. Slade
- Asian School of the Environment, Nanyang Technological University, 62 Nanyang Dr., 637459 Singapore
| | - Eduardo Somarriba
- Centro Agronómico Tropical de Investigación y Enseñanza, Turrialba, Costa Rica
| | - Joseph A. Tobias
- Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot SL5 7PY, UK
| | - Jason M. Tylianakis
- School of Biological Sciences, University of Canterbury, Private bag 4800, Christchurch 8140, New Zealand
| | - J. Nicolás Urbina-Cardona
- Department of Ecology and Territory, School of Rural and Environmental Studies, Pontificia Universidad Javeriana, Bogota, Colombia
| | - Jonathon J. Valente
- Forest Biodiversity Research Network, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331, USA
- Smithsonian Conservation Biology Institute, Migratory Bird Center, National Zoological Park, Washington, DC 20013, USA
| | - James I. Watling
- Department of Biology, John Carroll University, University Heights, OH 44118, USA
| | - Konstans Wells
- Department of Biosciences, Swansea University, Swansea SA2 8PP, Wales, UK
| | - Oliver R. Wearn
- Institute of Zoology, Zoological Society of London, Regent’s Park, London NW1 4RY, UK
| | - Eric Wood
- Department of Biological Sciences, California State University Los Angeles, 5151 State University Drive, Los Angeles, CA 90032, USA
| | - Richard Young
- Durrell Wildlife Conservation Trust, Les Augres Manor, Trinity, Jersey JE3 5BP, UK
| | - Robert M. Ewers
- Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot SL5 7PY, UK
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40
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Wolf C, Ripple WJ, Betts MG, Levi T, Peres CA. Eating plants and planting forests for the climate. Glob Chang Biol 2019; 25:3995. [PMID: 31613034 DOI: 10.1111/gcb.14835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 08/22/2019] [Indexed: 06/10/2023]
Abstract
The IPCC's Special Report on Climate Change and Land addresses the closely coupled relationship between land use and climate change. The report notes the climate change mitigation potential of dietary shifts and afforestation. Here, we briefly discuss how decreases in ruminant meat consumption associated with dietary shifts have the potential to free up area for forests, allowing for greater CO2 sequestration and benefiting biodiversity, while simultaneously reducing anthropogenic CO2 emissions.
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Affiliation(s)
- Christopher Wolf
- Forest Biodiversity Research Network, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - William J Ripple
- Forest Biodiversity Research Network, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Matthew G Betts
- Forest Biodiversity Research Network, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Taal Levi
- Forest Biodiversity Research Network, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Carlos A Peres
- Center for Ecology, Evolution & Conservation, School of Environmental Sciences, University of East Anglia, Norwich, UK
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41
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Fragoso JMV, Gonçalves F, Oliveira LFB, Overman H, Levi T, Silvius KM. Visual encounters on line transect surveys under-detect carnivore species: Implications for assessing distribution and conservation status. PLoS One 2019; 14:e0223922. [PMID: 31665170 PMCID: PMC6821099 DOI: 10.1371/journal.pone.0223922] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 10/01/2019] [Indexed: 11/19/2022] Open
Abstract
We compared the distribution and occurrence of 15 carnivore species with data collected monthly over three years by trained native trackers using both sign surveys and an encounter-based, visual-distance method in a well-preserved region of southern Guyana (Amazon / Guiana Shield). We found that a rigorously applied sign-based method was sufficient to describe the status of most carnivore species populations, including rare species such as jaguar and bush dog. We also found that even when accumulation curves for direct visual encounter data reached an asymptote, customarily an indication that sufficient sampling has occurred to describe populations, animal occurrence and distribution were grossly underestimated relative to the results of sign data. While other researchers have also found that sign are better than encounters or camera traps for large felids, our results are important in documenting the failure of even intensive levels of effort to raise encounter rates sufficiently to enable statistical analysis, and in describing the relationship between encounter and sign data for an entire community of carnivores including felids, canids, procyonids, and mustelids.
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Affiliation(s)
| | | | | | - Han Overman
- Environmental and Forest Biology, State University of New York-College of Environmental Science and Forestry, Syracuse, NY, United States of America
| | - Taal Levi
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, United States of America
| | - Kirsten M. Silvius
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, VA, United States of America
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42
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Pedrosa F, Bercê W, Levi T, Pires M, Galetti M. Seed dispersal effectiveness by a large‐bodied invasive species in defaunated landscapes. Biotropica 2019. [DOI: 10.1111/btp.12706] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Felipe Pedrosa
- Department of Ecology Institute of Biosciences São Paulo State University (UNESP) Rio Claro Brazil
- Department of Fisheries and Wildlife Oregon State University Corvallis OR USA
| | - William Bercê
- Department of Ecology Institute of Biosciences São Paulo State University (UNESP) Rio Claro Brazil
| | - Taal Levi
- Department of Fisheries and Wildlife Oregon State University Corvallis OR USA
| | - Mathias Pires
- Department of Animal Biology Institute of Biology Campinas State University (UNICAMP) Campinas Brazil
| | - Mauro Galetti
- Department of Ecology Institute of Biosciences São Paulo State University (UNESP) Rio Claro Brazil
- Department of Biology University of Miami Coral Gables FL USA
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43
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Spitz DB, Rowland MM, Clark DA, Wisdom MJ, Smith JB, Brown CL, Levi T. Behavioral changes and nutritional consequences to elk (
Cervus canadensis
) avoiding perceived risk from human hunters. Ecosphere 2019. [DOI: 10.1002/ecs2.2864] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Derek B. Spitz
- Department of Fisheries and Wildlife Oregon State University Corvallis Oregon 97331 USA
| | - Mary M. Rowland
- U.S. Forest Service Pacific Northwest Research Station La Grande Oregon 97850 USA
| | - Darren A. Clark
- Oregon Department of Fish and Wildlife La Grande Oregon 97850 USA
| | - Michael J. Wisdom
- U.S. Forest Service Pacific Northwest Research Station La Grande Oregon 97850 USA
| | - Joshua B. Smith
- Oregon Department of Fish and Wildlife La Grande Oregon 97850 USA
| | - Casey L. Brown
- Oregon Department of Fish and Wildlife La Grande Oregon 97850 USA
| | - Taal Levi
- Department of Fisheries and Wildlife Oregon State University Corvallis Oregon 97331 USA
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44
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Eriksson CE, Moriarty KM, Linnell MA, Levi T. Biotic factors influencing the unexpected distribution of a Humboldt marten (Martes caurina humboldtensis) population in a young coastal forest. PLoS One 2019; 14:e0214653. [PMID: 31042737 PMCID: PMC6493723 DOI: 10.1371/journal.pone.0214653] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 03/18/2019] [Indexed: 11/30/2022] Open
Abstract
Pacific martens (Martes caurina) are often associated with mature forests with complex structure for denning, resting, and efficient hunting. Nonetheless, a small isolated population of the Humboldt subspecies of Pacific martens (Martes caurina humboldtensis) occupies a narrow strip of young, coastal forest (< 70 years old) but not inland mature forest in the central Oregon Coast Range. We examined factors contributing to this unexpected distribution of martens by 1) analyzing marten diets using DNA metabarcoding to assess 90 scats, 2) using camera traps to assess differences in the relative abundances of prey, competitors, and predators across a coastal to inland gradient of vegetation types, and 3) quantifying differences in extent of fruit-producing shrubs and vegetation structure within vegetation types. Diets of martens were diverse (12, 10, and 3 species of birds, mammals, and amphibians respectively), and most fall and winter scats contained fruit. Voles, mice, and varied thrushes (Ixoreus naevius) were dominant prey items. Voles, mice, and most birds, but not varied thrushes, were more commonly observed in the coastal shrub-dominated forest than in inland forest. The coastal shrub-dominated forest had the highest diversity of vertebrates and potential prey overall. Bobcats (Lynx rufus), a key potential predator, were more commonly detected in inland forest. Of potential competitors, western spotted skunks (Spilogale gracilis) were more commonly detected in inland forest, with gray foxes (Urocyon cinereoargenteus) and raccoons (Procyon lotor) detected almost exclusively in coastal forests. Vegetation in coastal forests appears to provide, at least seasonally, more prey and fruit, and more overhead shrub cover compared with inland forest. Remaining plausible hypotheses for the restricted distribution of marten to coastal forests include increased prey, fruit, and overhead cover, and reduced predation risk from bobcats.
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Affiliation(s)
- Charlotte E. Eriksson
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, United States of America
| | - Katie M. Moriarty
- Pacific Northwest Research Station, USDA Forest Service, Olympia, WA, United States of America
| | - Mark A. Linnell
- Department of Forest Engineering, Resources, and Management, Oregon State University, Corvallis, OR, United States of America
| | - Taal Levi
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, United States of America
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45
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Levi T, Allen JM, Bell D, Joyce J, Russell JR, Tallmon DA, Vulstek SC, Yang C, Yu DW. Environmental DNA for the enumeration and management of Pacific salmon. Mol Ecol Resour 2019; 19:597-608. [DOI: 10.1111/1755-0998.12987] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/14/2018] [Accepted: 12/03/2018] [Indexed: 01/22/2023]
Affiliation(s)
- Taal Levi
- Department of Fisheries and Wildlife Oregon State University Corvallis Oregon
| | - Jennifer M. Allen
- Department of Fisheries and Wildlife Oregon State University Corvallis Oregon
| | - Donovan Bell
- Auke Bay Laboratories National Oceanic and Atmospheric Administration Juneau, Alaska
| | - John Joyce
- Auke Bay Laboratories National Oceanic and Atmospheric Administration Juneau, Alaska
| | - Joshua R. Russell
- Auke Bay Laboratories National Oceanic and Atmospheric Administration Juneau, Alaska
| | - David A. Tallmon
- Biology and Marine Biology Program University of Alaska Southeast Juneau, Alaska
| | - Scott C. Vulstek
- Auke Bay Laboratories National Oceanic and Atmospheric Administration Juneau, Alaska
| | - Chunyan Yang
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology, Chinese Academy of Sciences Kunming China
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology, Chinese Academy of Sciences Kunming China
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
- School of Biological Sciences University of East Anglia Norwich UK
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46
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Spitz DB, Clark DA, Wisdom MJ, Rowland MM, Johnson BK, Long RA, Levi T. Fire history influences large-herbivore behavior at circadian, seasonal, and successional scales. Ecol Appl 2018; 28:2082-2091. [PMID: 30179283 DOI: 10.1002/eap.1797] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 07/04/2018] [Accepted: 07/05/2018] [Indexed: 06/08/2023]
Abstract
Recurrent environmental changes often prompt animals to alter their behavior leading to predictable patterns across a range of temporal scales. The nested nature of circadian and seasonal behavior complicates tests for effects of rarer disturbance events like fire. Fire can dramatically alter plant community structure, with important knock-on effects at higher trophic levels, but the strength and timing of fire's effects on herbivores remain unclear. We combined prescribed fire treatments with fine-scale location data to quantify herbivore responses to fire across three temporal scales. Between 2001 and 2003, 26 stands of fir (Abies spp.) and Douglas-fir (Pseudotsuga menziesii) were thinned and burned; 27 similar stands were left untreated as experimental controls. Analyzing female elk (Cervus canadensis) locations across 21 yr (1996-2016), we found crepuscular, seasonal, and successional shifts in behavioral responses to fire. Elk displayed "commuting" behavior, avoiding burns during the day, but selecting them at night. Elk selection for burns was strongest in early summer and the relative probability of elk using burns peaked quickly (5 yr post burn) before gradually returning to pre-treatment levels (15 yr post burn). Our results demonstrate that fire history has complex, persistent effects on herbivore behavior, and suggest that herbivores benefit from heterogeneous landscapes containing a range of successional stages.
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Affiliation(s)
- Derek B Spitz
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Darren A Clark
- Oregon Department of Fish and Wildlife, La Grande, Oregon, 97850, USA
| | - Michael J Wisdom
- U.S. Forest Service Pacific Northwest Research Station, La Grande, Oregon, 97850, USA
| | - Mary M Rowland
- U.S. Forest Service Pacific Northwest Research Station, La Grande, Oregon, 97850, USA
| | - Bruce K Johnson
- Oregon Department of Fish and Wildlife, La Grande, Oregon, 97850, USA
| | - Ryan A Long
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, Idaho, 83844, USA
| | - Taal Levi
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon, 97331, USA
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47
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Wolf C, Betts MG, Levi T, Newsome TM, Ripple WJ. Large species within carnivora are large carnivores. R Soc Open Sci 2018; 5:181228. [PMID: 30839736 PMCID: PMC6170586 DOI: 10.1098/rsos.181228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 08/17/2018] [Indexed: 06/09/2023]
Affiliation(s)
- Christopher Wolf
- Global Trophic Cascades Program, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331, USA
| | - Matthew G. Betts
- Global Trophic Cascades Program, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331, USA
| | - Taal Levi
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR 97331, USA
| | - Thomas M. Newsome
- School of Life and Environmental Sciences, The University of Sydney, New South Wales 2006, Australia
| | - William J. Ripple
- Global Trophic Cascades Program, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331, USA
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48
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Affiliation(s)
- Yasaman N. Shakeri
- Department of Fisheries and Wildlife; Oregon State University; Corvallis Oregon 97331 USA
| | - Kevin S. White
- Division of Wildlife Conservation; Alaska Department of Fish and Game; Juneau Alaska 99811 USA
| | - Taal Levi
- Department of Fisheries and Wildlife; Oregon State University; Corvallis Oregon 97331 USA
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49
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Ostfeld RS, Levi T, Keesing F, Oggenfuss K, Canham CD. Tick‐borne disease risk in a forest food web. Ecology 2018; 99:1562-1573. [DOI: 10.1002/ecy.2386] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 03/06/2018] [Accepted: 04/12/2018] [Indexed: 01/27/2023]
Affiliation(s)
| | - Taal Levi
- Department of Fisheries and Wildlife Oregon State University Corvallis Oregon 97331 USA
| | - Felicia Keesing
- Program in Biology Bard College Annandale‐on‐Hudson New York 12504 USA
| | - Kelly Oggenfuss
- Cary Institute of Ecosystem Studies Millbrook New York 12545 USA
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50
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Linnell MA, Moriarty K, Green DS, Levi T. Density and population viability of coastal marten: a rare and geographically isolated small carnivore. PeerJ 2018; 6:e4530. [PMID: 29637018 PMCID: PMC5889706 DOI: 10.7717/peerj.4530] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 03/01/2018] [Indexed: 11/20/2022] Open
Abstract
Pacific martens (Martes caurina humboldtensis) in coastal forests of Oregon and northern California in the United States are rare and geographically isolated, prompting a petition for listing under the Endangered Species Act. If listed, regulations have the potential to influence land-use decisions on public and private lands, but no estimates of population size, density, or viability of remnant marten populations are available for evaluating their conservation status. We used GPS and VHF telemetry and spatial mark-resight to estimate home ranges, density, and population size of Pacific martens in the Oregon Dunes National Recreation Area, central coast Oregon, USA. We then estimated population viability at differing levels of human-caused mortality (e.g., vehicle mortality). Marten home ranges were small on average (females = 0.8 km2, males 1.5 km2) and density (1.13 martens/1 km2) was the highest reported for North American populations (M. caurina, M. americana). We estimated 71 adult martens (95% CRI [41–87]) across two subpopulations separated by a large barrier (Umpqua River). Using population viability analysis, extinction risk for a subpopulation of 30 martens, approximately the size of the subpopulation south of the Umpqua River, ranged from 32% to 99% with two or three annual human-caused mortalities within 30 years. Absent population expansion, limiting human-caused mortalities will likely have the greatest conservation impact.
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Affiliation(s)
- Mark A Linnell
- Department of Forest Engineering, Resources, and Management, Oregon State University, Corvallis, OR, United States of America
| | - Katie Moriarty
- Pacific Northwest Research Station, United States of America Department of Agriculture, Forest Service, Olympia, WA, United States of America
| | - David S Green
- Institute for Natural Resources, Oregon State University, Corvallis, OR, United States of America
| | - Taal Levi
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, United States of America
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