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Buzan E, Potočnik H, Pokorny B, Potušek S, Iacolina L, Gerič U, Urzi F, Kos I. Molecular analysis of scats revealed diet and prey choice of grey wolves and Eurasian lynx in the contact zone between the Dinaric Mountains and the Alps. Front Zool 2024; 21:9. [PMID: 38500207 PMCID: PMC10949697 DOI: 10.1186/s12983-024-00530-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 03/13/2024] [Indexed: 03/20/2024] Open
Abstract
A comprehensive understanding of the dietary habits of carnivores is essential to get ecological insights into their role in the ecosystem, potential competition with other carnivorous species, and their effect on prey populations. Genetic analysis of non-invasive samples, such as scats, can supplement behavioural or microscopic diet investigations. The objective of this study was to employ DNA metabarcoding to accurately determine the prey species in grey wolf (Canis lupus) and Eurasian lynx (Lynx lynx) scat samples collected in the Julian Alps and the Dinaric Mountains, Slovenia. The primary prey of wolves were red deer (Cervus elaphus) (detected in 96% scat samples), European roe deer (Capreolus capreolus) (68%), and wild boar (Sus scrofa) (45%). A smaller portion of their diet consisted of mesocarnivores, small mammals, and domestic animals. In contrast, the lynx diet mostly consisted of European roe deer (82%) and red deer (64%). However, small mammals and domestic animals were also present in lynx diet, albeit to a lesser extent. Our findings indicate that the dietary habits of wolves and lynx are influenced by geographical location. Snapshot dietary analyses using metabarcoding are valuable for comprehending the behaviour and ecology of predators, and for devising conservation measures aimed at sustainable management of both their natural habitats and prey populations. However, to gain a more detailed understanding of wolf and lynx dietary habits and ecological impact, it would be essential to conduct long-term genetic monitoring of their diet.
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Affiliation(s)
- Elena Buzan
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia
- Faculty of Environmental Protection, Trg mladosti 7, 3320, Velenje, Slovenia
| | - Hubert Potočnik
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Boštjan Pokorny
- Faculty of Environmental Protection, Trg mladosti 7, 3320, Velenje, Slovenia
- Slovenian Forestry Institute, Večna pot 2, 1000, Ljubljana, Slovenia
| | - Sandra Potušek
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia
| | - Laura Iacolina
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia
- Department of Chemistry and Bioscience, Aalborg University, Frederik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Urška Gerič
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia
| | - Felicita Urzi
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia.
| | - Ivan Kos
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
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2
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Rojas A, Germitsch N, Oren S, Sazmand A, Deak G. Wildlife parasitology: sample collection and processing, diagnostic constraints, and methodological challenges in terrestrial carnivores. Parasit Vectors 2024; 17:127. [PMID: 38481271 PMCID: PMC10938792 DOI: 10.1186/s13071-024-06226-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/01/2024] [Indexed: 03/17/2024] Open
Abstract
Wild terrestrial carnivores play a crucial role as reservoir, maintenance, and spillover hosts for a wide parasite variety. They may harbor, shed, and transmit zoonotic parasites and parasites of veterinary importance for domestic hosts. Although wild carnivores are globally distributed and comprise many different species, some living in close proximity to human settlements, only a few studies have investigated parasites of wild terrestrial carnivores using non-specific techniques. Access to samples of wild carnivores may be challenging as some species are protected, and others are secretive, possibly explaining the data paucity. Considering the importance of wild carnivores' health and ecological role, combined with the lack of specific diagnostic methodologies, this review aims to offer an overview of the diagnostic methods for parasite investigation in wild terrestrial carnivores, providing the precise techniques for collection and analysis of fecal, blood, and tissue samples, the environmental impact on said samples, and the limitations researchers currently face in analyzing samples of wild terrestrial carnivores. In addition, this paper offers some crucial information on how different environmental factors affect parasite detection postmortem and how insects can be used to estimate the time of death with a specific highlight on insect larvae. The paper contains a literature review of available procedures and emphasizes the need for diagnostic method standardization in wild terrestrial carnivores.
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Affiliation(s)
- Alicia Rojas
- Laboratory of Helminthology, Faculty of Microbiology, University of Costa Rica, San José, 11501-2060, Costa Rica.
- Centro de Investigación en Enfermedades Tropicales, University of Costa Rica, San José, 11501-2060, Costa Rica.
| | - Nina Germitsch
- Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave, Charlottetown, PEI, C1A 4P3, Canada.
| | - Stephanie Oren
- Department of Anatomic Pathology, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, 400372, Cluj-Napoca, Romania.
| | - Alireza Sazmand
- Department of Pathobiology, Faculty of Veterinary Medicine, Bu-Ali Sina University, Hamedan, 6517658978, Iran.
| | - Georgiana Deak
- Department of Parasitology and Parasitic Diseases, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, 400372, Cluj-Napoca, Romania.
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Tull A, Valdmann H, Tammeleht E, Kaasiku T, Rannap R, Saarma U. High overlap of zoonotic helminths between wild mammalian predators and rural dogs - an emerging One Health concern? Parasitology 2022; 149:1565-1574. [PMID: 35924728 PMCID: PMC11010195 DOI: 10.1017/s0031182022001032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 11/06/2022]
Abstract
The concept of One Health emphasizes the interdependence of human, animal and environmental health and is of growing significance, in part owing to the problems related to emerging infectious diseases of wildlife origin. Wild mammalian predators are a potential risk factor for transmission of zoonotic pathogens to domesticated animals and humans. This is especially relevant in rural areas, where transmission of zoonotic pathogens can occur particularly efficiently when free-ranging dogs are present. The main aim of this study was to determine helminth infections among wild mammalian predators and evaluate the overlap between helminth faunas of wild mammals and dogs. Scat samples of predators were collected in coastal areas of Western Estonia and genetic methodology applied for the correct identification of predator species from their scat. Parasitic helminths of mammalian predators in the scat samples were analysed and compared with dog data from a previous study. High helminth prevalence (~90%) was found in dominant predator species in the area, namely the red fox (Vulpes vulpes) and golden jackal (Canis aureus). Moreover, the helminth fauna of both wild species, including potentially zoonotic helminths, overlapped largely with that of rural dogs in the same area. The results, together with the ones from earlier parasitological studies among humans in Estonia, emphasize the potential risk of pathogen transmission from wild mammalian predators to dogs and from dogs to humans, making parasitic diseases of wildlife a One Health concern.
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Affiliation(s)
- Ants Tull
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
| | - Harri Valdmann
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
| | - Egle Tammeleht
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
| | - Triin Kaasiku
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
| | - Riinu Rannap
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
| | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
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Henger CS, Hargous E, Nagy CM, Weckel M, Wultsch C, Krampis K, Duncan N, Gormezano L, Munshi-South J. DNA metabarcoding reveals that coyotes in New York City consume wide variety of native prey species and human food. PeerJ 2022; 10:e13788. [PMID: 36164598 PMCID: PMC9508883 DOI: 10.7717/peerj.13788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 07/05/2022] [Indexed: 01/17/2023] Open
Abstract
Carnivores are currently colonizing cities where they were previously absent. These urban environments are novel ecosystems characterized by habitat degradation and fragmentation, availability of human food, and different prey assemblages than surrounding areas. Coyotes (Canis latrans) established a breeding population in New York City (NYC) over the last few decades, but their ecology within NYC is poorly understood. In this study, we used non-invasive scat sampling and DNA metabarcoding to profile vertebrate, invertebrate, and plant dietary items with the goal to compare the diets of urban coyotes to those inhabiting non-urban areas. We found that both urban and non-urban coyotes consumed a variety of plants and animals as well as human food. Raccoons (Procyon lotor) were an important food item for coyotes within and outside NYC. In contrast, white-tailed deer (Odocoileus virginianus) were mainly eaten by coyotes inhabiting non-urban areas. Domestic chicken (Gallus gallus) was the human food item found in most scats from both urban and non-urban coyotes. Domestic cats (Felis catus) were consumed by urban coyotes but were detected in only a small proportion of the scats (<5%), which differs markedly from high rates of cat depredation in some other cities. In addition, we compared our genetic metabarcoding analysis to a morphological analysis of the same scat samples. We found that the detection similarity between the two methods was low and it varied depending on the type of diet item.
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Affiliation(s)
- Carol S. Henger
- Louis Calder Biological Field Station, Fordham University, Armonk, New York, United States
| | - Emily Hargous
- Louis Calder Biological Field Station, Fordham University, Armonk, New York, United States
| | | | - Mark Weckel
- American Museum of Natural History, New York, New York, United States
| | - Claudia Wultsch
- American Museum of Natural History, New York, New York, United States,Bioinformatics and Computational Genomics Laboratory, City University of New York, Hunter College, New York, New York, United States
| | - Konstantinos Krampis
- Bioinformatics and Computational Genomics Laboratory, City University of New York, Hunter College, New York, New York, United States,Department of Biological Sciences, City University of New York, Hunter College, New York, New York, United States,Institute of Computational Biomedicine, Weill Medical College of Cornell University, New York, New York, United States
| | - Neil Duncan
- American Museum of Natural History, New York, New York, United States
| | - Linda Gormezano
- American Museum of Natural History, New York, New York, United States
| | - Jason Munshi-South
- Louis Calder Biological Field Station, Fordham University, Armonk, New York, United States
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Groen K, Trimbos KB, Hein S, Blaauw AI, van Bodegom PM, Hahne J, Jacob J. Establishment of a fecal DNA quantification technique for rare and cryptic diet constituents in small mammals. Mol Ecol Resour 2022; 22:2220-2231. [PMID: 35297564 DOI: 10.1111/1755-0998.13609] [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: 08/26/2021] [Revised: 02/25/2022] [Accepted: 03/04/2022] [Indexed: 11/27/2022]
Abstract
DNA-based approaches have highly improved the applicability of dietary studies aimed at investigating ecological processes. These studies have provided direct insights into, otherwise difficult to measure, interactions between species and trophic levels, food web structure and ecosystem functioning. However, despite these advances, DNA-based methods have been struggling to accurately quantify the whole breadth of diet constituents because of methodological biases, such as amplification bias and digestive processes. This study is, to our knowledge, the first diet study that used droplet digital PCR to quantify diet constituents. We manipulated the diet of wild caught wood mice (Apodemus sylvaticus) by feeding them with a known amount of small vegetable seeds (onion and carrot) and quantified the DNA traces of these diet constituents in fecal samples. The sensitivity of the technique combined with the control on the experimental design allowed mitigation of methodological bias. We were able to accurately determine DNA concentrations of small vegetable seeds in the diet of wood mice. Quantification of target DNA demonstrated significant differences in DNA content when one vs. five seeds were consumed. These differences remained significant when the age, sex, and other diet constituents of the mice were altered. Different DNA markers, targeting different parts of the chloroplast, influenced onion DNA detectability. However, all onion and carrot markers showed higher DNA content for higher seed numbers. Overall, the sensitive DNA based approach developed in this study allows for minimally-invasive quantification of small diet constituents in feces, which would otherwise be undetectable with traditional methods.
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Affiliation(s)
- Kevin Groen
- Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, Van Steenis Building Einsteinweg 2, 2333 CC, The Netherlands
| | - Krijn B Trimbos
- Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, Van Steenis Building Einsteinweg 2, 2333 CC, The Netherlands
| | - Susanne Hein
- Vertebrate Research, Institute for Plant Protection in Horticulture and Forests, Julius Kühn-Institute (JKI) Federal Research Institute for Cultivated Plants, Toppheideweg 88, 48161, Münster, Germany.,Present address: BASF SE, Agricultural Solutions - Global Ecotoxicology, Limburgerhof, Germany
| | - Astrid I Blaauw
- Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, Van Steenis Building Einsteinweg 2, 2333 CC, The Netherlands
| | - Peter M van Bodegom
- Environmental Biology, Institute of Environmental Sciences, Leiden University, Leiden, Van Steenis Building Einsteinweg 2, 2333 CC, The Netherlands
| | - Joerg Hahne
- Bayer AG, Crop Science Division, Terrestrial Vertebrates, Monheim am Rhein, Germany
| | - Jens Jacob
- Vertebrate Research, Institute for Plant Protection in Horticulture and Forests, Julius Kühn-Institute (JKI) Federal Research Institute for Cultivated Plants, Toppheideweg 88, 48161, Münster, Germany
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6
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Free-ranging rural dogs are highly infected with helminths, contaminating environment nine times more than urban dogs. J Helminthol 2022; 96:e19. [PMID: 35257647 DOI: 10.1017/s0022149x22000116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Regardless of the highly efficient anthelmintics available and the control measures taken by dog owners and veterinarians, gastrointestinal parasites, especially zoonotic helminths, are still abundant in dogs and pose a health risk to humans. Free-ranging dogs in rural areas can be an important source of helminth infection. The aims of the present work were to collect scats of rural dogs, determine the environmental contamination caused by helminth infections among rural dogs of Western Estonia, analyse how diet affects helminth infection rate and compare the findings to a previous study focusing on dog helminths in urban areas of Estonia. To differentiate the scats of dogs from other sympatric canids, a genetic method was applied. Of 328 samples, genetic analysis identified 84 scats belonging to dogs, of which 87.0% were infected with helminths. A high proportion of rural dog scats harboured eggs of Taeniidae (65.5%), followed by Trichuris spp./Eucoleus spp. (15.5%), Uncinaria stenocephala (14.7%) and Toxocara canis (4.3%). Coinfections occurred in 34.5% of the samples, being the most common between Taeniidae and U. stenocephala (41.4%). The intensity model indicated higher helminth infection rate in rural dogs preying on rodents and game. In comparison to urban dogs, rural dogs were nine times more likely to be infected with intestinal parasites. These results emphasize the need to implement measures to reduce helminth infections in dogs living in rural areas of Western Estonia. Among a complex of measures to be taken, we suggest that it is also important to diagnose which gastrointestinal parasite species infect dogs to determine specific anthelmintic treatment against these parasites.
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Draper J, Rodgers T, Young JK. Beating the heat: ecology of desert bobcats. BMC Ecol Evol 2022; 22:25. [PMID: 35246040 PMCID: PMC8896297 DOI: 10.1186/s12862-022-01973-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 02/09/2022] [Indexed: 11/30/2022] Open
Abstract
Background Relative to temperate regions, little is known about bobcats (Lynx rufus) in the Sonoran Desert portion of their range, in part due to the difficulty of sampling an elusive carnivore in harsh desert environments. Here, we quantify habitat selection and evaluate diet of bobcats at Kofa National Wildlife Refuge, Arizona, USA, using multiple sampling techniques including GPS telemetry, camera traps, and DNA metabarcoding. Results Home ranges during the hot season were smaller than during the cool season. Camera trapping failed to yield a high enough detection rate to identify habitat occupancy trends but third-order resource selection from GPS-collar data showed a preference for higher elevations and rugged terrain at lower elevations. Diet composition consisted of a diverse range of available small prey items, including a higher frequency of avian prey than previously observed in bobcats. Conclusions Desert bobcats in our study maintained smaller home ranges and primarily consumed smaller prey than their more northern relatives. This study illustrates the benefit of employing multiple, complementary sampling methods to understand the ecology of elusive species. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-01973-3.
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Affiliation(s)
- John Draper
- Ecology Center, Utah State University, Logan, UT, 84322, USA
| | - Torrey Rodgers
- Department of Wildland Resources, Utah State University, Logan, UT, 84322, USA
| | - Julie K Young
- Department of Wildland Resources, Utah State University, Logan, UT, 84322, USA. .,U.S. Department of Agriculture, National Wildlife Research Center - Predator Research Facility, Millville, UT, 84326, USA.
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MacAulay KM, Spilker EG, Berg JE, Hebblewhite M, Merrill EH. Beyond the encounter: Predicting multi‐predator risk to elk (
Cervus canadensis
) in summer using predator scats. Ecol Evol 2022; 12:e8589. [PMID: 35222962 PMCID: PMC8843817 DOI: 10.1002/ece3.8589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 12/23/2021] [Accepted: 01/10/2022] [Indexed: 11/08/2022] Open
Affiliation(s)
- Kara M. MacAulay
- Department of Biological Sciences University of Alberta Edmonton Alberta Canada
| | - Eric G. Spilker
- Department of Biological Sciences University of Alberta Edmonton Alberta Canada
| | - Jodi E. Berg
- Department of Biological Sciences University of Alberta Edmonton Alberta Canada
| | - Mark Hebblewhite
- Wildlife Biology Program Department of Ecosystem and Conservation Sciences W. A. Franke College of Forestry and Conservation University of Montana Missoula Montana USA
| | - Evelyn H. Merrill
- Department of Biological Sciences University of Alberta Edmonton Alberta Canada
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Pugesek G, Mumma MA, Mahoney SP, Waits LP. Molecular evaluation of American black bear prey consumption following diversionary feeding. URSUS 2021. [DOI: 10.2192/ursus-d-20-00027.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Genevieve Pugesek
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, Moscow, ID 83844, USA
| | - Matthew A. Mumma
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, Moscow, ID 83844, USA
| | - Shane P. Mahoney
- Department of Environment and Conservation, Government of Newfoundland and Labrador, St. John's, Newfoundland A1B 4J6, Canada
| | - Lisette P. Waits
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, Moscow, ID 83844, USA
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Di Bernardi C, Wikenros C, Hedmark E, Boitani L, Ciucci P, Sand H, Åkesson M. Multiple species-specific molecular markers using nanofluidic array as a tool to detect prey DNA from carnivore scats. Ecol Evol 2021; 11:11739-11748. [PMID: 34522337 PMCID: PMC8427573 DOI: 10.1002/ece3.7918] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 06/29/2021] [Accepted: 07/02/2021] [Indexed: 01/07/2023] Open
Abstract
Large carnivore feeding ecology plays a crucial role for management and conservation for predators and their prey. One of the keys to this kind of research is to identify the species composition in the predator diet, for example, prey determination from scat content. DNA-based methods applied to detect prey in predators' scats are viable alternatives to traditional macroscopic approaches, showing an increased reliability and higher prey detection rate. Here, we developed a molecular method for prey species identification in wolf (Canis lupus) scats using multiple species-specific marker loci on the cytochrome b gene for 18 target species. The final panel consisted of 80 assays, with a minimum of four markers per target species, and that amplified specifically when using a high-throughput Nanofluidic array technology (Fluidigm Inc.). As a practical example, we applied the method to identify target prey species DNA in 80 wolf scats collected in Sweden. Depending on the number of amplifying markers required to obtain a positive species call in a scat, the success in determining at least one prey species from the scats ranged from 44% to 92%. Although we highlight the need to evaluate the optimal number of markers for sensitive target species detection, the developed method is a fast and cost-efficient tool for prey identification in wolf scats and it also has the potential to be further developed and applied to other areas and large carnivores as well.
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Affiliation(s)
- Cecilia Di Bernardi
- Department of Biology and Biotechnologies "Charles Darwin" University of Rome La Sapienza Rome Italy
- Grimsö Wildlife Research Station Department of Ecology Swedish University of Agricultural Sciences Riddarhyttan Sweden
| | - Camilla Wikenros
- Grimsö Wildlife Research Station Department of Ecology Swedish University of Agricultural Sciences Riddarhyttan Sweden
| | - Eva Hedmark
- Grimsö Wildlife Research Station Department of Ecology Swedish University of Agricultural Sciences Riddarhyttan Sweden
| | - Luigi Boitani
- Department of Biology and Biotechnologies "Charles Darwin" University of Rome La Sapienza Rome Italy
| | - Paolo Ciucci
- Department of Biology and Biotechnologies "Charles Darwin" University of Rome La Sapienza Rome Italy
| | - Håkan Sand
- Grimsö Wildlife Research Station Department of Ecology Swedish University of Agricultural Sciences Riddarhyttan Sweden
| | - Mikael Åkesson
- Grimsö Wildlife Research Station Department of Ecology Swedish University of Agricultural Sciences Riddarhyttan Sweden
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11
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Huang RK, Webber QM, Laforge MP, Robitaille AL, Bonar M, Balluffi-Fry J, Zabihi-Seissan S, Vander Wal E. Coyote (Canis latrans) diet and spatial co-occurrence with woodland caribou (Rangifer tarandus caribou). CAN J ZOOL 2021. [DOI: 10.1139/cjz-2020-0253] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The interplay of predator encounters and antipredator responses is an integral part of understanding predator–prey interactions and spatial co-occurrence and avoidance can elucidate these interactions. We conducted hard-part dietary analysis of coyotes (Canis latrans Say, 1823) and space use of coyotes and woodland caribou (Rangifer tarandus caribou (Gmelin, 1788)) to test two competing hypotheses about coyote and caribou predator–prey spatial dynamics using resource selection functions. The high encounter hypothesis predicts that coyotes would maximize encounters with caribou via high spatial co-occurrence, whereas the predator stealth hypothesis predicts that through low spatial co-occurrence with caribou, coyotes act as stealth predators by avoiding habitats that caribou typically select. Our dietary analysis revealed that ∼46% of sampled coyote diet is composed of caribou. We found that coyote share space with caribou in lichen-barren habitat in both summer and winter and that coyotes co-occur with caribou in forested habitat during summer, but not during winter. Our findings support predictions associated with the high encounter predator hypothesis whereby coyotes and caribou have high spatial co-occurrence promoting caribou in coyote diet.
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Affiliation(s)
- Richard K.K. Huang
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John’s, NL A1B 3X9, Canada
| | - Quinn M.R. Webber
- Cognitive and Behavioural Ecology Interdisciplinary Program, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John’s, NL A1B 3X9, Canada
| | - Michel P. Laforge
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John’s, NL A1B 3X9, Canada
| | - Alec L. Robitaille
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John’s, NL A1B 3X9, Canada
| | - Maegwin Bonar
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John’s, NL A1B 3X9, Canada
| | - Juliana Balluffi-Fry
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John’s, NL A1B 3X9, Canada
| | - Sana Zabihi-Seissan
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John’s, NL A1B 3X9, Canada
| | - Eric Vander Wal
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John’s, NL A1B 3X9, Canada
- Cognitive and Behavioural Ecology Interdisciplinary Program, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John’s, NL A1B 3X9, Canada
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12
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eDNA metabarcoding for biodiversity assessment, generalist predators as sampling assistants. Sci Rep 2021; 11:6820. [PMID: 33767219 PMCID: PMC7994446 DOI: 10.1038/s41598-021-85488-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 02/24/2021] [Indexed: 01/31/2023] Open
Abstract
With an accelerating negative impact of anthropogenic actions on natural ecosystems, non-invasive biodiversity assessments are becoming increasingly crucial. As a consequence, the interest in the application of environmental DNA (eDNA) survey techniques has increased. The use of eDNA extracted from faeces from generalist predators, have recently been described as "biodiversity capsules" and suggested as a complementary tool for improving current biodiversity assessments. In this study, using faecal samples from two generalist omnivore species, the Eurasian badger and the red fox, we evaluated the applicability of eDNA metabarcoding in determining dietary composition, compared to macroscopic diet identification techniques. Subsequently, we used the dietary information obtained to assess its contribution to biodiversity assessments. Compared to classic macroscopic techniques, we found that eDNA metabarcoding detected more taxa, at higher taxonomic resolution, and proved to be an important technique to verify the species identification of the predator from field collected faeces. Furthermore, we showed how dietary analyses complemented field observations in describing biodiversity by identifying consumed flora and fauna that went unnoticed during field observations. While diet analysis approaches could not substitute field observations entirely, we suggest that their integration with other methods might overcome intrinsic limitations of single techniques in future biodiversity surveys.
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Smith BR, Yarnell RW, Uzal A, Whitehouse-Tedd K. The ecological effects of livestock guarding dogs (LGDs) on target and non-target wildlife. JOURNAL OF VERTEBRATE BIOLOGY 2020. [DOI: 10.25225/jvb.20103] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Bethany R. Smith
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, United Kingdom; e-mail: , , ,
| | - Richard W. Yarnell
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, United Kingdom; e-mail: , , ,
| | - Antonio Uzal
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, United Kingdom; e-mail: , , ,
| | - Katherine Whitehouse-Tedd
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, United Kingdom; e-mail: , , ,
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14
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Subrata SA, Siregar SRT, André A, Michaux JR. Identifying prey of the Javan mongoose (Urva javanica) in Java from fecal samples using next-generation sequencing. Mamm Biol 2020. [DOI: 10.1007/s42991-020-00086-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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15
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Bonin M, Dussault C, Taillon J, Lecomte N, Côté SD. Combining stable isotopes, morphological, and molecular analyses to reconstruct the diet of free-ranging consumers. Ecol Evol 2020; 10:6664-6676. [PMID: 32724540 PMCID: PMC7381590 DOI: 10.1002/ece3.6397] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/24/2020] [Accepted: 04/30/2020] [Indexed: 02/06/2023] Open
Abstract
Accurate estimates of animal diet composition are essential to untangle complex interactions in food webs. Biomarkers and molecular tools are increasingly used to estimate diet, sometimes alongside traditional dietary tracing methods. Yet only a few empirical studies have compared the outcomes and potential gains of using a combination of these methods, especially using free-ranging animals with distinct foraging preferences.We used stable isotopes, morphological, and molecular analyses to investigate the diet of free-ranging consumers with two distinct diet types, that is, carnivore and omnivore. By combining the three analytical methods to assess the diet of consumers during the same period, we aimed to identify the limits of each method and to assess the potential benefits of their combined use to derive diet estimates.Our results showed that the different methods led to a consistent diet description for carnivores, which have a relatively simple diet mixture, but their outcomes somewhat differed for omnivore, which have a more complex diet. Still, the combined use of morphological and molecular analyses enhanced the diversity of food sources detected compared to the use of a single method independently of diet types. Precision of diet estimates derived from stable isotope analyses was improved by the addition of priors obtained from morphological and molecular diet analyses of the same population.Although we used free-ranging animals without a known diet, our empirical testing of three of the most widely used methods of diet determination highlights the limits of relying over a single approach, especially in systems with few or no a priori information about the foraging habits of consumers. The choice of an appropriate approach of diet description should be a key step when planning dietary studies of free-ranging populations. We recommend using more than one dietary determination methods especially for species with complex diet mixtures.
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Affiliation(s)
- Michaël Bonin
- Caribou UngavaCentre d’études nordiquesUniversité LavalQuébecQCCanada
| | - Christian Dussault
- Caribou UngavaCentre d’études nordiquesUniversité LavalQuébecQCCanada
- Direction de l’expertise sur la faune terrestre, l’herpétofaune et l’avifauneMinistère des Forêts, de la Faune et des ParcsQuébecQCCanada
| | - Joëlle Taillon
- Caribou UngavaCentre d’études nordiquesUniversité LavalQuébecQCCanada
- Direction de l’expertise sur la faune terrestre, l’herpétofaune et l’avifauneMinistère des Forêts, de la Faune et des ParcsQuébecQCCanada
| | - Nicolas Lecomte
- Caribou UngavaCentre d’études nordiquesUniversité LavalQuébecQCCanada
- Chaire de recherche du Canada en écologie polaire et boréaleUniversité de MonctonMonctonNBCanada
| | - Steeve D. Côté
- Caribou UngavaCentre d’études nordiquesUniversité LavalQuébecQCCanada
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16
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Momeni S, Malekian M, Hemami MR. Molecular versus morphological approaches to diet analysis of the caracal ( Caracal caracal). MAMMALIA 2019. [DOI: 10.1515/mammalia-2017-0161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Diet analysis is an essential part in understanding the biology of a species and functioning of ecosystems. Traditional morphological identification of undigested remains in the scats and molecular analyses of prey species’ DNA have previously been used to assess diet. In the present study, caracal diet in the Abbasabad Wildlife Refuge, Central Iran, was investigated using both molecular and morphological methods. We collected 22 scat samples from caracal dens in the region. Feces were washed on sieves and their remaining components were morphologically identified. We also targeted a 307-base pair fragment of the cytochrome b gene to amplify and sequence the species’ DNA. Morphological analyses revealed that 76% of the diet comprised rodent species. We identified a total of nine prey taxa using the molecular method, including six rodents, one hare, one hedgehog and one wild goat. There was a general agreement between the molecular and morphological results; however, molecular methods tended to allow a better identification of the prey species. Therefore, the DNA-based approach acts as a valuable complement to current morphological methods in the study of a rare felid’s diet when no hair reference library exists.
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Affiliation(s)
- Sogol Momeni
- Department of Natural Resources , Isfahan University of Technology , Isfahan 84156-83111 , Iran
| | - Mansoureh Malekian
- Department of Natural Resources , Isfahan University of Technology , Isfahan 84156-83111 , Iran
| | - Mahmoud-Reza Hemami
- Department of Natural Resources , Isfahan University of Technology , Isfahan 84156-83111 , Iran
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17
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Morin DJ, Higdon SD, Lonsinger RC, Gosselin EN, Kelly MJ, Waits LP. Comparing methods of estimating carnivore diets with uncertainty and imperfect detection. WILDLIFE SOC B 2019. [DOI: 10.1002/wsb.1021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Dana J. Morin
- Department of Wildlife, Fisheries and AquacultureMississippi State University Box 9680 Mississippi State MS 39762 USA
| | - Summer D. Higdon
- School of Natural ResourcesUniversity of Missouri 302 Anheuser‐Busch Natural Resources Building Columbia MO 65211 USA
| | - Robert C. Lonsinger
- Department of Natural Resource ManagementSouth Dakota State University 1390 College Avenue Brookings SD 57007 USA
| | - Elyce N. Gosselin
- College of Natural ResourcesUniversity of Idaho 875 Perimeter Drive Moscow ID 83844 USA
| | - Marcella J. Kelly
- Department of Fish and Wildlife Conservation 100 Cheatham Hall, Virginia Tech Blacksburg VA 24061 USA
| | - Lisette P. Waits
- College of Natural ResourcesUniversity of Idaho 875 Perimeter Drive Moscow ID 83844 USA
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18
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Monterroso P, Godinho R, Oliveira T, Ferreras P, Kelly MJ, Morin DJ, Waits LP, Alves PC, Mills LS. Feeding ecological knowledge: the underutilised power of faecal
DNA
approaches for carnivore diet analysis. Mamm Rev 2018. [DOI: 10.1111/mam.12144] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Pedro Monterroso
- CIBIO/InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto. Campus de Vairão R. Padre Armando Quintas Vairão 4485‐661 Portugal
| | - Raquel Godinho
- CIBIO/InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto. Campus de Vairão R. Padre Armando Quintas Vairão 4485‐661 Portugal
- Departamento de BiologiaFaculdade de CiênciasUniversidade do Porto R. Campo Alegre s/n Porto 4169‐007 Portugal
| | - Teresa Oliveira
- CIBIO/InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto. Campus de Vairão R. Padre Armando Quintas Vairão 4485‐661 Portugal
- Departamento de BiologiaFaculdade de CiênciasUniversidade do Porto R. Campo Alegre s/n Porto 4169‐007 Portugal
| | - Pablo Ferreras
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC‐UCLM‐JCCM) Ronda de Toledo 12 Ciudad Real 13071 Spain
| | - Marcella J. Kelly
- Department of Fish and Wildlife ConservationVirginia Tech 146 Cheatham Hall Blacksburg VA 24061‐0321 USA
| | - Dana J. Morin
- Cooperative Wildlife Research LaboratorySouthern Illinois University 251 Lincoln Drive Carbondale IL 62901 USA
| | - Lisette P. Waits
- Department of Fish and Wildlife SciencesUniversity of Idaho 875 Perimeter Drive MS 1136 Moscow ID 83844‐1136 USA
| | - Paulo C. Alves
- CIBIO/InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto. Campus de Vairão R. Padre Armando Quintas Vairão 4485‐661 Portugal
- Departamento de BiologiaFaculdade de CiênciasUniversidade do Porto R. Campo Alegre s/n Porto 4169‐007 Portugal
- Wildlife Biology ProgramUniversity of Montana 32 Campus Drive Missoula MT 59812 USA
| | - L. Scott Mills
- Wildlife Biology ProgramUniversity of Montana 32 Campus Drive Missoula MT 59812 USA
- Office of Research and Creative ScholarshipUniversity of Montana 32 Campus Drive Missoula MT 59812 USA
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19
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Alberdi A, Aizpurua O, Bohmann K, Gopalakrishnan S, Lynggaard C, Nielsen M, Gilbert MTP. Promises and pitfalls of using high‐throughput sequencing for diet analysis. Mol Ecol Resour 2018; 19:327-348. [DOI: 10.1111/1755-0998.12960] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 09/19/2018] [Accepted: 10/05/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Antton Alberdi
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Ostaizka Aizpurua
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Kristine Bohmann
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
- School of Biological Sciences University of East Anglia Norwich Norfolk UK
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Christina Lynggaard
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Martin Nielsen
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Marcus Thomas Pius Gilbert
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
- NTNU University Museum Trondheim Norway
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20
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Glen AS, Veltman CJ. Search strategies for conservation detection dogs. WILDLIFE BIOLOGY 2018. [DOI: 10.2981/wlb.00393] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Alistair S. Glen
- A. S. Glen , Manaaki Whenna— Landcare Research, Private Bag 92170, Auc
| | - Clare J. Veltman
- C. J. Veltman, Dept of Conservation, c/o Manaaki Whenua — Landcare Research, Palmerston North, New Z
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21
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Towards more efficient large-scale DNA-based detection of terrestrial mammal predators from scats. MAMMAL RES 2018. [DOI: 10.1007/s13364-018-0369-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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22
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Bastille-Rousseau G, Schaefer JA, Peers MJL, Ellington EH, Mumma MA, Rayl ND, Mahoney SP, Murray DL. Climate change can alter predator–prey dynamics and population viability of prey. Oecologia 2017; 186:141-150. [DOI: 10.1007/s00442-017-4017-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 11/16/2017] [Indexed: 10/18/2022]
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23
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Gosselin EN, Lonsinger RC, Waits LP. Comparing morphological and molecular diet analyses and fecal DNA sampling protocols for a terrestrial carnivore. WILDLIFE SOC B 2017. [DOI: 10.1002/wsb.749] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Elyce N. Gosselin
- Department of Fish and Wildlife Sciences; University of Idaho; Moscow ID 83844-1136 USA
| | - Robert C. Lonsinger
- College of Natural Resources, University of Wisconsin-Stevens Point, Stevens Point, WI 54482, USA; Department of Fish and Wildlife Sciences; University of Idaho; Moscow ID 83844-1136 USA
| | - Lisette P. Waits
- Department of Fish and Wildlife Sciences; University of Idaho; Moscow ID 83844-1136 USA
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