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Schenekar T, Weiss A, Weiss SJ. Applying molecular genetic data at different scales to support conservation assessment of European Habitats Directive listed species: A case study of Eurasian otter in Austria. Evol Appl 2023; 16:1735-1752. [PMID: 38020875 PMCID: PMC10660814 DOI: 10.1111/eva.13597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/08/2023] [Accepted: 09/04/2023] [Indexed: 12/01/2023] Open
Abstract
Evaluating intraspecific genetic structure and diversity is fundamental to assessing a species' conservation status, but direct incorporation of such information into legal frameworks such as the EU's Habitats Directive is surprisingly rare. How genetic structure aligns with EU member state boundaries or biogeographic regions may be very important in designing management plans or achieving legislative goals. The Eurasian fish otter experienced a sharp population decline during the 20th century but is currently re-expanding in several countries. The species is listed under Annex II and IV of the European Habitats Directive, and member states are obliged to assess the species separately across different biogeographic regions. We genotyped 2492 otter spraints across four provinces in Austria, collected between 2017 and 2021. A total of 384 different genotypes were identified, supporting densities along river habitats from 0.1 to 0.47 otters per river km (mean: 0.306), with a resampling-based simulation supporting limited density overestimation at survey lengths of 20 km or more. Three distinct genetic clusters were revealed, two of them presumably reflecting two relict populations whereas the source of the third cluster is unknown. The geographic extent of the three clusters does not coincide with provincial or biogeographic boundaries, both relevant for assessment and management within existing national or European legislative frameworks. We advocate more consideration of genetic structure in the assessment and conservation management planning of species listed in the European Habitats Directive.
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Affiliation(s)
| | - Andreas Weiss
- NASA Postdoctoral Program FellowNASA Goddard Space Flight CenterGreenbeltMarylandUSA
- Institute of PhysicsUniversity of GrazGrazAustria
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Mitchell JD, Drymon JM, Vardon J, Coulson PG, Simpfendorfer CA, Scyphers SB, Kajiura SM, Hoel K, Williams S, Ryan KL, Barnett A, Heupel MR, Chin A, Navarro M, Langlois T, Ajemian MJ, Gilman E, Prasky E, Jackson G. Shark depredation: future directions in research and management. REVIEWS IN FISH BIOLOGY AND FISHERIES 2023; 33:475-499. [PMID: 36404946 PMCID: PMC9664043 DOI: 10.1007/s11160-022-09732-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 09/28/2022] [Indexed: 05/19/2023]
Abstract
Shark depredation is a complex social-ecological issue that affects a range of fisheries worldwide. Increasing concern about the impacts of shark depredation, and how it intersects with the broader context of fisheries management, has driven recent research in this area, especially in Australia and the United States. This review synthesises these recent advances and provides strategic guidance for researchers aiming to characterise the occurrence of depredation, identify the shark species responsible, and test deterrent and management approaches to reduce its impacts. Specifically, the review covers the application of social science approaches, as well as advances in video camera and genetic methods for identifying depredating species. The practicalities and considerations for testing magnetic, electrical, and acoustic deterrent devices are discussed in light of recent research. Key concepts for the management of shark depredation are reviewed, with recommendations made to guide future research and policy development. Specific management responses to address shark depredation are lacking, and this review emphasizes that a "silver bullet" approach for mitigating depredation does not yet exist. Rather, future efforts to manage shark depredation must rely on a diverse range of integrated approaches involving those in the fishery (fishers, scientists and fishery managers), social scientists, educators, and other stakeholders.
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Affiliation(s)
- J. D. Mitchell
- Queensland Government, Department of Agriculture and Fisheries, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102 Australia
| | - J. M. Drymon
- Mississippi State University, Coastal Research and Extension Center, 1815 Popps Ferry Road, Biloxi, MS 39532 USA
- Mississippi-Alabama Sea Grant Consortium, 703 East Beach Drive, Ocean Springs, MS 39564 USA
| | - J. Vardon
- Southern Cross University, Lismore, NSW Australia
| | - P. G. Coulson
- Department of Primary Industries and Regional Development, Western Australian Fisheries and Marine Research Laboratories, 39 Northside Drive, Hillarys, WA 6025 Australia
| | - C. A. Simpfendorfer
- Institute for Marine and Antarctic Studies, University of Tasmania, 20 Castray Esplanade, Battery Point, TAS 7004 Australia
| | - S. B. Scyphers
- Coastal Sustainability Institute, Department of Marine and Environmental Sciences, Northeastern University, Nahant, MA 01908 USA
- Social Science Environmental Health Research Institute, Northeastern University, Boston, MA 02115 USA
| | - S. M. Kajiura
- Department of Biological Sciences, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431 USA
| | - K. Hoel
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Bldg 34 James Cook Drive, Douglas, QLD 4811 Australia
| | - S. Williams
- Queensland Government, Department of Agriculture and Fisheries, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102 Australia
- School of Biological Sciences, The University of Queensland, St Lucia, Qld 4072 Australia
| | - K. L. Ryan
- Department of Primary Industries and Regional Development, Western Australian Fisheries and Marine Research Laboratories, 39 Northside Drive, Hillarys, WA 6025 Australia
| | - A. Barnett
- Biopixel Oceans Foundation, Cairns, QLD Australia
- Marine Data Technology Hub, James Cook University, Townsville, QLD 4811 Australia
| | - M. R. Heupel
- Institute for Marine and Antarctic Studies, University of Tasmania, 20 Castray Esplanade, Battery Point, TAS 7004 Australia
| | - A. Chin
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Bldg 34 James Cook Drive, Douglas, QLD 4811 Australia
| | - M. Navarro
- School of Biological Sciences, The University of Western Australia, Crawley, WA Australia
- The Oceans Institute, University of Western Australia, Crawley, WA Australia
| | - T. Langlois
- School of Biological Sciences, The University of Western Australia, Crawley, WA Australia
- The Oceans Institute, University of Western Australia, Crawley, WA Australia
| | - M. J. Ajemian
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 US 1 North, Fort Pierce, FL 34946 USA
| | - E. Gilman
- Pelagic Ecosystems Research Group, Honolulu, HI USA
- Heriot-Watt University, Edinburgh, UK
| | - E. Prasky
- Coastal Sustainability Institute, Department of Marine and Environmental Sciences, Northeastern University, Nahant, MA 01908 USA
- Social Science Environmental Health Research Institute, Northeastern University, Boston, MA 02115 USA
| | - G. Jackson
- Department of Primary Industries and Regional Development, Western Australian Fisheries and Marine Research Laboratories, 39 Northside Drive, Hillarys, WA 6025 Australia
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Kiffner C, Uthes S, Ostermann-Miyashita EF, Harms V, König HJ. Patterns of livestock loss associated with a recolonizing wolf population in Germany. FRONTIERS IN CONSERVATION SCIENCE 2022. [DOI: 10.3389/fcosc.2022.989368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Predation on livestock presents a daunting challenge for human–carnivore coexistence in agricultural landscapes. In Germany, the recolonization of wolves is ongoing and its consequences are insufficiently understood. Knowledge about which livestock species are susceptible to wolf predation, which farm types are predisposed to attacks by wolves, and when predation on livestock occurs is valuable for mitigating stakeholder conflicts. To this end, we analyzed 14 years of monitoring data and assessed the livestock prey spectrum, identified correlates between predation on livestock, farm type and livestock category, and described temporal patterns of livestock loss caused by a recolonizing wolf population in the state of Brandenburg (Germany). Among a total of 1387 recorded cases, 42% were unequivocally attributed to wolves (SCALP criteria C1 and C2) and 12% of cases were not caused by wolves. The number of head of livestock killed during a single wolf attack was mediated by farm type and livestock species; losses per event were greater in full-time farms vs. other farm types and greater in sheep, farmed deer and other livestock species, compared to cattle. While sheep were the most commonly killed livestock species, the increase in wolf territories over the investigation period was associated with a widening of the domestic prey species spectrum. Count regression models provided evidence for the increasing frequency of predation events over the 14-year period, along with an exponential increase in wolf territories. Predation on livestock occurred throughout the year, yet seasonality of events was evident and differed across livestock categories. Predation on sheep peaked in the fall, coinciding with the post-weaning period of wolf offspring. Predation on cattle peaked in the spring, coinciding with the cattle calving period. These results call for renewed investment in the implementation of prevention methods for all susceptible domestic species, particularly during times of elevated predation risk.
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Ganz TR, DeVivo MT, Reese EM, Prugh LR. Wildlife whodunnit: forensic identification of predators to inform wildlife management and conservation. WILDLIFE SOC B 2022. [DOI: 10.1002/wsb.1386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Taylor R. Ganz
- The University of Washington Box 352100 Seattle WA 98195‐2100 USA
| | - Melia T. DeVivo
- Washington Department of Fish and Wildlife 2315 North Discovery, Place, Spokane Valley Washington 99216‐1566 USA
| | - Ellen M. Reese
- The University of Washington Box 352100 Seattle WA 98195‐2100 USA
| | - Laura R. Prugh
- The University of Washington Box 352100 Seattle WA 98195‐2100 USA
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Iliopoulos Y, Astaras C, Chatzimichail E. Dogs, not wolves, most likely to have caused the death of a British tourist in northern Greece. NATURE CONSERVATION 2022. [DOI: 10.3897/natureconservation.50.81915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Wolf (Canis lupus) populations have recovered and expanded across many parts of the world thanks to conservation efforts, including improved legal status and restoration of their prey. Concurrently, public concerns regarding the risk of wolf attacks on humans and livestock are increasing as wolves occupy human-dominated landscapes. We examined a unique case in Europe allegedly involving wolves in the death of a female British tourist, aged 64, in northern Greece in September 2017. This incident received extensive international media attention and yet many fundamental details of the case area are lacking, including whether local livestock guarding dogs played a role. To assist in resolving the case, we conducted an extensive literature review which documented 13 criteria linked to the risk of either a wolf and/or a dog attacking a human. We also conducted a camera trap survey (October to December 2017) soon after the fatal attack to calculate the activity overlap among humans, dogs and wolves. Sufficient data were available for assessing 11 of the 13 criteria. For the remaining two, the required data were either not analysed (i.e. canid DNA collected from the attack site), not appropriately collected (i.e. DNA from the mouths of suspected dogs) or were collected, but misinterpreted (i.e. the post-consumption patterns of the victim’s corpse). Via this combination of evidence, we conclude that this case involved a fatal dog attack. This assertion is supported by evidence such as the: a) high dog-human activity overlap at the attack site which peaked during the attack time as opposed to near zero wolf-human activity overlap at the same time, b) presence of a large pack of unsupervised dogs, c) high ratio of male dogs in the dog pack, d) close vicinity of the attack site to dog owner’s property and e) previous documented aggression of these dogs towards humans. The consumption patterns, time scale and location of the victim’s remains indicate a posthumous consumption of the corpse possibly by the same dogs and/or by wild scavengers including wolves. A multidisciplinary approach, such as this one, in the assessment of putative wildlife attacks on humans can reduce misidentifications of the responsible species by forensic authorities and, therefore, prevent unfounded decrease in public tolerance for large carnivores.
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Hull KD, Jeckel S, Williams JM, Ciavaglia SA, Webster LMI, Fitzgerald E, Chang YM, Martineau HM. Fox ( Vulpes vulpes) involvement identified in a series of cat carcass mutilations. Vet Pathol 2021; 59:299-309. [PMID: 34872393 DOI: 10.1177/03009858211052661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
This study was designed to identify the cause of mutilation and death in 32 cats, part of a larger cohort found dead in Greater London, the United Kingdom, between 2016 and 2018. At the time, discussion in the media led to concerns of a human serial cat killer (dubbed The Croydon Cat Killer) pursuing domestic cats, causing a state of disquietude. Given the link between animal abuse and domestic violence, human intervention had to be ruled out. Using a combination of DNA testing, computed tomography imaging, and postmortem examination, no evidence was found to support any human involvement. Instead, a significant association between cat carcass mutilation and the presence of fox DNA was demonstrated. Gross examination identified shared characteristics including the pattern of mutilation, level of limb or vertebral disarticulation, wet fur, wound edges with shortened fur, and smooth or irregular contours, and marks in the skin, muscle, and bone consistent with damage from carnivore teeth. Together these findings supported the theory that the cause of mutilation was postmortem scavenging by red foxes (Vulpes vulpes). The probable cause of death was established in 26/32 (81%) carcasses: 10 were predated, 8 died from cardiorespiratory failure, 6 from blunt force trauma, one from ethylene glycol toxicity, and another from liver failure. In 6 carcasses a cause of death was not established due to autolysis and/or extensive mutilation. In summary, this study highlights the value of a multidisciplinary approach to fully investigate cases of suspected human-inflicted mutilation of animals.
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Affiliation(s)
- Kita D Hull
- The Royal Veterinary College, Hertfordshire, UK
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Forensic genetic identification of sharks involved in human attacks. Forensic Sci Int Genet 2021; 54:102558. [PMID: 34217058 DOI: 10.1016/j.fsigen.2021.102558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 11/22/2022]
Abstract
Each year, 75-100 unprovoked shark attacks on humans are recorded, most of them resulting in no or minor injuries, while a few are fatal. Often, shark identification responsible for attacks relies on visual observations or bite wound characteristics, which limits species determination and preclude individual identification. Here, we provide two genetic approaches to reliably identify species and/or individuals involved in shark attacks on humans based on a non-invasive DNA sampling (i.e. DNA traces present on bite wounds on victims), depending on the knowledge of previous attack history at the site. The first approach uses barcoding techniques allowing species identification without any a priori, while the second relies on microsatellite genotyping, allowing species identification confirmation and individual identification, but requiring an a priori of the potential species involved in the attack. Both approaches were validated by investigating two shark attacks that occurred in Reunion Island (southwestern Indian Ocean). According to both methods, each incident was attributed to a bull shark (Carcharhinus leucas), in agreement with suggestions derived from bite wound characteristics. Both approaches appear thus suitable for the reliable identification of species involved in shark attacks on humans. Moreover, microsatellite genotyping reveals, in the studied cases, that two distinct individuals were responsible of the bites. Applying these genetic identification methods will resolve ambiguities on shark species involved in attacks and allow the collection of individual data to better understand and mitigate shark risk.
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Non-invasive diagnostic PCRs for rapid detection of golden jackal, red fox, and gray wolf/domestic dog and application to validate golden jackal presence in Styria, Austria. EUR J WILDLIFE RES 2021. [DOI: 10.1007/s10344-021-01488-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractHuman-predator conflicts are frequently caused by livestock and/or game depredation. The golden jackal’s (Canis aureus) range expansion in Europe, as well as the recent re-expansion of several gray wolf (Canis lupus) populations, might increase risk of such conflicts. In Austria, golden jackal presence has been increasing since the 1990s including reports of wildlife and livestock kills, frequently occurring in the provinces Styria and Burgenland. We developed a rapid, two-step genetic screening protocol to (1) detect canid mtDNA from non-invasively collected samples like swabs from kills using diagnostic PCRs, and (2) assign this DNA to red fox (Vulpes vulpes), golden jackal, or gray wolf/dog. To monitor golden jackal presence in the region, a total of 167 signs of presence were collected over a period of 30 months throughout the Styrian province. Among these, 14 non-invasive genetic samples (13 swabs from kill sites and one scat) were screened with the developed protocol. Four of these samples revealed golden jackal mtDNA and six samples red fox mtDNA. The developed genetic screening protocol represents a quick and inexpensive method to assess canid presence, e.g., at kill sites, and therefore possesses high value for the conservation and wildlife management community.
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The rise of a large carnivore population in Central Europe: genetic evaluation of lynx reintroduction in the Harz Mountains. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01270-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AbstractLarge carnivores have made a successful comeback across human-dominated landscapes in Central Europe. The Eurasian lynx, for instance, has been actively reintroduced in different regions. Genetic diversity is quickly eroding in these isolated, small populations, questioning the long-term success of lynx reintroductions. To track population development and genetic diversity in a reintroduced lynx population, we used microsatellite analysis and mtDNA haplotyping based on 379 samples collected during the initial 15 year period of lynx reintroduction in the Harz mountains National Park, Germany. The Harz lynx population shows higher genetic diversity relative to other lynx reintroductions, due to initial cross-breeding of divergent captive source lineages and a comparably high founder size. While the population shows significant population growth and spread into adjacent regions, genetic diversity is continiously declining. Expected heterozygosity values dropped from 0.63 after reintroduction (2006/2007) to 0.55 within a 10 year period. Despite this, the Harz lynx population is currently a viable component to an envisioned lynx metapopulation spanning across Central Europe. The ongoing genetic erosion in the Harz population along with a lack of geneflow from adjacent populations indicates that such connectivity is urgently needed to ensure long-term population persistence.
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Zemanova MA. Towards more compassionate wildlife research through the 3Rs principles: moving from invasive to non-invasive methods. WILDLIFE BIOLOGY 2020. [DOI: 10.2981/wlb.00607] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Miriam A. Zemanova
- M. A. Zemanova (https://orcid.org/0000-0002-5002-3388) ✉ , Dept of Philosophy, Univ. of Basel, Steinengraben 5, CH-4051 Basel, Switzerland
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Interval of detectability of predator DNA after livestock (and wild animal) predation. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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12
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Piaggio AJ, Shriner SA, Young JK, Griffin DL, Callahan P, Wostenberg DJ, Gese EM, Hopken MW. DNA persistence in predator saliva from multiple species and methods for optimal recovery from depredated carcasses. J Mammal 2019. [DOI: 10.1093/jmammal/gyz156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
AbstractMolecular forensics is an important component of wildlife research and management. Using DNA from noninvasive samples collected at predation sites, we can identify predator species and obtain individual genotypes, improving our understanding of predator–prey dynamics and impacts of predators on livestock and endangered species. To improve sample collection strategies, we tested two sample collection methods and estimated degradation rates of predator DNA on the carcasses of multiple prey species. We fed carcasses of calves (Bos taurus) and lambs (Ovis aires) to three captive predator species: wolves (Canis lupus), coyotes (C. latrans), and mountain lions (Puma concolor). We swabbed the carcass in the field, as well as removed a piece of hide from the carcasses and then swabbed it in the laboratory. We swabbed all tissue samples through time and attempted to identify the predator involved in the depredation using salivary DNA. We found the most successful approach for yielding viable salivary DNA was removing hide from the prey and swabbing it in the laboratory. As expected, genotyping error increased through time and our ability to obtain complete genotypes decreased over time, the latter falling below 50% after 24 h. We provide guidelines for sampling salivary DNA from tissues of depredated carcasses for maximum probability of detection.
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Affiliation(s)
- Antoinette J Piaggio
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO, USA
| | - Susan A Shriner
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO, USA
| | - Julie K Young
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center-Predator Research Facility, Utah State University, Logan, UT,USA
| | - Doreen L Griffin
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO, USA
| | | | - Darren J Wostenberg
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO, USA
| | - Eric M Gese
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center-Predator Research Facility, Utah State University, Logan, UT,USA
| | - Matthew W Hopken
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO, USA
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Peelle LE, Wirsing AJ, Pilgrim KL, Schwartz MK. Identifying predators from saliva at kill sites with limited remains. WILDLIFE SOC B 2019. [DOI: 10.1002/wsb.992] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Laurel E. Peelle
- University of WashingtonSchool of Environmental and Forest Sciences Box 352100, 3715 West Stevens Way NE Seattle WA 98195 USA
| | - Aaron J. Wirsing
- University of WashingtonSchool of Environmental and Forest Sciences Box 352100, 3715 West Stevens Way NE Seattle WA 98195 USA
| | - Kristine L. Pilgrim
- U.S. Forest Service, Rocky Mountain Research Station 800 East Beckwith Avenue Missoula MT 59801 USA
| | - Michael K. Schwartz
- U.S. Forest Service, Rocky Mountain Research Station 800 East Beckwith Avenue Missoula MT 59801 USA
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Karssene Y, Nowak C, Chammem M, Cocchiararo B, Nouira S. Genetic diversity of the genus Vulpes (Red fox and Fennec fox) in Tunisia based on mitochondrial DNA and noninvasive DNA sampling. Mamm Biol 2019. [DOI: 10.1016/j.mambio.2018.09.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Srinivasan K, Buys EM. Insights into the role of bacteria in vitamin A biosynthesis: Future research opportunities. Crit Rev Food Sci Nutr 2019; 59:3211-3226. [PMID: 30638045 DOI: 10.1080/10408398.2018.1546670] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Significant efforts have been made to address the hidden hunger challenges due to iron, zinc, iodine, and vitamin A since the beginning of the 21st century. Prioritizing the vitamin A deficiency (VAD) disorders, many countries are looking for viable alternative strategies such as biofortification. One of the leading causes of VAD is the poor bioconversion of β-carotene into retinoids. This review is focused on the opportunities of bacterial biosynthesis of retinoids, in particular, through the gut microbiota. The proposed hypothesis starts with the premise that an animal can able to store and timely convert carotenoids into retinoids in the liver and intestinal tissues. This theory is experimental with many scientific insights. The syntrophic metabolism, potential crosstalk of bile acids, lipocalins and lipopolysaccharides of gut microbiota are reported to contribute significantly to the retinoid biosynthesis. The gut bacteria respond to these kinds of factors by genetic restructuring driven mainly by events like horizontal gene transfer. A phylogenetic analysis of β-carotene 15, 15'-mono (di) oxygenase enzymes among a selected group of prokaryotes and eukaryotes was carried out to validate the hypotheses. Shedding light on the probiotic strategies through non-genetically modified organism such as gut bacteria capable of synthesizing vitamin A would address the VAD disorders.
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Affiliation(s)
- K Srinivasan
- Department of Consumer and Food Sciences, University of Pretoria, Hatfield Campus, Pretoria, South Africa
| | - Elna M Buys
- Department of Consumer and Food Sciences, University of Pretoria, Hatfield Campus, Pretoria, South Africa
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Monge O, Dumas D, Baus I. Environmental DNA from avian residual saliva in fruits and its potential uses in population genetics. CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-018-1074-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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17
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Noninvasive genetic assessment provides evidence of extensive gene flow and possible high movement ability in the African golden wolf. Mamm Biol 2018. [DOI: 10.1016/j.mambio.2018.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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18
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Improved genotyping and sequencing success rates for North American river otter (Lontra canadensis). EUR J WILDLIFE RES 2018. [DOI: 10.1007/s10344-018-1177-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Plumer L, Talvi T, Männil P, Saarma U. Assessing the roles of wolves and dogs in livestock predation with suggestions for mitigating human–wildlife conflict and conservation of wolves. CONSERV GENET 2018. [DOI: 10.1007/s10592-017-1045-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Assessing SNP genotyping of noninvasively collected wildlife samples using microfluidic arrays. Sci Rep 2017; 7:10768. [PMID: 28883428 PMCID: PMC5589735 DOI: 10.1038/s41598-017-10647-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/11/2017] [Indexed: 11/09/2022] Open
Abstract
Noninvasively collected samples are a common source of DNA in wildlife genetic studies. Currently, single nucleotide polymorphism (SNP) genotyping using microfluidic arrays is emerging as an easy-to-use and cost-effective methodology. Here we assessed the performance of microfluidic SNP arrays in genotyping noninvasive samples from grey wolves, European wildcats and brown bears, and we compared results with traditional microsatellite genotyping. We successfully SNP-genotyped 87%, 80% and 97% of the wolf, cat and bear samples, respectively. Genotype recovery was higher based on SNPs, while both marker types identified the same individuals and provided almost identical estimates of pairwise differentiation. We found that samples for which all SNP loci were scored had no disagreements across the three replicates (except one locus in a wolf sample). Thus, we argue that call rate (amplification success) can be used as a proxy for genotype quality, allowing the reduction of replication effort when call rate is high. Furthermore, we used cycle threshold values of real-time PCR to guide the choice of protocols for SNP amplification. Finally, we provide general guidelines for successful SNP genotyping of degraded DNA using microfluidic technology.
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Heers T, van Neer A, Becker A, Grilo ML, Siebert U, Abdulmawjood A. Loop-mediated isothermal amplification (LAMP) assay-A rapid detection tool for identifying red fox (Vulpes vulpes) DNA in the carcasses of harbour porpoises (Phocoena phocoena). PLoS One 2017; 12:e0184349. [PMID: 28863185 PMCID: PMC5581184 DOI: 10.1371/journal.pone.0184349] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 08/22/2017] [Indexed: 11/18/2022] Open
Abstract
Carcasses of wild animals are often visited by different scavengers. However, determining which scavenger caused certain types of bite marks is particularly difficult and knowledge thereof is lacking. Therefore, a loop-mediated isothermal amplification (LAMP) assay (target sequence cytochrome b) was developed to detect red fox DNA in carcasses of harbour porpoises. The MSwab™ method for direct testing without prior DNA isolation was validated. As a detection device, the portable real-time fluorometer Genie® II was used, which yields rapid results and can be used in field studies without huge laboratory equipment. In addition to in vitro evaluation and validation, a stranded and scavenged harbour porpoise carcass was successfully examined for red fox DNA residues. The developed LAMP method is a valuable diagnostic tool for confirming presumable red fox bite wounds in harbour porpoises without further DNA isolation steps.
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Affiliation(s)
- Teresa Heers
- Institute for Food Quality and Food Safety, Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Abbo van Neer
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - André Becker
- Institute for Food Quality and Food Safety, Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Miguel Luca Grilo
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Ursula Siebert
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Amir Abdulmawjood
- Institute for Food Quality and Food Safety, Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
- * E-mail:
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22
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Engelhardt A, Muniz L, Perwitasari-Farajallah D, Widdig A. Highly Polymorphic Microsatellite Markers for the Assessment of Male Reproductive Skew and Genetic Variation in Critically Endangered Crested Macaques ( Macaca nigra). INT J PRIMATOL 2017; 38:672-691. [PMID: 28845069 PMCID: PMC5550527 DOI: 10.1007/s10764-017-9973-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 05/11/2017] [Indexed: 11/24/2022]
Abstract
Genetic analyses based on noninvasively collected samples have become an important tool for evolutionary biology and conservation. Crested macaques (Macaca nigra), endemic to Sulawesi, Indonesia, are important for our understanding of primate evolution as Sulawesi macaques represent an exceptional example of primate adaptive radiation. Crested macaques are also Critically Endangered. However, to date we know very little about their genetics. The aim of our study was to find and validate microsatellite markers useful for evolutionary, conservation, and other genetic studies on wild crested macaques. Using fecal samples of 176 wild macaques living in the Tangkoko Reserve, Sulawesi, we identified 12 polymorphic microsatellite loci through cross-species polymerase chain reaction amplification with later modification of some of these primers. We tested their suitability by investigating and exploring patterns of paternity, observed heterozygosity, and evidence for inbreeding. We assigned paternity to 63 of 65 infants with high confidence. Among cases with solved paternity, we found no evidence of extragroup paternity and natal breeding. We found a relatively steep male reproductive skew B index of 0.330 ± 0.267; mean ± SD) and mean alpha paternity of 65% per year with large variation across groups and years (29–100%). Finally, we detected an excess in observed heterozygosity and no evidence of inbreeding across our three study groups, with an observed heterozygosity of 0.766 ± 0.059 and expected heterozygosity of 0.708 ± 0.059, and an inbreeding coefficient of −0.082 ± 0.035. Our results indicate that the selected markers are useful for genetic studies on wild crested macaques, and possibly also on other Sulawesi and closely related macaques. They further suggest that the Tangkoko population of crested macaques is still genetically variable despite its small size, isolation, and the species’ reproductive patterns. This gives us hope that other endangered primate species living in small, isolated populations may also retain a healthy gene pool, at least in the short term.
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Affiliation(s)
- Antje Engelhardt
- School of Natural Sciences and Psychology, Liverpool John Moores University, L3 3AF, Liverpool, UK.,Junior Research Group of Primate Sexual Selection, German Primate Center, 37077 Göttingen, Germany.,Courant Research Center Evolution of Social Behavior, Georg August University, 37077 Göttingen, Germany
| | - Laura Muniz
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.,Research Group of Behavioural Ecology, Institute of Biology, University of Leipzig, 04103 Leipzig, Germany
| | - Dyah Perwitasari-Farajallah
- Primate Research Centre, Bogor Agricultural University, Bogor, Indonesia.,Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Bogor, Indonesia
| | - Anja Widdig
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.,Research Group of Behavioural Ecology, Institute of Biology, University of Leipzig, 04103 Leipzig, Germany.,German Center for Integrative Biodiversity Research, 04103 Leipzig, Germany
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23
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Nakamura M, Godinho R, Rio-Maior H, Roque S, Kaliontzopoulou A, Bernardo J, Castro D, Lopes S, Petrucci-Fonseca F, Álvares F. Evaluating the predictive power of field variables for species and individual molecular identification on wolf noninvasive samples. EUR J WILDLIFE RES 2017. [DOI: 10.1007/s10344-017-1112-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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24
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Wheat RE, Allen JM, Miller SDL, Wilmers CC, Levi T. Environmental DNA from Residual Saliva for Efficient Noninvasive Genetic Monitoring of Brown Bears (Ursus arctos). PLoS One 2016; 11:e0165259. [PMID: 27828988 PMCID: PMC5102439 DOI: 10.1371/journal.pone.0165259] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 10/07/2016] [Indexed: 11/21/2022] Open
Abstract
Noninvasive genetic sampling is an important tool in wildlife ecology and management, typically relying on hair snaring or scat sampling techniques, but hair snaring is labor and cost intensive, and scats yield relatively low quality DNA. New approaches utilizing environmental DNA (eDNA) may provide supplementary, cost-effective tools for noninvasive genetic sampling. We tested whether eDNA from residual saliva on partially-consumed Pacific salmon (Oncorhynchus spp.) carcasses might yield suitable DNA quality for noninvasive monitoring of brown bears (Ursus arctos). We compared the efficiency of monitoring brown bear populations using both fecal DNA and salivary eDNA collected from partially-consumed salmon carcasses in Southeast Alaska. We swabbed a range of tissue types from 156 partially-consumed salmon carcasses from a midseason run of lakeshore-spawning sockeye (O. nerka) and a late season run of stream-spawning chum (O. keta) salmon in 2014. We also swabbed a total of 272 scats from the same locations. Saliva swabs collected from the braincases of salmon had the best amplification rate, followed by swabs taken from individual bite holes. Saliva collected from salmon carcasses identified unique individuals more quickly and required much less labor to locate than scat samples. Salmon carcass swabbing is a promising method to aid in efficient and affordable monitoring of bear populations, and suggests that the swabbing of food remains or consumed baits from other animals may be an additional cost-effective and valuable tool in the study of the ecology and population biology of many elusive and/or wide-ranging species.
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Affiliation(s)
- Rachel E. Wheat
- Department of Environmental Studies, Center for Integrated Spatial Research, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail:
| | - Jennifer M. Allen
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon, United States of America
| | - Sophie D. L. Miller
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Christopher C. Wilmers
- Department of Environmental Studies, Center for Integrated Spatial Research, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Taal Levi
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon, United States of America
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25
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Hopken MW, Orning EK, Young JK, Piaggio AJ. Molecular forensics in avian conservation: a DNA-based approach for identifying mammalian predators of ground-nesting birds and eggs. BMC Res Notes 2016; 9:14. [PMID: 26738484 PMCID: PMC4704294 DOI: 10.1186/s13104-015-1797-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 12/11/2015] [Indexed: 11/23/2022] Open
Abstract
Background The greater sage-grouse (Centrocercus urophasianus) is a ground-nesting bird from the Northern Rocky Mountains and a species at risk of extinction in in multiple U.S. states and Canada. Herein we report results from a proof of concept that mitochondrial and nuclear DNAs from mammalian predator saliva could be non-invasively collected from depredated greater sage-grouse eggshells and carcasses and used for predator species identification. Molecular forensic approaches have been applied to identify predators from depredated remains as one strategy to better understand predator–prey dynamics and guide management strategies. This can aid conservation efforts by correctly identifying predators most likely to impact threatened and endangered species. DNA isolated from non-invasive samples around nesting sites (e.g. fecal or hair samples) is one method that can increase the success and accuracy of predator species identification when compared to relying on nest remains alone. Results Predator saliva DNA was collected from depredated eggshells and carcasses using swabs. We sequenced two partial fragments of two mitochondrial genes and obtained microsatellite genotypes using canid specific primers for species and individual identification, respectively. Using this multilocus approach we were able to identify predators, at least down to family, from 11 out of 14 nests (79 %) and three out of seven carcasses (47 %). Predators detected most frequently were canids (86 %), while other taxa included rodents, a striped skunk, and cattle. We attempted to match the genotypes of individual coyotes obtained from eggshells and carcasses with those obtained from fecal samples and coyotes collected in the areas, but no genotype matches were found. Conclusion Predation is a main cause of nest failure in ground-nesting birds and can impact reproduction and recruitment. To inform predator management for ground-nesting bird conservation, accurate identification of predator species is necessary. Considering predation can have a high impact on recruitment, predation events are very difficult to observe, and predator species are difficult to identify visually from nest remains, molecular approaches that reduce the need to observe or handle animals offer an additional tool to better understand predator–prey dynamics at nesting sites. Electronic supplementary material The online version of this article (doi:10.1186/s13104-015-1797-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthew W Hopken
- United States Department of Agriculture, Wildlife Services, National Wildlife Research Center, Fort Collins, CO, USA.
| | - Elizabeth K Orning
- Department of Wildland Resources, Utah State University, Logan, UT, USA. .,Oregon Cooperative Fish and Wildlife Research Unit, Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA.
| | - Julie K Young
- Department of Wildland Resources, Utah State University, Logan, UT, USA. .,United States Department of Agriculture, Wildlife Services, National Wildlife Research Center, Logan, UT, USA.
| | - Antoinette J Piaggio
- United States Department of Agriculture, Wildlife Services, National Wildlife Research Center, Fort Collins, CO, USA.
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26
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de Groot GA, Nowak C, Skrbinšek T, Andersen LW, Aspi J, Fumagalli L, Godinho R, Harms V, Jansman HA, Liberg O, Marucco F, Mysłajek RW, Nowak S, Pilot M, Randi E, Reinhardt I, Śmietana W, Szewczyk M, Taberlet P, Vilà C, Muñoz-Fuentes V. Decades of population genetic research reveal the need for harmonization of molecular markers: the grey wolf C
anis lupus
as a case study. Mamm Rev 2015. [DOI: 10.1111/mam.12052] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- G. Arjen de Groot
- Animal Ecology; Alterra, Wageningen UR; P.O. Box 47 6700 AA Wageningen The Netherlands
| | - Carsten Nowak
- Conservation Genetics Group; Senckenberg Research Institute and Natural History Museum Frankfurt; Clamecystrasse 12 63571 Gelnhausen Germany
| | - Tomaž Skrbinšek
- Department of Biology; Biotechnical Faculty; University of Ljubljana; Večna pot 111 Ljubljana 1000 Slovenia
| | | | - Jouni Aspi
- Department of Biology, Genetics and Physiology; University of Oulu; P.O. Box 3000 90014 Oulu Finland
| | - Luca Fumagalli
- Department of Ecology and Evolution; Laboratory for Conservation Biology; Biophore Building; University of Lausanne; 1015 Lausanne Switzerland
| | - Raquel Godinho
- Research Center in Biodiversity and Genetic Resources; CIBIO/InBio; Campus Agrário de Vairão 4485-661 Vairão Portugal
- Department of Biology; Faculty of Sciences; University of Porto; Rua do Campo Alegre s/n 4169-007 Porto Portugal
- Department of Zoology; Faculty of Sciences; University of Johannesburg; Auckland Park 2006 Johannesburg South Africa
| | - Verena Harms
- Conservation Genetics Group; Senckenberg Research Institute and Natural History Museum Frankfurt; Clamecystrasse 12 63571 Gelnhausen Germany
| | - Hugh A.H. Jansman
- Animal Ecology; Alterra, Wageningen UR; P.O. Box 47 6700 AA Wageningen The Netherlands
| | - Olof Liberg
- Swedish University of Agricultural Sciences (SLU); Grimsö Wildlife Research Station SE-730 91 Riddarhyttan Sweden
| | - Francesca Marucco
- Parco Naturale Alpi Marittime; Centro Gestione e Conservazione Grandi Carnivori; Piazza Regina Elena 30 12010 Valdieri Italy
| | - Robert W. Mysłajek
- Institute of Genetics and Biotechnology; Faculty of Biology; University of Warsaw; Pawińskiego 5a 02-106 Warszawa Poland
| | - Sabina Nowak
- Association for Nature ‘Wolf’; Twardorzeczka 229 34-324 Lipowa Poland
| | - Małgorzata Pilot
- School of Life Sciences; University of Lincoln; Green Lane Lincoln LN6 7DL UK
| | - Ettore Randi
- Laboratorio di Genetica; Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA); Via Cà Fornacetta 9 40064 Ozzano dell'Emilia (BO) Italy
- Aalborg University; Department 18/Section of Environmental Engineering; Sohngårdsholmsvej 57 9000 Aalborg Denmark
| | - Ilka Reinhardt
- LUPUS - German Institute for Wolf Monitoring and Research; Dorfstraße 20 02979 Spreewitz Germany
| | - Wojciech Śmietana
- Polish Academy of Sciences; Institute of Nature Conservation; Mickiewicza 33 31-120 Kraków Poland
| | - Maciej Szewczyk
- Institute of Genetics and Biotechnology; Faculty of Biology; University of Warsaw; Pawińskiego 5a 02-106 Warszawa Poland
| | - Pierre Taberlet
- Centre National de la Recherche Scientifique; Laboratoire d'Ecologie Alpine (LECA); F-38000 Grenoble France
- Université Grenoble Alpes; Laboratoire d'Ecologie Alpine (LECA); F-38000 Grenoble France
| | - Carles Vilà
- Doñana Biological Station (EBD-CSIC); Avenida Americo Vespucio s/n 41092 Sevilla Spain
| | - Violeta Muñoz-Fuentes
- Conservation Genetics Group; Senckenberg Research Institute and Natural History Museum Frankfurt; Clamecystrasse 12 63571 Gelnhausen Germany
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