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Fukuda Y, Moritz C, Jang N, Webb G, Campbell H, Christian K, Lindner G, Banks S. Environmental resistance and habitat quality influence dispersal of the saltwater crocodile. Mol Ecol 2021; 31:1076-1092. [PMID: 34865283 PMCID: PMC9299799 DOI: 10.1111/mec.16310] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 11/15/2021] [Accepted: 11/22/2021] [Indexed: 11/29/2022]
Abstract
Landscape genetics commonly focuses on the effects of environmental resistance on animal dispersal patterns, but there is an emerging focus on testing environmental effects on emigration and settlement choices. In this study, we used landscape genetics approaches to quantify dispersal patterns in the world's largest crocodilian, the saltwater crocodile (Crocodylus porosus), and demonstrated environmental influences on three processes that comprise dispersal: emigration, movement and settlement. We found that both environmental resistance and properties of the source and destination catchments (proportion of breeding habitat) were important factors influencing observed dispersal events. Our habitat quality variables related to hypotheses about resource competition and represented the ratio of breeding habitat (which limits carrying capacity), suggesting that competition for habitat influences emigration and settlement choices, together with the strong effect of environmental resistance to movement (where high-quality habitat was associated with greatest environmental permeability). Approximately 42% of crocodiles were migrants from populations other than their sampling locations and some outstandingly productive populations had a much higher proportion of emigration rather than immigration. The distance most commonly travelled between source and destination was 150-200 km although a few travelled much longer distances, up to 600-700 km. Given the extensive dispersal range, individual catchments or hydrographic regions that combine two or three adjacent catchments are an appropriate scale for population management.
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Affiliation(s)
- Yusuke Fukuda
- Research School of Biology and Center for Biodiversity Analysis, The Australian National University, Canberra, ACT, Australia.,Department of Environment, Parks and Water Security, Northern Territory Government, Darwin, Northern Territory, Australia
| | - Craig Moritz
- Research School of Biology and Center for Biodiversity Analysis, The Australian National University, Canberra, ACT, Australia
| | - Namchul Jang
- Namchul Photography, Palmerston, Northern Territory, Australia
| | - Grahame Webb
- Wildlife Management International Pty Ltd, Darwin, Northern Territory, Australia
| | - Hamish Campbell
- Research Institute for the Environment and Livelihoods, College of Engineering, IT and the Environment, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Keith Christian
- Research Institute for the Environment and Livelihoods, College of Engineering, IT and the Environment, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Garry Lindner
- Parks Australia, Australian Government, Jabiru, Northern Territory, Australia
| | - Sam Banks
- Research Institute for the Environment and Livelihoods, College of Engineering, IT and the Environment, Charles Darwin University, Darwin, Northern Territory, Australia
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2
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Demographic modeling informs functional connectivity and management interventions in Graham’s beardtongue. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01392-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AbstractFunctional connectivity (i.e., the movement of individuals across a landscape) is essential for the maintenance of genetic variation and persistence of rare species. However, illuminating the processes influencing functional connectivity and ultimately translating this knowledge into management practice remains a fundamental challenge. Here, we combine various population structure analyses with pairwise, population-specific demographic modeling to investigate historical functional connectivity in Graham’s beardtongue (Penstemon grahamii), a rare plant narrowly distributed across a dryland region of the western US. While principal component and population structure analyses indicated an isolation-by-distance pattern of differentiation across the species’ range, spatial inferences of effective migration exposed an abrupt shift in population ancestry near the range center. To understand these seemingly conflicting patterns, we tested various models of historical gene flow and found evidence for recent admixture (~ 3400 generations ago) between populations near the range center. This historical perspective reconciles population structure patterns and suggests management efforts should focus on maintaining connectivity between these previously isolated lineages to promote the ongoing transfer of genetic variation. Beyond providing species-specific knowledge to inform management options, our study highlights how understanding demographic history may be critical to guide conservation efforts when interpreting population genetic patterns and inferring functional connectivity.
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3
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Dellinger JA, Gustafson KD, Gammons DJ, Ernest HB, Torres SG. Minimum habitat thresholds required for conserving mountain lion genetic diversity. Ecol Evol 2020; 10:10687-10696. [PMID: 33072289 PMCID: PMC7548186 DOI: 10.1002/ece3.6723] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 07/31/2020] [Accepted: 08/05/2020] [Indexed: 11/24/2022] Open
Abstract
Jointly considering the ecology (e.g., habitat use) and genetics (e.g., population genetic structure and diversity) of a species can increase understanding of current conservation status and inform future management practices. Previous analyses indicate that mountain lion (Puma concolor) populations in California are genetically structured and exhibit extreme variation in population genetic diversity. Although human development may have fragmented gene flow, we hypothesized the quantity and quality of remaining habitat available would affect the genetic viability of each population. Our results indicate that area of suitable habitat, determined via a resource selection function derived using 843,500 location fixes from 263 radio‐collared mountain lions, is strongly and positively associated with population genetic diversity and viability metrics, particularly with effective population size. Our results suggested that contiguous habitat of ≥10,000 km2 may be sufficient to alleviate the negative effects of genetic drift and inbreeding, allowing mountain lion populations to maintain suitable effective population sizes. Areas occupied by five of the nine geographic–genetic mountain lion populations in California fell below this habitat threshold, and two (Santa Monica Area and Santa Ana) of those five populations lack connectivity to nearby populations. Enhancing ecological conditions by protection of greater areas of suitable habitat and facilitating positive evolutionary processes by increasing connectivity (e.g., road‐crossing structures) might promote persistence of small or isolated populations. The conservation status of suitable habitat also appeared to influence genetic diversity of populations. Thus, our results demonstrate that both the area and status (i.e., protected or unprotected) of suitable habitat influence the genetic viability of mountain lion populations.
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Affiliation(s)
| | - Kyle D Gustafson
- Department of Biological Sciences Arkansas State University Jonesboro Arkansas USA.,Wildlife Genomics and Disease Ecology Laboratory University of Wyoming Laramie Wyoming USA
| | - Daniel J Gammons
- California Department of Fish and Wildlife Sacramento California USA
| | - Holly B Ernest
- Wildlife Genomics and Disease Ecology Laboratory University of Wyoming Laramie Wyoming USA
| | - Steven G Torres
- California Department of Fish and Wildlife Sacramento California USA
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4
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Ford BM, Cornellas A, Leonard JA, Weir RD, Russello MA. Spatiotemporal analyses suggest the role of glacial history and the ice-free corridor in shaping American badger population genetic variation. Ecol Evol 2020; 10:8345-8357. [PMID: 32788984 PMCID: PMC7417222 DOI: 10.1002/ece3.6541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 06/03/2020] [Accepted: 06/10/2020] [Indexed: 11/07/2022] Open
Abstract
Recurring glacial cycles through the Quaternary period drastically altered the size and distribution of natural populations of North American flora and fauna. The "southerly refugia model" has been the longstanding framework for testing the effects of glaciation on contemporary genetic patterns; however, insights from ancient DNA have contributed to the reconstruction of more complex histories for some species. The American badger, Taxidea taxus, provides an interesting species for exploring the genetic legacy of glacial history, having been hypothesized to have postglacially emerged from a single, southerly refugium to recolonize northern latitudes. However, previous studies have lacked genetic sampling from areas where distinct glacial refugia have been hypothesized, including the Pacific Northwest and American Far North (Yukon, Alaska). In order to further investigate the phylogeographic history of American badgers, we collected mitochondrial DNA sequence data from ancient subfossil material collected within the historical range (Alaska, Yukon) and combined them with new and previously published data from across the species' contemporary distribution (n = 1,207). We reconstructed a mostly unresolved phylogenetic tree and star-like haplotype network indicative of emergence from a largely panmictic glacial refugium and recent population expansion, the latter further punctuated by significantly negative Tajima's D and Fu's Fs values. Although directionality of migration cannot be unequivocally inferred, the moderate to high levels of genetic variation exhibited by American badgers, alongside the low frequency of haplotypes with indels in the Midwest, suggest a potential recolonization into central North America after the hypothesized ice-free corridor reopened ~13,000 years ago. Overall, the expanded reconstruction of phylogeographic history of American badgers offers a broader understanding of contemporary range-wide patterns and identifies unique genetic units that can likely be used to inform conservation of at-risk populations at the northern periphery.
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Affiliation(s)
- Brett M. Ford
- Department of BiologyUniversity of British ColumbiaKelownaBCCanada
| | - Anna Cornellas
- Conservation and Evolutionary Genetics GroupEstación Biológica de Doñana (EBD‐CSIC)SevilleSpain
| | - Jennifer A. Leonard
- Conservation and Evolutionary Genetics GroupEstación Biológica de Doñana (EBD‐CSIC)SevilleSpain
| | - Richard D. Weir
- British Columbia Ministry of Environment and Climate Change StrategyVictoriaBCCanada
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5
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Dellinger JA, Cristescu B, Ewanyk J, Gammons DJ, Garcelon D, Johnston P, Martins Q, Thompson C, Vickers TW, Wilmers CC, Wittmer HU, Torres SG. Using Mountain Lion Habitat Selection in Management. J Wildl Manage 2019. [DOI: 10.1002/jwmg.21798] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Justin A. Dellinger
- California Department of Fish and Wildlife 1701 Nimbus Rd., Suite D Rancho Cordova CA 95670 USA
| | - Bogdan Cristescu
- Center for Integrated Spatial Research, Environmental Studies Department University of California 1156 High St. Santa Cruz CA 95064 USA
| | - Jonathan Ewanyk
- Institute for Wildlife Studies PO Box 1104 Arcata CA 95518 USA
| | - Daniel J. Gammons
- California Department of Fish and Wildlife 787 N Main St., Suite 220 Bishop CA 93514 USA
| | - David Garcelon
- Institute for Wildlife Studies PO Box 1104 Arcata CA 95518 USA
| | | | | | - Craig Thompson
- United States Forest Service, Northern Region 26 Fort Missoula Rd. Missoula MT 59804 USA
| | - T. Winston Vickers
- Wildlife Health Center University of California 1089 Veterinary Medicine Dr. Davis CA 95616 USA
| | - Christopher C. Wilmers
- Center for Integrated Spatial Research, Environmental Studies Department University of California 1156 High St. Santa Cruz CA 95064 USA
| | - Heiko U. Wittmer
- School of Biological Sciences Victoria University of Wellington PO Box 600 Wellington 6140 NZ
| | - Steven G. Torres
- California Department of Fish and Wildlife 1701 Nimbus Rd., Suite D Rancho Cordova CA 95670 USA
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Trumbo DR, Salerno PE, Logan KA, Alldredge MW, Gagne RB, Kozakiewicz CP, Kraberger S, Fountain-Jones NM, Craft ME, Carver S, Ernest HB, Crooks KR, VandeWoude S, Funk WC. Urbanization impacts apex predator gene flow but not genetic diversity across an urban-rural divide. Mol Ecol 2019; 28:4926-4940. [PMID: 31587398 DOI: 10.1111/mec.15261] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 08/11/2019] [Accepted: 09/20/2019] [Indexed: 02/06/2023]
Abstract
Apex predators are important indicators of intact natural ecosystems. They are also sensitive to urbanization because they require broad home ranges and extensive contiguous habitat to support their prey base. Pumas (Puma concolor) can persist near human developed areas, but urbanization may be detrimental to their movement ecology, population structure, and genetic diversity. To investigate potential effects of urbanization in population connectivity of pumas, we performed a landscape genomics study of 130 pumas on the rural Western Slope and more urbanized Front Range of Colorado, USA. Over 12,000 single nucleotide polymorphisms (SNPs) were genotyped using double-digest, restriction site-associated DNA sequencing (ddRADseq). We investigated patterns of gene flow and genetic diversity, and tested for correlations between key landscape variables and genetic distance to assess the effects of urbanization and other landscape factors on gene flow. Levels of genetic diversity were similar for the Western Slope and Front Range, but effective population sizes were smaller, genetic distances were higher, and there was more admixture in the more urbanized Front Range. Forest cover was strongly positively associated with puma gene flow on the Western Slope, while impervious surfaces restricted gene flow and more open, natural habitats enhanced gene flow on the Front Range. Landscape genomic analyses revealed differences in puma movement and gene flow patterns in rural versus urban settings. Our results highlight the utility of dense, genome-scale markers to document subtle impacts of urbanization on a wide-ranging carnivore living near a large urban center.
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Affiliation(s)
- Daryl R Trumbo
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | | | | | | | - Roderick B Gagne
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | | | - Simona Kraberger
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | | | - Meggan E Craft
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, USA
| | - Scott Carver
- Department of Biological Sciences, University of Tasmania, Hobart, TAS., Australia
| | - Holly B Ernest
- Department of Veterinary Sciences, University of Wyoming, Laramie, WY, USA
| | - Kevin R Crooks
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO, USA
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - W Chris Funk
- Department of Biology, Colorado State University, Fort Collins, CO, USA.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
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Dellinger JA, Darby NW, Torres SG. FACTORS INFLUENCING OCCUPANCY AND DETECTION RATES OF MOUNTAIN LIONS IN THE MOJAVE DESERT OF CALIFORNIA. SOUTHWEST NAT 2019. [DOI: 10.1894/0038-4909-63-4-248] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Justin A. Dellinger
- Wildlife Investigations Laboratory, California Department of Fish and Wildlife, 1701 Nimbus Road, Rancho Cordova, CA 95670 (JAD, SGT)
| | - Neal W. Darby
- Mojave National Preserve, 2701 Barstow Road, Barstow, CA 92311 (NWD)
| | - Steven G. Torres
- Wildlife Investigations Laboratory, California Department of Fish and Wildlife, 1701 Nimbus Road, Rancho Cordova, CA 95670 (JAD, SGT)
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Cristescu B, Bose S, Elbroch LM, Allen ML, Wittmer HU. Habitat selection when killing primary versus alternative prey species supports prey specialization in an apex predator. J Zool (1987) 2019. [DOI: 10.1111/jzo.12718] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- B. Cristescu
- Environmental Studies Department University of California Santa Cruz CA USA
| | - S. Bose
- School of Biological Sciences Victoria University of Wellington Wellington New Zealand
| | | | - M. L. Allen
- School of Biological Sciences Victoria University of Wellington Wellington New Zealand
- Illinois Natural History Survey University of Illinois Champaign IL USA
| | - H. U. Wittmer
- School of Biological Sciences Victoria University of Wellington Wellington New Zealand
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9
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Lai S, Quiles A, Lambourdière J, Berteaux D, Lalis A. Fine-scale population genetic structure of arctic foxes (Vulpes lagopus) in the High Arctic. BMC Res Notes 2017; 10:663. [PMID: 29191239 PMCID: PMC5710073 DOI: 10.1186/s13104-017-3002-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 11/25/2017] [Indexed: 11/18/2022] Open
Abstract
Objective The arctic fox (Vulpes lagopus) is a circumpolar species inhabiting all accessible Arctic tundra habitats. The species forms a panmictic population over areas connected by sea ice, but recently, kin clustering and population differentiation were detected even in regions where sea ice was present. The purpose of this study was to examine the genetic structure of a population in the High Arctic using a robust panel of highly polymorphic microsatellites. Results We analyzed the genotypes of 210 individuals from Bylot Island, Nunavut, Canada, using 15 microsatellite loci. No pattern of isolation-by-distance was detected, but a spatial principal component analysis (sPCA) revealed the presence of genetic subdivisions. Overall, the sPCA revealed two spatially distinct genetic clusters corresponding to the northern and southern parts of the study area, plus another subdivision within each of these two clusters. The north–south genetic differentiation partly matched the distribution of a snow goose colony, which could reflect a preference for settling into familiar ecological environments. Secondary clusters may result from higher-order social structures (neighbourhoods) that use landscape features to delimit their borders. The cryptic genetic subdivisions found in our population may highlight ecological processes deserving further investigations in arctic foxes at larger, regional spatial scales. Electronic supplementary material The online version of this article (10.1186/s13104-017-3002-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sandra Lai
- Canada Research Chair on Northern Biodiversity, Centre for Northern Studies and Quebec Center for Biodiversity Science, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski, QC, G5L 3A1, Canada.
| | - Adrien Quiles
- UMR7205 ISYEB CNRS-MNHN-EPHE-UPMC, Muséum National d'Histoire Naturelle, CP 51, 75231, Paris Cedex 05, France
| | - Josie Lambourdière
- UMS 2700 OMSI Service de Systématique Moléculaire, Muséum National d'Histoire Naturelle, CP 26, 75231, Paris Cedex 05, France
| | - Dominique Berteaux
- Canada Research Chair on Northern Biodiversity, Centre for Northern Studies and Quebec Center for Biodiversity Science, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski, QC, G5L 3A1, Canada
| | - Aude Lalis
- UMR7205 ISYEB CNRS-MNHN-EPHE-UPMC, Muséum National d'Histoire Naturelle, CP 51, 75231, Paris Cedex 05, France
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10
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Maletzke B, Kertson B, Swanson M, Koehler G, Beausoleil R, Wielgus R, Cooley H. Cougar response to a gradient of human development. Ecosphere 2017. [DOI: 10.1002/ecs2.1828] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Benjamin Maletzke
- School of the Environment Washington State University Pullman Washington 99164 USA
| | - Brian Kertson
- Wildlife Science Group School of Forest Resources College of the Environment University of Washington Seattle Washington 98195 USA
| | - Mark Swanson
- School of the Environment Washington State University Pullman Washington 99164 USA
| | - Gary Koehler
- Washington Department of Fish and Wildlife 2218 Stephanie Brooke Wenatchee Washington 98801 USA
| | - Richard Beausoleil
- Washington Department of Fish and Wildlife 3515 State Highway 97A Wenatchee Washington 98801 USA
| | - Robert Wielgus
- School of the Environment Washington State University Pullman Washington 99164 USA
| | - Hilary Cooley
- School of the Environment Washington State University Pullman Washington 99164 USA
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11
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Filla M, Premier J, Magg N, Dupke C, Khorozyan I, Waltert M, Bufka L, Heurich M. Habitat selection by Eurasian lynx ( Lynx lynx) is primarily driven by avoidance of human activity during day and prey availability during night. Ecol Evol 2017; 7:6367-6381. [PMID: 28861240 PMCID: PMC5574813 DOI: 10.1002/ece3.3204] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/31/2017] [Indexed: 12/03/2022] Open
Abstract
The greatest threat to the protected Eurasian lynx (Lynx lynx) in Central Europe is human‐induced mortality. As the availability of lynx prey often peaks in human‐modified areas, lynx have to balance successful prey hunting with the risk of encounters with humans. We hypothesized that lynx minimize this risk by adjusting habitat choices to the phases of the day and over seasons. We predicted that (1) due to avoidance of human‐dominated areas during daytime, lynx range use is higher at nighttime, that (2) prey availability drives lynx habitat selection at night, whereas high cover, terrain inaccessibility, and distance to human infrastructure drive habitat selection during the day, and that (3) habitat selection also differs between seasons, with altitude being a dominant factor in winter. To test these hypotheses, we analyzed telemetry data (GPS, VHF) of 10 lynx in the Bohemian Forest Ecosystem (Germany, Czech Republic) between 2005 and 2013 using generalized additive mixed models and considering various predictor variables. Night ranges exceeded day ranges by more than 10%. At night, lynx selected open habitats, such as meadows, which are associated with high ungulate abundance. By contrast, during the day, lynx selected habitats offering dense understorey cover and rugged terrain away from human infrastructure. In summer, land‐cover type greatly shaped lynx habitats, whereas in winter, lynx selected lower altitudes. We concluded that open habitats need to be considered for more realistic habitat models and contribute to future management and conservation (habitat suitability, carrying capacity) of Eurasian lynx in Central Europe.
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Affiliation(s)
- Marc Filla
- Workgroup on Endangered Species J.F. Blumenbach Institute of Zoology and Anthropology Georg-August University of Göttingen Göttingen Germany
| | - Joseph Premier
- Global Change Ecology University of Bayreuth Bayreuth Germany
| | - Nora Magg
- Forest Research Institute of Baden-Württemberg Freiburg Germany
| | - Claudia Dupke
- Department of Biometry and Environmental System Analysis University of Freiburg Freiburg Germany
| | - Igor Khorozyan
- Workgroup on Endangered Species J.F. Blumenbach Institute of Zoology and Anthropology Georg-August University of Göttingen Göttingen Germany
| | - Matthias Waltert
- Workgroup on Endangered Species J.F. Blumenbach Institute of Zoology and Anthropology Georg-August University of Göttingen Göttingen Germany
| | - Luděk Bufka
- Faculty of Forestry and Wood Sciences Czech University of Life Sciences Prague Czech Republic.,Department of Research and Nature Protection Šumava National Park Administration Kašperské Hory Czech Republic
| | - Marco Heurich
- Chair of Wildlife Ecology and Management Faculty of Environment and Natural Resources University of Freiburg Freiburg Germany.,Department of Conservation and Research Bavarian Forest National Park Grafenau Germany
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