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Ma R, Ma S, Liu H, Hu L, Li Y, He K, Zhu Y. Seasonal changes in invertebrate diet of breeding black-necked cranes ( Grus nigricollis). Ecol Evol 2024; 14:e70234. [PMID: 39219571 PMCID: PMC11362503 DOI: 10.1002/ece3.70234] [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: 04/24/2024] [Revised: 08/06/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024] Open
Abstract
Invertebrates greatly support the growth, development, and reproduction of insectivorous birds. However, the influence of human activity (e.g., pesticide use, deforestation, and urbanization) inevitably leads to a decrease in global arthropods. The diversity and variation in invertebrate diet influence the food composition of birds, especially species living in rapidly changing environments, such as the Tibetan Plateau. However, little is known of the seasonal variation in invertebrate diet in response to environmental changes. Here, we characterized the invertebrate diet composition in pre- and post-breeding black-necked crane (Grus nigricollis) using fecal metabarcoding. We identified 38 invertebrate genera; the top three were Tipula (82.1% of relative abundance), Ceramica (3.0%), and unclassified_Hymenoptera (2.5%), with Tipula predominated the diet in both seasons. We also observed 20 and 16 unique genera in the pre- and post-breeding periods, and the genera composition was distinct between seasons (R = .036, p = .024). In pre-breeding, black-necked cranes tended to consume more diverse foods, and individual cranes exhibited greater heterogeneity at the genus level. At the genera and species level, pre-breeding black-necked cranes showed a wider dietary niche than post-breeding cranes. We observed season-specific features, with Tipula (common crane fly) and Stethophyma (grasshoppers) being enriched in the post-breeding period and Ceramica (moth) being more abundant in the pre-breeding period. Three Tipula species had the greatest importance in discriminating between seasonal diets. This study demonstrated a seasonal pattern of invertebrate diet in the black-necked crane, suggesting diet composition in response to resource and species availability. These results elaborate on the foraging ecology of highland birds and can inform the management of black-necked crane conservation.
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Affiliation(s)
- Ruifeng Ma
- College of Grassland Resources, Institute of Qinghai‐Tibetan Plateau, Sichuan Provincial Forest and Grassland Key Laboratory of Alpine Grassland Conservation and Utilization of Qinghai‐Tibetan PlateauSouthwest Minzu UniversityChengduSichuanChina
| | - Shujuan Ma
- College of Grassland Resources, Institute of Qinghai‐Tibetan Plateau, Sichuan Provincial Forest and Grassland Key Laboratory of Alpine Grassland Conservation and Utilization of Qinghai‐Tibetan PlateauSouthwest Minzu UniversityChengduSichuanChina
| | - Hongyi Liu
- The Co‐Innovation Center for Sustainable Forestry in Southern China, College of Life SciencesNanjing Forestry UniversityNanjingChina
| | - Lei Hu
- College of Grassland Resources, Institute of Qinghai‐Tibetan Plateau, Sichuan Provincial Forest and Grassland Key Laboratory of Alpine Grassland Conservation and Utilization of Qinghai‐Tibetan PlateauSouthwest Minzu UniversityChengduSichuanChina
| | - Yudong Li
- Sichuan Province Laboratory for Natural Resources Protection and Sustainable UtilizationSichuan Provincial Academy of Natural Resource SciencesChengduChina
| | - Ke He
- College of Animal Science and Technology, College of Veterinary MedicineZhejiang A&F UniversityHangzhouChina
| | - Ying Zhu
- College of Grassland Resources, Institute of Qinghai‐Tibetan Plateau, Sichuan Provincial Forest and Grassland Key Laboratory of Alpine Grassland Conservation and Utilization of Qinghai‐Tibetan PlateauSouthwest Minzu UniversityChengduSichuanChina
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Tobe A, Sato Y, Wachi N, Nakanishi N, Izawa M. Seasonal diet partition among top predators of a small island, Iriomote Island in the Ryukyu Archipelago, Japan. Sci Rep 2024; 14:7727. [PMID: 38565931 PMCID: PMC10987585 DOI: 10.1038/s41598-024-58204-6] [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: 01/29/2024] [Accepted: 03/26/2024] [Indexed: 04/04/2024] Open
Abstract
Small islands tend to lack predators because species at higher trophic levels often cannot survive. However, two exceptional top predators-the Iriomote cat Prionailurus bengalensis iriomotensis, and the Crested Serpent Eagle Spilornis cheela perplexus-live on the small Iriomote Island in the Ryukyu Archipelago. To understand how these predators coexist with limited resources, we focused on their seasonal diets between which conflicts are considered to occur. To compare the diets, we used DNA metabarcoding analysis of faecal samples. In the summer, we identified 16 unique prey items from Iriomote cat faecal samples and 15 unique prey items from Crested Serpent Eagle faecal samples. In the winter, we identified 37 and 14, respectively. Using a non-metric multidimensional scaling and a permutational multivariate analysis of variance, our study reveals significant differences in the diet composition at the order level between the predators during both seasons. Furthermore, although some prey items at the species-to-order level overlapped between them, the frequency of occurrence of most prey items differed in both seasons. These results suggest that this difference in diets is one of the reasons why the Iriomote cat and the Crested Serpent Eagle are able to coexist on such a small island.
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Affiliation(s)
- Alisa Tobe
- Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan.
- Wildlife Research Center, Kyoto University, Sakyo, Kyoto, Japan.
| | - Yukuto Sato
- Center for Strategic Research Project, Organization for Research Promotion, University of the Ryukyus, Nishihara, Okinawa, Japan
- Research Laboratory Center, Faculty of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Nakatada Wachi
- Center for Strategic Research Project, Organization for Research Promotion, University of the Ryukyus, Nishihara, Okinawa, Japan
- Iriomote Station, Tropical Biosphere Research Center, University of the Ryukyus, Taketomi, Okinawa, Japan
| | - Nozomi Nakanishi
- Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan
- Kitakyushu Museum of Natural History and Human History, Kitakyushu, Fukuoka, Japan
| | - Masako Izawa
- Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan.
- Kitakyushu Museum of Natural History and Human History, Kitakyushu, Fukuoka, Japan.
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3
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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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4
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Youngmann JL, Lance SL, Kilgo JC, Ruth C, Cantrell J, D’Angelo GJ. Assessing springtime vertebrate prey of sympatric mesopredators in the southeastern United States using metabarcoding analysis. PLoS One 2023; 18:e0293270. [PMID: 37878654 PMCID: PMC10599563 DOI: 10.1371/journal.pone.0293270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 10/01/2023] [Indexed: 10/27/2023] Open
Abstract
Coyotes (Canis latrans) colonized the eastern United States over the last century and formed a 3-species predator guild with bobcats (Lynx rufus) and gray foxes (Urocyon cinereoargenteus) across much of the southeastern United States. Diets among the three species vary along with respective impacts on game species such as white-tailed deer (Odocoileus virginianus) and wild turkeys (Meleagris gallopavo). To determine predation impacts on vertebrate prey and dietary overlap in consumption of prey items, we assessed diets of coyote, bobcat, and gray fox during spring, coinciding with white-tailed deer fawning and wild turkey nesting and brood rearing. We sampled across three sites along the Savannah River in South Carolina from mid-May through mid-June of 2020-2021. We collected 180 scat samples along 295.9 kilometers (71.1-122.4 km/site) of unpaved secondary roads and used DNA metabarcoding to determine vertebrate diet items. We identified predator species of scat using DNA metabarcoding and species-specific mtDNA fragment analysis (153 were coyote, 20 bobcat, and seven gray fox). Overall, we found evidence that two species, coyote and bobcat, consumed deer while all three consumed turkeys. Frequency of deer in the diet varied across sites for coyotes from 62-86% and wild turkey was present with a frequency of occurrence of 9% for coyotes, 5% for bobcats, and 14% for gray fox. Vertebrate diet specialization was evident across predator species with high frequency of deer in coyote diets, rabbits and small mammals in bobcat diets, and herpetofauna in gray fox diets. During deer fawning and wild turkey nesting and brood rearing, dietary overlap appears to be mediated by disparate selection of prey items, which reduced competition among coyotes, bobcats, and gray foxes. Use of DNA metabarcoding may augment our understanding of dietary preferences within this predator guild by providing increased resolution of diet composition among important game species.
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Affiliation(s)
- Jordan L. Youngmann
- Daniel B. Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
| | - Stacey L. Lance
- Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina, United States of America
| | - John C. Kilgo
- United States Department of Agriculture Forest Service, Southern Research Station, New Ellenton, South Carolina, United States of America
| | - Charles Ruth
- South Carolina Department of Natural Resources, Columbia, South Carolina, United States of America
| | - Jay Cantrell
- South Carolina Department of Natural Resources, Columbia, South Carolina, United States of America
| | - Gino J. D’Angelo
- Daniel B. Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
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5
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Mroue-Ruiz FH, Pacheco-Sandoval A, Lago-Lestón A, Giffard-Mena I, Abadía-Cardoso A, Chong-Robles J, Schramm Y. Metabarcoding Used for the First Time to Identify Prey of Wild Totoaba macdonaldi. Integr Comp Biol 2023; 63:276-287. [PMID: 37164934 DOI: 10.1093/icb/icad030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/01/2023] [Accepted: 05/04/2023] [Indexed: 05/12/2023] Open
Abstract
Totoaba macdonaldi is an endangered endemic fish of the Gulf of California. Overexploitation resulted in the Mexican government banning the fishing of this species in 1975, and it being listed as endangered. However, the species is still subject to illegal fishing. Despite its conservation status, little is known about totoaba biology. The present study aimed to implement, for the first time, a metabarcoding protocol to describe the totoaba diet. Four wild totoaba individuals, seized by Mexican law enforcement agents, were dissected, and their stomach contents were collected. Three representative amplicon libraries were generated for cephalopods, chordates, and eukaryotes. After sequencing, 18 different taxa were identified, of which 11 species were recognized as prey. The totoaba were found to have consumed Pacific anchovy (Cetengraulis mysticetus), flathead grey mullet (Mugil cephalus), bigeye croaker (Micropogonias megalops), northern anchovy (Engraulis mordax), ocean whitefish (Caulolatilus princeps), milkfish (Chanos chanos), and Pacific sardine (Sardinops sagax). Members of the Euphausiidae family (krill) were also identified. This study identified up to four times more species in much fewer samples than previous studies based on morphological recognition, thus confirming metabarcoding as an effective method for studying the feeding habits of this species and one providing the tools required for further analysis of the totoaba diet.
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Affiliation(s)
- F H Mroue-Ruiz
- Facultad de Ciencias, Universidad Autónoma de Baja California, 22860 Ensenada, Baja California, Mexico
| | - A Pacheco-Sandoval
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, 22860 Ensenada, Baja California, Mexico
- Posgrado en Ciencias de la Vida, Centro de Investigación Científica y de Educación Superior de Ensenada, 22860 Ensenada, Baja California, Mexico
| | - A Lago-Lestón
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, 22860 Ensenada, Baja California, Mexico
| | - I Giffard-Mena
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, 22860 Ensenada, Baja California, Mexico
| | - A Abadía-Cardoso
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, 22860 Ensenada, Baja California, Mexico
| | - J Chong-Robles
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, 22860 Ensenada, Baja California, Mexico
| | - Y Schramm
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, 22860 Ensenada, Baja California, Mexico
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6
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Esmaeili S, King SRB, Schoenecker KA. Browsers or Grazers? New Insights into Feral Burro Diet Using a Non-Invasive Sampling and Plant DNA Metabarcoding Approach. Animals (Basel) 2023; 13:2683. [PMID: 37627474 PMCID: PMC10451565 DOI: 10.3390/ani13162683] [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: 05/18/2023] [Revised: 07/14/2023] [Accepted: 07/17/2023] [Indexed: 08/27/2023] Open
Abstract
Ungulates play a large role in shaping ecosystems and communities by influencing plant composition, structure, and productivity. We investigated the summer diets of feral burros in two ecosystems in which they are found in the United States: a subtropical desert in Arizona and a temperate juniper shrubland in Utah. Between 24 June and 16 July of 2019, we gathered 50 burro fecal samples from each location and used plant DNA metabarcoding to determine the burros' diets. We found that during our sampling period the burros in the Sonoran Desert consumed a higher proportion of woody browse and had a narrower dietary niche breadth and lower degree of diet diversity compared to the burros in the juniper shrubland ecosystem, where the burros consumed higher proportions of graminoids and forbs and had a higher diet diversity index and broader dietary niche breadth. The burros in the Sonoran Desert relied primarily on Prosopis spp. (mesquite) and Poaceae grasses, whereas the burros in the juniper shrubland relied on a wider variety of forb and grass species, likely due to the greater variability in the forage species temporally and spatially available in that temperate ecosystem. We found that feral burros are highly adaptable with respect to diet and appear to be employing a mixed feeding strategy, similar to their ancestor, the African wild ass, to meet their nutritional needs in whichever ecosystem they are found.
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Affiliation(s)
- Saeideh Esmaeili
- Natural Resource Ecology Laboratory, Colorado State University, and in Cooperation with USGS Fort Collins Science Center, Fort Collins, CO 80523, USA;
| | - Sarah R. B. King
- Natural Resource Ecology Laboratory, Colorado State University, and in Cooperation with USGS Fort Collins Science Center, Fort Collins, CO 80523, USA;
| | - Kathryn A. Schoenecker
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, CO 80526, USA;
- Ecosystem Science and Sustainability, Colorado State University, Fort Collins, CO 80523, USA
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7
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Navarro-Castilla Á, Hernández MC, Barja I. An Experimental Study in Wild Wood Mice Testing Elemental and Isotope Analysis in Faeces to Determine Variations in Food Intake Amount. Animals (Basel) 2023; 13:ani13071176. [PMID: 37048432 PMCID: PMC10093285 DOI: 10.3390/ani13071176] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/16/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
The analysis of carbon and nitrogen elemental (C, N) and isotopic compositions (δ13C, δ15N) in faeces are considered reliable methodologies for the study of diet in wildlife. Here, we tested the suitability of these techniques to detect variations in the amount of food intake. We captured wild wood mice (Apodemus sylvaticus) with Sherman live traps where bait access was initially free, and later it was experimentally limited inside by four different devices to cause intended variations in the amount ingested. The total C and N (%) and stable δ13C and δ15N isotopic values were determined for the bait and in mice faecal samples. Faecal values were lower than bait ones except for N, likely due to animal matter ingested before capture. No significant differences in total C, N and δ13C were found due to individual traits. However, breeding males showed higher δ15N values than breeding females, probably due to differences in energy and protein demands between both sexes during the breeding season. Only δ13C detected food intake variations (≥2 g). Despite further research being needed, these results initially support the potential of δ13C to provide information on the amount ingested, thus being useful to complement trophic ecology studies.
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Affiliation(s)
- Álvaro Navarro-Castilla
- Eco- and Ethophysiology Lab, Departamento de Biología, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, C. Darwin 2, 28049 Madrid, Spain
- Correspondence:
| | - M. Carmen Hernández
- Eco- and Ethophysiology Lab, Departamento de Biología, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Isabel Barja
- Eco- and Ethophysiology Lab, Departamento de Biología, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, C. Darwin 2, 28049 Madrid, Spain
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Abstract
Food webs are indispensable maps of community organization, but most are crudely drawn - an inconvenient truth that ecologists must confront. A new DNA metabarcoding study quantifies predator-prey interactions and ecological-network structure with long-overdue precision, supplying insight into how large and small carnivores coexist.
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Affiliation(s)
- Erin M Phillips
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Robert M Pringle
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.
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9
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Tosa MI, Lesmeister DB, Allen JM, Levi T. Multi‐locus
DNA
metabarcoding reveals seasonality of foraging ecology of western spotted skunks in the Pacific Northwest. Ecosphere 2023. [DOI: 10.1002/ecs2.4386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Marie I. Tosa
- Department of Fisheries, Wildlife, and Conservation Sciences Oregon State University Corvallis Oregon USA
| | - Damon B. Lesmeister
- Department of Fisheries, Wildlife, and Conservation Sciences Oregon State University Corvallis Oregon USA
- Pacific Northwest Research Station U.S. Department of Agriculture Forest Service Corvallis Oregon USA
| | - Jennifer M. Allen
- Department of Fisheries, Wildlife, and Conservation Sciences Oregon State University Corvallis Oregon USA
| | - Taal Levi
- Department of Fisheries, Wildlife, and Conservation Sciences Oregon State University Corvallis Oregon USA
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10
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Wanniarachchi S, Swan M, Nevil P, York A. Using eDNA metabarcoding to understand the effect of fire on the diet of small mammals in a woodland ecosystem. Ecol Evol 2022; 12:e9457. [PMID: 36381390 PMCID: PMC9643072 DOI: 10.1002/ece3.9457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/30/2022] [Accepted: 10/05/2022] [Indexed: 11/11/2022] Open
Abstract
Food acquisition is a fundamental process that drives animal distribution and abundance, influencing how species respond to changing environments. Disturbances such as fire create significant shifts in available dietary resources, yet, for many species, we lack basic information about what they eat, let alone how they respond to a changing resource base. In order to create effective management strategies, faunal conservation in flammable landscapes requires a greater understanding of what animals eat and how this change following a fire. What animals eat in postfire environments has received little attention due to the time-consuming methodologies and low-resolution identification of food taxa. Recently, molecular techniques have been developed to identify food DNA in scats, making it possible to identify animal diets with enhanced resolution. The primary aim of this study was to utilize eDNA metabarcoding to obtain an improved understanding of the diet of three native Australian small mammal species: yellow-footed antechinus (Antechinus flavipes), heath mouse (Pseudomys shortridgei), and bush rat (Rattus fuscipes). Specifically, we sought to understand the difference in the overall diet of the three species and how diet changed over time after fire. Yellow-footed antechinus diets mostly consisted of moths, and plants belonging to myrtles and legume families while bush rats consumed legumes, myrtles, rushes, and beetles. Heath mouse diet was dominated by rushes. All three species shifted their diets over time after fire, with most pronounced shifts in the bush rats and least for heath mice. Identifying critical food resources for native animals will allow conservation managers to consider the effect of fire management actions on these resources and help conserve the species that use them.
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Affiliation(s)
- Saumya Wanniarachchi
- School of Ecosystem and Forest SciencesThe University of MelbourneCreswickVictoriaAustralia
| | - Matthew Swan
- School of Ecosystem and Forest SciencesThe University of MelbourneCreswickVictoriaAustralia
| | - Paul Nevil
- Trace and Environmental DNA Laboratory, School of Life and Molecular SciencesCurtin UniversityPerthWestern AustraliaAustralia
| | - Alan York
- School of Ecosystem and Forest SciencesThe University of MelbourneCreswickVictoriaAustralia
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11
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A Nearctic cat in the Neotropics: spatial biases in the existing knowledge of bobcats in Mexico (1988–2019). EUR J WILDLIFE RES 2022. [DOI: 10.1007/s10344-022-01614-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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Fleming PA, Stobo-Wilson AM, Crawford HM, Dawson SJ, Dickman CR, Doherty TS, Fleming PJS, Newsome TM, Palmer R, Thompson JA, Woinarski JCZ. Distinctive diets of eutherian predators in Australia. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220792. [PMID: 36312571 PMCID: PMC9554524 DOI: 10.1098/rsos.220792] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/16/2022] [Indexed: 06/01/2023]
Abstract
Introduction of the domestic cat and red fox has devastated Australian native fauna. We synthesized Australian diet analyses to identify traits of prey species in cat, fox and dingo diets, which prey were more frequent or distinctive to the diet of each predator, and quantified dietary overlap. Nearly half (45%) of all Australian terrestrial mammal, bird and reptile species occurred in the diets of one or more predators. Cat and dingo diets overlapped least (0.64 ± 0.27, n = 24 location/time points) and cat diet changed little over 55 years of study. Cats were more likely to have eaten birds, reptiles and small mammals than foxes or dingoes. Dingo diet remained constant over 53 years and constituted the largest mammal, bird and reptile prey species, including more macropods/potoroids, wombats, monotremes and bandicoots/bilbies than cats or foxes. Fox diet had greater overlap with both cats (0.79 ± 0.20, n = 37) and dingoes (0.73 ± 0.21, n = 42), fewer distinctive items (plant material, possums/gliders) and significant spatial and temporal heterogeneity over 69 years, suggesting the opportunity for prey switching (especially of mammal prey) to mitigate competition. Our study reinforced concerns about mesopredator impacts upon scarce/threatened species and the need to control foxes and cats for fauna conservation. However, extensive dietary overlap and opportunism, as well as low incidence of mesopredators in dingo diets, precluded resolution of the debate about possible dingo suppression of foxes and cats.
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Affiliation(s)
- Patricia A. Fleming
- Centre for Terrestrial Ecosystem Science and Sustainability, Harry Butler Institute, Murdoch University, 90 South Street, Murdoch, Western Australia 6150, Australia
| | - Alyson M. Stobo-Wilson
- NESP Threatened Species Recovery Hub, Charles Darwin University, Casuarina, Northern Territory 0909, Australia
- CSIRO Land and Water, PMB 44, Winnellie, Northern Territory 0822, Australia
| | - Heather M. Crawford
- Centre for Terrestrial Ecosystem Science and Sustainability, Harry Butler Institute, Murdoch University, 90 South Street, Murdoch, Western Australia 6150, Australia
| | - Stuart J. Dawson
- Centre for Terrestrial Ecosystem Science and Sustainability, Harry Butler Institute, Murdoch University, 90 South Street, Murdoch, Western Australia 6150, Australia
- Department of Primary Industries and Regional Development, 3 Baron-Hay Court, South Perth, Western Australia 6151, Australia
| | - Chris R. Dickman
- Desert Ecology Research Group, School of Life and Environmental Sciences, The University of Sydney, Heydon-Laurence Building A08, Camperdown, New South Wales 2006, Australia
| | - Tim S. Doherty
- School of Life and Environmental Sciences, The University of Sydney, Heydon-Laurence Building A08, Camperdown, New South Wales 2006, Australia
| | - Peter J. S. Fleming
- Vertebrate Pest Research Unit, NSW Department of Primary Industries, Orange Agricultural Institute, 1447 Forest Road, Orange, New South Wales 2800, Australia
- Ecosystem Management, School of Environmental and Rural Science, University of New England, Armidale, New South Wales 2351, Australia
- Institute for Agriculture and the Environment, Centre for Sustainable Agricultural Systems, University of Southern Queensland, Toowoomba, Queensland 4350, Australia.
| | - Thomas M. Newsome
- School of Life and Environmental Sciences, The University of Sydney, Heydon-Laurence Building A08, Camperdown, New South Wales 2006, Australia
| | - Russell Palmer
- Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Western Australia 6983, Australia
| | - Jim A. Thompson
- Queensland Museum Network, PO Box 3300, South Brisbane BC, Queensland 4101, Australia
| | - John C. Z. Woinarski
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Casuarina, Northern Territory 0909, Australia
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13
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Feeding ecology of the endangered Asiatic wild dogs (Cuon alpinus) across tropical forests of the Central Indian Landscape. Sci Rep 2022; 12:14029. [PMID: 35982090 PMCID: PMC9388674 DOI: 10.1038/s41598-022-17906-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 08/02/2022] [Indexed: 11/21/2022] Open
Abstract
Studies on resource utilisation by carnivores are essential as they aid in assessing their role in a community, by unravelling predator–prey relationships. Globally, prey depletion is one of the primary causes of declining Asiatic wild dog (dhole) populations. Therefore, it is essential to examine their diet across their range. Our study presents insights into dhole feeding ecology across multiple sites from the central Indian landscape of Maharashtra, India, for the first time. We conducted scat analysis using a subset of genetically identified scats and collected additional data from kills observed while tracking radio-collared dholes and other known packs from 2 study sites. We analysed 861 scats, and 191 dhole kills to identify species and age class of prey. We estimated the relative contribution of various prey, utilising non-linear biomass models of prey consumption. Overall, wild ungulates like sambar and chital were the principal prey in terms of biomass (sambar 61.08%; chital 19.08%) and number of prey consumed (sambar 39.28%; chital 13.83%). An analysis of kill data also suggested that dholes strongly preferred the two deer species; and differential selection of age classes was observed at the 2 study sites. Our study can potentially help manage and conserve this important population of an endangered carnivore.
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14
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Wang Q, Wang Z, Zheng K, Zhang P, Shen L, Chen W, Fan P, Zhang L. Assessing the Diet of a Predator Using a DNA Metabarcoding Approach. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.902412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The diet of top predators is vital information needed to determine their ecological function and for their conservation management. However, the elusive habit and low population density of many predators constrains determination of their diets. While the morphological identification of scat contents is the traditional method, DNA metabarcoding has lately proven a more efficient and accurate method of identifying prey taxa. We applied DNA metabarcoding to analyzing the diet of the Eurasian otter (Lutra lutra), a top predator in freshwater ecosystems, using 12S and 16S rRNA mitochondrial primers target vertebrate prey. Diet did not vary among different data removal thresholds of 0.1, 1, 3, and 5%, comprising fishes (>90%), amphibians and birds (>2%), and occasionally mammals (<2%). Both 12S and 16S primers revealed similar otter diets, indicating that a single set of primers with a higher threshold is cost-effective for detecting the main prey taxa. Using 12S primers and a 5% threshold, we found no seasonal variation of otter diet in the Tangjiahe National Nature Reserve. A different prey community was found outside the reserve, which resulted in different prey composition for otters. However, prey taxon richness was not different between otters in- and outside the reserve. Otters preferred Schizothorax spp., the largest-sized fish species in the reserve, whereas they mainly preyed on Triplophysa bleekeri, a small-sized fish species, outside the reserve. Otters’ flexible feeding strategy reflect their high adaptability. However, greater human disturbance outside the reserve may present significant challenges to otters by altering prey communities and reducing prey profitability. Combining fecal DNA metabarcoding and local fish survey will provide opportunities for more detailed studies on the impact of different levels of human disturbances on prey communities and otters.
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15
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Assessing Asiatic cheetah’s individual diet using metabarcoding and its implication for conservation. Sci Rep 2022; 12:11403. [PMID: 35794196 PMCID: PMC9259742 DOI: 10.1038/s41598-022-15065-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 05/09/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractKnowledge on diet composition allows defining well-targeted conservation measures of large carnivores. Little is known about ecology of critically endangered Asiatic cheetah, especially the overall diet and its possible regional differences. We used cheetah scats, metabarcoding technique and microsatellite markers to assess the individual and overall diet composition of the species across its entire range in Asia. Cheetahs were primarily predating on mouflon; following by ibex, cape hare and goitered gazelle. Despite their high availability, small-sized livestock was never detected. Goitered gazelles were only detected in an area where the habitat is mainly flatlands. In hilly areas, mouflon was the most frequent prey item taken. Ibex was typically taken in rugged terrain, but mouflon was still the most frequently consumed item in these habitats. High consumption of mouflon in comparison to goitered gazelle suggests that human pressure on lowland habitats has possibly forced Asiatic cheetahs to occupy suboptimal habitats where gazelles are less abundant. The protection of flatlands and the removal of livestock from them are needed to ensure the long-term survival of Asiatic cheetah. The laboratory and bioinformatics pipelines used in this study are replicable and can be used to address similar questions in other threatened carnivores.
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16
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Schilling AK, Mazzamuto MV, Romeo C. A Review of Non-Invasive Sampling in Wildlife Disease and Health Research: What's New? Animals (Basel) 2022; 12:1719. [PMID: 35804619 PMCID: PMC9265025 DOI: 10.3390/ani12131719] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 12/14/2022] Open
Abstract
In the last decades, wildlife diseases and the health status of animal populations have gained increasing attention from the scientific community as part of a One Health framework. Furthermore, the need for non-invasive sampling methods with a minimal impact on wildlife has become paramount in complying with modern ethical standards and regulations, and to collect high-quality and unbiased data. We analysed the publication trends on non-invasive sampling in wildlife health and disease research and offer a comprehensive review on the different samples that can be collected non-invasively. We retrieved 272 articles spanning from 1998 to 2021, with a rapid increase in number from 2010. Thirty-nine percent of the papers were focussed on diseases, 58% on other health-related topics, and 3% on both. Stress and other physiological parameters were the most addressed research topics, followed by viruses, helminths, and bacterial infections. Terrestrial mammals accounted for 75% of all publications, and faeces were the most widely used sample. Our review of the sampling materials and collection methods highlights that, although the use of some types of samples for specific applications is now consolidated, others are perhaps still underutilised and new technologies may offer future opportunities for an even wider use of non-invasively collected samples.
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Affiliation(s)
- Anna-Katarina Schilling
- Previously Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK;
| | - Maria Vittoria Mazzamuto
- Haub School of Environment and Natural Resources, University of Wyoming, 1000 E. University Ave., Laramie, WY 82072, USA;
- Department of Theoretical and Applied Sciences, University of Insubria, Via J.H. Dunant 3, 21100 Varese, Italy
| | - Claudia Romeo
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), Via Bianchi 9, 25124 Brescia, Italy
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17
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Karandikar H, Serota MW, Sherman WC, Green JR, Verta G, Kremen C, Middleton AD. Dietary patterns of a versatile large carnivore, the puma ( Puma concolor). Ecol Evol 2022; 12:e9002. [PMID: 35784054 PMCID: PMC9240727 DOI: 10.1002/ece3.9002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 11/11/2022] Open
Abstract
Large carnivores play critical roles in terrestrial ecosystems but have suffered dramatic range contractions over the past two centuries. Developing an accurate understanding of large carnivore diets is an important first step towards an improved understanding of their ecological roles and addressing the conservation challenges faced by these species.The puma is one of seven large felid species in the world and the only one native to the non-tropical regions of the New World. We conducted a meta-analysis of puma diets across the species' range in the Americas and assessed the impact of varying environmental conditions, niche roles, and human activity on puma diets. Pumas displayed remarkable dietary flexibility, consuming at least 232 different prey species, including one Critically Endangered and five Endangered species.Our meta-analysis found clear patterns in puma diets with changing habitat and environmental conditions. Pumas consumed more larger-bodied prey species with increasing distance from the equator, but consumption of medium-sized species showed the opposite trend.Puma diets varied with their realized niche; however, contrary to our expectations, puma consumption of large species did not change with their trophic position, and pumas consumed more small prey and birds as apex predators. Consumption of domestic species was negatively correlated with consumption of medium-sized wild species, a finding which underscores the importance of maintaining intact native prey assemblages.The tremendous dietary flexibility displayed by pumas represents both an opportunity and a challenge for understanding the puma's role in ecosystems and for the species' management and conservation. Future studies should explore the linkages between availability and selection of primary and other wild prey, and consequent impacts on predation of domestic species, in order to guide conservation actions and reduce conflict between pumas and people.
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Affiliation(s)
- Harshad Karandikar
- Department of Environmental Science, Policy & ManagementMulford HallUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Mitchell W. Serota
- Department of Environmental Science, Policy & ManagementMulford HallUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Wilson C. Sherman
- Department of Environmental Science, Policy & ManagementMulford HallUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Jennifer R. Green
- Department of Environmental Science, Policy & ManagementMulford HallUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Guadalupe Verta
- Department of Environmental Science, Policy & ManagementMulford HallUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Claire Kremen
- Department of Environmental Science, Policy & ManagementMulford HallUniversity of CaliforniaBerkeleyCaliforniaUSA
- Institute for Resources, Environment and SustainabilityUniversity of British ColumbiaVancouverBritish ColumbiaCanada
- Department of ZoologyBiodiversity Research CentreUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Arthur D. Middleton
- Department of Environmental Science, Policy & ManagementMulford HallUniversity of CaliforniaBerkeleyCaliforniaUSA
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18
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Cristescu B, Elbroch LM, Forrester TD, Allen ML, Spitz DB, Wilmers CC, Wittmer HU. Standardizing protocols for determining the cause of mortality in wildlife studies. Ecol Evol 2022; 12:e9034. [PMID: 35784072 PMCID: PMC9219102 DOI: 10.1002/ece3.9034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 04/15/2022] [Accepted: 05/26/2022] [Indexed: 12/05/2022] Open
Abstract
Mortality site investigations of telemetered wildlife are important for cause-specific survival analyses and understanding underlying causes of observed population dynamics. Yet, eroding ecoliteracy and a lack of quality control in data collection can lead researchers to make incorrect conclusions, which may negatively impact management decisions for wildlife populations. We reviewed a random sample of 50 peer-reviewed studies published between 2000 and 2019 on survival and cause-specific mortality of ungulates monitored with telemetry devices. This concise review revealed extensive variation in reporting of field procedures, with many studies omitting critical information for the cause of mortality inference. Field protocols used to investigate mortality sites and ascertain the cause of mortality are often minimally described and frequently fail to address how investigators dealt with uncertainty. We outline a step-by-step procedure for mortality site investigations of telemetered ungulates, including evidence that should be documented in the field. Specifically, we highlight data that can be useful to differentiate predation from scavenging and more conclusively identify the predator species that killed the ungulate. We also outline how uncertainty in identifying the cause of mortality could be acknowledged and reported. We demonstrate the importance of rigorous protocols and prompt site investigations using data from our 5-year study on survival and cause-specific mortality of telemetered mule deer (Odocoileus hemionus) in northern California. Over the course of our study, we visited mortality sites of neonates (n = 91) and adults (n = 23) to ascertain the cause of mortality. Rapid site visitations significantly improved the successful identification of the cause of mortality and confidence levels for neonates. We discuss the need for rigorous and standardized protocols that include measures of confidence for mortality site investigations. We invite reviewers and journal editors to encourage authors to provide supportive information associated with the identification of causes of mortality, including uncertainty.
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Affiliation(s)
- Bogdan Cristescu
- Environmental Studies DepartmentUniversity of CaliforniaSanta CruzCaliforniaUSA
| | | | - Tavis D. Forrester
- Oregon Department of Fish and WildlifeWildlife ResearchLa GrandeOregonUSA
| | | | - Derek B. Spitz
- Environmental Studies DepartmentUniversity of CaliforniaSanta CruzCaliforniaUSA
| | | | - Heiko U. Wittmer
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
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19
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Jensen AJ, Marneweck CJ, Kilgo JC, Jachowski DS. Coyote diet in North America: geographic and ecological patterns during range expansion. Mamm Rev 2022. [DOI: 10.1111/mam.12299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Alex J. Jensen
- Department of Forestry and Environmental Conservation Clemson University Clemson South Carolina 29631 USA
| | - Courtney J. Marneweck
- Department of Forestry and Environmental Conservation Clemson University Clemson South Carolina 29631 USA
| | - John C. Kilgo
- USDA Forest Service, Southern Research Station New Ellenton South Carolina 29809 USA
| | - David S. Jachowski
- Department of Forestry and Environmental Conservation Clemson University Clemson South Carolina 29631 USA
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20
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Lingle S, Breiter C, Schowalter DB, Wilmshurst JF. Prairie dogs, cattle subsidies and alternative prey: seasonal and spatial variation in coyote diet in a temperate grassland. WILDLIFE BIOLOGY 2022. [DOI: 10.1002/wlb3.01048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Susan Lingle
- Dept of Biology, Univ. of Winnipeg Winnipeg MB Canada
| | - C‐Jae Breiter
- Research and Conservation Dept, Assiniboine Park Zoo Winnipeg MB Canada
| | | | - John F. Wilmshurst
- Dept of Geography and Planning, Univ. of Saskatchewan Saskatoon SK Canada
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21
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McLennan EA, Wise P, Lee AV, Grueber CE, Belov K, Hogg CJ. DNA metabarcoding reveals a broad dietary range for Tasmanian devils introduced to a naive ecosystem. Ecol Evol 2022; 12:e8936. [PMID: 35600680 PMCID: PMC9120209 DOI: 10.1002/ece3.8936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 11/08/2022] Open
Abstract
Top carnivores are essential for maintaining ecosystem stability and biodiversity. Yet, carnivores are declining globally and current in situ threat mitigations cannot halt population declines. As such, translocations of carnivores to historic sites or those outside the species' native range are becoming increasingly common. As carnivores are likely to impact herbivore and small predator populations, understanding how carnivores interact within an ecosystem following translocation is necessary to inform potential remedial management and future translocations. Dietary analyses provide a preliminary assessment of the direct influence of translocated carnivores on a recipient ecosystem. We used a metabarcoding approach to quantify the diet of Tasmanian devils introduced to Maria Island, Tasmania, a site outside the species' native range. We extracted DNA from 96 scats and used a universal primer set targeting the vertebrate 12S rRNA gene to identify diet items. Tasmanian devils on Maria Island had an eclectic diet, with 63 consumed taxa identified. Cat DNA was detected in 14% of scats, providing the first instance of cats appearing as part of Tasmanian devil diets either via predation or scavenging. Short-tail shearwaters and little penguins were commonly consumed, corresponding with previous surveys showing sharp population declines in these species since the introduction of Tasmanian devils. Our results indicate that the introduction of carnivores to novel ecosystems can be very successful for the focal species, but that commonly consumed species should be closely monitored to identify any vulnerable species in need of remedial management.
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Affiliation(s)
- Elspeth A. McLennan
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
| | - Phil Wise
- Save the Tasmanian Devil ProgramNREHobartTasmaniaAustralia
| | - Andrew V. Lee
- Save the Tasmanian Devil ProgramNREHobartTasmaniaAustralia
| | - Catherine E. Grueber
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
| | - Katherine Belov
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
| | - Carolyn J. Hogg
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
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22
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Parker LD, Quinta JD, Rivera I, Cypher BL, Kelly EC, Campana MG, Fleischer RC, Boarman R, Boarman WI, Maldonado JE. Genetic analyses are more sensitive than morphological inspection at detecting the presence of threatened Mojave desert tortoise (
Gopherus agassizii
) remains in canid scat and raven pellets. CONSERVATION SCIENCE AND PRACTICE 2022. [DOI: 10.1111/csp2.12689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Lillian D. Parker
- Center for Conservation Genomics Smithsonian Conservation Biology Institute and National Zoological Park Washington District of Columbia USA
- School of Systems Biology George Mason University Virginia USA
| | - Jessica D. Quinta
- Center for Conservation Genomics Smithsonian Conservation Biology Institute and National Zoological Park Washington District of Columbia USA
| | - Isabel Rivera
- Center for Conservation Genomics Smithsonian Conservation Biology Institute and National Zoological Park Washington District of Columbia USA
| | - Brian L. Cypher
- Endangered Species Recovery Program California State University Stanislaus Turlock California USA
| | - Erica C. Kelly
- Endangered Species Recovery Program California State University Stanislaus Turlock California USA
| | - Michael G. Campana
- Center for Conservation Genomics Smithsonian Conservation Biology Institute and National Zoological Park Washington District of Columbia USA
- School of Systems Biology George Mason University Virginia USA
- Department of Environmental Science and Policy George Mason University Virginia USA
| | - Robert C. Fleischer
- Center for Conservation Genomics Smithsonian Conservation Biology Institute and National Zoological Park Washington District of Columbia USA
| | - Ryan Boarman
- Conservation Science Research and Consultation Spring Valley California USA
| | - William I. Boarman
- Conservation Science Research and Consultation Spring Valley California USA
| | - Jesús E. Maldonado
- Center for Conservation Genomics Smithsonian Conservation Biology Institute and National Zoological Park Washington District of Columbia USA
- School of Systems Biology George Mason University Virginia USA
- Department of Environmental Science and Policy George Mason University Virginia USA
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23
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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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24
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Mutoro NM, Chira R, Gichuki N, Kariuki E, Eberle J, Habel JC, Wykstra M. Dietary preference of cheetahs ( Acinonyx jubatus) in south-eastern Kenya. Ecol Evol 2022; 12:e8556. [PMID: 35342561 PMCID: PMC8932225 DOI: 10.1002/ece3.8556] [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: 03/19/2021] [Revised: 09/22/2021] [Accepted: 09/30/2021] [Indexed: 11/11/2022] Open
Abstract
The conversion of natural ecosystems due to anthropogenic activities has led to the destruction of natural habitats and to the deterioration of habitat quality. Top predators particularly respond sensitively to changes in habitat structures, including the availability of prey. The cheetah Acinonyx jubatus prefers small-medium-sized, wild ungulate prey due to the cheetah's morphological adaptations. However, the majority of the species' population is found beyond protected areas, where habitat structures, species abundances, and community composition are highly influenced by human activities. Only few studies have analyzed the diet preference of cheetahs in relation to prey availability and abundance for rangelands beyond protected areas in Eastern Africa. The study aimed to determine cheetah prey preference in the rangelands of south-eastern Kenya based on scat analyses. We compared dietary preference of cheetah with prey availability. For this purpose, we conducted standardized game counts. We analyzed 27 cheetah scat samples collected across the same study area where we also conducted game counts. We found that Grant's gazelle Gazella granti contributed the highest portion of cheetah's diet, although Thomson's gazelle Gazella thomsonii was the most abundant medium-sized ungulate prey in the study areas. We also recorded two primate species, yellow baboon Papio cynocephalus and vervet monkey Chlorocebus pygerythrus, as well as the rock hyrax Procavia capensis in the cheetah diet. These species have never been documented as cheetah prey before. Furthermore, our results document livestock as potential prey for cheetahs. These observations underline that cheetah use diverse prey in rangelands outside protected areas, and that the abundance of specific prey does not influence cheetah prey preference.
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Affiliation(s)
- Noreen M Mutoro
- Evolutionary Zoology Department of Environment and Biodiversity University of Salzburg Salzburg Austria
- School of Biological Sciences University of Nairobi Nairobi Kenya
- Action for Cheetahs in Kenya Nairobi Kenya
| | - Robert Chira
- School of Biological Sciences University of Nairobi Nairobi Kenya
| | - Nathan Gichuki
- School of Biological Sciences University of Nairobi Nairobi Kenya
| | | | - Jonas Eberle
- Evolutionary Zoology Department of Environment and Biodiversity University of Salzburg Salzburg Austria
| | - Jan Christian Habel
- Evolutionary Zoology Department of Environment and Biodiversity University of Salzburg Salzburg Austria
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25
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Mitchell G, Wilson PJ, Manseau M, Redquest B, Patterson BR, Rutledge LY. DNA metabarcoding of faecal pellets reveals high consumption of yew ( Taxus spp.) by caribou ( Rangifer tarandus) in a lichen-poor environment. Facets (Ott) 2022. [DOI: 10.1139/facets-2021-0071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Woodland caribou ( Rangifer tarandus caribou) are threatened in Canada because of the drastic decline in population size caused primarily by human-induced landscape changes that decrease habitat and increase predation risk. Conservation efforts have largely focused on reducing predators and protecting critical habitat, whereas research on dietary niches and the role of potential food constraints in lichen-poor environments is limited. To improve our understanding of dietary niche variability, we used a next-generation sequencing approach with metabarcoding of DNA extracted from faecal pellets of woodland caribou located on Lake Superior in lichen-rich (mainland) and lichen-poor (island) environments. Amplicon sequencing of fungal ITS2 region revealed lichen-associated fungi as predominant in samples from both populations, but amplification at the chloroplast trnL region, which was only successful on island samples, revealed primary consumption of yew ( Taxus spp.) based on relative read abundance (83.68%) with dogwood ( Cornus spp.; 9.67%) and maple ( Acer spp.; 4.10%) also prevalent. These results suggest that conservation efforts for caribou need to consider the availability of food resources beyond lichen to ensure successful outcomes. More broadly, we provide a reliable methodology for assessing ungulate diet from archived faecal pellets that could reveal important dietary shifts over time in response to climate change.
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Affiliation(s)
- Greniqueca Mitchell
- Biology Department, Trent University, Life and Health Sciences Building, 2089 East Bank Drive, Peterborough, ON K9L 1Z8, Canada
| | - Paul J. Wilson
- Biology Department, Trent University, Life and Health Sciences Building, 2089 East Bank Drive, Peterborough, ON K9L 1Z8, Canada
| | - Micheline Manseau
- Biology Department, Trent University, Life and Health Sciences Building, 2089 East Bank Drive, Peterborough, ON K9L 1Z8, Canada
- Landscape Science and Technology Division, Environment and Climate Change Canada, 1125 Colonel By Drive, Ottawa, ON K1S 5R1, Canada
| | - Bridgett Redquest
- Biology Department, Trent University, Life and Health Sciences Building, 2089 East Bank Drive, Peterborough, ON K9L 1Z8, Canada
| | - Brent R. Patterson
- Ontario Ministry of Natural Resources and Forestry, Trent University, DNA Building, Peterborough, ON K9L 1Z8, Canada
| | - Linda Y. Rutledge
- Biology Department, Trent University, Life and Health Sciences Building, 2089 East Bank Drive, Peterborough, ON K9L 1Z8, Canada
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26
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OUP accepted manuscript. J Mammal 2022. [DOI: 10.1093/jmammal/gyac003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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27
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Schultz AJ, Strickland K, Cristescu RH, Hanger J, de Villiers D, Frère CH. Testing the effectiveness of genetic monitoring using genetic non-invasive sampling. Ecol Evol 2022; 12:e8459. [PMID: 35127011 PMCID: PMC8794716 DOI: 10.1002/ece3.8459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 10/26/2021] [Accepted: 11/26/2021] [Indexed: 01/07/2023] Open
Abstract
Effective conservation requires accurate data on population genetic diversity, inbreeding, and genetic structure. Increasingly, scientists are adopting genetic non-invasive sampling (gNIS) as a cost-effective population-wide genetic monitoring approach. gNIS has, however, known limitations which may impact the accuracy of downstream genetic analyses. Here, using high-quality single nucleotide polymorphism (SNP) data from blood/tissue sampling of a free-ranging koala population (n = 430), we investigated how the reduced SNP panel size and call rate typical of genetic non-invasive samples (derived from experimental and field trials) impacts the accuracy of genetic measures, and also the effect of sampling intensity on these measures. We found that gNIS at small sample sizes (14% of population) can provide accurate population diversity measures, but slightly underestimated population inbreeding coefficients. Accurate measures of internal relatedness required at least 33% of the population to be sampled. Accurate geographic and genetic spatial autocorrelation analysis requires between 28% and 51% of the population to be sampled. We show that gNIS at low sample sizes can provide a powerful tool to aid conservation decision-making and provide recommendations for researchers looking to apply these techniques to free-ranging systems.
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Affiliation(s)
- Anthony James Schultz
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQldAustralia
- Icelandic Museum of Natural History (Náttúruminjasafn Íslands)ReykjavikIceland
| | - Kasha Strickland
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQldAustralia
- Department of Aquaculture and Fish BiologyHólar UniversityHólarIceland
| | - Romane H. Cristescu
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQldAustralia
| | | | | | - Céline H. Frère
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQldAustralia
- School of Biological SciencesUniversity of QueenslandSt LuciaQldAustralia
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Lu Q, Xiao L, Cheng C, Lu Z, Zhao J, Yao M. Snow Leopard Dietary Preferences and Livestock Predation Revealed by Fecal DNA Metabarcoding: No Evidence for Apparent Competition Between Wild and Domestic Prey. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.783546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Accurate assessments of the patterns and drivers of livestock depredation by wild carnivores are vital for designing effective mitigation strategies to reduce human-wildlife conflict. Snow leopard’s (Panthera uncia) range extensively overlaps pastoralist land-use and livestock predation there is widely reported, but the ecological determinants of livestock consumption by snow leopards remain obscure. We investigated snow leopard dietary habits at seven sites across the Sanjiangyuan region of the Qinghai–Tibetan Plateau (QTP), an area central to the species’ global range. Snow leopard abundance, wild prey composition, and livestock density varied among those sites, thus allowing us to test the effects of various factors on snow leopard diet and livestock predation. Using DNA metabarcoding, we obtained highly resolved dietary data from 351 genetically verified snow leopard fecal samples. We then analyzed the prey preferences of snow leopards and examined ecological factors related to their livestock consumption. Across the sites, snow leopard prey was composed mainly of wild ungulates (mean = 81.5% of dietary sequences), particularly bharal (Pseudois nayaur), and supplemented with livestock (7.62%) and smaller mammals (marmots, pikas, mice; 10.7%). Snow leopards showed a strong preference for bharal, relative to livestock, based on their densities. Interestingly, both proportional and total livestock consumption by snow leopards increased linearly with local livestock biomass, but not with livestock density. That, together with a slight negative relationship with bharal density, supports apparent facilitation between wild and domestic prey. We also found a significant positive correlation between population densities of snow leopard and bharal, yet those densities showed slight negative relationships with livestock density. Our results highlight the importance of sufficient wild ungulate abundance to the conservation of viable snow leopard populations. Additionally, livestock protection is critically needed to reduce losses to snow leopard depredation, especially where local livestock abundances are high.
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Vigués J, Menci S, Wilkinson C, Le Vaillant M, Angerbjörn A, Norén K. A beacon of dung: using lemming (Lemmus lemmus) winter nests and DNA analysis of faeces to further understand predator–prey dynamics in Northern Sweden. Polar Biol 2021. [DOI: 10.1007/s00300-021-02958-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Abstract The hypothesis that predation is the cause of the regular small rodent population oscillations observed in boreal and Arctic regions has long been debated. Within this hypothesis, it is proposed that the most likely predators to cause these destabilizing effects are sedentary specialists, with small mustelids being possible candidates. One such case would be the highly specialized least weasel (Mustela nivalis) driving the Norwegian lemming (Lemmus lemmus) cycle in Fennoscandia. These predators are often elusive and therefore distribution data can only be based on field signs, which is problematic when various mustelid species are sympatric, such as weasels and stoats (Mustela erminea). Here we present the results of using mustelid faeces in predated winter lemming nests to correctly identify the predator and thus discern which species exerts the strongest predation pressure on lemming winter populations. Samples were obtained during different phases in the lemming cycle, spanning 6 years, to account for different prey densities. Faecal mitochondrial DNA extraction and amplification of a 400-bp fragment was successful in 92/114 samples (81%); the sequencing of these samples proved that most predation occurrences (83%) could be attributed to the least weasel. These findings support the hypothesis that weasels in particular show high specificity in predation and could therefore be candidates to driving the lemming cycle in this area. We conclude that DNA analysis of faecal remains around predated nests can be a useful tool for further investigations concerning predator–prey interactions in the tundra.
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Nielsen SS, Alvarez J, Bicout DJ, Calistri P, Canali E, Drewe JA, Garin‐Bastuji B, Gonzales Rojas JL, Schmidt C, Herskin M, Michel V, Padalino B, Pasquali P, Roberts HC, Spoolder H, Stahl K, Velarde A, Winckler C, Blome S, Boklund A, Bøtner A, Dhollander S, Rapagnà C, Van der Stede Y, Miranda Chueca MA. Research priorities to fill knowledge gaps in wild boar management measures that could improve the control of African swine fever in wild boar populations. EFSA J 2021; 19:e06716. [PMID: 34354769 PMCID: PMC8319816 DOI: 10.2903/j.efsa.2021.6716] [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] [Indexed: 11/11/2022] Open
Abstract
The European Commission asked EFSA to provide study designs for the investigation of four research domains (RDs) according to major gaps in knowledge identified by EFSA in a report published in 2019: (RD 1) African swine fever (ASF) epidemiology in wild boar; (RD 2) ASF transmission by vectors; (RD 3) African swine fever virus (ASFV) survival in the environment, and (RD 4) the patterns of seasonality of ASF in wild boar and domestic pigs in the EU. In this Scientific Opinion, the second RD on ASF epidemiology in wild boar is addressed. Twenty-nine research objectives were proposed by the working group and broader ASF expert networks and 23 of these research objectives met a prespecified inclusion criterion. Fourteen of these 23 research objectives met the predefined threshold for selection and so were prioritised based on the following set of criteria: (1) the impact on ASF management; (2) the feasibility or practicality to carry out the study; (3) the potential implementation of study results in practice; (4) a possible short time-frame study (< 1 year); (5) the novelty of the study; and (6) if it was a priority for risk managers. Finally, after further elimination of three of the proposed research objectives due to overlapping scope of studies published during the development of this opinion, 11 research priorities were elaborated into short research proposals, considering the potential impact on ASF management and the period of one year for the research activities.
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Hinton JW, Rountree K, Chamberlain MJ. Diet of Coyotes on the Tensas River National Wildlife Refuge During the White-Tailed Deer Pre-Fawning and Fawning Seasons. SOUTHEAST NAT 2021. [DOI: 10.1656/058.020.0201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Joseph W. Hinton
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931
| | - Kaitlyn Rountree
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA 30602
| | - Michael J. Chamberlain
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA 30602
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Cardoso B, Pessoa B, Figueiredo P, Rinaldi L, Cringoli G, Díaz A, Gomes L, Santos N, de Carvalho LM. Comparative survey of gastrointestinal parasites in sympatric Iberian ibex (Capra pyrenaica) and domestic goats using molecular host specific identification. Parasitol Res 2021; 120:2291-2296. [PMID: 33969442 DOI: 10.1007/s00436-021-07174-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 04/26/2021] [Indexed: 11/29/2022]
Abstract
An isolated population of several hundred Iberian ibex (Capra pyrenaica) inhabits the Gerês-Xurés Transboundary Biosphere Reserve (GXTBR) in north-western Iberian Peninsula, in partial sympatry with tens of thousands domestic goats (Capra hircus). This study aimed to assess the prevalence and shedding intensity of gastrointestinal parasites from sympatric herds of domestic goat and Iberian ibex in autumn 2018. A total of 93 pooled faecal samples were collected from GXTBR (39 from domestic goats and 54 from Iberian ibex) and the host species was identified using molecular techniques, whenever defecation was not visualised in the field. Parasitological analysis was achieved by joint Willis flotation/sedimentation, McMaster and Mini-FLOTAC techniques. Seventy-two samples (25 domestic goats and 47 Iberian ibex) were retained for analysis after discarding the least fresh and those with uncertain specific identification. Generalized linear mixed models compared prevalence and shedding intensity between caprine species. Domestic goats showed a non-significant tendency to be more parasitized than Iberian ibex, as assessed by overall prevalence (100.0%, CI95 86.7-100.0 vs. 74.5%, CI95 69.5-84.8), and shedding intensity. This study reveals a similar community of gastrointestinal parasites in an abundant livestock species and an isolated population of wild caprine, living in partial sympatry. It is the first study on the health status of this endangered Iberian ibex population, in close contact with livestock, highlighting the need for further sanitary surveillance.
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Affiliation(s)
- Beatriz Cardoso
- IREC - Instituto de Investigación en Recursos Cinegéticos, UCLM-CSIC-JCCM, Ronda Toledo 12, 13071, Ciudad Real, Spain.,CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vila do Conde, Porto, Portugal
| | - Beatriz Pessoa
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - Patrícia Figueiredo
- CIISA - Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477, Lisboa, Portugal
| | - Laura Rinaldi
- Department of Veterinary Medicine and Animal Production, University of Napoli Federico II, CREMOPAR, Corso Umberto I, 40, 80138, Napoli, Italy
| | - Giuseppe Cringoli
- Department of Veterinary Medicine and Animal Production, University of Napoli Federico II, CREMOPAR, Corso Umberto I, 40, 80138, Napoli, Italy
| | - Adriana Díaz
- Grupo de Investigación en Medicina Veterinaria y Zootecnia, Universidade Pedagógica e Tecnológica de Colômbia, Avenida Central del Norte 39-115, 150003, Tunja, Boyacá, Colombia
| | - Lídia Gomes
- CIISA - Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477, Lisboa, Portugal
| | - Nuno Santos
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vila do Conde, Porto, Portugal. .,CIISA - Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477, Lisboa, Portugal.
| | - Luís Madeira de Carvalho
- CIISA - Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477, Lisboa, Portugal
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Prey partitioning between sympatric wild carnivores revealed by DNA metabarcoding: a case study on wolf (Canis lupus) and coyote (Canis latrans) in northeastern Washington. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01337-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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34
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van Zinnicq Bergmann MPM, Postaire BD, Gastrich K, Heithaus MR, Hoopes LA, Lyons K, Papastamatiou YP, Schneider EVC, Strickland BA, Talwar BS, Chapman DD, Bakker J. Elucidating shark diets with DNA metabarcoding from cloacal swabs. Mol Ecol Resour 2021; 21:1056-1067. [PMID: 33527665 DOI: 10.1111/1755-0998.13315] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 12/07/2020] [Accepted: 12/18/2020] [Indexed: 12/20/2022]
Abstract
Animal dietary information provides the foundation for understanding trophic relationships, which is essential for ecosystem management. Yet, in marine systems, high-resolution diet reconstruction tools are currently under-developed. This is particularly pertinent for large marine vertebrates, for which direct foraging behaviour is difficult or impossible to observe and, due to their conservation status, the collection of stomach contents at adequate sample sizes is frequently impossible. Consequently, the diets of many groups, such as sharks, have largely remained unresolved. To address this knowledge gap, we applied metabarcoding to prey DNA in faecal residues (fDNA) collected on cotton swabs from the inside of a shark's cloaca. We used a previously published primer set targeting a small section of the 12S rRNA mitochondrial gene to amplify teleost prey species DNA. We tested the utility of this method in a controlled feeding experiment with captive juvenile lemon sharks (Negaprion brevirostris) and on free-ranging juvenile bull sharks (Carcharhinus leucas). In the captive trial, we successfully isolated and correctly identified teleost prey DNA without incurring environmental DNA contamination from the surrounding seawater. In the field, we were able to reconstruct high-resolution teleost dietary information from juvenile C. leucas fDNA that was generally consistent with expectations based on published diet studies of this species. While further investigation is needed to validate the method for larger sharks and other species, it is expected to be broadly applicable to aquatic vertebrates and provides an opportunity to advance our understanding of trophic interactions in marine and freshwater systems.
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Affiliation(s)
- Maurits P M van Zinnicq Bergmann
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA.,Bimini Biological Field Station Foundation, Bimini, The Bahamas
| | - Bautisse D Postaire
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA
| | - Kirk Gastrich
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA
| | - Michael R Heithaus
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA
| | | | | | - Yannis P Papastamatiou
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA
| | - Eric V C Schneider
- Exuma Sound Ecosystem Research Project, Cape Eleuthera Institute, Eleuthera, The Bahamas
| | - Bradley A Strickland
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA
| | - Brendan S Talwar
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA.,Exuma Sound Ecosystem Research Project, Cape Eleuthera Institute, Eleuthera, The Bahamas
| | - Demian D Chapman
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA
| | - Judith Bakker
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA
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Factors influencing genotyping success and genotyping error rate of Eurasian otter (Lutra lutra) faeces collected in temperate Central Europe. EUR J WILDLIFE RES 2020. [DOI: 10.1007/s10344-020-01444-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
AbstractThe use of non-invasively collected DNA source material for genetic and genomic applications is usually characterized by low target DNA concentration and quality, genotyping errors and cost-intensive lab procedures. However, for otters (Lutrinae) as elusive species of conservation concern, genetic non-invasive sampling has become an important tool to study their ecology and demography. To increase cost-efficiency of monitoring programmes and to promote the expansion of genomic approaches to non-invasive samples, we aimed to refine sample collection and preparation. Therefore, we examined the effects of intrinsic sample characteristics (including diet), environmental conditions in the field and sample treatment in the molecular laboratory on the success of genotyping and allelic dropout (ADO) rates using microsatellite markers in 1970 fresh Eurasian otter (Lutra lutra) scats. Using fresh samples only, we probably eliminated one of the most important impediments of genotyping DNA from otter faecal samples beforehand. But, we observed higher genotyping success and lower ADO rates for anal glad secretions and faecal samples containing high proportions of mucus. Moist conditions during sample collection may promote DNA degradation and PCR inhibition, leading to decreased genotyping success rates. ADO was further affected by the type of extraction kit. However, a high proportion of variance remaining unexplained by our models implied that additional parameters were acting (amount of PCR inhibitors, non-uniform distribution of intestinal cells, efficiency of PCRs, specific microclimate at marking sites). We summarized influential factors maximizing genotyping quality of otter scats and give recommendations for sample collection, storage and DNA extraction based on our results and current literature.
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36
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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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Skorupski J. Fifty Years of Research on European Mink Mustela lutreola L., 1761 Genetics: Where Are We Now in Studies on One of the Most Endangered Mammals? Genes (Basel) 2020; 11:E1332. [PMID: 33187363 PMCID: PMC7696698 DOI: 10.3390/genes11111332] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/28/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023] Open
Abstract
The purpose of this review is to present the current state of knowledge about the genetics of European mink Mustela lutreola L., 1761, which is one of the most endangered mammalian species in the world. This article provides a comprehensive description of the studies undertaken over the last 50 years in terms of cytogenetics, molecular genetics, genomics (including mitogenomics), population genetics of wild populations and captive stocks, phylogenetics, phylogeography, and applied genetics (including identification by genetic methods, molecular ecology, and conservation genetics). An extensive and up-to-date review and critical analysis of the available specialist literature on the topic is provided, with special reference to conservation genetics. Unresolved issues are also described, such as the standard karyotype, systematic position, and whole-genome sequencing, and hotly debated issues are addressed, like the origin of the Southwestern population of the European mink and management approaches of the most distinct populations of the species. Finally, the most urgent directions of future research, based on the research questions arising from completed studies and the implementation of conservation measures to save and restore M. lutreola populations, are outlined. The importance of the popularization of research topics related to European mink genetics among scientists is highlighted.
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Affiliation(s)
- Jakub Skorupski
- Institute of Marine and Environmental Sciences, University of Szczecin, Adama Mickiewicza 16 St., 70-383 Szczecin, Poland; ; Tel.: +48-914-441-685
- Polish Society for Conservation Genetics LUTREOLA, Maciejkowa 21 St., 71-784 Szczecin, Poland
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38
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Schroeder H, Palczewski S, Degen B. Development of D-Loop mitochondrial markers for amplification of prey DNA from wolf scat. CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01169-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AbstractAnalysis of wolves dietary is a currently important theme because of the discussion about wolves preying on livestock as sheep or goats. We developed molecular markers to especially amplify the DNA of the prey out of wolf scat. For this purpose, we used the mitochondrial D-Loop using public available sequences for wolf and seven potential prey species (even-toed ungulates). We developed special primers amplifying either the wolves DNA or the prey DNA. In a fragment of 223-225 basepairs (bp) length we identified 21 SNPs, two 1-bp indels and one 3-bp indel, and three microsatellites to separate seven prey species from each other. Validation of the markers was performed by sequencing the PCR products of 12 fresh prey tissues and 20 wolf scat samples using the different primer pairs.
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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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LaBarge LR, Hill RA, Berman CM, Margulis SW, Allan ATL. Anthropogenic influences on primate antipredator behavior and implications for research and conservation. Am J Primatol 2020; 82:e23087. [PMID: 31894614 DOI: 10.1002/ajp.23087] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 11/10/2022]
Abstract
Predation risk affects prey species' behavior, even in the absence of a direct threat, but human-induced environmental change may disturb ecologically significant predator-prey interactions. Here, we propose various ways in which knowledge of antipredator tactics, behavioral risk effects, and primate-predator interactions could assist in identifying human-caused disruption to natural systems. Using behavior to evaluate primate responses to the ongoing environmental change should be a potentially effective way to make species conservation more predictive by identifying issues before a more dramatic population declines. A key challenge here is that studies of predation on primates often use data collected via direct observations of habituated animals and human presence can deter carnivores and influence subjects' perception of risk. Hence, we also review various indirect data collection methods to evaluate their effectiveness in identifying where environmental change threatens wild species, while also minimizing observer bias.
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Affiliation(s)
- Laura R LaBarge
- Department of Environment and Sustainability, Program in Evolution, Ecology, and Behavior, The State University of New York at Buffalo, Amherst, New York.,Primate and Predator Project, Lajuma Research Centre, Louis Trichardt, South Africa
| | - Russell A Hill
- Primate and Predator Project, Lajuma Research Centre, Louis Trichardt, South Africa.,Department of Anthropology, Durham University, Durham, UK.,Department of Zoology, University of Venda, Thohoyandou, South Africa
| | - Carol M Berman
- Department of Environment and Sustainability, Program in Evolution, Ecology, and Behavior, The State University of New York at Buffalo, Amherst, New York.,Department of Anthropology, The State University of New York at Buffalo, Amherst, New York
| | - Susan W Margulis
- Department of Animal Behavior, Ecology, and Conservation, Canisius College, Buffalo, New York.,Department of Biology, Canisius College, Buffalo, New York
| | - Andrew T L Allan
- Primate and Predator Project, Lajuma Research Centre, Louis Trichardt, South Africa.,Department of Anthropology, Durham University, Durham, UK
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Srivathsan A, Nagarajan N, Meier R. Boosting natural history research via metagenomic clean-up of crowdsourced feces. PLoS Biol 2019; 17:e3000517. [PMID: 31697678 PMCID: PMC6863569 DOI: 10.1371/journal.pbio.3000517] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 11/19/2019] [Indexed: 12/22/2022] Open
Abstract
Biodiversity is in crisis due to habitat destruction and climate change. The conservation of many noncharismatic species is hampered by the lack of data. Yet, natural history research—a major source of information on noncharismatic species—is in decline. We here suggest a remedy for many mammal species, i.e., metagenomic clean-up of fecal samples that are “crowdsourced” during routine field surveys. Based on literature data, we estimate that this approach could yield natural history information for circa 1,000 species within a decade. Metagenomic analysis would simultaneously yield natural history data on diet and gut parasites while enhancing our understanding of host genetics, gut microbiome, and the functional interactions between traditional and new natural history data. We document the power of this approach by carrying out a “metagenomic clean-up” on fecal samples collected during a single night of small mammal trapping in one of Alfred Wallace’s favorite collecting sites. Natural history research is in crisis and non-charismatic species are increasingly ignored; this Community Page article argues and demonstrates that shotgun sequencing of serendipitously obtained faecal samples could reverse this trend for 1000 mammal species within 10 years.
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Affiliation(s)
- Amrita Srivathsan
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Niranjan Nagarajan
- Computational and Systems Biology, Genome Institute of Singapore, Singapore
- School of Medicine, National University of Singapore, Singapore
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore
- Tropical Marine Science Institute, National University of Singapore, Singapore
- * E-mail:
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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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Novel real-time PCR species identification assays for British and Irish bats and their application to a non-invasive survey of bat roosts in Ireland. Mamm Biol 2019. [DOI: 10.1016/j.mambio.2019.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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