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Podar NA, Carrell AA, Cassidy KA, Klingeman DM, Yang Z, Stahler EA, Smith DW, Stahler DR, Podar M. From wolves to humans: oral microbiome resistance to transfer across mammalian hosts. mBio 2024; 15:e0334223. [PMID: 38299854 PMCID: PMC10936156 DOI: 10.1128/mbio.03342-23] [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: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 02/02/2024] Open
Abstract
The mammalian mouth is colonized by complex microbial communities, adapted to specific niches, and in homeostasis with the host. Individual microbes interact metabolically and rely primarily on nutrients provided by the host, with which they have potentially co-evolved along the mammalian lineages. The oral environment is similar across mammals, but the diversity, specificity, and evolution of community structure in related or interacting mammals are little understood. Here, we compared the oral microbiomes of dogs with those of wild wolves and humans. In dogs, we found an increased microbial diversity relative to wolves, possibly related to the transition to omnivorous nutrition following domestication. This includes a larger diversity of Patescibacteria than previously reported in any other oral microbiota. The oral microbes are most distinct at bacterial species or strain levels, with few if any shared between humans and canids, while the close evolutionary relationship between wolves and dogs is reflected by numerous shared taxa. More taxa are shared at higher taxonomic levels including with humans, supporting their more ancestral common mammalian colonization followed by diversification. Phylogenies of selected oral bacterial lineages do not support stable human-dog microbial transfers but suggest diversification along mammalian lineages (apes and canids). Therefore, despite millennia of cohabitation and close interaction, the host and its native community controls and limits the assimilation of new microbes, even if closely related. Higher resolution metagenomic and microbial physiological studies, covering a larger mammalian diversity, should help understand how oral communities assemble, adapt, and interact with their hosts.IMPORTANCENumerous types of microbes colonize the mouth after birth and play important roles in maintaining oral health. When the microbiota-host homeostasis is perturbed, proliferation of some bacteria leads to diseases such as caries and periodontitis. Unlike the gut microbiome, the diversity of oral microbes across the mammalian evolutionary space is not understood. Our study compared the oral microbiomes of wild wolves, dogs, and apes (humans, chimpanzees, and bonobos), with the aim of identifying if microbes have been potentially exchanged between humans and dogs as a result of domestication and cohabitation. We found little if any evidence for such exchanges. The significance of our research is in finding that the oral microbiota and/or the host limit the acquisition of exogenous microbes, which is important in the context of natural exclusion of potential novel pathogens. We provide a framework for expanded higher-resolution studies across domestic and wild animals to understand resistance/resilience.
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Affiliation(s)
- Nicholas A. Podar
- School of Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Alyssa A. Carrell
- Biosciences Department, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Kira A. Cassidy
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Dawn M. Klingeman
- Biosciences Department, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Zamin Yang
- Biosciences Department, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Erin A. Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Douglas W. Smith
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Daniel R. Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Mircea Podar
- Biosciences Department, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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Inzalaco HN, Brandell EE, Wilson SP, Hunsaker M, Stahler DR, Woelfel K, Walsh DP, Nordeen T, Storm DJ, Lichtenberg SS, Turner WC. Detection of prions from spiked and free-ranging carnivore feces. Sci Rep 2024; 14:3804. [PMID: 38360908 PMCID: PMC10869337 DOI: 10.1038/s41598-023-44167-7] [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: 06/06/2023] [Accepted: 10/04/2023] [Indexed: 02/17/2024] Open
Abstract
Chronic wasting disease (CWD) is a highly contagious, fatal neurodegenerative disease caused by infectious prions (PrPCWD) affecting wild and captive cervids. Although experimental feeding studies have demonstrated prions in feces of crows (Corvus brachyrhynchos), coyotes (Canis latrans), and cougars (Puma concolor), the role of scavengers and predators in CWD epidemiology remains poorly understood. Here we applied the real-time quaking-induced conversion (RT-QuIC) assay to detect PrPCWD in feces from cervid consumers, to advance surveillance approaches, which could be used to improve disease research and adaptive management of CWD. We assessed recovery and detection of PrPCWD by experimental spiking of PrPCWD into carnivore feces from 9 species sourced from CWD-free populations or captive facilities. We then applied this technique to detect PrPCWD from feces of predators and scavengers in free-ranging populations. Our results demonstrate that spiked PrPCWD is detectable from feces of free-ranging mammalian and avian carnivores using RT-QuIC. Results show that PrPCWD acquired in natural settings is detectable in feces from free-ranging carnivores, and that PrPCWD rates of detection in carnivore feces reflect relative prevalence estimates observed in the corresponding cervid populations. This study adapts an important diagnostic tool for CWD, allowing investigation of the epidemiology of CWD at the community-level.
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Affiliation(s)
- H N Inzalaco
- Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin, Madison, Madison, WI, 53706, USA.
| | - E E Brandell
- Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin, Madison, Madison, WI, 53706, USA
| | - S P Wilson
- Nebraska Game and Parks Commission, 2200 N 33rd St., P.O. Box 30370, Lincoln, NE, 68503, USA
| | - M Hunsaker
- Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin, Madison, Madison, WI, 53706, USA
| | - D R Stahler
- Yellowstone Center for Resources, Yellowstone National Park, WY, 82190, USA
| | - K Woelfel
- Wild and Free Wildlife Rehabilitation Program, 27264 MN-18, Garrison, MN, 56450, USA
| | - D P Walsh
- U.S. Geological Survey, Montana Cooperative Wildlife Research Unit, University of Montana, Missoula, MT, USA
| | - T Nordeen
- Nebraska Game and Parks Commission, 2200 N 33rd St., P.O. Box 30370, Lincoln, NE, 68503, USA
| | - D J Storm
- Wisconsin Department of Natural Resources, Eau Claire, WI, 54701, USA
| | - S S Lichtenberg
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN, 55108, USA
| | - W C Turner
- U.S. Geological Survey, Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin - Madison, Madison, WI, 53706, USA
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vonHoldt BM, Stahler DR, Brzeski KE, Musiani M, Peterson R, Phillips M, Stephenson J, Laudon K, Meredith E, Vucetich JA, Leonard JA, Wayne RK. Demographic history shapes North American gray wolf genomic diversity and informs species' conservation. Mol Ecol 2024; 33:e17231. [PMID: 38054561 DOI: 10.1111/mec.17231] [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: 06/05/2023] [Revised: 11/19/2023] [Accepted: 11/21/2023] [Indexed: 12/07/2023]
Abstract
Effective population size estimates are critical information needed for evolutionary predictions and conservation decisions. This is particularly true for species with social factors that restrict access to breeding or experience repeated fluctuations in population size across generations. We investigated the genomic estimates of effective population size along with diversity, subdivision, and inbreeding from 162,109 minimally filtered and 81,595 statistically neutral and unlinked SNPs genotyped in 437 grey wolf samples from North America collected between 1986 and 2021. We found genetic structure across North America, represented by three distinct demographic histories of western, central, and eastern regions of the continent. Further, grey wolves in the northern Rocky Mountains have lower genomic diversity than wolves of the western Great Lakes and have declined over time. Effective population size estimates revealed the historical signatures of continental efforts of predator extermination, despite a quarter century of recovery efforts. We are the first to provide molecular estimates of effective population size across distinct grey wolf populations in North America, which ranged between Ne ~ 275 and 3050 since early 1980s. We provide data that inform managers regarding the status and importance of effective population size estimates for grey wolf conservation, which are on average 5.2-9.3% of census estimates for this species. We show that while grey wolves fall above minimum effective population sizes needed to avoid extinction due to inbreeding depression in the short term, they are below sizes predicted to be necessary to avoid long-term risk of extinction.
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Affiliation(s)
- Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Daniel R Stahler
- Yellowstone Center for Resources, Yellowstone National Park, Wyoming, USA
| | - Kristin E Brzeski
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Marco Musiani
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, Bologna, Italy
| | - Rolf Peterson
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | | | | | - Kent Laudon
- California Department of Fish and Wildlife, Northern Region, Redding, California, USA
| | - Erin Meredith
- California Department of Fish and Wildlife, Wildlife Forensic Laboratory, Sacramento, California, USA
| | - John A Vucetich
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, USA
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4
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Passoni G, Coulson T, Cagnacci F, Hudson P, Stahler DR, Smith DW, Lachish S. Investigating tritrophic interactions using bioenergetic demographic models. Ecology 2024; 105:e4197. [PMID: 37897692 DOI: 10.1002/ecy.4197] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 07/27/2023] [Accepted: 09/18/2023] [Indexed: 10/30/2023]
Abstract
A central debate in ecology has been the long-running discussion on the role of apex predators in affecting the abundance and dynamics of their prey. In terrestrial systems, research has primarily relied on correlational approaches, due to the challenge of implementing robust experiments with replication and appropriate controls. A consequence of this is that we largely suffer from a lack of mechanistic understanding of the population dynamics of interacting species, which can be surprisingly complex. Mechanistic models offer an opportunity to examine the causes and consequences of some of this complexity. We present a bioenergetic mechanistic model of a tritrophic system where the primary vegetation resource follows a seasonal growth function, and the herbivore and carnivore species are modeled using two integral projection models (IPMs) with body mass as the phenotypic trait. Within each IPM, the demographic functions are structured according to bioenergetic principles, describing how animals acquire and transform resources into body mass, energy reserves, and breeding potential. We parameterize this model to reproduce the population dynamics of grass, elk, and wolves in northern Yellowstone National Park (USA) and investigate the impact of wolf reintroduction on the system. Our model generated predictions that closely matched the observed population sizes of elk and wolf in Yellowstone prior to and following wolf reintroduction. The introduction of wolves into our basal grass-elk bioenergetic model resulted in a population of 99 wolves and a reduction in elk numbers by 61% (from 14,948 to 5823) at equilibrium. In turn, vegetation biomass increased by approximately 25% in the growing season and more than threefold in the nongrowing season. The addition of wolves to the model caused the elk population to switch from being food-limited to being predator-limited and had a stabilizing effect on elk numbers across different years. Wolf predation also led to a shift in the phenotypic composition of the elk population via a small increase in elk average body mass. Our model represents a novel approach to the study of predator-prey interactions, and demonstrates that explicitly considering and linking bioenergetics, population demography and body mass phenotypes can provide novel insights into the mechanisms behind complex ecosystem processes.
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Affiliation(s)
- Gioele Passoni
- Department of Biology, University of Oxford, Oxford, UK
- Animal Ecology Unit, Research and Innovation Centre (CRI), Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Tim Coulson
- Department of Biology, University of Oxford, Oxford, UK
| | - Francesca Cagnacci
- Animal Ecology Unit, Research and Innovation Centre (CRI), Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Peter Hudson
- The Huck Institutes, Penn State University, State College, Pennsylvania, USA
| | - Daniel R Stahler
- Yellowstone Center for Resources, Yellowstone National Park, Wyoming, USA
| | - Douglas W Smith
- Yellowstone Center for Resources, Yellowstone National Park, Wyoming, USA
| | - Shelly Lachish
- Commonwealth Scientific Industrial Research Organisation (CSIRO) Environment Unit, Dutton Park, Queensland, Australia
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5
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vonHoldt BM, DeCandia AL, Cassidy KA, Stahler EE, Sinsheimer JS, Smith DW, Stahler DR. Patterns of reproduction and autozygosity distinguish the breeding from non-breeding gray wolves of Yellowstone National Park. J Hered 2023:esad062. [PMID: 37793153 DOI: 10.1093/jhered/esad062] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Indexed: 10/06/2023] Open
Abstract
For species of management concern, accurate estimates of inbreeding and associated consequences on reproduction are crucial for predicting their future viability. However, few studies have partitioned this aspect of genetic viability with respect to reproduction in a group-living social mammal. We investigated the contributions of foundation stock lineages, putative fitness consequences of inbreeding, and genetic diversity of the breeding versus non-reproductive segment of the Yellowstone National Park gray wolf population. Our dataset spans 25 years and seven generations since reintroduction, encompassing 152 nuclear families and 329 litters. We found over 87% of the pedigree foundation genomes persisted and report influxes of allelic diversity from two translocated wolves from a divergent source in Montana. As expected for group-living species, mean kinship significantly increased over time but with minimal loss of observed heterozygosity. Strikingly, the reproductive portion of the population carried a significantly lower genome-wide inbreeding coefficients, autozygosity, and more rapid decay for linkage disequilibrium relative to the non-breeding population. Breeding wolves had significantly longer lifespans and lower inbreeding coefficients than non-breeding wolves. Our model revealed that the number of litters was negatively significantly associated with heterozygosity (R=-0.11). Our findings highlight genetic contributions to fitness, and the importance of the reproductively active individuals in a population to counteract loss of genetic variation in a wild, free-ranging social carnivore. It is crucial for managers to mitigate factors that significantly reduce effective population size and genetic connectivity, which supports the dispersion of genetic variation that aids in rapid evolutionary responses to environmental challenges.
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Affiliation(s)
- Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, 106A Guyot Hall, Princeton University, Princeton NJ
| | - Alexandra L DeCandia
- Department of Biology, Georgetown University, Washington DC
- Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC
| | - Kira A Cassidy
- Yellowstone Wolf Project, PO Box 168, Yellowstone National Park, WY
| | - Erin E Stahler
- Yellowstone Wolf Project, PO Box 168, Yellowstone National Park, WY
| | - Janet S Sinsheimer
- Department of Biostatistics, Fielding School of Public Health and Departments of Human Genetics and Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA
| | - Douglas W Smith
- Yellowstone Wolf Project, PO Box 168, Yellowstone National Park, WY
| | - Daniel R Stahler
- Yellowstone Wolf Project, PO Box 168, Yellowstone National Park, WY
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6
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Tucker MA, Schipper AM, Adams TSF, Attias N, Avgar T, Babic NL, Barker KJ, Bastille-Rousseau G, Behr DM, Belant JL, Beyer DE, Blaum N, Blount JD, Bockmühl D, Pires Boulhosa RL, Brown MB, Buuveibaatar B, Cagnacci F, Calabrese JM, Černe R, Chamaillé-Jammes S, Chan AN, Chase MJ, Chaval Y, Chenaux-Ibrahim Y, Cherry SG, Ćirović D, Çoban E, Cole EK, Conlee L, Courtemanch A, Cozzi G, Davidson SC, DeBloois D, Dejid N, DeNicola V, Desbiez ALJ, Douglas-Hamilton I, Drake D, Egan M, Eikelboom JAJ, Fagan WF, Farmer MJ, Fennessy J, Finnegan SP, Fleming CH, Fournier B, Fowler NL, Gantchoff MG, Garnier A, Gehr B, Geremia C, Goheen JR, Hauptfleisch ML, Hebblewhite M, Heim M, Hertel AG, Heurich M, Hewison AJM, Hodson J, Hoffman N, Hopcraft JGC, Huber D, Isaac EJ, Janik K, Ježek M, Johansson Ö, Jordan NR, Kaczensky P, Kamaru DN, Kauffman MJ, Kautz TM, Kays R, Kelly AP, Kindberg J, Krofel M, Kusak J, Lamb CT, LaSharr TN, Leimgruber P, Leitner H, Lierz M, Linnell JDC, Lkhagvaja P, Long RA, López-Bao JV, Loretto MC, Marchand P, Martin H, Martinez LA, McBride RT, McLaren AAD, Meisingset E, Melzheimer J, Merrill EH, Middleton AD, Monteith KL, Moore SA, Van Moorter B, Morellet N, Morrison T, Müller R, Mysterud A, Noonan MJ, O'Connor D, Olson D, Olson KA, Ortega AC, Ossi F, Panzacchi M, Patchett R, Patterson BR, de Paula RC, Payne J, Peters W, Petroelje TR, Pitcher BJ, Pokorny B, Poole K, Potočnik H, Poulin MP, Pringle RM, Prins HHT, Ranc N, Reljić S, Robb B, Röder R, Rolandsen CM, Rutz C, Salemgareyev AR, Samelius G, Sayine-Crawford H, Schooler S, Şekercioğlu ÇH, Selva N, Semenzato P, Sergiel A, Sharma K, Shawler AL, Signer J, Silovský V, Silva JP, Simon R, Smiley RA, Smith DW, Solberg EJ, Ellis-Soto D, Spiegel O, Stabach J, Stacy-Dawes J, Stahler DR, Stephenson J, Stewart C, Strand O, Sunde P, Svoboda NJ, Swart J, Thompson JJ, Toal KL, Uiseb K, VanAcker MC, Velilla M, Verzuh TL, Wachter B, Wagler BL, Whittington J, Wikelski M, Wilmers CC, Wittemyer G, Young JK, Zięba F, Zwijacz-Kozica T, Huijbregts MAJ, Mueller T. Behavioral responses of terrestrial mammals to COVID-19 lockdowns. Science 2023; 380:1059-1064. [PMID: 37289888 DOI: 10.1126/science.abo6499] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/27/2023] [Indexed: 06/10/2023]
Abstract
COVID-19 lockdowns in early 2020 reduced human mobility, providing an opportunity to disentangle its effects on animals from those of landscape modifications. Using GPS data, we compared movements and road avoidance of 2300 terrestrial mammals (43 species) during the lockdowns to the same period in 2019. Individual responses were variable with no change in average movements or road avoidance behavior, likely due to variable lockdown conditions. However, under strict lockdowns 10-day 95th percentile displacements increased by 73%, suggesting increased landscape permeability. Animals' 1-hour 95th percentile displacements declined by 12% and animals were 36% closer to roads in areas of high human footprint, indicating reduced avoidance during lockdowns. Overall, lockdowns rapidly altered some spatial behaviors, highlighting variable but substantial impacts of human mobility on wildlife worldwide.
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Affiliation(s)
- Marlee A Tucker
- Department of Environmental Science, Radboud Institute for Biological and Environmental Sciences, Radboud University, P.O. Box 9010, 6500, GL Nijmegen, the Netherlands
| | - Aafke M Schipper
- Department of Environmental Science, Radboud Institute for Biological and Environmental Sciences, Radboud University, P.O. Box 9010, 6500, GL Nijmegen, the Netherlands
| | | | - Nina Attias
- Instituto de Conservação de Animais Silvestres (ICAS), Campo Grande, Mato Grosso do Sul, Brazil
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, USA
| | - Tal Avgar
- Department of Wildland Resources and the Ecology Center, Utah State University, Logan, UT 84322 USA
| | - Natarsha L Babic
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Kristin J Barker
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720 USA
| | | | - Dominik M Behr
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH - 8057 Zürich
- Botswana Predator Conservation, Private Bag 13, Maun, Botswana
| | - Jerrold L Belant
- Department of Fisheries and Wildlife, Michigan State University, 480 Wilson Road, East Lansing, MI 48824, USA
| | - Dean E Beyer
- Department of Fisheries and Wildlife, Michigan State University, 480 Wilson Road, East Lansing, MI 48824, USA
| | - Niels Blaum
- University of Potsdam, Plant Ecology and Nature Conservation, Am Mühlenberg 3, 14476 Potsdam, Germany
| | - J David Blount
- School of Biological Sciences, University of Utah, 257 S 1400 E, Salt Lake City, UT 84112, USA
| | - Dirk Bockmühl
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | | | - Michael B Brown
- Giraffe Conservation Foundation, Eros, PO Box 86099, Windhoek, Namibia
- Smithsonian National Zoo and Conservation Biology Institute, Conservation Ecology Center, 1500 Remount Rd, Front Royal, VA, 22630, USA
| | | | - Francesca Cagnacci
- Animal Ecology Unit, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige, Italy
| | - Justin M Calabrese
- Center for Advanced Systems Understanding (CASUS), Goerlitz, Germany
- Department of Biology, University of Maryland, College Park, 4094 Campus Dr, College Park, MA, USA
| | - Rok Černe
- Slovenia Forest service, Večna pot 2, 1000 Ljubljana, Slovenia
| | - Simon Chamaillé-Jammes
- CEFE, CNRS, Univ Montpellier, EPHE, IRD, Montpellier, France
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, South Africa
| | - Aung Nyein Chan
- Smithsonian National Zoo and Conservation Biology Institute, Conservation Ecology Center, 1500 Remount Rd, Front Royal, VA, 22630, USA
- Dept. Fish, Wildlife and Conservation Biology, Colorado State University, Fort Collins, CO 80525, USA
| | | | - Yannick Chaval
- Université de Toulouse, INRAE, CEFS, F-31326 Castanet-Tolosan, France
- LTSER ZA PYRénées GARonne, F-31320 Auzeville-Tolosane, France
| | - Yvette Chenaux-Ibrahim
- Department of Biology and Environment, Grand Portage Band of Lake Superior Chippewa, Grand Portage, MN 55605 USA
| | - Seth G Cherry
- Parks Canada Agency, Box 220, Radium Hot Springs, BC, V0A 1M0, Canada
| | - Duško Ćirović
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia
| | - Emrah Çoban
- KuzeyDoğa Society, Ortakapı Mah. Şehit Yusuf Cad. 69, 36100 Kars, Turkey
| | - Eric K Cole
- U.S. Fish and Wildlfe Service, National Elk Refuge, PO Box 510, Jackson, WY 83001
| | - Laura Conlee
- Missouri Department of Conservation, Columbia, MO, 65201, USA
| | | | - Gabriele Cozzi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH - 8057 Zürich
- Botswana Predator Conservation, Private Bag 13, Maun, Botswana
| | - Sarah C Davidson
- Department of Migration, Max Planck Institute of Animal Behavior, 78315 Radolfzell, Germany
- Department of Biology, University of Konstanz, 78464 Konstanz, Germany
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, 43210 Columbus, OH, USA
| | | | - Nandintsetseg Dejid
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | | | - Arnaud L J Desbiez
- Instituto de Conservação de Animais Silvestres (ICAS), Campo Grande, Mato Grosso do Sul, Brazil
- Royal Zoological Society of Scotland (RZSS), Murrayfield, Edinburgh, UK
- Instituto de Pesquisas Ecológicas (IPÊ), Nazaré Paulista, São Paulo, Brazil
| | - Iain Douglas-Hamilton
- Save the Elephants, Marula Manor, Marula Lane, Karen, Nairobi 00200, Kenya
- Department of Zoology, Oxford University, Oxford OX1 3PS, UK
| | - David Drake
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI, 53706 USA
| | - Michael Egan
- Cooperative Wildlife Research Laboratory, Southern Illinois University, Carbondale, IL, 62901
- LTSER ZA PYRénées GARonne, F-31320 Auzeville-Tolosane, France
| | - Jasper A J Eikelboom
- Wildlife Ecology and Conservation Group, Wageningen University and Research, Droevendaalsesteeg 3a, 6708 PB, Wageningen, Netherlands
| | - William F Fagan
- Department of Biology, University of Maryland, College Park, 4094 Campus Dr, College Park, MA, USA
| | - Morgan J Farmer
- Department of Forest and Wildlife Ecology, University of Wisconsin, 1630 Linden Drive, Madison, WI 53706 USA
| | - Julian Fennessy
- Giraffe Conservation Foundation, Eros, PO Box 86099, Windhoek, Namibia
| | - Shannon P Finnegan
- Global Wildlife Conservation Center, State University of New York College of Environmental Science and Forestry, 1 Forestry Drive, Syracuse, NY 13210, USA
| | - Christen H Fleming
- Department of Biology, University of Maryland, College Park, 4094 Campus Dr, College Park, MA, USA
- Smithsonian Conservation Biology Institute, 1500 Remount Rd, Front Royal, VA, USA
| | - Bonnie Fournier
- Wildlife and Fish Division, Department of Environment and Natural Resources, Government of the Northwest Territories, P.O. Box 1320, Yellowknife, NT, Canada
| | - Nicholas L Fowler
- Global Wildlife Conservation Center, State University of New York College of Environmental Science and Forestry, 1 Forestry Drive, Syracuse, NY 13210, USA
- Alaska Department of Fish and Game, 43961 Kalifornsky Beach Road, Suite B, Soldotna, AK 99669, USA
| | - Mariela G Gantchoff
- State University of New York College of Environmental Science and Forestry, Syracuse, NY 13210, USA
- Department of Biology, College of Arts and Sciences, University of Dayton, Dayton, OH 45469 USA
| | - Alexandre Garnier
- Université de Toulouse, INRAE, CEFS, F-31326 Castanet-Tolosan, France
- Parc National des Pyrénées, 65000 Tarbes, France
| | - Benedikt Gehr
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Chris Geremia
- Yellowstone Center for Resources, PO Box 168, Yellowstone National Park, WY 82190
| | - Jacob R Goheen
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071 USA
| | - Morgan L Hauptfleisch
- Biodiversity Research Centre, Namibia University of Science and Technnology Pvt bag 13388 Windhoek, Namibia
| | - Mark Hebblewhite
- Wildlife Biology Program, Franke College of Forestry and Conservation, University of Montana, Missoula, MT, 59801
| | - Morten Heim
- Norwegian Institute for Nature Research, Terrestrial Ecology Department, P.O. Box 5685 Torgarden, 7485 Trondheim, Norway
| | - Anne G Hertel
- Behavioural Ecology, Department of Biology, Ludwig Maximilian University of Munich, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
| | - Marco Heurich
- Department of Visitor Management and National Park Monitoring, Bavarian Forest National Park, Freyunger Straße 2, 94481 Grafenau, Germany
- Chair of Wildlife Ecology and Conservation Biology, Faculty of Environment and Natural Resources, University of Freiburg, Tennenbacher Straße 4, 79106 Freiburg, Germany
- Institute for forest and wildlife management, Faculty of Applied Ecology, Agricultural Sciences and Biotechnology, Campus Evenstad, Inland Norway University of Applied Science, NO-2480 Koppang, Norway
| | - A J Mark Hewison
- Université de Toulouse, INRAE, CEFS, F-31326 Castanet-Tolosan, France
- LTSER ZA PYRénées GARonne, F-31320 Auzeville-Tolosane, France
| | - James Hodson
- Wildlife and Fish Division, Department of Environment and Natural Resources, Government of the Northwest Territories, P.O. Box 1320, Yellowknife, NT Canada X1A 2L9
| | - Nicholas Hoffman
- Ecological Program, Pennsylvania Department of Military and Veterans Affairs, Fort Indiantown Gap National Guard Training Center, Annville, PA 17003, USA
| | - J Grant C Hopcraft
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow UK G12 8QQ
| | - Djuro Huber
- Veterinary Biology Department, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, HR-10000 Zagreb, Croatia
| | - Edmund J Isaac
- Department of Biology and Environment, Grand Portage Band of Lake Superior Chippewa, Grand Portage, MN 55605 USA
| | - Karolina Janik
- City of New York Parks and Recreation, Wildlife Unit, 1234 5th Avenue, 5th Floor, NY 10029
| | - Miloš Ježek
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Czech Republic
| | - Örjan Johansson
- Grimsö Wildlife Research Station, Swedish University of Agricultural Sciences, 739 93, Riddarhyttan, Sweden
- Snow Leopard Trust, 4649 Sunnyside Avenue North, Seattle, WA 98103, USA
| | - Neil R Jordan
- Botswana Predator Conservation, Private Bag 13, Maun, Botswana
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
- Taronga Institute of Science and Learning, Taronga Conservation Society, Sydney, NSW, 2088, Australia
| | - Petra Kaczensky
- Inland Norway University of Applied Sciences, Department of Forestry and Wildlife Management, Norway
- University of Veterinary Medicine Vienna, Research Institute of Wildlife Ecology, Austria
| | - Douglas N Kamaru
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071 USA
- Wildlife Department, Ol Pejeta Conservancy, Private Bag-10400, Nanyuki, Kenya
| | - Matthew J Kauffman
- U.S. Geological Survey, Wyoming Cooperative Fish and Wildlife Research Unit, Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
| | - Todd M Kautz
- Global Wildlife Conservation Center, State University of New York College of Environmental Science and Forestry, 1 Forestry Drive, Syracuse, NY 13210, USA
| | - Roland Kays
- North Carolina Museum of Natural Sciences, Raleigh, NC, 27601, USA
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
| | - Allicia P Kelly
- Department of Environment and Natural Resources, Government of the Northwest Territories, P.O. Box 2668, Yellowknife, NT Canada X1A 2P9
| | - Jonas Kindberg
- Norwegian Institute for Nature Research, NO-7484 Trondheim, Norway
- Department of Wildlife, Fish and Environmental studies, Swedish University of Agricultural Sciences, SE- 901 83 Umeå, Sweden
| | - Miha Krofel
- Department of Forestry, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research, Alfred- Kowalke- Str. 17, 10315 Berlin, Germany
| | - Josip Kusak
- Veterinary Biology Department, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, HR-10000 Zagreb, Croatia
| | - Clayton T Lamb
- Biological Sciences Centre, University of Alberta, Edmonton, Alberta, T6G 2E9 Canada
| | - Tayler N LaSharr
- Haub School of Environment and Natural Resources, Wyoming Cooperative Fish and Wildlife Research Unit, Department of Zoology and Physiology, University of Wyoming, 804 East Fremont, Laramie, WY 82072
| | - Peter Leimgruber
- Smithsonian National Zoo and Conservation Biology Institute, Conservation Ecology Center, 1500 Remount Rd, Front Royal, VA, 22630, USA
| | - Horst Leitner
- Büro für Wildökologie und Forstwirtschaft, Klagenfurth, Austria
| | - Michael Lierz
- Clinic for birds, reptiles, amphibians and fish, Justus-Liebig-University Giessen, Germany
| | - John D C Linnell
- Norwegian Institute for Nature Research, Terrestrial Ecology Department, P.O. Box 5685 Torgarden, 7485 Trondheim, Norway
- Inland Norway University of Applied Sciences, Department of Forestry and Wildlife Management, Anne Evenstads vei 80, 2480 Koppang, Norway
| | | | - Ryan A Long
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID 83844 USA
| | - José Vicente López-Bao
- Biodiversity Research Institute (CSIC - Oviedo University - Principality of Asturias), Oviedo University, E-33600 Mieres, Spain
| | - Matthias-Claudio Loretto
- Department of Migration, Max Planck Institute of Animal Behavior, 78315 Radolfzell, Germany
- Technical University of Munich, TUM School of Life Sciences, Ecosystem Dynamics and Forest Management Group, 85354 Freising, Germany
- Berchtesgaden National Park, 83471 Berchtesgaden, Germany
| | - Pascal Marchand
- Office Français de la Biodiversité, Direction de la Recherche et de l'Expertise, Unité Ongulés Sauvages, Juvignac, France
| | - Hans Martin
- Wildlife Biology Program, Franke College of Forestry and Conservation, University of Montana, Missoula, MT, 59801
| | - Lindsay A Martinez
- Wyoming Cooperative Fish and Wildlife Research Unit, Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
| | - Roy T McBride
- Faro Moro Eco Research, Estancia Faro Moro, Departmento de Boquerón, Paraguay
| | - Ashley A D McLaren
- Ontario Ministry of Natural Resources and Forestry, Wildlife Research and Monitoring Section, Trent University, 2140 East Bank Drive, Peterborough, Ontario, K9J 7B8, Canada
- Department of Environment and Natural Resources, Government of the Northwest Territories, Highway 5, PO Box 900, Fort Smith, Northwest Territories, X0E 0P0, Canada
| | - Erling Meisingset
- Department of Forestry and Forestry resources, Norwegian Institute of Bioeconomy Research, Tingvoll gard, NO-6630 Tingvoll, Norway
| | - Joerg Melzheimer
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Evelyn H Merrill
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Arthur D Middleton
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Kevin L Monteith
- Haub School of Environment and Natural Resources, Wyoming Cooperative Fish and Wildlife Research Unit, Department of Zoology and Physiology, University of Wyoming, 804 East Fremont, Laramie, WY 82072
| | - Seth A Moore
- Department of Biology and Environment, Grand Portage Band of Lake Superior Chippewa, Grand Portage, MN 55605 USA
| | - Bram Van Moorter
- Norwegian Institute for Nature Research, Terrestrial Ecology Department, P.O. Box 5685 Torgarden, 7485 Trondheim, Norway
| | - Nicolas Morellet
- Université de Toulouse, INRAE, CEFS, F-31326 Castanet-Tolosan, France
- LTSER ZA PYRénées GARonne, F-31320 Auzeville-Tolosane, France
| | - Thomas Morrison
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow UK G12 8QQ
| | - Rebekka Müller
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Atle Mysterud
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, NO-0316 Oslo, Norway
| | - Michael J Noonan
- Department of Biology, University of British Columbia Okanagan, Kelowna, British Columbia, Canada
| | - David O'Connor
- Save Giraffe Now, 8333 Douglas Avenue, Suite 300, Dallas, Texas 75225
- The Faculty of Biological Sciences, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- National Geographic Partners, 1145 17th Street NW, Washington DC 20036, USA
| | | | - Kirk A Olson
- Wildlife Conservation Society, Mongolia Program. Post 20A, Box 21, Ulaanbaatar 14200, Mongolia
| | - Anna C Ortega
- Wyoming Cooperative Fish and Wildlife Research Unit, Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
- Program in Ecology, University of Wyoming, Laramie, WY 82071 USA
| | - Federico Ossi
- Animal Ecology Unit, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige, Italy
| | - Manuela Panzacchi
- Norwegian Institute for Nature Research, Terrestrial Ecology Department, P.O. Box 5685 Torgarden, 7485 Trondheim, Norway
| | - Robert Patchett
- Centre for Biological Diversity, School of Biology, University of St Andrews, Sir Harold Mitchell Building, St Andrews, KY16 9TH, UK
| | - Brent R Patterson
- Department of Environmental and Life Sciences, Trent University, 2140 East Bank Drive, Peterborough, Ontario K9J 7B8, Canada
- Ontario Ministry of Natural Resources and Forestry, Wildlife Research and Monitoring Section, Trent University, 2140 East Bank Drive, Peterborough, Ontario K9J 7B8, Canada
| | - Rogerio Cunha de Paula
- Centro Nacional de Pesquisa e Conservação de Mamíferos Carnívoros, Instituto Chico Mendes de Conservação da Biodiversidade, Atibaia, SP, 12952011 Brazil
| | - John Payne
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
| | - Wibke Peters
- Department of Biodiversity, Conservation and Wildlife Management, Bavarian State Institute for Forestry, Hans-Carl-von Carlowitz Platz 1, 85354 Freising
| | - Tyler R Petroelje
- Global Wildlife Conservation Center, State University of New York College of Environmental Science and Forestry, 1 Forestry Drive, Syracuse, NY 13210, USA
| | - Benjamin J Pitcher
- Taronga Institute of Science and Learning, Taronga Conservation Society, Sydney, NSW, 2088, Australia
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, NSW, 2109, Australia
| | - Boštjan Pokorny
- Faculty of Environmental Protection, Trg mladosti 7, 3320 Velenje, Slovenia
- Slovenian Forestry Institute, Večna pot 2, 1000 Ljubljana, Slovenia
- Department of Biodiversity, Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia
| | - Kim Poole
- Aurora Wildlife Research, 1918 Shannon Point Rd., Nelson, BC, V1L 6K1 Canada
| | - Hubert Potočnik
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Marie-Pier Poulin
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY, 82071 USA
| | - Robert M Pringle
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544 USA
| | - Herbert H T Prins
- Department of Animal Sciences, Wageningen University and Research, De Elst 1, 6708 WD, Wageningen, Netherlands
| | - Nathan Ranc
- Animal Ecology Unit, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige, Italy
- Université de Toulouse, INRAE, CEFS, F-31326 Castanet-Tolosan, France
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge MA 02138, USA
| | - Slaven Reljić
- Veterinary Biology Department, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, HR-10000 Zagreb, Croatia
- Oikon Ltd, Institute of Applied Ecology, Trg Senjskih uskoka 1-2, HR-10020 Zagreb, Croatia
| | - Benjamin Robb
- Wyoming Cooperative Fish and Wildlife Research Unit, Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
| | - Ralf Röder
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Christer M Rolandsen
- Norwegian Institute for Nature Research, Terrestrial Ecology Department, P.O. Box 5685 Torgarden, 7485 Trondheim, Norway
| | - Christian Rutz
- Centre for Biological Diversity, School of Biology, University of St Andrews, Sir Harold Mitchell Building, St Andrews, KY16 9TH, UK
| | - Albert R Salemgareyev
- Association for the Conservation of Biodiversity of Kazakhstan (ACBK), Nur-Sultan, 010000, Kazakhstan
| | - Gustaf Samelius
- Snow Leopard Trust, 4649 Sunnyside Avenue North, Seattle, WA 98103, USA
- Nordens Ark, 456 93 Hunnebostrand, Sweden
| | - Heather Sayine-Crawford
- Wildlife and Fish Division, Department of Environment and Natural Resources, Government of the Northwest Territories, P.O. Box 1320, Yellowknife, NT Canada X1A 2L9
| | - Sarah Schooler
- Global Wildlife Conservation Center, State University of New York College of Environmental Science and Forestry, 1 Forestry Drive, Syracuse, NY 13210, USA
| | - Çağan H Şekercioğlu
- School of Biological Sciences, University of Utah, 257 S 1400 E, Salt Lake City, UT 84112, USA
- KuzeyDoğa Society, Ortakapı Mah. Şehit Yusuf Cad. 69, 36100 Kars, Turkey
- Koç University Department of Molecular Biology and Genetics, Faculty of Sciences, Rumelifeneri, Istanbul, Sarıyer, Turkey
| | - Nuria Selva
- Institute of Nature Conservation Polish Academy of Sciences, Adama Mickiewicza 33, 31-120 Kraków, Poland
- Departamento de Ciencias Integradas, Facultad de Ciencias Experimentales, Centro de Estudios Avanzados en Física, Matemáticas y Computación, Universidad de Huelva, 21071 Huelva, Spain
| | - Paola Semenzato
- Animal Ecology Unit, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige, Italy
- Dimension Research, Ecology and Environment (D.R.E.Am. Italia), Via Garibaldi, 3, 52015 Pratovecchio Stia (AR), Italy
| | - Agnieszka Sergiel
- Institute of Nature Conservation Polish Academy of Sciences, Adama Mickiewicza 33, 31-120 Kraków, Poland
| | - Koustubh Sharma
- Snow Leopard Trust, Seattle, WA 98103, USA
- Global Snow Leopard and Ecosystem Protection Program, Bishkek, Kyrgyzstan
- Snow Leopard Foundation, Kyrgyzstan Bishkek, Kyrgyzstan
- Nature Conservation Foundation, Mysore 570002, India
| | - Avery L Shawler
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Johannes Signer
- Wildlife Sciences, Faculty of Forest Sciences and Forest Ecology, University of Goettingen, Göttingen Germany
| | - Václav Silovský
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Czech Republic
| | - João Paulo Silva
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Richard Simon
- City of New York Parks and Recreation, Wildlife Unit, 1234 5th Avenue, 5th Floor, NY, NY, 10029
| | - Rachel A Smiley
- Haub School of Environment and Natural Resources, Wyoming Cooperative Fish and Wildlife Research Unit, Department of Zoology and Physiology, University of Wyoming, 804 East Fremont, Laramie, WY 82072
| | - Douglas W Smith
- Yellowstone Center for Resources, PO Box 168, Yellowstone National Park, WY 82190
| | - Erling J Solberg
- Norwegian Institute for Nature Research, Terrestrial Ecology Department, P.O. Box 5685 Torgarden, 7485 Trondheim, Norway
| | - Diego Ellis-Soto
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
- Center for Biodiversity and Global Change, Yale University, New Haven, CT
- Max Planck - Yale Center for Biodiversity Movement and Global Change, Yale University
| | - Orr Spiegel
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jared Stabach
- Smithsonian National Zoo and Conservation Biology Institute, Conservation Ecology Center, 1500 Remount Rd, Front Royal, VA, 22630, USA
| | - Jenna Stacy-Dawes
- San Diego Zoo Wildlife Alliance, 15600 San Pasqual Valley Road, Escondido, CA, 92027 USA
| | - Daniel R Stahler
- Yellowstone Center for Resources, PO Box 168, Yellowstone National Park, WY 82190
| | - John Stephenson
- Grand Teton National Park, PO Drawer 170, Moose, Wyoming 83012 USA
| | - Cheyenne Stewart
- Wyoming Game and Fish Department, 700 Valley View Dr. Sheridan, WY 82801
| | - Olav Strand
- Norwegian Institute for Nature Research, Terrestrial Ecology Department, P.O. Box 5685 Torgarden, 7485 Trondheim, Norway
| | - Peter Sunde
- Aarhus University, Department of Ecoscience - Wildlife Ecology, C.F. Møllers Allé 4-8, 8000 Aarhus C, Denmark
| | | | - Jonathan Swart
- Welgevonden Game Reserve, P.O. Box 433, Vaalwater, South Africa
| | - Jeffrey J Thompson
- Guyra Paraguay - CONACYT, Asunción, Paraguay
- Instituto Saite, Asunción, Paraguay
| | - Katrina L Toal
- City of New York Parks and Recreation, Wildlife Unit, 1234 5th Avenue, 5th Floor, NY, NY, 10029
| | - Kenneth Uiseb
- Ministry of Environment, Forestry and Tourism, Windhoek, Namibia
| | - Meredith C VanAcker
- Smithsonian National Zoo and Conservation Biology Institute, Conservation Ecology Center, 1500 Remount Rd, Front Royal, VA, 22630, USA
- Ecology, Evolution and Environmental Biology, Columbia University, NY, NY 10027
| | - Marianela Velilla
- Guyra Paraguay - CONACYT, Asunción, Paraguay
- Instituto Saite, Asunción, Paraguay
- School of Natural Resources, University of Arizona, 1064 E Lowell St, Tucson, AZ 85719, USA
| | - Tana L Verzuh
- Haub School of Environment and Natural Resources, Wyoming Cooperative Fish and Wildlife Research Unit, Department of Zoology and Physiology, University of Wyoming, 804 East Fremont, Laramie, WY 82072
| | - Bettina Wachter
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Brittany L Wagler
- Haub School of Environment and Natural Resources, Wyoming Cooperative Fish and Wildlife Research Unit, Department of Zoology and Physiology, University of Wyoming, 804 East Fremont, Laramie, WY 82072
| | - Jesse Whittington
- Park Canada, Banff National Park Resource Conservation. PO Box 900, Banff, Alberta, Canada. T1L 1K2
| | - Martin Wikelski
- Department of Migration, Max Planck Institute of Animal Behavior, 78315 Radolfzell, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, 78457 Konstanz, Germany
| | - Christopher C Wilmers
- Center for Integrated Spatial Research, Environmental Studies Department, University of California, Santa Cruz CA, 95064 USA
| | - George Wittemyer
- Save the Elephants, Marula Manor, Marula Lane, Karen, Nairobi 00200, Kenya
- Department of Fish, Wildlife and Conservation Biology, Colorado State University, Fort Collins, CO 80523
| | - Julie K Young
- USDA National Wildlife Research Center, Predator Research Facility, Millville, UT 84326 USA
- Department of Wildland Resources, Utah State University, Logan, UT 84322 USA
| | - Filip Zięba
- Tatra National Park, Kuźnice 1, 34-500, Zakopane, Poland
| | | | - Mark A J Huijbregts
- Department of Environmental Science, Radboud Institute for Biological and Environmental Sciences, Radboud University, P.O. Box 9010, 6500, GL Nijmegen, the Netherlands
| | - Thomas Mueller
- Smithsonian National Zoo and Conservation Biology Institute, Conservation Ecology Center, 1500 Remount Rd, Front Royal, VA, 22630, USA
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Department of Biological Sciences, Goethe University, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany
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Smith BJ, MacNulty DR, Stahler DR, Smith DW, Avgar T. Density-dependent habitat selection alters drivers of population distribution in northern Yellowstone elk. Ecol Lett 2023; 26:245-256. [PMID: 36573288 PMCID: PMC10107875 DOI: 10.1111/ele.14155] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 12/28/2022]
Abstract
Although it is well established that density dependence drives changes in organismal abundance over time, relatively little is known about how density dependence affects variation in abundance over space. We tested the hypothesis that spatial trade-offs between food and safety can change the drivers of population distribution, caused by opposing patterns of density-dependent habitat selection (DDHS) that are predicted by the multidimensional ideal free distribution. We addressed this using winter aerial survey data of northern Yellowstone elk (Cervus canadensis) spanning four decades. Supporting our hypothesis, we found positive DDHS for food (herbaceous biomass) and negative DDHS for safety (openness and roughness), such that the primary driver of habitat selection switched from food to safety as elk density decreased from 9.3 to 2.0 elk/km2 . Our results demonstrate how population density can drive landscape-level shifts in population distribution, confounding habitat selection inference and prediction and potentially affecting community-level interactions.
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Affiliation(s)
- Brian J Smith
- Department of Wildland Resources and Ecology Center, Utah State University, Logan, Utah, USA
| | - Daniel R MacNulty
- Department of Wildland Resources and Ecology Center, Utah State University, Logan, Utah, USA
| | - Daniel R Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Douglas W Smith
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Tal Avgar
- Department of Wildland Resources and Ecology Center, Utah State University, Logan, Utah, USA.,Biodiversity Pathways Ltd., British Columbia, Canada
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SunderRaj J, Rabe JW, Cassidy KA, McIntyre R, Stahler DR, Smith DW. Breeding displacement in gray wolves (Canis lupus): Three males usurp breeding position and pup rearing from a neighboring pack in Yellowstone National Park. PLoS One 2022; 17:e0256618. [PMID: 36449452 PMCID: PMC9710779 DOI: 10.1371/journal.pone.0256618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/02/2022] [Indexed: 12/02/2022] Open
Abstract
Gray Wolves (Canis lupus) are territorial, group living carnivores that live in packs typically consisting of a dominant breeding pair and their offspring. Breeding tenures are relatively short and competitive, with vacancies usually occurring following a breeder's death, and are often filled by unrelated immigrants or by relatives of the previous breeder. The frequency and conditions of active breeder displacements are poorly understood. Position changes in the dominance hierarchy are common yet rarely documented in detail. We describe a male breeding position turnover in a wolf pack by males from a neighboring pack in mid-summer 2016 in Yellowstone National Park. Over the course of two months, three males from the Mollie's pack displaced the breeding male of the neighboring Wapiti Lake pack, joined the pack's two adult females, and subsequently raised the previous male's four approximately three-month old pups. In the five years following the displacement (2017 to 2021), at least one of the intruding males has successfully bred with the dominant female and most years with a subordinate female (who was one of the pups at the time of displacement). The pack reared pups to adulthood each year. Male breeding displacements are likely influenced by male-male competition and female mate choice. These changes are the result of individuals competing to improve breeding position and may lead to increased pack stability and greater reproductive success. We report in detail on the behavior of a closely observed breeding displacement and we discuss the adaptive benefits of the change.
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Affiliation(s)
- Jeremy SunderRaj
- Yellowstone Wolf Project, Yellowstone Center for Resources, Yellowstone National Park, Wyoming, United States of America
- * E-mail:
| | - Jack W. Rabe
- Yellowstone Wolf Project, Yellowstone Center for Resources, Yellowstone National Park, Wyoming, United States of America
- Department of Fisheries, Wildlife, and Conservation Biology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Kira A. Cassidy
- Yellowstone Wolf Project, Yellowstone Center for Resources, Yellowstone National Park, Wyoming, United States of America
| | - Rick McIntyre
- Yellowstone Wolf Project, Yellowstone Center for Resources, Yellowstone National Park, Wyoming, United States of America
| | - Daniel R. Stahler
- Yellowstone Wolf Project, Yellowstone Center for Resources, Yellowstone National Park, Wyoming, United States of America
| | - Douglas W. Smith
- Yellowstone Wolf Project, Yellowstone Center for Resources, Yellowstone National Park, Wyoming, United States of America
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9
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Meyer CJ, Cassidy KA, Stahler EE, Brandell EE, Anton CB, Stahler DR, Smith DW. Parasitic infection increases risk-taking in a social, intermediate host carnivore. Commun Biol 2022; 5:1180. [PMID: 36424436 PMCID: PMC9691632 DOI: 10.1038/s42003-022-04122-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 11/24/2021] [Accepted: 10/17/2022] [Indexed: 11/26/2022] Open
Abstract
Toxoplasma gondii is a protozoan parasite capable of infecting any warm-blooded species and can increase risk-taking in intermediate hosts. Despite extensive laboratory research on the effects of T. gondii infection on behaviour, little is understood about the effects of toxoplasmosis on wild intermediate host behavior. Yellowstone National Park, Wyoming, USA, has a diverse carnivore community including gray wolves (Canis lupus) and cougars (Puma concolor), intermediate and definitive hosts of T. gondii, respectively. Here, we used 26 years of wolf behavioural, spatial, and serological data to show that wolf territory overlap with areas of high cougar density was an important predictor of infection. In addition, seropositive wolves were more likely to make high-risk decisions such as dispersing and becoming a pack leader, both factors critical to individual fitness and wolf vital rates. Due to the social hierarchy within a wolf pack, we hypothesize that the behavioural effects of toxoplasmosis may create a feedback loop that increases spatial overlap and disease transmission between wolves and cougars. These findings demonstrate that parasites have important implications for intermediate hosts, beyond acute infections, through behavioural impacts. Particularly in a social species, these impacts can surge beyond individuals to affect groups, populations, and even ecosystem processes.
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Affiliation(s)
- Connor J. Meyer
- grid.454846.f0000 0001 2331 3972Yellowstone Wolf Project, Yellowstone Center for Resources, P.O. Box 168, Yellowstone National Park, WY 82190 USA ,grid.253613.00000 0001 2192 5772Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, W. A. Franke College of Forestry and Conservation, University of Montana, Missoula, MT 59812 USA
| | - Kira A. Cassidy
- grid.454846.f0000 0001 2331 3972Yellowstone Wolf Project, Yellowstone Center for Resources, P.O. Box 168, Yellowstone National Park, WY 82190 USA
| | - Erin E. Stahler
- grid.454846.f0000 0001 2331 3972Yellowstone Wolf Project, Yellowstone Center for Resources, P.O. Box 168, Yellowstone National Park, WY 82190 USA
| | - Ellen E. Brandell
- grid.454846.f0000 0001 2331 3972Yellowstone Wolf Project, Yellowstone Center for Resources, P.O. Box 168, Yellowstone National Park, WY 82190 USA
| | - Colby B. Anton
- grid.454846.f0000 0001 2331 3972Yellowstone Wolf Project, Yellowstone Center for Resources, P.O. Box 168, Yellowstone National Park, WY 82190 USA
| | - Daniel R. Stahler
- grid.454846.f0000 0001 2331 3972Yellowstone Wolf Project, Yellowstone Center for Resources, P.O. Box 168, Yellowstone National Park, WY 82190 USA
| | - Douglas W. Smith
- grid.454846.f0000 0001 2331 3972Yellowstone Wolf Project, Yellowstone Center for Resources, P.O. Box 168, Yellowstone National Park, WY 82190 USA
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10
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Brandell EE, Jackson MK, Cross PC, Piaggio AJ, Taylor DR, Smith DW, Boufana B, Stahler DR, Hudson PJ. Evaluating noninvasive methods for estimating cestode prevalence in a wild carnivore population. PLoS One 2022; 17:e0277420. [PMID: 36378663 PMCID: PMC9665365 DOI: 10.1371/journal.pone.0277420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022] Open
Abstract
Helminth infections are cryptic and can be difficult to study in wildlife species. Helminth research in wildlife hosts has historically required invasive animal handling and necropsy, while results from noninvasive parasite research, like scat analysis, may not be possible at the helminth species or individual host levels. To increase the utility of noninvasive sampling, individual hosts can be identified by applying molecular methods. This allows for longitudinal sampling of known hosts and can be paired with individual-level covariates. Here we evaluate a combination of methods and existing long-term monitoring data to identify patterns of cestode infections in gray wolves in Yellowstone National Park. Our goals were: (1) Identify the species and apparent prevalence of cestodes infecting Yellowstone wolves; (2) Assess the relationships between wolf biological and social characteristics and cestode infections; (3) Examine how wolf samples were affected by environmental conditions with respect to the success of individual genotyping. We collected over 200 wolf scats from 2018-2020 and conducted laboratory analyses including individual wolf genotyping, sex identification, cestode identification, and fecal glucocorticoid measurements. Wolf genotyping success rate was 45%, which was higher in the winter but decreased with higher precipitation and as more time elapsed between scat deposit and collection. One cestode species was detected in 28% of all fecal samples, and 38% of known individuals. The most common infection was Echinococcus granulosus sensu lato (primarily E. canadensis). Adult wolves had 4x greater odds of having a cestode infection than pups, as well as wolves sampled in the winter. Our methods provide an alternative approach to estimate cestode prevalence and to linking parasites to known individuals in a wild host system, but may be most useful when employed in existing study systems and when field collections are designed to minimize the time between fecal deposition and collection.
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Affiliation(s)
- Ellen E. Brandell
- Center for Infectious Disease Dynamics, Department of Biology, Huck Institutes of Life Sciences, Pennsylvania State University, University Park, PA, United States of America
- * E-mail:
| | - Madeline K. Jackson
- Yellowstone Center for Resources, Yellowstone National Park, WY, United States of America
| | - Paul C. Cross
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Bozeman, MT, United States of America
| | - Antoinette J. Piaggio
- National Wildlife Research Center, U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, Fort Collins, CO, United States of America
| | - Daniel R. Taylor
- National Wildlife Research Center, U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, Fort Collins, CO, United States of America
| | - Douglas W. Smith
- Yellowstone Center for Resources, Yellowstone National Park, WY, United States of America
| | - Belgees Boufana
- National Wildlife Management Centre, National Reference Laboratory for Parasites (Trichinella and Echinococcus), Animal and Plant Health Agency, York, United Kingdom
| | - Daniel R. Stahler
- Yellowstone Center for Resources, Yellowstone National Park, WY, United States of America
| | - Peter J. Hudson
- Center for Infectious Disease Dynamics, Department of Biology, Huck Institutes of Life Sciences, Pennsylvania State University, University Park, PA, United States of America
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11
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Cubaynes S, Brandell EE, Stahler DR, Smith DW, Almberg ES, Schindler S, Wayne RK, Dobson AP, vonHoldt BM, MacNulty DR, Cross PC, Hudson PJ, Coulson T. Disease outbreaks select for mate choice and coat color in wolves. Science 2022; 378:300-303. [PMID: 36264784 DOI: 10.1126/science.abi8745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
We know much about pathogen evolution and the emergence of new disease strains, but less about host resistance and how it is signaled to other individuals and subsequently maintained. The cline in frequency of black-coated wolves (Canis lupus) across North America is hypothesized to result from a relationship with canine distemper virus (CDV) outbreaks. We tested this hypothesis using cross-sectional data from wolf populations across North America that vary in the prevalence of CDV and the allele that makes coats black, longitudinal data from Yellowstone National Park, and modeling. We found that the frequency of CDV outbreaks generates fluctuating selection that results in heterozygote advantage that in turn affects the frequency of the black allele, optimal mating behavior, and black wolf cline across the continent.
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Affiliation(s)
- Sarah Cubaynes
- CEFE, University of Montpellier, CNRS, EPHE-PSL University, IRD, 34090 Montpellier, France
| | - Ellen E Brandell
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, State College, PA 16802, USA
| | - Daniel R Stahler
- Yellowstone Center for Resources, Yellowstone National Park, WY 82190, USA
| | - Douglas W Smith
- Yellowstone Center for Resources, Yellowstone National Park, WY 82190, USA
| | - Emily S Almberg
- Wildlife Division, Montana Fish Wildlife & Park, Bozeman, MT 59718, USA
| | - Susanne Schindler
- School of Biological Sciences, University of Bristol, Bristol BS8 1QU, UK
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Andrew P Dobson
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.,Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Daniel R MacNulty
- Department of Wildland Resources and Ecology Center, Utah State University, Logan, UT 84322, USA
| | - Paul C Cross
- US Geological Survey, Northern Rocky Mountain Science Center, Bozeman, MT 59715, USA
| | - Peter J Hudson
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, State College, PA 16802, USA
| | - Tim Coulson
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
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12
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Brandell EE, Cross PC, Smith DW, Rogers W, Galloway N, MacNulty DR, Stahler DR, Treanor J, Hudson PJ. Examination of the interaction between age-specific predation and chronic disease in the Greater Yellowstone Ecosystem. J Anim Ecol 2022; 91:1373-1384. [PMID: 34994978 PMCID: PMC9912199 DOI: 10.1111/1365-2656.13661] [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] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/28/2021] [Indexed: 11/27/2022]
Abstract
Predators may create healthier prey populations by selectively removing diseased individuals. Predators typically prefer some ages of prey over others, which may, or may not, align with those prey ages that are most likely to be diseased. The interaction of age-specific infection and predation has not been previously explored and likely has sizable effects on disease dynamics. We hypothesize that predator cleansing effects will be greater when the disease and predation occur in the same prey age groups. We examine the predator cleansing effect using a model where both vulnerability to predators and pathogen prevalence vary with age. We tailor this model to chronic wasting disease (CWD) in mule deer and elk populations in the Greater Yellowstone Ecosystem, with empirical data from Yellowstone grey wolves and cougars. Model results suggest that under moderate, yet realistic, predation pressure from cougars and wolves independently, predators may decrease CWD outbreak size substantially and delay the accumulation of symptomatic deer and elk. The magnitude of this effect is driven by the ability of predators to selectively remove late-stage CWD infections that are likely the most responsible for transmission, but this may not be the age class they typically select. Thus, predators that select for infected young adults over uninfected juveniles have a stronger cleansing effect, and these effects are strengthened when transmission rates increase with increasing prey morbidity. There are also trade-offs from a management perspective-that is, increasing predator kill rates can result in opposing forces on prey abundance and CWD prevalence. Our modelling exploration shows that predators have the potential to reduce prevalence in prey populations when prey age and disease severity are considered, yet the strength of this effect is influenced by predators' selection for demography or body condition. Current CWD management focuses on increasing cervid hunting as the primary management tool, and our results suggest predators may also be a useful tool under certain conditions, but not necessarily without additional impacts on host abundance and demography. Protected areas with predator populations will play a large role in informing the debate over predator impacts on disease.
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Affiliation(s)
- Ellen E. Brandell
- Center for Infectious Disease Dynamics and Department of Biology, Huck Institutes of the Life SciencesPennsylvania State UniversityUniversity ParkPAUSA,Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife EcologyUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Paul C. Cross
- U.S. Geological SurveyNorthern Rocky Mountain Science CenterBozemanMTUSA
| | - Douglas W. Smith
- Yellowstone Center for ResourcesYellowstone National ParkWyomingWYUSA
| | - Will Rogers
- Department of EcologyMontana State UniversityBozemanMTUSA
| | | | | | - Daniel R. Stahler
- Yellowstone Center for ResourcesYellowstone National ParkWyomingWYUSA
| | - John Treanor
- Yellowstone Center for ResourcesYellowstone National ParkWyomingWYUSA
| | - Peter J. Hudson
- Center for Infectious Disease Dynamics and Department of Biology, Huck Institutes of the Life SciencesPennsylvania State UniversityUniversity ParkPAUSA
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13
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Tallian A, Ordiz A, Metz MC, Zimmermann B, Wikenros C, Smith DW, Stahler DR, Wabakken P, Swenson JE, Sand H, Kindberg J. Of wolves and bears: Seasonal drivers of interference and exploitation competition between apex predators. ECOL MONOGR 2021. [DOI: 10.1002/ecm.1498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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)
- Aimee Tallian
- Norwegian Institute for Nature Research NO‐7485 Trondheim Norway
| | - Andrés Ordiz
- Grimsӧ Wildlife Research Station Department of Ecology Swedish University of Agricultural Sciences SE‐739 93 Riddarhyttan Sweden
- Faculty of Environmental Sciences and Natural Resource Management Norwegian University of Life Sciences Postbox 5003, NO‐1432 Ås Norway
- Dpto. de Biodiversidad y Gestión Ambiental Área de Zoología Facultad de Ciencias Biológicas y Ambientales Universidad de León Campus de Vegazana s/n 24071 León Spain
| | - Matthew C. Metz
- Wildlife Biology Program Department of Ecosystem and Conservation Sciences University of Montana Missoula Montana 59812 USA
- Yellowstone Center for Resources Yellowstone National Park Box 168, Mammoth Hot Springs WY 82190 USA
| | - Barbara Zimmermann
- Faculty of Applied Ecology, Agricultural Sciences and Biotechnology Inland Norway University of Applied Sciences Evenstad NO‐2480 Koppang Norway
| | - Camilla Wikenros
- Grimsӧ Wildlife Research Station Department of Ecology Swedish University of Agricultural Sciences SE‐739 93 Riddarhyttan Sweden
| | - Douglas W. Smith
- Yellowstone Center for Resources Yellowstone National Park Box 168, Mammoth Hot Springs WY 82190 USA
| | - Daniel R. Stahler
- Yellowstone Center for Resources Yellowstone National Park Box 168, Mammoth Hot Springs WY 82190 USA
| | - Petter Wabakken
- Faculty of Applied Ecology, Agricultural Sciences and Biotechnology Inland Norway University of Applied Sciences Evenstad NO‐2480 Koppang Norway
| | - Jon E. Swenson
- Faculty of Environmental Sciences and Natural Resource Management Norwegian University of Life Sciences Postbox 5003, NO‐1432 Ås Norway
| | - Håkan Sand
- Grimsӧ Wildlife Research Station Department of Ecology Swedish University of Agricultural Sciences SE‐739 93 Riddarhyttan Sweden
| | - Jonas Kindberg
- Norwegian Institute for Nature Research NO‐7485 Trondheim Norway
- Department of Wildlife, Fish, and Environmental Studies Swedish University of Agricultural Sciences SE‐901 83 Umeå Sweden
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14
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Hoy SR, MacNulty DR, Metz MC, Smith DW, Stahler DR, Peterson RO, Vucetich JA. Negative frequency-dependent prey selection by wolves and its implications on predator–prey dynamics. Anim Behav 2021. [DOI: 10.1016/j.anbehav.2021.06.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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Johnston RA, Rheinwald JG, vonHoldt BM, Stahler DR, Lowry W, Tung J, Wayne RK. K Locus Effects in Gray Wolves: Experimental Assessment of TLR3 Signaling and the Gene Expression Response to Canine Distemper Virus. J Hered 2021; 112:458-468. [PMID: 34132805 PMCID: PMC8567826 DOI: 10.1093/jhered/esab029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 12/31/2020] [Revised: 02/04/2021] [Accepted: 05/06/2021] [Indexed: 12/21/2022] Open
Abstract
In North American gray wolves, black coat color is dominantly inherited via a 3 base pair coding deletion in the canine beta defensin 3 (CBD103) gene. This 3 base pair deletion, called the KB allele, was introduced through hybridization with dogs and subsequently underwent a selective sweep that increased its frequency in wild wolves. Despite apparent positive selection, KBB wolves have lower fitness than wolves with the KyB genotype, even though the 2 genotypes show no observable differences in black coat color. Thus, the KB allele is thought to have pleiotropic effects on as-yet unknown phenotypes. Given the role of skin-expressed CBD103 in innate immunity, we hypothesized that the KB allele influences the keratinocyte gene expression response to TLR3 pathway stimulation and/or infection by canine distemper virus (CDV). To test this hypothesis, we developed a panel of primary epidermal keratinocyte cell cultures from 24 wild North American gray wolves of both Kyy and KyB genotypes. In addition, we generated an immortalized Kyy line and used CRISPR/Cas9 editing to produce a KyB line on the same genetic background. We assessed the transcriptome-wide responses of wolf keratinocytes to the TLR3 agonist polyinosinic:polycytidylic acid (polyI:C), and to live CDV. K locus genotype did not predict the transcriptional response to either challenge, suggesting that variation in the gene expression response does not explain pleiotropic effects of the KB allele on fitness. This study supports the feasibility of using cell culture methods to investigate the phenotypic effects of naturally occurring genetic variation in wild mammals.
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Affiliation(s)
- Rachel A Johnston
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
| | - James G Rheinwald
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Daniel R Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, WY, USA
| | - William Lowry
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Jenny Tung
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Department of Biology, Duke University, Durham, NC, USA
- Duke Population Research Institute, Duke University, Durham, NC, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
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16
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DeCandia AL, Cassidy KA, Stahler DR, Stahler EA, vonHoldt BM. Social environment and genetics underlie body site-specific microbiomes of Yellowstone National Park gray wolves ( Canis lupus). Ecol Evol 2021; 11:9472-9488. [PMID: 34306636 PMCID: PMC8293786 DOI: 10.1002/ece3.7767] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/20/2021] [Accepted: 05/24/2021] [Indexed: 12/17/2022] Open
Abstract
The host-associated microbiome is an important player in the ecology and evolution of species. Despite growing interest in the medical, veterinary, and conservation communities, there remain numerous questions about the primary factors underlying microbiota, particularly in wildlife. We bridged this knowledge gap by leveraging microbial, genetic, and observational data collected in a wild, pedigreed population of gray wolves (Canis lupus) inhabiting Yellowstone National Park. We characterized body site-specific microbes across six haired and mucosal body sites (and two fecal samples) using 16S rRNA amplicon sequencing. At the phylum level, we found that the microbiome of gray wolves primarily consists of Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria, consistent with previous studies within Mammalia and Canidae. At the genus level, we documented body site-specific microbiota with functions relevant to microenvironment and local physiological processes. We additionally employed observational and RAD sequencing data to examine genetic, demographic, and environmental correlates of skin and gut microbiota. We surveyed individuals across several levels of pedigree relationships, generations, and social groups, and found that social environment (i.e., pack) and genetic relatedness were two primary factors associated with microbial community composition to differing degrees between body sites. We additionally reported body condition and coat color as secondary factors underlying gut and skin microbiomes, respectively. We concluded that gray wolf microbiota resemble similar host species, differ between body sites, and are shaped by numerous endogenous and exogenous factors. These results provide baseline information for this long-term study population and yield important insights into the evolutionary history, ecology, and conservation of wild wolves and their associated microbes.
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Affiliation(s)
- Alexandra L. DeCandia
- Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNJUSA
- Smithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | - Kira A. Cassidy
- Yellowstone Center for ResourcesNational Park ServiceYellowstone National ParkWYUSA
| | - Daniel R. Stahler
- Yellowstone Center for ResourcesNational Park ServiceYellowstone National ParkWYUSA
| | - Erin A. Stahler
- Yellowstone Center for ResourcesNational Park ServiceYellowstone National ParkWYUSA
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17
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DeCandia AL, Schrom EC, Brandell EE, Stahler DR, vonHoldt BM. Sarcoptic mange severity is associated with reduced genomic variation and evidence of selection in Yellowstone National Park wolves ( Canis lupus). Evol Appl 2021; 14:429-445. [PMID: 33664786 PMCID: PMC7896714 DOI: 10.1111/eva.13127] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/28/2020] [Accepted: 08/25/2020] [Indexed: 01/25/2023] Open
Abstract
Population genetic theory posits that molecular variation buffers against disease risk. Although this "monoculture effect" is well supported in agricultural settings, its applicability to wildlife populations remains in question. In the present study, we examined the genomics underlying individual-level disease severity and population-level consequences of sarcoptic mange infection in a wild population of canids. Using gray wolves (Canis lupus) reintroduced to Yellowstone National Park (YNP) as our focal system, we leveraged 25 years of observational data and biobanked blood and tissue to genotype 76,859 loci in over 400 wolves. At the individual level, we reported an inverse relationship between host genomic variation and infection severity. We additionally identified 410 loci significantly associated with mange severity, with annotations related to inflammation, immunity, and skin barrier integrity and disorders. We contextualized results within environmental, demographic, and behavioral variables, and confirmed that genetic variation was predictive of infection severity. At the population level, we reported decreased genome-wide variation since the initial gray wolf reintroduction event and identified evidence of selection acting against alleles associated with mange infection severity. We concluded that genomic variation plays an important role in disease severity in YNP wolves. This role scales from individual to population levels, and includes patterns of genome-wide variation in support of the monoculture effect and specific loci associated with the complex mange phenotype. Results yielded system-specific insights, while also highlighting the relevance of genomic analyses to wildlife disease ecology, evolution, and conservation.
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Affiliation(s)
| | - Edward C. Schrom
- Ecology & Evolutionary BiologyPrinceton UniversityPrincetonNJUSA
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18
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Brandell EE, Fountain-Jones NM, Gilbertson ML, Cross PC, Hudson PJ, Smith DW, Stahler DR, Packer C, Craft ME. Group density, disease, and season shape territory size and overlap of social carnivores. J Anim Ecol 2021; 90:87-101. [PMID: 32654133 PMCID: PMC9844152 DOI: 10.1111/1365-2656.13294] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 05/22/2020] [Indexed: 01/19/2023]
Abstract
The spatial organization of a population can influence the spread of information, behaviour and pathogens. Group territory size and territory overlap and components of spatial organization, provide key information as these metrics may be indicators of habitat quality, resource dispersion, contact rates and environmental risk (e.g. indirectly transmitted pathogens). Furthermore, sociality and behaviour can also shape space use, and subsequently, how space use and habitat quality together impact demography. Our study aims to identify factors shaping the spatial organization of wildlife populations and assess the impact of epizootics on space use. We further aim to explore the mechanisms by which disease perturbations could cause changes in spatial organization. Here we assessed the seasonal spatial organization of Serengeti lions and Yellowstone wolves at the group level. We use network analysis to describe spatial organization and connectivity of social groups. We then examine the factors predicting mean territory size and mean territory overlap for each population using generalized additive models. We demonstrate that lions and wolves were similar in that group-level factors, such as number of groups and shaped spatial organization more than population-level factors, such as population density. Factors shaping territory size were slightly different than factors shaping territory overlap; for example, wolf pack size was an important predictor of territory overlap, but not territory size. Lion spatial networks were more highly connected, while wolf spatial networks varied seasonally. We found that resource dispersion may be more important for driving territory size and overlap for wolves than for lions. Additionally, canine distemper epizootics may have altered lion spatial organization, highlighting the importance of including infectious disease epizootics in studies of behavioural and movement ecology. We provide insight about when we might expect to observe the impacts of resource dispersion, disease perturbations, and other ecological factors on spatial organization. Our work highlights the importance of monitoring and managing social carnivore populations at the group level. Future research should elucidate the complex relationships between demographics, social and spatial structure, abiotic and biotic conditions and pathogen infections.
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Affiliation(s)
- Ellen E. Brandell
- Center for Infectious Disease Dynamics & Department of Biology, Huck Institute for Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA 16802
| | | | - Marie L.J. Gilbertson
- Department of Veterinary Population Medicine, University of Minnesota, St Paul, Minnesota 55108
| | - Paul C. Cross
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Bozeman, Montana, USA 59715
| | - Peter J. Hudson
- Center for Infectious Disease Dynamics & Department of Biology, Huck Institute for Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA 16802
| | - Douglas W. Smith
- Yellowstone Center for Resources, Wolf Project, P.O. Box 168, Yellowstone National Park, WY 82190, USA
| | - Daniel R. Stahler
- Yellowstone Center for Resources, Wolf Project, P.O. Box 168, Yellowstone National Park, WY 82190, USA
| | - Craig Packer
- Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, Minnesota 55108
| | - Meggan E. Craft
- Department of Veterinary Population Medicine, University of Minnesota, St Paul, Minnesota 55108
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19
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Anton CB, Smith DW, Suraci JP, Stahler DR, Duane TP, Wilmers CC. Gray wolf habitat use in response to visitor activity along roadways in Yellowstone National Park. Ecosphere 2020. [DOI: 10.1002/ecs2.3164] [Citation(s) in RCA: 5] [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: 11/07/2022] Open
Affiliation(s)
- Colby B. Anton
- Yellowstone Center for Resources National Park Service Yellowstone National Park Wyoming 82190 USA
- Environmental Studies Department Center for Integrated Spatial Research University of California Santa Cruz California 95064 USA
| | - Douglas W. Smith
- Yellowstone Center for Resources National Park Service Yellowstone National Park Wyoming 82190 USA
| | - Justin P. Suraci
- Environmental Studies Department Center for Integrated Spatial Research University of California Santa Cruz California 95064 USA
| | - Daniel R. Stahler
- Yellowstone Center for Resources National Park Service Yellowstone National Park Wyoming 82190 USA
| | - Timothy P. Duane
- Environmental Studies Department University of California Santa Cruz California 95064 USA
| | - Christopher C. Wilmers
- Environmental Studies Department Center for Integrated Spatial Research University of California Santa Cruz California 95064 USA
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20
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Metz MC, SunderRaj J, Smith DW, Stahler DR, Kohl MT, Cassidy KA, Hebblewhite M. Accounting for imperfect detection in observational studies: modeling wolf sightability in Yellowstone National Park. Ecosphere 2020. [DOI: 10.1002/ecs2.3152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Matthew C. Metz
- Wildlife Biology Program Department of Ecosystem and Conservation Sciences W.A. Franke College of Forestry and Conservation University of Montana Missoula Montana 59812 USA
- Yellowstone Wolf Project Yellowstone Center for Resources Yellowstone National Park Wyoming 82190 USA
| | - Jeremy SunderRaj
- Wildlife Biology Program Department of Ecosystem and Conservation Sciences W.A. Franke College of Forestry and Conservation University of Montana Missoula Montana 59812 USA
| | - Douglas W. Smith
- Yellowstone Wolf Project Yellowstone Center for Resources Yellowstone National Park Wyoming 82190 USA
| | - Daniel R. Stahler
- Yellowstone Wolf Project Yellowstone Center for Resources Yellowstone National Park Wyoming 82190 USA
| | - Michel T. Kohl
- Warnell School of Forestry and Natural Resources University of Georgia Athens Georgia 30602 USA
| | - Kira A. Cassidy
- Yellowstone Wolf Project Yellowstone Center for Resources Yellowstone National Park Wyoming 82190 USA
| | - Mark Hebblewhite
- Wildlife Biology Program Department of Ecosystem and Conservation Sciences W.A. Franke College of Forestry and Conservation University of Montana Missoula Montana 59812 USA
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21
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Wilmers CC, Metz MC, Stahler DR, Kohl MT, Geremia C, Smith DW. How climate impacts the composition of wolf-killed elk in northern Yellowstone National Park. J Anim Ecol 2020; 89:1511-1519. [PMID: 32145069 PMCID: PMC7317765 DOI: 10.1111/1365-2656.13200] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 07/08/2019] [Accepted: 02/04/2020] [Indexed: 11/30/2022]
Abstract
While the functional response of predators is commonly measured, recent work has revealed that the age and sex composition of prey killed is often a better predictor of prey population dynamics because the reproductive value of adult females is usually higher than that of males or juveniles. Climate is often an important mediating factor in determining the composition of predator kills, but we currently lack a mechanistic understanding of how the multiple facets of climate interact with prey abundance and demography to influence the composition of predator kills. Over 20 winters, we monitored 17 wolf packs in Yellowstone National Park and recorded the sex, age and nutritional condition of kills of their dominant prey—elk—in both early and late winter periods when elk are in relatively good and relatively poor condition, respectively. Nutritional condition (as indicated by per cent marrow fat) of wolf‐killed elk varied markedly with summer plant productivity, snow water equivalent (SWE) and winter period. Moreover, marrow was poorer for wolf‐killed bulls and especially for calves than it was for cows. Wolf prey composition was influenced by a complex set of climatic and endogenous variables. In early winter, poor plant growth in either year t or t − 1, or relatively low elk abundance, increased the odds of wolves killing bulls relative to cows. Calves were most likely to get killed when elk abundance was high and when the forage productivity they experienced in utero was poor. In late winter, low SWE and a relatively large elk population increased the odds of wolves killing calves relative to cows, whereas low SWE and poor vegetation productivity 1 year prior together increased the likelihood of wolves killing a bull instead of a cow. Since climate has a strong influence on whether wolves prey on cows (who, depending on their age, are the key reproductive components of the population) or lower reproductive value of calves and bulls, our results suggest that climate can drive wolf predation to be more or less additive from year to year.
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Affiliation(s)
- Christopher C Wilmers
- Center for Integrated Spatial Research, Environmental Studies Department, University of California, Santa Cruz, CA, USA
| | - Matthew C Metz
- Yellowstone Center for Resources, Yellowstone National Park, WY, USA.,Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, MT, USA
| | - Daniel R Stahler
- Yellowstone Center for Resources, Yellowstone National Park, WY, USA
| | - Michel T Kohl
- Department of Wildland Resources and Ecology Center, Utah State University, Logan, UT, USA
| | - Chris Geremia
- Yellowstone Center for Resources, Yellowstone National Park, WY, USA
| | - Douglas W Smith
- Yellowstone Center for Resources, Yellowstone National Park, WY, USA
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22
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vonHoldt BM, DeCandia AL, Heppenheimer E, Janowitz-Koch I, Shi R, Zhou H, German CA, Brzeski KE, Cassidy KA, Stahler DR, Sinsheimer JS. Heritability of interpack aggression in a wild pedigreed population of North American grey wolves. Mol Ecol 2020; 29:1764-1775. [PMID: 31905256 DOI: 10.1111/mec.15349] [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: 04/24/2018] [Revised: 12/16/2019] [Accepted: 12/17/2019] [Indexed: 12/24/2022]
Abstract
Aggression is a quantitative trait deeply entwined with individual fitness. Mapping the genomic architecture underlying such traits is complicated by complex inheritance patterns, social structure, pedigree information and gene pleiotropy. Here, we leveraged the pedigree of a reintroduced population of grey wolves (Canis lupus) in Yellowstone National Park, Wyoming, USA, to examine the heritability of and the genetic variation associated with aggression. Since their reintroduction, many ecological and behavioural aspects have been documented, providing unmatched records of aggressive behaviour across multiple generations of a wild population of wolves. Using a linear mixed model, a robust genetic relationship matrix, 12,288 single nucleotide polymorphisms (SNPs) and 111 wolves, we estimated the SNP-based heritability of aggression to be 37% and an additional 14% of the phenotypic variation explained by shared environmental exposures. We identified 598 SNP genotypes from 425 grey wolves to resolve a consensus pedigree that was included in a heritability analysis of 141 individuals with SNP genotype, metadata and aggression data. The pedigree-based heritability estimate for aggression is 14%, and an additional 16% of the phenotypic variation was explained by shared environmental exposures. We find strong effects of breeding status and relative pack size on aggression. Through an integrative approach, these results provide a framework for understanding the genetic architecture of a complex trait that influences individual fitness, with linkages to reproduction, in a social carnivore. Along with a few other studies, we show here the incredible utility of a pedigreed natural population for dissecting a complex, fitness-related behavioural trait.
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Affiliation(s)
| | | | | | | | - Ruoyao Shi
- BioKnow Health Informatics Lab, College of Life Sciences, Jilin University, Changchun, China
| | - Hua Zhou
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA, USA
| | - Christopher A German
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA, USA
| | - Kristin E Brzeski
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA
| | - Kira A Cassidy
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, WY, USA
| | - Daniel R Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, WY, USA
| | - Janet S Sinsheimer
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA, USA.,Department of Human Genetics and Computational Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
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23
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Hoy SR, MacNulty DR, Smith DW, Stahler DR, Lambin X, Peterson RO, Ruprecht JS, Vucetich JA. Fluctuations in age structure and their variable influence on population growth. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13431] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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)
- Sarah R. Hoy
- School of Forest Resources and Environmental Science Michigan Technological University Houghton MI USA
| | - Daniel R. MacNulty
- Department of Wildland Resources and Ecology Center Utah State University Logan UT USA
| | - Douglas W. Smith
- Yellowstone Centre for Resources Yellowstone National Park WY USA
| | | | - Xavier Lambin
- School of Biological Sciences University of Aberdeen Aberdeen UK
| | - Rolf O. Peterson
- School of Forest Resources and Environmental Science Michigan Technological University Houghton MI USA
| | - Joel S. Ruprecht
- Department of Fisheries and Wildlife Oregon State University Corvallis OR USA
| | - John A. Vucetich
- School of Forest Resources and Environmental Science Michigan Technological University Houghton MI USA
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24
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Saremi NF, Supple MA, Byrne A, Cahill JA, Coutinho LL, Dalén L, Figueiró HV, Johnson WE, Milne HJ, O'Brien SJ, O'Connell B, Onorato DP, Riley SPD, Sikich JA, Stahler DR, Villela PMS, Vollmers C, Wayne RK, Eizirik E, Corbett-Detig RB, Green RE, Wilmers CC, Shapiro B. Author Correction: Puma genomes from North and South America provide insights into the genomic consequences of inbreeding. Nat Commun 2019; 10:5276. [PMID: 31754100 PMCID: PMC6872549 DOI: 10.1038/s41467-019-13096-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Nedda F Saremi
- Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Megan A Supple
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Ashley Byrne
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - James A Cahill
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA.,Laboratory of Neurogenetics of Language, Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Luiz Lehmann Coutinho
- Laboratório de Biotecnologia Animal, Departamento de Zootecnia, ESALQ, Universidade de São Paulo, Caixa Postal 09, Piracicaba, SP, 13418-900, Brazil
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, Stockholm, 10405, Sweden
| | - Henrique V Figueiró
- Escola de Ciências, Pontifical Catholic University of Rio Grande do Sul, Avenida Ipiranga, 6681-Partenon, Porto Alegre-RS, 90619-900, Brazil
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, Smithsonian Institution, 600 Maryland Avenue SW, Washington, DC, 20002, USA.,Walter Reed Biosystematics Unit, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD, 20746, USA
| | - Heather J Milne
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, 41 Sredniy Prospekt, Saint Petersburg, 199004, Russia
| | - Brendan O'Connell
- Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA.,Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, 3181 S.W. Sam Jackson Park Road, Portland, OR, 97239-3098, USA
| | - David P Onorato
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, 298 Sabal Palm Road, Naples, FL, 34114, USA
| | - Seth P D Riley
- Santa Monica Mountains National Recreation Area, 401 West Hillcrest Drive, Thousand Oaks, CA, 91360, USA.,Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 610 Charles E. Young Drive South, Los Angeles, CA, 90095-1601, USA
| | - Jeff A Sikich
- Santa Monica Mountains National Recreation Area, 401 West Hillcrest Drive, Thousand Oaks, CA, 91360, USA
| | - Daniel R Stahler
- Yellowstone Center for Resources, P.O. Box 168, Yellowstone National Park, WY, 82190, USA
| | | | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 610 Charles E. Young Drive South, Los Angeles, CA, 90095-1601, USA
| | - Eduardo Eizirik
- Escola de Ciências, Pontifical Catholic University of Rio Grande do Sul, Avenida Ipiranga, 6681-Partenon, Porto Alegre-RS, 90619-900, Brazil
| | - Russell B Corbett-Detig
- Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Christopher C Wilmers
- Environmental Studies Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA. .,Howard Hughes Medical Institute, 400 Jones Bridge Road, Chevy Chase, MD, 20815, USA.
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25
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Koch EM, Schweizer RM, Schweizer TM, Stahler DR, Smith DW, Wayne RK, Novembre J. De Novo Mutation Rate Estimation in Wolves of Known Pedigree. Mol Biol Evol 2019; 36:2536-2547. [PMID: 31297530 PMCID: PMC6805234 DOI: 10.1093/molbev/msz159] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 06/18/2019] [Accepted: 06/24/2019] [Indexed: 12/11/2022] Open
Abstract
Knowledge of mutation rates is crucial for calibrating population genetics models of demographic history in units of years. However, mutation rates remain challenging to estimate because of the need to identify extremely rare events. We estimated the nuclear mutation rate in wolves by identifying de novo mutations in a pedigree of seven wolves. Putative de novo mutations were discovered by whole-genome sequencing and were verified by Sanger sequencing of parents and offspring. Using stringent filters and an estimate of the false negative rate in the remaining observable genome, we obtain an estimate of ∼4.5 × 10-9 per base pair per generation and provide conservative bounds between 2.6 × 10-9 and 7.1 × 10-9. Although our estimate is consistent with recent mutation rate estimates from ancient DNA (4.0 × 10-9 and 3.0-4.5 × 10-9), it suggests a wider possible range. We also examined the consequences of our rate and the accompanying interval for dating several critical events in canid demographic history. For example, applying our full range of rates to coalescent models of dog and wolf demographic history implies a wide set of possible divergence times between the ancestral populations of dogs and extant Eurasian wolves (16,000-64,000 years ago) although our point estimate indicates a date between 25,000 and 33,000 years ago. Aside from one study in mice, ours provides the only direct mammalian mutation rate outside of primates and is likely to be vital to future investigations of mutation rate evolution.
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Affiliation(s)
- Evan M Koch
- Department of Ecology and Evolution, University of Chicago, Chicago, IL
| | - Rena M Schweizer
- Division of Biological Sciences, University of Montana, Missoula, MT
| | - Teia M Schweizer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA
- Department of Biology, Colorado State University, Fort Collins, CO
| | - Daniel R Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, WY
| | - Douglas W Smith
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, WY
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA
| | - John Novembre
- Department of Ecology and Evolution, University of Chicago, Chicago, IL
- Department of Human Genetics, University of Chicago, Chicago, IL
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26
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Saremi NF, Supple MA, Byrne A, Cahill JA, Coutinho LL, Dalén L, Figueiró HV, Johnson WE, Milne HJ, O'Brien SJ, O'Connell B, Onorato DP, Riley SPD, Sikich JA, Stahler DR, Villela PMS, Vollmers C, Wayne RK, Eizirik E, Corbett-Detig RB, Green RE, Wilmers CC, Shapiro B. Puma genomes from North and South America provide insights into the genomic consequences of inbreeding. Nat Commun 2019; 10:4769. [PMID: 31628318 PMCID: PMC6800433 DOI: 10.1038/s41467-019-12741-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 09/26/2019] [Indexed: 11/09/2022] Open
Abstract
Pumas are the most widely distributed felid in the Western Hemisphere. Increasingly, however, human persecution and habitat loss are isolating puma populations. To explore the genomic consequences of this isolation, we assemble a draft puma genome and a geographically broad panel of resequenced individuals. We estimate that the lineage leading to present-day North American pumas diverged from South American lineages 300-100 thousand years ago. We find signatures of close inbreeding in geographically isolated North American populations, but also that tracts of homozygosity are rarely shared among these populations, suggesting that assisted gene flow would restore local genetic diversity. The genome of a Florida panther descended from translocated Central American individuals has long tracts of homozygosity despite recent outbreeding. This suggests that while translocations may introduce diversity, sustaining diversity in small and isolated populations will require either repeated translocations or restoration of landscape connectivity. Our approach provides a framework for genome-wide analyses that can be applied to the management of similarly small and isolated populations.
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Affiliation(s)
- Nedda F Saremi
- Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Megan A Supple
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Ashley Byrne
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - James A Cahill
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA.,Laboratory of Neurogenetics of Language, Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Luiz Lehmann Coutinho
- Laboratório de Biotecnologia Animal, Departamento de Zootecnia, ESALQ, Universidade de São Paulo, Caixa Postal 09, Piracicaba, SP, 13418-900, Brazil
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, Stockholm, 10405, Sweden
| | - Henrique V Figueiró
- Escola de Ciências, Pontifical Catholic University of Rio Grande do Sul, Avenida Ipiranga, 6681-Partenon, Porto Alegre-RS, 90619-900, Brazil
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, Smithsonian Institution, 600 Maryland Avenue SW, Washington, DC, 20002, USA.,Walter Reed Biosystematics Unit, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD, 20746, USA
| | - Heather J Milne
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, 41 Sredniy Prospekt, Saint Petersburg, 199004, Russia
| | - Brendan O'Connell
- Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA.,Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, 3181 S.W. Sam Jackson Park Road, Portland, OR, 97239-3098, USA
| | - David P Onorato
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, 298 Sabal Palm Road, Naples, FL, 34114, USA
| | - Seth P D Riley
- Santa Monica Mountains National Recreation Area, 401 West Hillcrest Drive, Thousand Oaks, CA, 91360, USA.,Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 610 Charles E. Young Drive South, Los Angeles, CA, 90095-1601, USA
| | - Jeff A Sikich
- Santa Monica Mountains National Recreation Area, 401 West Hillcrest Drive, Thousand Oaks, CA, 91360, USA
| | - Daniel R Stahler
- Yellowstone Center for Resources, P.O. Box 168, Yellowstone National Park, WY, 82190, USA
| | | | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 610 Charles E. Young Drive South, Los Angeles, CA, 90095-1601, USA
| | - Eduardo Eizirik
- Escola de Ciências, Pontifical Catholic University of Rio Grande do Sul, Avenida Ipiranga, 6681-Partenon, Porto Alegre-RS, 90619-900, Brazil
| | - Russell B Corbett-Detig
- Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Christopher C Wilmers
- Environmental Studies Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA. .,Howard Hughes Medical Institute, 400 Jones Bridge Road, Chevy Chase, MD, 20815, USA.
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27
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Van Valkenburgh B, Peterson RO, Smith DW, Stahler DR, Vucetich JA. Tooth fracture frequency in gray wolves reflects prey availability. eLife 2019; 8:48628. [PMID: 31549963 PMCID: PMC6759352 DOI: 10.7554/elife.48628] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 05/21/2019] [Accepted: 08/21/2019] [Indexed: 11/20/2022] Open
Abstract
Exceptionally high rates of tooth fracture in large Pleistocene carnivorans imply intensified interspecific competition, given that tooth fracture rises with increased bone consumption, a behavior that likely occurs when prey are difficult to acquire. To assess the link between prey availability and dental attrition, we documented dental fracture rates over decades among three well-studied populations of extant gray wolves that differed in prey:predator ratio and levels of carcass utilization. When prey:predator ratios declined, kills were more fully consumed, and rates of tooth fracture more than doubled. This supports tooth fracture frequency as a relative measure of the difficulty of acquiring prey, and reveals a rapid response to diminished food levels in large carnivores despite risks of infection and reduced fitness due to dental injuries. More broadly, large carnivore tooth fracture frequency likely reflects energetic stress, an aspect of predator success that is challenging to quantify in wild populations. Gray wolves roam many European and American landscapes, where they prey on large animals such as elk and moose. A healthy dentition is essential for these predators to kill, eat and defend themselves. As a result, they tend to avoid biting down on tough body parts, such as bones, so that their teeth do not break. If food becomes scarce however, the wolves may resort to consuming these hard elements, eating more of the carcasses and leading to more damaged teeth. It could therefore be possible to assess the food levels available to existing (or even extinct) wolf populations based on how many broken teeth the animals have. However, older individuals are also more likely to have more damaged teeth, so age would need to be taken into consideration. Van Valkenburgh et al. decided to evaluate whether it was indeed possible to deduce how much food was available to groups of wolves based on teeth damage. Tooth wear and fracture were quantified in three current populations of gray wolves whose skulls had been collected and preserved in natural history collections. For each group, there were data available about the variations of number of moose per wolf over time, and how much of the carcasses the wolves were consuming. The analyses showed that indeed, when prey became less abundant, the wolves ate more of the remains – including the bones – and therefore broke more teeth. These conclusions can be applied to other large predators and even to extinct species such as dire wolves or sabertooth cats. Tapping into the potential of museum specimens could help to retrace environmental conditions and the history of animals now long gone.
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Affiliation(s)
- Blaire Van Valkenburgh
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, United States
| | - Rolf O Peterson
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, United States
| | - Douglas W Smith
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, United States
| | - Daniel R Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, United States
| | - John A Vucetich
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, United States
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28
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Kohl MT, Ruth TK, Metz MC, Stahler DR, Smith DW, White PJ, MacNulty DR. Do prey select for vacant hunting domains to minimize a multi-predator threat? Ecol Lett 2019; 22:1724-1733. [PMID: 31373137 DOI: 10.1111/ele.13319] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [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: 01/02/2019] [Revised: 02/13/2019] [Accepted: 05/09/2019] [Indexed: 01/02/2023]
Abstract
Many ecosystems contain sympatric predator species that hunt in different places and times. We tested whether this provides vacant hunting domains, places and times where and when predators are least active, that prey use to minimize threats from multiple predators simultaneously. We measured how northern Yellowstone elk (Cervus elaphus) responded to wolves (Canis lupus) and cougars (Puma concolor), and found that elk selected for areas outside the high-risk domains of both predators consistent with the vacant domain hypothesis. This enabled elk to avoid one predator without necessarily increasing its exposure to the other. Our results demonstrate how the diel cycle can serve as a key axis of the predator hunting domain that prey exploit to manage predation risk from multiple sources. We argue that a multi-predator, spatiotemporal framework is vital to understand the causes and consequences of prey spatial response to predation risk in environments with more than one predator.
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Affiliation(s)
- Michel T Kohl
- Department of Wildland Resources and Ecology Center, Utah State University, Logan, UT, 84322, USA
| | - Toni K Ruth
- Hornocker Wildlife Institute/Wildlife Conservation Society, Bozeman, MT, 59715, USA.,Salmon Valley Stewardship, Salmon, ID, 83467, USA
| | - Matthew C Metz
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, WY, 82190, USA.,Wildlife Biology Program, University of Montana, Missoula, MT, 59812, USA
| | - Daniel R Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, WY, 82190, USA
| | - Douglas W Smith
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, WY, 82190, USA
| | - P J White
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, WY, 82190, USA
| | - Daniel R MacNulty
- Department of Wildland Resources and Ecology Center, Utah State University, Logan, UT, 84322, USA
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29
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Cusack JJ, Kohl MT, Metz MC, Coulson T, Stahler DR, Smith DW, MacNulty DR. Weak spatiotemporal response of prey to predation risk in a freely interacting system. J Anim Ecol 2019; 89:120-131. [PMID: 30838656 PMCID: PMC7003944 DOI: 10.1111/1365-2656.12968] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 09/20/2018] [Accepted: 12/19/2018] [Indexed: 11/26/2022]
Abstract
The extent to which prey space use actively minimizes predation risk continues to ignite controversy. Methodological reasons that have hindered consensus include inconsistent measurements of predation risk, biased spatiotemporal scales at which responses are measured and lack of robust null expectations. We addressed all three challenges in a comprehensive analysis of the spatiotemporal responses of adult female elk (Cervus elaphus) to the risk of predation by wolves (Canis lupus) during winter in northern Yellowstone, USA. We quantified spatial overlap between the winter home ranges of GPS‐collared elk and three measures of predation risk: the intensity of wolf space use, the distribution of wolf‐killed elk and vegetation openness. We also assessed whether elk varied their use of areas characterized by more or less predation risk across hours of the day, and estimated encounter rates between simultaneous elk and wolf pack trajectories. We determined whether observed values were significantly lower than expected if elk movements were random with reference to predation risk using a null model approach. Although a small proportion of elk did show a tendency to minimize use of open vegetation at specific times of the day, overall we highlight a notable absence of spatiotemporal response by female elk to the risk of predation posed by wolves in northern Yellowstone. Our results suggest that predator–prey interactions may not always result in strong spatiotemporal patterns of avoidance.
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Affiliation(s)
- Jeremy J Cusack
- Department of Zoology, University of Oxford, Oxford, UK.,Biological and Environmental Sciences, University of Stirling, Stirling, UK
| | - Michel T Kohl
- Department of Wildland Resources and Ecology Center, Utah State University, Logan, Utah
| | - Matthew C Metz
- Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, Montana
| | - Tim Coulson
- Department of Zoology, University of Oxford, Oxford, UK
| | - Daniel R Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming
| | - Douglas W Smith
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming
| | - Daniel R MacNulty
- Department of Wildland Resources and Ecology Center, Utah State University, Logan, Utah
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30
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Schweizer RM, Durvasula A, Smith J, Vohr SH, Stahler DR, Galaverni M, Thalmann O, Smith DW, Randi E, Ostrander EA, Green RE, Lohmueller KE, Novembre J, Wayne RK. Natural Selection and Origin of a Melanistic Allele in North American Gray Wolves. Mol Biol Evol 2019; 35:1190-1209. [PMID: 29688543 DOI: 10.1093/molbev/msy031] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Pigmentation is often used to understand how natural selection affects genetic variation in wild populations since it can have a simple genetic basis, and can affect a variety of fitness-related traits (e.g., camouflage, thermoregulation, and sexual display). In gray wolves, the K locus, a β-defensin gene, causes black coat color via a dominantly inherited KB allele. The allele is derived from dog-wolf hybridization and is at high frequency in North American wolf populations. We designed a DNA capture array to probe the geographic origin, age, and number of introgression events of the KB allele in a panel of 331 wolves and 20 dogs. We found low diversity in KB, but not ancestral ky, wolf haplotypes consistent with a selective sweep of the black haplotype across North America. Further, North American wolf KB haplotypes are monophyletic, suggesting that a single adaptive introgression from dogs to wolves most likely occurred in the Northwest Territories or Yukon. We use a new analytical approach to date the origin of the KB allele in Yukon wolves to between 1,598 and 7,248 years ago, suggesting that introgression with early Native American dogs was the source. Using population genetic simulations, we show that the K locus is undergoing natural selection in four wolf populations. We find evidence for balancing selection, specifically in Yellowstone wolves, which could be a result of selection for enhanced immunity in response to distemper. With these data, we demonstrate how the spread of an adaptive variant may have occurred across a species' geographic range.
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Affiliation(s)
- Rena M Schweizer
- Division of Biological Sciences, University of Montana, Missoula, MT.,Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA
| | - Arun Durvasula
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA
| | - Joel Smith
- Department of Ecology and Evolution, University of Chicago, Chicago, IL
| | - Samuel H Vohr
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA
| | - Daniel R Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, WY
| | | | - Olaf Thalmann
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Douglas W Smith
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, WY
| | - Ettore Randi
- Department of Biology, University of Bologna, Bologna, Italy.,Department of Chemistry and Bioscience, Faculty of Engineering and Science, University of Aalborg, Aalborg, Denmark
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA
| | - John Novembre
- Department of Ecology and Evolution, University of Chicago, Chicago, IL.,Department of Human Genetics, University of Chicago, IL
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA
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31
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Walker LE, Marzluff JM, Metz MC, Wirsing AJ, Moskal LM, Stahler DR, Smith DW. Population responses of common ravens to reintroduced gray wolves. Ecol Evol 2018; 8:11158-11168. [PMID: 30519433 PMCID: PMC6262918 DOI: 10.1002/ece3.4583] [Citation(s) in RCA: 6] [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: 11/20/2017] [Revised: 05/11/2018] [Accepted: 09/05/2018] [Indexed: 11/08/2022] Open
Abstract
Top predators have cascading effects throughout the food web, but their impacts on scavenger abundance are largely unknown. Gray wolves (Canis lupus) provide carrion to a suite of scavenger species, including the common raven (Corvus corax). Ravens are wide-ranging and intelligent omnivores that commonly take advantage of anthropogenic food resources. In areas where they overlap with wolves, however, ravens are numerous and ubiquitous scavengers of wolf-acquired carrion. We aimed to determine whether subsidies provided through wolves are a limiting factor for raven populations in general and how the wolf reintroduction to Yellowstone National Park in 1995-1997 affected raven population abundance and distribution on the Yellowstone's Northern Range specifically. We counted ravens throughout Yellowstone's Northern Range in March from 2009 to 2017 in both human-use areas and wolf habitat. We then used statistics related to the local wolf population and the winter weather conditions to model raven abundance during our study period and predict raven abundance on the Northern Range both before and after the wolf reintroduction. In relatively severe winters with greater snowpack, raven abundance increased in areas of human use and decreased in wolf habitat. When wolves were able to acquire more carrion, however, ravens increased in wolf habitat and decreased in areas with anthropogenic resources. Raven populations prior to the wolf reintroduction were likely more variable and heavily dependent on ungulate winter-kill and hunter-provided carcasses. The wolf recovery in Yellowstone helped stabilize raven populations by providing a regular food supply, regardless of winter severity. This stabilization has important implications for effective land management as wolves recolonize the west and global climate patterns change.
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Affiliation(s)
- Lauren E. Walker
- Yellowstone Center for ResourcesYellowstone National ParkWyoming
- College of the Environment, School of Environmental and Forest SciencesUniversity of WashingtonSeattleWashington
| | - John M. Marzluff
- College of the Environment, School of Environmental and Forest SciencesUniversity of WashingtonSeattleWashington
| | - Matthew C. Metz
- Yellowstone Center for ResourcesYellowstone National ParkWyoming
- College of Forestry and ConservationUniversity of MontanaMissoulaMontana
| | - Aaron J. Wirsing
- College of the Environment, School of Environmental and Forest SciencesUniversity of WashingtonSeattleWashington
| | - L. Monika Moskal
- College of the Environment, School of Environmental and Forest SciencesUniversity of WashingtonSeattleWashington
| | | | - Douglas W. Smith
- Yellowstone Center for ResourcesYellowstone National ParkWyoming
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32
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Cross PC, van Manen FT, Viana M, Almberg ES, Bachen D, Brandell EE, Haroldson MA, Hudson PJ, Stahler DR, Smith DW. Estimating distemper virus dynamics among wolves and grizzly bears using serology and Bayesian state-space models. Ecol Evol 2018; 8:8726-8735. [PMID: 30271540 PMCID: PMC6157674 DOI: 10.1002/ece3.4396] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [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: 03/12/2018] [Revised: 05/08/2018] [Accepted: 06/27/2018] [Indexed: 02/05/2023] Open
Abstract
Many parasites infect multiple hosts, but estimating the transmission across host species remains a key challenge in disease ecology. We investigated the within and across host species dynamics of canine distemper virus (CDV) in grizzly bears (Ursus arctos) and wolves (Canis lupus) of the Greater Yellowstone Ecosystem (GYE). We hypothesized that grizzly bears may be more likely to be exposed to CDV during outbreaks in the wolf population because grizzly bears often displace wolves while scavenging carcasses. We used serological data collected from 1984 to 2014 in conjunction with Bayesian state-space models to infer the temporal dynamics of CDV. These models accounted for the unknown timing of pathogen exposure, and we assessed how different testing thresholds and the potential for testing errors affected our conclusions. We identified three main CDV outbreaks (1999, 2005, and 2008) in wolves, which were more obvious when we used higher diagnostic thresholds to qualify as seropositive. There was some evidence for increased exposure rates in grizzly bears in 2005, but the magnitude of the wolf effect on bear exposures was poorly estimated and depended upon our prior distributions. Grizzly bears were exposed to CDV prior to wolf reintroduction and during time periods outside of known wolf outbreaks, thus wolves are only one of several potential routes for grizzly bear exposures. Our modeling approach accounts for several of the shortcomings of serological data and is applicable to many wildlife disease systems, but is most informative when testing intervals are short. CDV circulates in a wide range of carnivore species, but it remains unclear whether the disease persists locally within the GYE carnivore community or is periodically reintroduced from distant regions with larger host populations.
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Affiliation(s)
- Paul C. Cross
- U.S. Geological SurveyNorthern Rocky Mountain Science CenterBozemanMontana
| | - Frank T. van Manen
- U.S. Geological SurveyNorthern Rocky Mountain Science CenterBozemanMontana
| | - Mafalda Viana
- Boyd Orr Centre for Population and Ecosystem HealthInstitute of Biodiversity, Animal Health and Comparative MedicineCollege of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
| | | | | | - Ellen E. Brandell
- Department of BiologyHuck Institutes of the Life SciencesPennsylvania State UniversityUniversity ParkPennsylvania
| | - Mark A. Haroldson
- U.S. Geological SurveyNorthern Rocky Mountain Science CenterBozemanMontana
| | - Peter J. Hudson
- Department of BiologyHuck Institutes of the Life SciencesPennsylvania State UniversityUniversity ParkPennsylvania
| | - Daniel R. Stahler
- Yellowstone Wolf ProjectYellowstone National Park, National Park ServiceGardinerWyoming
| | - Douglas W. Smith
- Yellowstone Wolf ProjectYellowstone National Park, National Park ServiceGardinerWyoming
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33
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Kohl MT, Stahler DR, Metz MC, Forester JD, Kauffman MJ, Varley N, White PJ, Smith DW, MacNulty DR. Diel predator activity drives a dynamic landscape of fear. ECOL MONOGR 2018. [DOI: 10.1002/ecm.1313] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Michel T. Kohl
- Department of Wildland Resources and Ecology Center; Utah State University; Logan Utah 84322 USA
| | - Daniel R. Stahler
- Yellowstone Center for Resources; National Park Service; Yellowstone National Park; Wyoming Montana 82190 USA
| | - Matthew C. Metz
- Yellowstone Center for Resources; National Park Service; Yellowstone National Park; Wyoming Montana 82190 USA
- Wildlife Biology Program; University of Montana; Missoula Montana 59812 USA
| | - James D. Forester
- Department of Fisheries, Wildlife, and Conservation Biology; University of Minnesota; St. Paul Minnesota 55108 USA
| | - Matthew J. Kauffman
- U.S. Geological Survey; Wyoming Cooperative Fish and Wildlife Research Unit; Department of Zoology and Physiology; University of Wyoming; Laramie Wyoming 82071 USA
| | - Nathan Varley
- Department of Biological Sciences; University of Alberta; Edmonton Alberta T6G 2E9 Canada
| | - P. J. White
- Yellowstone Center for Resources; National Park Service; Yellowstone National Park; Wyoming Montana 82190 USA
| | - Douglas W. Smith
- Yellowstone Center for Resources; National Park Service; Yellowstone National Park; Wyoming Montana 82190 USA
| | - Daniel R. MacNulty
- Department of Wildland Resources and Ecology Center; Utah State University; Logan Utah 84322 USA
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34
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vonHoldt BM, Ji SS, Aardema ML, Stahler DR, Udell MAR, Sinsheimer JS. Activity of Genes with Functions in Human Williams-Beuren Syndrome Is Impacted by Mobile Element Insertions in the Gray Wolf Genome. Genome Biol Evol 2018; 10:1546-1553. [PMID: 29860323 PMCID: PMC6007319 DOI: 10.1093/gbe/evy112] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2018] [Indexed: 12/13/2022] Open
Abstract
In canines, transposon dynamics have been associated with a hyper-social behavioral syndrome, although the functional mechanism has yet to be described. We investigate the epigenetic and transcriptional consequences of these behavior-associated mobile element insertions (MEIs) in dogs and Yellowstone gray wolves. We posit that the transposons themselves may not be the causative feature; rather, their transcriptional regulation may exert the functional impact. We survey four outlier transposons associated with hyper-sociability, with the expectation that they are targeted for epigenetic silencing. We predict hyper-methylation of MEIs, suggestive that the epigenetic silencing of and not the MEIs themselves may be driving dysregulation of nearby genes. We found that transposon-derived sequences are significantly hyper-methylated, regardless of their copy number or species. Further, we have assessed transcriptome sequence data and found evidence that MEIs impact the expression levels of six genes (WBSCR17, LIMK1, GTF2I, WBSCR27, BAZ1B, and BCL7B), all of which have known roles in human Williams-Beuren syndrome due to changes in copy number, typically hemizygosity. Although further evidence is needed, our results suggest that a few insertions alter local expression at multiple genes, likely through a cis-regulatory mechanism that excludes proximal methylation.
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Affiliation(s)
- Bridgett M vonHoldt
- Department of Ecology & Evolutionary Biology, Princeton University, New Jersey
| | - Sarah S Ji
- Department of Biostatistics, UCLA Fielding School of Public Health, Los Angeles, California
| | - Matthew L Aardema
- Department of Biology, Montclair State University, New Jersey
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York
| | - Daniel R Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming
| | - Monique A R Udell
- Department of Animal & Rangeland Sciences, Oregon State University, Oregon
| | - Janet S Sinsheimer
- Department of Biostatistics, UCLA Fielding School of Public Health, Los Angeles, California
- Departments of Human Genetics and Biomathematics, David Geffen School of Medicine at UCLA, Los Angeles, California
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35
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Uboni A, Smith DW, Stahler DR, Vucetich JA. Selecting habitat to what purpose? The advantage of exploring the habitat–fitness relationship. Ecosphere 2017. [DOI: 10.1002/ecs2.1705] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Alessia Uboni
- School of Forest Resources and Environmental Science Michigan Technological University 1400 Townsend Dr. Houghton Michigan 49931 USA
| | - Douglas W. Smith
- Yellowstone Center for Resources Wolf Project PO Box 168 Yellowstone National Park Wyoming 82190 USA
| | - Daniel R. Stahler
- Yellowstone Center for Resources Wolf Project PO Box 168 Yellowstone National Park Wyoming 82190 USA
| | - John A. Vucetich
- School of Forest Resources and Environmental Science Michigan Technological University 1400 Townsend Dr. Houghton Michigan 49931 USA
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Tallian A, Smith DW, Stahler DR, Metz MC, Wallen RL, Geremia C, Ruprecht J, Wyman CT, MacNulty DR. Predator foraging response to a resurgent dangerous prey. Funct Ecol 2017. [DOI: 10.1111/1365-2435.12866] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Aimee Tallian
- Department of Wildland Resources & Ecology Center Utah State University 5230 Old Main Hill Logan UT84322 USA
| | - Douglas W. Smith
- Yellowstone Center for Resources Yellowstone National Park Box 168 Mammoth Hot Springs WY82190 USA
| | - Daniel R. Stahler
- Yellowstone Center for Resources Yellowstone National Park Box 168 Mammoth Hot Springs WY82190 USA
| | - Matthew C. Metz
- Yellowstone Center for Resources Yellowstone National Park Box 168 Mammoth Hot Springs WY82190 USA
- Wildlife Biology Program Department of Ecosystem and Conservation Sciences University of Montana Missoula MT59812 USA
| | - Rick L. Wallen
- Yellowstone Center for Resources Yellowstone National Park Box 168 Mammoth Hot Springs WY82190 USA
| | - Chris Geremia
- Yellowstone Center for Resources Yellowstone National Park Box 168 Mammoth Hot Springs WY82190 USA
| | - Joel Ruprecht
- Department of Fisheries and Wildlife Oregon State University 104 Nash Hall Corvallis OR97331 USA
| | - C. Travis Wyman
- Yellowstone Center for Resources Yellowstone National Park Box 168 Mammoth Hot Springs WY82190 USA
| | - Daniel R. MacNulty
- Department of Wildland Resources & Ecology Center Utah State University 5230 Old Main Hill Logan UT84322 USA
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37
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Tallian A, Ordiz A, Metz MC, Milleret C, Wikenros C, Smith DW, Stahler DR, Kindberg J, MacNulty DR, Wabakken P, Swenson JE, Sand H. Competition between apex predators? Brown bears decrease wolf kill rate on two continents. Proc Biol Sci 2017; 284:20162368. [PMID: 28179516 PMCID: PMC5310606 DOI: 10.1098/rspb.2016.2368] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 01/16/2017] [Indexed: 11/12/2022] Open
Abstract
Trophic interactions are a fundamental topic in ecology, but we know little about how competition between apex predators affects predation, the mechanism driving top-down forcing in ecosystems. We used long-term datasets from Scandinavia (Europe) and Yellowstone National Park (North America) to evaluate how grey wolf (Canis lupus) kill rate was affected by a sympatric apex predator, the brown bear (Ursus arctos). We used kill interval (i.e. the number of days between consecutive ungulate kills) as a proxy of kill rate. Although brown bears can monopolize wolf kills, we found no support in either study system for the common assumption that they cause wolves to kill more often. On the contrary, our results showed the opposite effect. In Scandinavia, wolf packs sympatric with brown bears killed less often than allopatric packs during both spring (after bear den emergence) and summer. Similarly, the presence of bears at wolf-killed ungulates was associated with wolves killing less often during summer in Yellowstone. The consistency in results between the two systems suggests that brown bear presence actually reduces wolf kill rate. Our results suggest that the influence of predation on lower trophic levels may depend on the composition of predator communities.
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Affiliation(s)
- Aimee Tallian
- Department of Wildland Resources and Ecology Center, Utah State University, 5230 Old Main Hill, Logan, UT 84322, USA
- Grimsö Wildlife Research Station, Department of Ecology, Swedish University of Agricultural Sciences, 730 91 Riddarhyttan, Sweden
| | - Andrés Ordiz
- Grimsö Wildlife Research Station, Department of Ecology, Swedish University of Agricultural Sciences, 730 91 Riddarhyttan, Sweden
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Postbox 5003, 1432 Ås, Norway
| | - Matthew C Metz
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, MT 59812, USA
- Yellowstone Center for Resources, Yellowstone National Park, Box 168, Mammoth Hot Springs, WY 82190, USA
| | - Cyril Milleret
- Faculty of Applied Ecology and Agricultural Sciences, Inland Norway University of Applied Sciences, Evenstad, 2480 Koppang, Norway
| | - Camilla Wikenros
- Grimsö Wildlife Research Station, Department of Ecology, Swedish University of Agricultural Sciences, 730 91 Riddarhyttan, Sweden
| | - Douglas W Smith
- Yellowstone Center for Resources, Yellowstone National Park, Box 168, Mammoth Hot Springs, WY 82190, USA
| | - Daniel R Stahler
- Yellowstone Center for Resources, Yellowstone National Park, Box 168, Mammoth Hot Springs, WY 82190, USA
| | - Jonas Kindberg
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden
- Norwegian Institute for Nature Research, 7485 Trondheim, Norway
| | - Daniel R MacNulty
- Department of Wildland Resources and Ecology Center, Utah State University, 5230 Old Main Hill, Logan, UT 84322, USA
| | - Petter Wabakken
- Faculty of Applied Ecology and Agricultural Sciences, Inland Norway University of Applied Sciences, Evenstad, 2480 Koppang, Norway
| | - Jon E Swenson
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Postbox 5003, 1432 Ås, Norway
- Norwegian Institute for Nature Research, 7485 Trondheim, Norway
| | - Håkan Sand
- Grimsö Wildlife Research Station, Department of Ecology, Swedish University of Agricultural Sciences, 730 91 Riddarhyttan, Sweden
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Cassidy KA, Mech LD, MacNulty DR, Stahler DR, Smith DW. Sexually dimorphic aggression indicates male gray wolves specialize in pack defense against conspecific groups. Behav Processes 2017; 136:64-72. [PMID: 28143722 DOI: 10.1016/j.beproc.2017.01.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [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: 05/18/2016] [Revised: 11/25/2016] [Accepted: 01/18/2017] [Indexed: 10/20/2022]
Abstract
Aggression directed at conspecific groups is common among gregarious, territorial species, and for some species such as gray wolves (Canis lupus) intraspecific strife is the leading cause of natural mortality. Each individual in a group likely has different measures of the costs and benefits associated with a group task, such as an aggressive attack on another group, which can alter motivation and behavior. We observed 292 inter-pack aggressive interactions in Yellowstone National Park between 1 April 1995 and 1 April 2011 (>5300days of observation) in order to determine the role of both sexes, and the influence of pack, age, and other traits on aggression. We recorded the behaviors and characteristics of all individuals present during the interactions (n=534 individuals) and which individuals participated in each step (i.e. chase, attack, kill, flight) of the interaction. Overall, all wolves were more likely to chase rivals if they outnumbered their opponent, suggesting packs accurately assess their opponent's size during encounters and individuals adjust their behavior based on relative pack size. Males were more likely than females to chase rival packs and gray-colored wolves were more aggressive than black-colored wolves. Male wolves and gray-colored wolves also recorded higher cortisol levels than females and black-colored wolves, indicating hormonal support for more intense aggressive behavior. Further, we found a positive correlation between male age and probability of chasing, while age-specific participation for females remained constant. Chasing behavior was influenced by the sex of lone intruders, with males more likely to chase male intruders. This difference in behavior suggests male and female wolves may have different strategies and motivations during inter-pack aggressive interactions related to gray wolf mating systems. A division of labor between pack members concerning resource and territory defense suggests selection for specific traits related to aggression is an adaptive response to intense competition between groups of conspecifics.
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Affiliation(s)
- Kira A Cassidy
- Natural Resource Science and Management, 115 Green Hall, 1530 Cleveland Avenue N, University of Minnesota, St. Paul, MN, 55108, USA; Yellowstone Wolf Project, PO Box 168, Yellowstone Center for Resources, Yellowstone National Park, WY, 82190, USA.
| | - L David Mech
- U. S. Geological Survey, Northern Prairie Wildlife Research Center, 8711-37th St., S.E., Jamestown, ND, 58401-7317, USA
| | - Daniel R MacNulty
- Department of Wildland Resources, Utah State University, Logan, UT, 84322, USA
| | - Daniel R Stahler
- Yellowstone Wolf Project, PO Box 168, Yellowstone Center for Resources, Yellowstone National Park, WY, 82190, USA
| | - Douglas W Smith
- Yellowstone Wolf Project, PO Box 168, Yellowstone Center for Resources, Yellowstone National Park, WY, 82190, USA
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39
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Smith DW, White PJ, Stahler DR, Wydeven A, Hallac DE. Managing wolves in the Yellowstone area: Balancing goals across jurisdictional boundaries. WILDLIFE SOC B 2016. [DOI: 10.1002/wsb.677] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [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]
Affiliation(s)
| | - P. J. White
- Yellowstone National Park; P.O. Box 168 Mammoth WY 82190 USA
| | | | - Adrian Wydeven
- Wisconsin Department of Natural Resources; 875 S 4th Avenue Park Falls WI 54552 USA
| | - David E. Hallac
- Cape Hatteras National Seashore; 1401 National Park Drive Manteo NC 27954 USA
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40
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Ausband DE, Mitchell MS, Bassing SB, Nordhagen M, Smith DW, Stahler DR. Dog days of summer: influences on decision of wolves to move pups. J Mammal 2016. [DOI: 10.1093/jmammal/gyw114] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [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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41
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Charruau P, Johnston RA, Stahler DR, Lea A, Snyder-Mackler N, Smith DW, vonHoldt BM, Cole SW, Tung J, Wayne RK. Pervasive Effects of Aging on Gene Expression in Wild Wolves. Mol Biol Evol 2016; 33:1967-78. [PMID: 27189566 DOI: 10.1093/molbev/msw072] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Gene expression levels change as an individual ages and responds to environmental conditions. With the exception of humans, such patterns have principally been studied under controlled conditions, overlooking the array of developmental and environmental influences that organisms encounter under conditions in which natural selection operates. We used high-throughput RNA sequencing (RNA-Seq) of whole blood to assess the relative impacts of social status, age, disease, and sex on gene expression levels in a natural population of gray wolves (Canis lupus). Our findings suggest that age is broadly associated with gene expression levels, whereas other examined factors have minimal effects on gene expression patterns. Further, our results reveal evolutionarily conserved signatures of senescence, such as immunosenescence and metabolic aging, between wolves and humans despite major differences in life history and environment. The effects of aging on gene expression levels in wolves exhibit conservation with humans, but the more rapid expression differences observed in aging wolves is evolutionarily appropriate given the species' high level of extrinsic mortality due to intraspecific aggression. Some expression changes that occur with age can facilitate physical age-related changes that may enhance fitness in older wolves. However, the expression of these ancestral patterns of aging in descendant modern dogs living in highly modified domestic environments may be maladaptive and cause disease. This work provides evolutionary insight into aging patterns observed in domestic dogs and demonstrates the applicability of studying natural populations to investigate the mechanisms of aging.
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Affiliation(s)
- Pauline Charruau
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles
| | - Rachel A Johnston
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles
| | - Daniel R Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park
| | | | | | - Douglas W Smith
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park
| | | | - Steven W Cole
- Department of Medicine, University of California, Los Angeles Cousins Center for Psychoneuroimmunology, Semel Institute, University of California, Los Angeles
| | - Jenny Tung
- Department of Biology, Duke University Department of Evolutionary Anthropology, Duke University
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles
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42
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Hedrick PW, Smith DW, Stahler DR. Negative-assortative mating for color in wolves. Evolution 2016; 70:757-66. [PMID: 26988852 DOI: 10.1111/evo.12906] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [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: 10/20/2015] [Revised: 02/13/2016] [Accepted: 03/01/2016] [Indexed: 12/01/2022]
Abstract
There is strong negative-assortative mating for gray and black pelage color in the iconic wolves in Yellowstone National Park. This is the first documented case of significant negative-assortative mating in mammals and one of only a very few cases in vertebrates. Of 261 matings documented from 1995 to 2015, 63.6% were between gray and black wolves and the correlation between mates for color was -0.266. There was a similar excess of matings of both gray males × black females and black males × gray females. Using the observed frequency of negative-assortative mating in a model with both random and negative-assortative mating, the estimated proportion of negative-assortative mating was 0.430. The estimated frequency of black wolves in the population from 1996 to 2014 was 0.452 and these frequencies appear stable over this 19-year period. Using the estimated level of negative-assortative mating, the predicted equilibrium frequency of the dominant allele was 0.278, very close to the mean value of 0.253 observed. In addition, the patterns of genotype frequencies, that is, the observed proportion of black homozygotes and the observed excess of black heterozygotes, are consistent with negative-assortative mating. Importantly these results demonstrate that negative-assortative mating could be entirely responsible for the maintenance of this well-known color polymorphism.
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Affiliation(s)
- Philip W Hedrick
- School of Life Sciences, Arizona State University, Tempe, Arizona, 85287.
| | - Douglas W Smith
- Yellowstone Wolf Project, Yellowstone Center for Resources, Yellowstone National Park, Wyoming, 82190
| | - Daniel R Stahler
- Yellowstone Wolf Project, Yellowstone Center for Resources, Yellowstone National Park, Wyoming, 82190
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43
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Janowitz Koch I, Clark MM, Thompson MJ, Deere-Machemer KA, Wang J, Duarte L, Gnanadesikan GE, McCoy EL, Rubbi L, Stahler DR, Pellegrini M, Ostrander EA, Wayne RK, Sinsheimer JS, vonHoldt BM. The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves. Mol Ecol 2016; 25:1838-55. [PMID: 27112634 PMCID: PMC4849173 DOI: 10.1111/mec.13480] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [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: 07/01/2015] [Revised: 11/09/2015] [Accepted: 11/12/2015] [Indexed: 12/21/2022]
Abstract
The process of domestication can exert intense trait-targeted selection on genes and regulatory regions. Specifically, rapid shifts in the structure and sequence of genomic regulatory elements could provide an explanation for the extensive, and sometimes extreme, variation in phenotypic traits observed in domesticated species. Here, we explored methylation differences from >24 000 cytosines distributed across the genomes of the domesticated dog (Canis familiaris) and the grey wolf (Canis lupus). PCA and model-based cluster analyses identified two primary groups, domestic vs. wild canids. A scan for significantly differentially methylated sites (DMSs) revealed species-specific patterns at 68 sites after correcting for cell heterogeneity, with weak yet significant hypermethylation typical of purebred dogs when compared to wolves (59% and 58%, P < 0.05, respectively). Additionally, methylation patterns at eight genes significantly deviated from neutrality, with similar trends of hypermethylation in purebred dogs. The majority (>66%) of differentially methylated regions contained or were associated with repetitive elements, indicative of a genotype-mediated trend. However, DMSs were also often linked to functionally relevant genes (e.g. neurotransmitters). Finally, we utilized known genealogical relationships among Yellowstone wolves to survey transmission stability of methylation marks, from which we found a substantial fraction that demonstrated high heritability (both H(2) and h(2 ) > 0.99). These analyses provide a unique epigenetic insight into the molecular consequences of recent selection and radiation of our most ancient domesticated companion, the dog. These findings suggest selection has acted on methylation patterns, providing a new genomic perspective on phenotypic diversification in domesticated species.
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Affiliation(s)
- Ilana Janowitz Koch
- Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Michelle M Clark
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Michael J Thompson
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | | | - Jun Wang
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48085, USA
| | - Lionel Duarte
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | | | - Eskender L McCoy
- Yale School of Management, Yale University, New Haven, CT, 06511, USA
| | - Liudmilla Rubbi
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Daniel R Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, WY, 82190, USA
| | - Matteo Pellegrini
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Robert K Wayne
- Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Janet S Sinsheimer
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Human Genetics and Biomathematics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Bridgett M vonHoldt
- Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
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Smith DW, Metz MC, Cassidy KA, Stahler EE, McIntyre RT, Almberg ES, Stahler DR. Infanticide in wolves: seasonality of mortalities and attacks at dens support evolution of territoriality. J Mammal 2015. [DOI: 10.1093/jmammal/gyv125] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Abstract
Interannual variability in space use and how that variation is influenced by density-dependent and density-independent factors are important processes in population ecology. Nevertheless, interannual variability has been neglected by the majority of space use studies. We assessed that variation for wolves living in 15 different packs within Yellowstone National Park during a 13-year period (1996-2008). We estimated utilization distributions to quantify the intensity of space use within each pack's territory each year in summer and winter. Then, we used the volume of intersection index (VI) to quantify the extent to which space use varied from year to year. This index accounts for both the area of overlap and differences in the intensity of use throughout a territory and ranges between 0 and 1. The mean VI index was 0.49, and varied considerably, with approximately 20% of observations (n = 230) being <0.3 or >0.7. In summer, 42% of the variation was attributable to differences between packs. These differences can be attributable to learned behaviors and had never been thought to have such an influence on space use. In winter, 34% of the variation in overlap between years was attributable to interannual differences in precipitation and pack size. This result reveals the strong influence of climate on predator space use and underlies the importance of understanding how climatic factors are going to affect predator populations in the occurrence of climate change. We did not find any significant association between overlap and variables representing density-dependent processes (elk and wolf densities) or intraspecific competition (ratio of wolves to elk). This last result poses a challenge to the classic view of predator-prey systems. On a small spatial scale, predator space use may be driven by factors other than prey distribution.
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Almberg ES, Cross PC, Dobson AP, Smith DW, Metz MC, Stahler DR, Hudson PJ, Festa-Bianchet M. Social living mitigates the costs of a chronic illness in a cooperative carnivore. Ecol Lett 2015; 18:660-7. [PMID: 25983011 PMCID: PMC4676290 DOI: 10.1111/ele.12444] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 01/06/2015] [Accepted: 04/01/2015] [Indexed: 11/28/2022]
Abstract
Infection risk is assumed to increase with social group size, and thus be a cost of group living. We assess infection risk and costs with respect to group size using data from an epidemic of sarcoptic mange (Sarcoptes scabiei) among grey wolves (Canis lupus). We demonstrate that group size does not predict infection risk and that individual costs of infection, in terms of reduced survival, can be entirely offset by having sufficient numbers of pack-mates. Infected individuals experience increased mortality hazards with increasing proportions of infected pack-mates, but healthy individuals remain unaffected. The social support of group hunting and territory defence are two possible mechanisms mediating infection costs. This is likely a common phenomenon among other social species and chronic infections, but difficult to detect in systems where infection status cannot be measured continuously over time.
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Affiliation(s)
- E S Almberg
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State UniversityUniversity Park, PA, USA
| | - P C Cross
- US Geological Survey, Northern Rocky Mountain Science CenterBozeman, MT, USA
| | - A P Dobson
- Department of Ecology and Evolutionary Biology, Princeton UniversityPrinceton, NJ, USA
- Santa Fe InstituteSanta Fe, NM, USA
| | - D W Smith
- Yellowstone Wolf ProjectYellowstone National Park, WY, USA
| | - M C Metz
- Yellowstone Wolf ProjectYellowstone National Park, WY, USA
- College of Forestry and Conservation, University of MontanaMissoula, MT, USA
| | - D R Stahler
- Yellowstone Wolf ProjectYellowstone National Park, WY, USA
| | - P J Hudson
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State UniversityUniversity Park, PA, USA
| | - Marco Festa-Bianchet
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State UniversityUniversity Park, PA, USA
- US Geological Survey, Northern Rocky Mountain Science CenterBozeman, MT, USA
- Department of Ecology and Evolutionary Biology, Princeton UniversityPrinceton, NJ, USA
- Santa Fe InstituteSanta Fe, NM, USA
- Yellowstone Wolf ProjectYellowstone National Park, WY, USA
- College of Forestry and Conservation, University of MontanaMissoula, MT, USA
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47
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Cassidy KA, MacNulty DR, Stahler DR, Smith DW, Mech LD. Group composition effects on aggressive interpack interactions of gray wolves in Yellowstone National Park. Behav Ecol 2015. [DOI: 10.1093/beheco/arv081] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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48
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Affiliation(s)
- Alessia Uboni
- School of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931 USA
| | - Douglas W. Smith
- Yellowstone Center for Resources, Wolf Project, P.O. Box 168, Yellowstone National Park, Wyoming 82190 USA
| | - Julie S. Mao
- Colorado Parks and Wildlife, 0088 Wildlife Way, Glenwood Springs, Colorado 81601 USA
| | - Daniel R. Stahler
- Yellowstone Center for Resources, Wolf Project, P.O. Box 168, Yellowstone National Park, Wyoming 82190 USA
| | - John A. Vucetich
- School of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931 USA
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49
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Abstract
An intriguing aspect of social foraging behaviour is that large groups are often no better at capturing prey than are small groups, a pattern that has been attributed to diminished cooperation (i.e., free riding) in large groups. Although this suggests the formation of large groups is unrelated to prey capture, little is known about cooperation in large groups that hunt hard-to-catch prey. Here, we used direct observations of Yellowstone wolves (Canis lupus) hunting their most formidable prey, bison (Bison bison), to test the hypothesis that large groups are more cooperative when hunting difficult prey. We quantified the relationship between capture success and wolf group size, and compared it to previously reported results for Yellowstone wolves hunting elk (Cervus elaphus), a prey that was, on average, 3 times easier to capture than bison. Whereas improvement in elk capture success levelled off at 2-6 wolves, bison capture success levelled off at 9-13 wolves with evidence that it continued to increase beyond 13 wolves. These results are consistent with the hypothesis that hunters in large groups are more cooperative when hunting more formidable prey. Improved ability to capture formidable prey could therefore promote the formation and maintenance of large predator groups, particularly among predators that specialize on such prey.
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Affiliation(s)
- Daniel R. MacNulty
- Department of Wildland Resources, Utah State University, Logan, UT, United States of America
| | - Aimee Tallian
- Department of Wildland Resources and the Ecology Center, Utah State University, Logan, Utah, United States of America
| | - Daniel R. Stahler
- Yellowstone Wolf Project, Yellowstone Center for Resources, Yellowstone National Park, Mammoth, WY, United States of America
| | - Douglas W. Smith
- Yellowstone Wolf Project, Yellowstone Center for Resources, Yellowstone National Park, Mammoth, WY, United States of America
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50
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Cubaynes S, MacNulty DR, Stahler DR, Quimby KA, Smith DW, Coulson T. Density-dependent intraspecific aggression regulates survival in northern Yellowstone wolves (Canis lupus). J Anim Ecol 2014; 83:1344-56. [PMID: 24749694 DOI: 10.1111/1365-2656.12238] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [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: 12/19/2013] [Accepted: 04/11/2014] [Indexed: 11/30/2022]
Abstract
Understanding the population dynamics of top-predators is essential to assess their impact on ecosystems and to guide their management. Key to this understanding is identifying the mechanisms regulating vital rates. Determining the influence of density on survival is necessary to understand the extent to which human-caused mortality is compensatory or additive. In wolves (Canis lupus), empirical evidence for density-dependent survival is lacking. Dispersal is considered the principal way in which wolves adjust their numbers to prey supply or compensate for human exploitation. However, studies to date have primarily focused on exploited wolf populations, in which density-dependent mechanisms are likely weak due to artificially low wolf densities. Using 13 years of data on 280 collared wolves in Yellowstone National Park, we assessed the effect of wolf density, prey abundance and population structure, as well as winter severity, on age-specific survival in two areas (prey-rich vs. prey-poor) of the national park. We further analysed cause-specific mortality and explored the factors driving intraspecific aggression in the prey-rich northern area of the park. Overall, survival rates decreased during the study. In northern Yellowstone, density dependence regulated adult survival through an increase in intraspecific aggression, independent of prey availability. In the interior of the park, adult survival was less variable and density-independent, despite reduced prey availability. There was no effect of prey population structure in northern Yellowstone, or of winter severity in either area. Survival was similar among yearlings and adults, but lower for adults older than 6 years. Our results indicate that density-dependent intraspecific aggression is a major driver of adult wolf survival in northern Yellowstone, suggesting intrinsic density-dependent mechanisms have the potential to regulate wolf populations at high ungulate densities. When low prey availability or high removal rates maintain wolves at lower densities, limited inter-pack interactions may prevent density-dependent survival, consistent with our findings in the interior of the park.
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Affiliation(s)
- Sarah Cubaynes
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Daniel R MacNulty
- Department of Wildland Resources, Utah State University, Logan, UT, 84322, USA
| | - Daniel R Stahler
- Yellowstone Wolf Project, Yellowstone Center for Resources, Yellowstone National Park, Mammoth, WY, 82190, USA
| | - Kira A Quimby
- Yellowstone Wolf Project, Yellowstone Center for Resources, Yellowstone National Park, Mammoth, WY, 82190, USA
| | - Douglas W Smith
- Yellowstone Wolf Project, Yellowstone Center for Resources, Yellowstone National Park, Mammoth, WY, 82190, USA
| | - Tim Coulson
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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