1
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Peter N, Schantz AV, Dörge DD, Steinhoff A, Cunze S, Skaljic A, Klimpel S. Evidence of predation pressure on sensitive species by raccoons based on parasitological studies. Int J Parasitol Parasites Wildl 2024; 24:100935. [PMID: 38638363 PMCID: PMC11024658 DOI: 10.1016/j.ijppaw.2024.100935] [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: 03/14/2024] [Revised: 04/05/2024] [Accepted: 04/07/2024] [Indexed: 04/20/2024]
Abstract
To demonstrate predation and potential impacts of raccoons on various species, a total of 108 raccoons from aquatic-associated nature reserves and natural areas in three federal states of Germany, Hesse (n = 36), Saxony-Anhalt (n = 36) and Brandenburg (n = 36), were investigated from a dietary ecological perspective in the present study. Fecal analyses and stomach content examinations were conducted for this purpose. Additionally, as a supplementary method for analyzing the dietary spectrum of raccoons, the parasite fauna was considered, as metazoan parasites, in particular, can serve as indicators for the species and origin of food organisms. While stomach content analyses allow for a detailed recording of trophic relationships solely at the time of sampling, parasitological examinations enable inferences about more distant interaction processes. With their different developmental stages and heteroxenous life cycles involving specific, sometimes obligate, intermediate hosts, they utilize the food web to reach their definitive host. The results of this study clearly demonstrate that spawning areas of amphibians and reptiles were predominantly utilized as food resources by raccoons in the study areas. Thus, common toad (Bufo bufo), common newt (Lissotriton vulgaris), grass frog (Rana temporaria), and grass snake (Natrix natrix) were identified as food organisms for raccoons. The detection of the parasite species Euryhelmis squamula, Isthmiophora melis, and Physocephalus sexalatus with partially high infestation rates also suggests that both amphibians and reptiles belong to the established dietary components of raccoons from an ecological perspective, as amphibians and reptiles are obligate intermediate hosts in the respective parasitic life cycles of the detected parasites. The study clearly demonstrates that raccoons have a significant impact on occurrence-sensitive animal species in certain areas and, as an invasive species, can exert a negative influence on native species and ecosystems.
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Affiliation(s)
- Norbert Peter
- Institute for Ecology, Evolution and Diversity, Goethe-University, Max-von-Laue-Str. 13, Frankfurt/Main, D-60439, Germany
| | - Anna V. Schantz
- Institute for Ecology, Evolution and Diversity, Goethe-University, Max-von-Laue-Str. 13, Frankfurt/Main, D-60439, Germany
| | - Dorian D. Dörge
- Institute for Ecology, Evolution and Diversity, Goethe-University, Max-von-Laue-Str. 13, Frankfurt/Main, D-60439, Germany
| | - Anne Steinhoff
- Institute for Ecology, Evolution and Diversity, Goethe-University, Max-von-Laue-Str. 13, Frankfurt/Main, D-60439, Germany
| | - Sarah Cunze
- Institute for Ecology, Evolution and Diversity, Goethe-University, Max-von-Laue-Str. 13, Frankfurt/Main, D-60439, Germany
| | - Ajdin Skaljic
- Institute for Ecology, Evolution and Diversity, Goethe-University, Max-von-Laue-Str. 13, Frankfurt/Main, D-60439, Germany
| | - Sven Klimpel
- Institute for Ecology, Evolution and Diversity, Goethe-University, Max-von-Laue-Str. 13, Frankfurt/Main, D-60439, Germany
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, Frankfurt/Main, D-60325, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, D-60325, Frankfurt/Main, Germany
- Branch Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392, Giessen, Germany
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2
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Thongjued K, Garcia K, Scott D, Gonthier DJ, Dupuis JR. DNA metabarcoding diet analysis in a generalist omnivore: feeding trials reveal the efficacy of extraction kits and a multi-locus approach for identifying diverse diets. Integr Zool 2024. [PMID: 38297429 DOI: 10.1111/1749-4877.12806] [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] [Indexed: 02/02/2024]
Abstract
Metabarcoding-based diet analysis is a valuable tool for understanding the feeding behavior of a wide range of species. However, many studies using these methods for wild animals assume accuracy and precision without experimental evaluation with known positive control food items. Here, we conducted a feeding trial experiment with a positive control community in pasture-raised chickens and assessed the efficacy of several commonly used DNA extraction kits and primer sets. We hand-fed 22 known food items, including insects and plants, to six backyard laying hens and collected their excreta for eight h. We evaluated the efficacy of three DNA extraction kits, three primer sets for plant identification (targeting rbcL, trnL, and internal transcribed spacer 2 [ITS2]), and three primer sets for arthropod identification (targeting cytochrome oxidase subunit I [COI]). The detection success rate of our positive control food items was highly variable, ranging from 2.04% to 93.88% for all kit/primer combinations and averaging 37.35% and 43.57% for the most effective kit/primer combination for plants and insects, respectively. Extraction kits using bead-based homogenization positively affected the recovery proportion of plant and insect DNA in excreta samples. The minimum time to detect known food items was 44 min post-feeding. Two COI primer sets significantly outperformed the third, and both recovery proportion and taxonomic resolution from ITS2 were significantly higher than those from rbcL and trnL. Taken together, these results display the potential variability that can be inherently present in DNA-based diet analyses and highlight the utility of experimental feeding trials in validating such approaches, particularly for omnivores with diverse diets.
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Affiliation(s)
- Kantima Thongjued
- Department of Entomology, University of Kentucky, Agricultural Science Center, Lexington, Kentucky, USA
| | - Karina Garcia
- Department of Entomology, University of Kentucky, Agricultural Science Center, Lexington, Kentucky, USA
| | - Delia Scott
- Department of Entomology, University of Kentucky, Agricultural Science Center, Lexington, Kentucky, USA
| | - David J Gonthier
- Department of Entomology, University of Kentucky, Agricultural Science Center, Lexington, Kentucky, USA
| | - Julian R Dupuis
- Department of Entomology, University of Kentucky, Agricultural Science Center, Lexington, Kentucky, USA
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3
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Browett SS, Synnott R, O'Meara DB, Antwis RE, Browett SS, Bown KJ, Wangensteen OS, Dawson DA, Searle JB, Yearsley JM, McDevitt AD. Resource competition drives an invasion-replacement event among shrew species on an island. J Anim Ecol 2023; 92:698-709. [PMID: 36617677 DOI: 10.1111/1365-2656.13855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/17/2022] [Indexed: 01/10/2023]
Abstract
Invasive mammals are responsible for the majority of native species extinctions on islands. While most of these extinction events will be due to novel interactions between species (e.g. exotic predators and naive prey), it is more unusual to find incidences where a newly invasive species causes the decline/extinction of a native species on an island when they normally coexist elsewhere in their overlapping mainland ranges. We investigated if resource competition between two insectivorous small mammals was playing a significant role in the rapid replacement of the native pygmy shrew Sorex minutus in the presence of the recently invading greater white-toothed shrew Crocidura russula on the island of Ireland. We used DNA metabarcoding of gut contents from >300 individuals of both species to determine each species' diet and measured the body size (weight and length) during different stages of the invasion in Ireland (before, during and after the species come into contact with one another) and on a French island where both species have long coexisted (acting as a natural 'control' site). Dietary composition, niche width and overlap and body size were compared in these different stages. The body size of the invasive C. russula and composition of its diet changes between when it first invades an area and after it becomes established. During the initial stages of the invasion, individual shrews are larger and consume larger sized invertebrate prey species. During later stages of the invasion, C. russula switches to consuming smaller prey taxa that are more essential for the native species. As a result, the level of interspecific dietary overlap increases from between 11% and 14% when they first come into contact with each other to between 39% and 46% after the invasion. Here we show that an invasive species can quickly alter its dietary niche in a new environment, ultimately causing the replacement of a native species. In addition, the invasive shrew could also be potentially exhausting local resources of larger invertebrate species. These subsequent changes in terrestrial invertebrate communities could have severe impacts further downstream on ecosystem functioning and services.
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Affiliation(s)
- Samuel S Browett
- School of Science, Engineering and Environment, University of Salford, Salford, UK.,Molecular Ecology Research Group, Eco-Innovation Research Centre, School of Science and Computing, South East Technological University, Waterford, Ireland.,NERC Environmental Omics Facility, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Rebecca Synnott
- Molecular Ecology Research Group, Eco-Innovation Research Centre, School of Science and Computing, South East Technological University, Waterford, Ireland
| | - Denise B O'Meara
- Molecular Ecology Research Group, Eco-Innovation Research Centre, School of Science and Computing, South East Technological University, Waterford, Ireland
| | - Rachael E Antwis
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Stephen S Browett
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Kevin J Bown
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Owen S Wangensteen
- Norwegian College of Fishery Science, University of Tromsø, Tromsø, Norway
| | - Deborah A Dawson
- NERC Environmental Omics Facility, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Jeremy B Searle
- Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, New York, USA
| | - Jon M Yearsley
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Allan D McDevitt
- School of Science, Engineering and Environment, University of Salford, Salford, UK.,Department of Natural Sciences and the Environment, School of Science and Computing, Atlantic Technological University, Galway, Ireland
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4
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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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5
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Pinho CJ, Lopes EP, Paupério J, Gomes I, Romeiras MM, Vasconcelos R. Trust your guts? The effect of gut section on diet composition and impact of
Mus musculus
on islands using metabarcoding. Ecol Evol 2022; 12:e8638. [PMID: 35309743 PMCID: PMC8901889 DOI: 10.1002/ece3.8638] [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: 08/06/2021] [Revised: 01/20/2022] [Accepted: 01/27/2022] [Indexed: 11/11/2022] Open
Abstract
DNA metabarcoding is widely used to characterize the diet of species, and it becomes very relevant for biodiversity conservation, allowing the understanding of trophic chains and the impact of invasive species. The need for cost‐effective biodiversity monitoring methods fostered advances in this technique. One question that arises is which sample type provides a better diet representation. Therefore, with this study, we intended to evaluate if there were differences in diet estimates according to the section of the gastrointestinal tract analysed and which section(s) provided the best diet representation. Additionally, we intended to infer the ecological/economic impacts of an invader as a model of the potential effects in an originally mammal‐free ecosystem. We examined the gut contents of the house mouse Mus musculus introduced to Cabo Verde, considering three sections: stomach, small intestine, and large intestine. We applied a DNA‐metabarcoding approach using two genetic markers, one specific for plants and another for invertebrates. We showed that this invader consumed 131 taxa (73 plants and 58 invertebrates). We obtained significant differences in the composition of two of the three sections, with a higher incidence of invertebrates in the stomach and plants in the intestines. This may be due to stomach inhibitors acting on plants and/or to faster absorption of soft‐body invertebrates compared to the plant fibers in the intestines. We verified that the impact of this invader in the ecosystem is predominantly negative, as at least 50% of the ingested items were native, endemic, or economically important taxa, and only 19% of the diet items were exotics. Overall, results showed the need to analyse only two gastrointestinal tract sections to obtain robust diet data, increasing the cost‐effectiveness of the method. Furthermore, by uncovering the native taxa most frequently preyed on by mice, this DNA‐metabarcoding approach allowed us to evaluate efficiently which are at the highest risk.
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Affiliation(s)
- Catarina J. Pinho
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do PortoVairão Portugal
- Departamento de Biologia Faculdade de Ciências da Universidade do Porto Porto Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning CIBIO, Campus de Vairão Vairão Portugal
| | - Evandro P. Lopes
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do PortoVairão Portugal
- Departamento de Biologia Faculdade de Ciências da Universidade do Porto Porto Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning CIBIO, Campus de Vairão Vairão Portugal
- ISECMAR‐UTA Instituto Engenharia e Ciências do Mar da Universidade Técnica do AtlânticoMindelo Cabo Verde
| | - Joana Paupério
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do PortoVairão Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning CIBIO, Campus de Vairão Vairão Portugal
| | - Isildo Gomes
- INIDA Instituto Nacional de Investigação e Desenvolvimento AgrárioSantiago Cabo Verde
| | - Maria M. Romeiras
- LEAF‐ISA Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia Universidade de Lisboa Lisboa Portugal
| | - Raquel Vasconcelos
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do PortoVairão Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning CIBIO, Campus de Vairão Vairão Portugal
- ISECMAR‐UTA Instituto Engenharia e Ciências do Mar da Universidade Técnica do AtlânticoMindelo Cabo Verde
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6
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Cuff JP, Windsor FM, Tercel MPTG, Kitson JJN, Evans DM. Overcoming the pitfalls of merging dietary metabarcoding into ecological networks. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13796] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Jordan P. Cuff
- School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
| | - Fredric M. Windsor
- School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
| | - Maximillian P. T. G. Tercel
- School of Biosciences Cardiff University Cardiff UK
- Durrell Wildlife Conservation Trust Jersey Channel Islands
| | - James J. N. Kitson
- School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
| | - Darren M. Evans
- School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
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7
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Liu G, Zhang S, Zhao X, Li C, Gong M. Advances and Limitations of Next Generation Sequencing in Animal Diet Analysis. Genes (Basel) 2021; 12:genes12121854. [PMID: 34946803 PMCID: PMC8701983 DOI: 10.3390/genes12121854] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 02/07/2023] Open
Abstract
Diet analysis is a critical content of animal ecology and the diet analysis methods have been constantly improving and updating. Contrary to traditional methods of high labor intensity and low resolution, the next generation sequencing (NGS) approach has been suggested as a promising tool for dietary studies, which greatly improves the efficiency and broadens the application range. Here we present a framework of adopting NGS and DNA metabarcoding into diet analysis, and discuss the application in aspects of prey taxa composition and structure, intra-specific and inter-specific trophic links, and the effects of animal feeding on environmental changes. Yet, the generation of NGS-based diet data and subsequent analyses and interpretations are still challenging with several factors, making it possible still not as widely used as might be expected. We suggest that NGS-based diet methods must be furthered, analytical pipelines should be developed. More application perspectives, including nutrient geometry, metagenomics and nutrigenomics, need to be incorporated to encourage more ecologists to infer novel insights on they work.
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Affiliation(s)
- Gang Liu
- Key Laboratory of Wetland Ecological Function and Restoration in Beijing City, Wetland Research Institute of Chinese Academy of Forestry Sciences, Beijing 100091, China; (G.L.); (X.Z.); (C.L.)
| | - Shumiao Zhang
- Beijing Milu Ecological Research Center, Beijing 100076, China;
| | - Xinsheng Zhao
- Key Laboratory of Wetland Ecological Function and Restoration in Beijing City, Wetland Research Institute of Chinese Academy of Forestry Sciences, Beijing 100091, China; (G.L.); (X.Z.); (C.L.)
| | - Chao Li
- Key Laboratory of Wetland Ecological Function and Restoration in Beijing City, Wetland Research Institute of Chinese Academy of Forestry Sciences, Beijing 100091, China; (G.L.); (X.Z.); (C.L.)
| | - Minghao Gong
- Key Laboratory of Wetland Ecological Function and Restoration in Beijing City, Wetland Research Institute of Chinese Academy of Forestry Sciences, Beijing 100091, China; (G.L.); (X.Z.); (C.L.)
- Correspondence: ; Tel.: +86-010-62884159
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8
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Tercel MPTG, Symondson WOC, Cuff JP. The problem of omnivory: A synthesis on omnivory and DNA metabarcoding. Mol Ecol 2021; 30:2199-2206. [PMID: 33772967 DOI: 10.1111/mec.15903] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/09/2021] [Accepted: 03/22/2021] [Indexed: 01/03/2023]
Abstract
Dietary analysis using DNA metabarcoding is a powerful tool that is increasingly being used to further our knowledge of trophic interactions in highly complex food webs but is not without limitations. Omnivores, the most generalist of consumers, pose unique challenges when using such methods. Here, we provide the rationale to understand the problems associated with analysing the complex diets of omnivores. By reviewing existing metabarcoding studies of omnivorous diet, and constructing hypothetical scenarios arising from each, we outline that great caution is required when interpreting sequencing data in such cases. In essence, the problems of accidental consumption and secondary ingestion are significant sources of error when investigating omnivorous diets. The integration of multiple high throughput sequencing markers increases the taxonomic breadth of taxa detected but we reveal how some detections may be misleading. Disentangling which taxa have been deliberately or accidentally consumed by the focal omnivore is challenging and can falsely emphasise those that were not intentionally consumed, obscuring biologically meaningful interactions. Although we suggest ways to disentangle these issues, we urge that the results of such analyses should be interpreted with caution and all possible scenarios for the presence of biota within omnivores given due consideration.
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Affiliation(s)
- Maximillian P T G Tercel
- School of Biosciences, Cardiff University, Cardiff, Wales, UK.,Durrell Wildlife Conservation Trust, Trinity, Jersey, Channel Islands
| | | | - Jordan P Cuff
- School of Biosciences, Cardiff University, Cardiff, Wales, UK.,Rothamsted Insect Survey, Rothamsted Research, West Common, Harpenden, Hertfordshire, UK
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9
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Browett SS, Curran TG, O’Meara DB, Harrington AP, Sales NG, Antwis RE, O’Neill D, McDevitt AD. Primer biases in the molecular assessment of diet in multiple insectivorous mammals. Mamm Biol 2021. [DOI: 10.1007/s42991-021-00115-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
AbstractOur understanding of trophic interactions of small insectivorous mammals has been drastically improved with the advent of DNA metabarcoding. The technique has continued to be optimised over the years, with primer choice repeatedly being a vital factor for dietary inferences. However, the majority of dietary studies examining the effect of primer choice often rely on in silico analyses or comparing between species that occupy an identical niche type. Here, we apply DNA metabarcoding to empirically compare the prey detection capabilities of two widely used primer sets when assessing the diets of a flying (lesser horseshoe bat; Rhinolophus hipposideros) and two ground-dwelling insectivores (greater white-toothed shrew; Crocidura russula and pygmy shrew; Sorex minutus). Although R. hipposideros primarily rely on two prey orders (Lepidoptera and Diptera), the unique taxa detected by each primer shows that a combination of primers may be the best approach to fully describe bat trophic ecology. However, random forest classifier analysis suggests that one highly degenerate primer set detected the majority of both shrews’ diet despite higher levels of host amplification. The wide range of prey consumed by ground-dwelling insectivores can therefore be accurately documented from using a single broad-range primer set, which can decrease cost and labour. The results presented here show that dietary inferences will differ depending on the primer or primer combination used for insectivores occupying different niches (i.e., hunting in the air or ground) and demonstrate the importance of performing empirical pilot studies for novel study systems.
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10
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Castle ST, Allan N, Clifford D, Aylward CM, Ramsey J, Fascetti AJ, Pesapane R, Roy A, Statham M, Sacks B, Foley J. Diet composition analysis provides new management insights for a highly specialized endangered small mammal. PLoS One 2020; 15:e0240136. [PMID: 33007017 PMCID: PMC7531790 DOI: 10.1371/journal.pone.0240136] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 09/20/2020] [Indexed: 01/04/2023] Open
Abstract
The critically endangered Amargosa vole (Microtus californicus scirpensis) is found only in rare marsh habitat near Tecopa, California in a plant community dominated by three-square bulrush (Schoenoplectus americanus). Since the earliest research on the Amargosa vole, the existing paradigm has been that these voles are obligatorily dependent on bulrush as their only food source and for the three-dimensional canopy and litter structure it provides for predator avoidance. However, no prior research has confirmed the diet of the Amargosa vole. In this study we characterized the Amargosa vole' nutritional needs, analyzed the quality of bulrush by forage analysis, and performed microhistological and metabarcoding analyses of vole feces to determine what foods were consumed in the wild. All bulrush plant tissues analyzed were low in fat (from 0.9% of dry matter in roots to 3.6% in seeds), high in neutral detergent fiber (from 5.9% in rhizomes to 33.6% in seeds), and low in protein (7.3-8.4%). These findings support the conclusion that bulrush alone is unlikely to support vole survival and reproduction. Fecal microhistology and DNA metabarcoding revealed relatively diverse diets including plants in 14 families, with rushes (Juncaceae), bulrushes (Cyperaceae), and grasses (Poaceae) being the most common diet items. On microhistology, all analyzed samples contained bulrush, sedges (Carex sp.), rushes (Juncus sp.), and beaked spikerush (Eleocharis rostrellata) even from marshes where non-bulrush plants were uncommon. There was evidence of insects at <1% in two marshes but none in the remaining marshes. Metabarcoding detected ten genera of plants. When considering non-Schoenoplectus targets, for which metabarcoding had poor sensitivity, saltgrass (Distichlis spicata) was the most commonly detected species, with prominent contributions from seaside arrowgrass (Triglochin concinna) and yerba mansa (Anemopsis californica) as well. Diversity of vole diets generally increased with increasing site plant diversity, but differences were not statistically significant. Confirming details about dietary behaviors is critical for informing appropriate conservation planning including habitat management and reintroduction of voles into new sites.
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Affiliation(s)
- Stephanie T. Castle
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States of America
- Wildlife Investigations Lab, California Department of Fish and Wildlife, Rancho Cordova, CA, United States of America
| | - Nora Allan
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Deana Clifford
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States of America
- Wildlife Investigations Lab, California Department of Fish and Wildlife, Rancho Cordova, CA, United States of America
| | - Cody M. Aylward
- Department of Fish, Wildlife and Conservation Biology, University of California, Davis, CA, United States of America
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, CA, United States of America
| | - Jon Ramsey
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Andrea J. Fascetti
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Risa Pesapane
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Austin Roy
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Mark Statham
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, CA, United States of America
| | - Benjamin Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, CA, United States of America
- Department of Population Health, and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Janet Foley
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States of America
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11
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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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12
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Browett SS, O'Meara DB, McDevitt AD. Genetic tools in the management of invasive mammals: recent trends and future perspectives. Mamm Rev 2020. [DOI: 10.1111/mam.12189] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Samuel S. Browett
- Ecosystems and Environment Research Centre School of Science, Engineering and Environment University of Salford Salford M5 4WTUK
| | - Denise B. O'Meara
- Molecular Ecology Research Group Eco‐Innovation Research Centre School of Science and Computing Waterford Institute of Technology Waterford Ireland
| | - Allan D. McDevitt
- Ecosystems and Environment Research Centre School of Science, Engineering and Environment University of Salford Salford M5 4WTUK
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13
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Woinarski JCZ, Legge SM, Woolley LA, Palmer R, Dickman CR, Augusteyn J, Doherty TS, Edwards G, Geyle H, McGregor H, Riley J, Turpin J, Murphy BP. Predation by introduced cats Felis catus on Australian frogs: compilation of species records and estimation of numbers killed. WILDLIFE RESEARCH 2020. [DOI: 10.1071/wr19182] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Abstract
ContextWe recently estimated the numbers of reptiles, birds and mammals killed by cats (Felis catus) in Australia, with these assessments providing further evidence that cats have significant impacts on Australian wildlife. No previous studies have estimated the numbers of frogs killed by cats in Australia and there is limited comparable information from elsewhere in the world.
AimsWe sought to (1) estimate the numbers of frogs killed by cats in Australia and (2) compile a list of Australian frog species known to be killed by cats.
MethodsFor feral cats, we estimated the number of frogs killed from information on their frequency of occurrence in 53 cat dietary studies (that examined stomach contents), the mean number of frogs in dietary samples that contained frogs, and the numbers of cats in Australia. We collated comparable information for take of frogs by pet cats, but the information base was far sparser.
Key resultsFrogs were far more likely to be reported in studies that sampled cat stomachs than cat scats. The mean frequency of occurrence of frogs in cat stomachs was 1.5%. The estimated annual per capita consumption by feral cats in Australia’s natural environments is 44 frogs, and, hence, the annual total take is estimated at 92 million frogs. The estimated annual per capita consumption by pet cats is 0.26 frogs, for a total annual kill of one million frogs by pet cats. Thirty native frog species (13% of the Australian frog fauna) are known to be killed by cats: this tally does not include any of the 51 threatened frog species, but this may simply be because no cat dietary studies have occurred within the small ranges typical of threatened frog species.
ConclusionsThe present study indicated that cats in Australia kill nearly 100 million frogs annually, but further research is required to understand the conservation significance of such predation rates.
ImplicationsThe present study completed a set of reviews of the impacts of cats on Australian terrestrial vertebrates. Cat predation on Australian frogs is substantial, but is likely to be markedly less than that on Australian reptiles, birds and mammals.
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14
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Egeter B, Roe C, Peixoto S, Puppo P, Easton LJ, Pinto J, Bishop PJ, Robertson BC. Using molecular diet analysis to inform invasive species management: A case study of introduced rats consuming endemic New Zealand frogs. Ecol Evol 2019; 9:5032-5048. [PMID: 31110660 PMCID: PMC6509367 DOI: 10.1002/ece3.4903] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 12/07/2018] [Accepted: 12/13/2018] [Indexed: 12/25/2022] Open
Abstract
The decline of amphibians has been of international concern for more than two decades, and the global spread of introduced fauna is a major factor in this decline. Conservation management decisions to implement control of introduced fauna are often based on diet studies. One of the most common metrics to report in diet studies is Frequency of Occurrence (FO), but this can be difficult to interpret, as it does not include a temporal perspective. Here, we examine the potential for FO data derived from molecular diet analysis to inform invasive species management, using invasive ship rats (Rattus rattus) and endemic frogs (Leiopelma spp.) in New Zealand as a case study. Only two endemic frog species persist on the mainland. One of these, Leiopelma archeyi, is Critically Endangered (IUCN 2017) and ranked as the world's most evolutionarily distinct and globally endangered amphibian (EDGE, 2018). Ship rat stomach contents were collected by kill-trapping and subjected to three methods of diet analysis (one morphological and two DNA-based). A new primer pair was developed targeting all anuran species that exhibits good coverage, high taxonomic resolution, and reasonable specificity. Incorporating a temporal parameter allowed us to calculate the minimum number of ingestion events per rat per night, providing a more intuitive metric than the more commonly reported FO. We are not aware of other DNA-based diet studies that have incorporated a temporal parameter into FO data. The usefulness of such a metric will depend on the study system, in particular the feeding ecology of the predator. Ship rats are consuming both species of native frogs present on mainland New Zealand, and this study provides the first detections of remains of these species in mammalian stomach contents.
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Affiliation(s)
- Bastian Egeter
- CIBIO‐InBio, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
- Department of ZoologyUniversity of OtagoDunedinNew Zealand
| | - Cailín Roe
- Department of ZoologyUniversity of OtagoDunedinNew Zealand
| | - Sara Peixoto
- Faculdade de Ciências daUniversidade do PortoPortoPortugal
| | - Pamela Puppo
- CIBIO‐InBio, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
| | - Luke J. Easton
- Department of ZoologyUniversity of OtagoDunedinNew Zealand
| | - Joana Pinto
- CIBIO‐InBio, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
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15
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Taylor CM, Keppel G, O'Sullivan S, Peters S, Kerr GD, Williams CR. Indiscriminate feeding by an alien population of the spotted-thighed frog (Litoria cyclorhyncha) in southern Australia and potential impacts on native biodiversity. AUST J ZOOL 2019. [DOI: 10.1071/zo19042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Litoria cyclorhyncha (Hylidae) is native to southern Western Australia, but a naturalised population has established on the Eyre Peninsula, South Australia. We investigated the diet of this exotic population to assess potential impacts on biodiversity and ecosystems. Seventy-six frogs were collected from three different habitats and their diet items assigned to parataxonomic units (PU) within orders. Stomach contents were diverse, containing 467 prey items from 19 orders and 135 PU, with extrapolation suggesting a diet of ~200 PU. Shannon diversity estimates of prey items consumed produced different rankings for the three habitats at the PU and order level. Therefore, estimates at the order level may not be representative of the actual diversity of prey items. L. cyclorhyncha consumed mainly arthropods and low numbers of conspecific young frogs, geckos and a juvenile house mouse. This generalist, indiscriminate predatory diet is similar to that of other hylids and implies that the species poses a risk to native biodiversity and ecosystem processes by predation and competition. Therefore, further spread of this species needs to be prevented. Our findings can inform effective policies and management actions to mitigate future impacts of L. cyclorhyncha.
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16
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Forin-Wiart MA, Poulle ML, Piry S, Cosson JF, Larose C, Galan M. Evaluating metabarcoding to analyse diet composition of species foraging in anthropogenic landscapes using Ion Torrent and Illumina sequencing. Sci Rep 2018; 8:17091. [PMID: 30459313 PMCID: PMC6244006 DOI: 10.1038/s41598-018-34430-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 10/18/2018] [Indexed: 01/01/2023] Open
Abstract
DNA metabarcoding of faecal samples is being successfully used to study the foraging niche of species. We assessed the ability of two benchtop high-throughput sequencing (HTS) platforms, to identify a large taxonomic array of food items from domestic cats Felis silvestris catus, including prey and human-related food taxa (pet food and leftovers leaving undetectable solid remains in faeces). Scats from a captive feeding trial (n = 41) and from free-ranging individuals (n = 326) were collected and analysed using a cytb mini-barcode in independent PCR replicates on the Ion PGM and the MiSeq platforms. Outputs from MiSeq were more sensitive and reproducible than those from Ion PGM due to a higher sequencing depth and sequence quality on MiSeq. DNA from intact prey taxa was detected more often (82% of the expected occurrences) than DNA from pet food (54%) and raw fish and meat (31%). We assumed that this variability was linked to different degree of DNA degradation: The Ion PGM detected significantly less human-linked food, birds, field voles, murids and shrews in the field-collected samples than the MiSeq platform. Pooling the replicates from both platforms and filtering the data allowed identification of at least one food item in 87.4% of the field-collected samples. Our DNA metabarcoding approach identified 29 prey taxa, of which 25 to species level (90% of items) including 9 rodents, 3 insectivores, 12 birds and 1 reptile and 33 human-related food taxa of which 23 were identified to genus level (75% of items). Our results demonstrate that using HTS platforms such as MiSeq, which provide reads of sufficiently high quantity and quality, with sufficient numbers of technical replicates, is a robust and non-invasive approach for further dietary studies on animals foraging on a wide range of food items in anthropogenic landscapes.
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Affiliation(s)
- Marie-Amélie Forin-Wiart
- Université de Reims Champagne-Ardenne, EA 7510 ESCAPE, UFR de Médecine, 51 rue Cognacq Jay, 51095, Reims Cedex, France.
- Université de Reims Champagne-Ardenne, Centre d'Etude et de Formation en Eco-Ethologie (CERFE), 5 rue de la Héronnière, 08240, Boult-aux-Bois, France.
- Université de Strasbourg, CNRS, IPHC, UMR 7178, Département Ecologie, Physiologie et Ethologie (DEPE), 67087, Strasbourg, France.
| | - Marie-Lazarine Poulle
- Université de Reims Champagne-Ardenne, EA 7510 ESCAPE, UFR de Médecine, 51 rue Cognacq Jay, 51095, Reims Cedex, France
- Université de Reims Champagne-Ardenne, Centre d'Etude et de Formation en Eco-Ethologie (CERFE), 5 rue de la Héronnière, 08240, Boult-aux-Bois, France
| | - Sylvain Piry
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, 755 avenue du Campus Agropolis, CS 300 16, 34988, Montferrier-sur-Lez cedex, France
| | - Jean-François Cosson
- UMR BIPAR, Animal Health Laboratory, INRA, ANSES, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, Maisons-Alfort, France
| | - Claire Larose
- DIANA PetFood Division, Z.A. du Gohélis, 56250, Elven, France
| | - Maxime Galan
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, 755 avenue du Campus Agropolis, CS 300 16, 34988, Montferrier-sur-Lez cedex, France
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17
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Deagle BE, Thomas AC, McInnes JC, Clarke LJ, Vesterinen EJ, Clare EL, Kartzinel TR, Eveson JP. Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data? Mol Ecol 2018; 28:391-406. [PMID: 29858539 PMCID: PMC6905394 DOI: 10.1111/mec.14734] [Citation(s) in RCA: 276] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/28/2018] [Accepted: 05/30/2018] [Indexed: 02/06/2023]
Abstract
Advances in DNA sequencing technology have revolutionized the field of molecular analysis of trophic interactions, and it is now possible to recover counts of food DNA sequences from a wide range of dietary samples. But what do these counts mean? To obtain an accurate estimate of a consumer's diet should we work strictly with data sets summarizing frequency of occurrence of different food taxa, or is it possible to use relative number of sequences? Both approaches are applied to obtain semi-quantitative diet summaries, but occurrence data are often promoted as a more conservative and reliable option due to taxa-specific biases in recovery of sequences. We explore representative dietary metabarcoding data sets and point out that diet summaries based on occurrence data often overestimate the importance of food consumed in small quantities (potentially including low-level contaminants) and are sensitive to the count threshold used to define an occurrence. Our simulations indicate that using relative read abundance (RRA) information often provides a more accurate view of population-level diet even with moderate recovery biases incorporated; however, RRA summaries are sensitive to recovery biases impacting common diet taxa. Both approaches are more accurate when the mean number of food taxa in samples is small. The ideas presented here highlight the need to consider all sources of bias and to justify the methods used to interpret count data in dietary metabarcoding studies. We encourage researchers to continue addressing methodological challenges and acknowledge unanswered questions to help spur future investigations in this rapidly developing area of research.
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Affiliation(s)
- Bruce E Deagle
- Australian Antarctic Division, Channel Highway, Kingston, TAS, Australia
| | | | - Julie C McInnes
- Australian Antarctic Division, Channel Highway, Kingston, TAS, Australia
| | - Laurence J Clarke
- Australian Antarctic Division, Channel Highway, Kingston, TAS, Australia.,Antarctic Climate & Ecosystems Cooperative Research Centre, University of Tasmania, Hobart, TAS, Australia
| | - Eero J Vesterinen
- Biodiversity Unit and Department of Biology, University of Turku, Turku, Finland.,Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Elizabeth L Clare
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Tyler R Kartzinel
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island
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18
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Kamenova S, Mayer R, Rubbmark OR, Coissac E, Plantegenest M, Traugott M. Comparing three types of dietary samples for prey DNA decay in an insect generalist predator. Mol Ecol Resour 2018; 18:966-973. [PMID: 29509995 DOI: 10.1111/1755-0998.12775] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 02/04/2018] [Accepted: 02/13/2018] [Indexed: 11/28/2022]
Abstract
The rapidly growing field of molecular diet analysis is becoming increasingly popular among ecologists, especially when investigating methodologically challenging groups, such as invertebrate generalist predators. Prey DNA detection success is known to be affected by multiple factors; however, the type of dietary sample has rarely been considered. Here, we address this knowledge gap by comparing prey DNA detection success from three types of dietary samples. In a controlled feeding experiment, using the carabid beetle Pterostichus melanarius as a model predator, we collected regurgitates, faeces and whole consumers (including their gut contents) at different time points postfeeding. All dietary samples were analysed using multiplex PCR, targeting three different length DNA fragments (128, 332 and 612 bp). Our results show that both the type of dietary sample and the size of the DNA fragment contribute to a significant part of the variation found in the detectability of prey DNA. Specifically, we observed that in both regurgitates and whole consumers, prey DNA was detectable significantly longer for all fragment sizes than for faeces. Based on these observations, we conclude that prey DNA detected from regurgitates and whole consumers DNA extracts are comparable, whereas prey DNA detected from faeces, though still sufficiently reliable for ecological studies, will not be directly comparable to the former. Therefore, regurgitates and faeces constitute a useful, nonlethal source for dietary information that could be applied to field studies in situations when invertebrate predators should not be killed.
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Affiliation(s)
- Stefaniya Kamenova
- Centre d'Etudes Biologiques de Chizé, Villiers-en-Bois, France
- Agrocampus Ouest UMR1349 IGEPP, Rennes, France
- Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Rebecca Mayer
- Mountain Agriculture Research Unit, Institute of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Oskar R Rubbmark
- Mountain Agriculture Research Unit, Institute of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Eric Coissac
- Laboratoire d'Ecologie Alpine (LECA), Université Grenoble-Alpes, Grenoble, France
- Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique, Grenoble, France
| | | | - Michael Traugott
- Mountain Agriculture Research Unit, Institute of Ecology, University of Innsbruck, Innsbruck, Austria
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19
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Thalinger B, Oehm J, Obwexer A, Traugott M. The influence of meal size on prey DNA detectability in piscivorous birds. Mol Ecol Resour 2017; 17:e174-e186. [PMID: 28776942 PMCID: PMC5725817 DOI: 10.1111/1755-0998.12706] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 07/14/2017] [Accepted: 07/25/2017] [Indexed: 12/01/2022]
Abstract
Molecular methods allow noninvasive assessment of vertebrate predator-prey systems at high taxonomic resolution by examining dietary samples such as faeces and pellets. To facilitate the interpretation of field-derived data, feeding trials, investigating the impacts of biological, methodological and environmental factors on prey DNA detection, have been conducted. The effect of meal size, however, has not yet been explicitly considered for vertebrate consumers. Moreover, different noninvasively obtained sample types remain to be compared in such experiments. Here, we present a feeding trial on abundant piscivorous birds, Great Cormorants (Phalacrocorax carbo), to assess meal size effects on postfeeding prey DNA detection success. Faeces and pellets were sampled twice a day after the feed of large (350-540 g), medium (190-345 g) and small (15-170 g) fish meals contributing either a large (>79%) or small (<38%) share to the daily consumption. Samples were examined for prey DNA and fish hard parts. Molecular analysis of faeces revealed that both large meal size and share had a significantly positive effect on prey DNA detection rate postfeeding. Furthermore, large meals were detectable for a significantly longer time span with a detection limit at ~76 hr and a 50% detection probability at ~32 hr postfeeding. In pellets, molecular methods reliably identified the meal consumed the previous day, which was not possible via morphological analysis or when examining individual faeces. The less reliable prey DNA detection of small meals or meal shares in faeces signifies the importance of large numbers of dietary samples to obtain reliable trophic data.
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Affiliation(s)
| | - Johannes Oehm
- Institute of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Armin Obwexer
- Institute of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Michael Traugott
- Institute of Ecology, University of Innsbruck, Innsbruck, Austria
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20
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Gosselin EN, Lonsinger RC, Waits LP. Comparing morphological and molecular diet analyses and fecal DNA sampling protocols for a terrestrial carnivore. WILDLIFE SOC B 2017. [DOI: 10.1002/wsb.749] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Elyce N. Gosselin
- Department of Fish and Wildlife Sciences; University of Idaho; Moscow ID 83844-1136 USA
| | - Robert C. Lonsinger
- College of Natural Resources, University of Wisconsin-Stevens Point, Stevens Point, WI 54482, USA; Department of Fish and Wildlife Sciences; University of Idaho; Moscow ID 83844-1136 USA
| | - Lisette P. Waits
- Department of Fish and Wildlife Sciences; University of Idaho; Moscow ID 83844-1136 USA
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21
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Oehm J, Thalinger B, Eisenkölbl S, Traugott M. Diet analysis in piscivorous birds: What can the addition of molecular tools offer? Ecol Evol 2017; 7:1984-1995. [PMID: 28331605 PMCID: PMC5355203 DOI: 10.1002/ece3.2790] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 12/29/2016] [Accepted: 01/05/2017] [Indexed: 11/21/2022] Open
Abstract
In trophic studies on piscivorous birds, it is vital to know which kind of dietary sample provides the information of interest and how the prey can be identified reliably and efficiently. Often, noninvasively obtained dietary samples such as regurgitated pellets, feces, and regurgitated fish samples are the preferred source of information. Fish prey has usually been identified via morphological analysis of undigested hard parts, but molecular approaches are being increasingly used for this purpose. What remains unknown, however, is which dietary sample type is best suited for molecular diet analysis and how the molecular results compare to those obtained by morphological analysis. Pellets, feces, and regurgitated fish samples of Great Cormorants (Phalacrocorax carbo sinensis) were examined for prey using both morphological hard part analysis and molecular prey identification. The sample types and methods were compared regarding number of species detected (overall and per sample) as well as the prey species composition and its variability among individual samples. Via molecular analysis, significantly higher numbers of prey species were detected in pellets, feces, and fish samples. Of the three sample types, pellets contained the most comprehensive trophic information and could be obtained with the lowest sampling effort. Contrastingly, dietary information obtained from feces was least informative and most variable. For all sample types, the molecular approach outperformed morphological hard part identification regarding the detectable prey spectrum and prey species composition. We recommend the use of pellets in combination with molecular prey identification to study the diet of piscivorous birds.
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Affiliation(s)
- Johannes Oehm
- Institute of Ecology University of Innsbruck Innsbruck Austria
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22
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Kamenova S, Bartley T, Bohan D, Boutain J, Colautti R, Domaizon I, Fontaine C, Lemainque A, Le Viol I, Mollot G, Perga ME, Ravigné V, Massol F. Invasions Toolkit. ADV ECOL RES 2017. [DOI: 10.1016/bs.aecr.2016.10.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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23
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Morin DJ, Higdon SD, Holub JL, Montague DM, Fies ML, Waits LP, Kelly MJ. Bias in carnivore diet analysis resulting from misclassification of predator scats based on field identification. WILDLIFE SOC B 2016. [DOI: 10.1002/wsb.723] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Dana J. Morin
- Department of Fish and Wildlife Conservation; Virginia Tech; Blacksburg VA 24061 USA
| | - Summer D. Higdon
- Department of Fish and Wildlife Conservation; Virginia Tech; Blacksburg VA 24061 USA
| | - Jennifer L. Holub
- Department of Fish and Wildlife Conservation; Virginia Tech; Blacksburg VA 24061 USA
| | - David M. Montague
- Department of Fish and Wildlife Conservation; Virginia Tech; Blacksburg VA 24061 USA
| | - Michael L. Fies
- Virginia Department of Game and Inland Fisheries; Verona VA 24482 USA
| | - Lisette P. Waits
- Department of Fish and Wildlife Science; University of Idaho; Moscow ID 83844 USA
| | - Marcella J. Kelly
- Department of Fish and Wildlife Conservation; Virginia Tech; Blacksburg VA 24061 USA
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24
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Oehm J, Thalinger B, Mayr H, Traugott M. Maximizing dietary information retrievable from carcasses of Great Cormorants Phalacrocorax carbo using a combined morphological and molecular analytical approach. THE IBIS 2016; 158:51-60. [PMID: 26877544 PMCID: PMC4739555 DOI: 10.1111/ibi.12337] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 11/03/2015] [Indexed: 05/11/2023]
Abstract
Avian carcasses can provide important information on the trophic ecology of birds. Usually, the number of carcasses available for examination is limited and therefore it is important to gain as much dietary information per specimen as possible. In piscivorous birds and raptors, the stomach has been the primary source of dietary information, whereas the gut (intestine) has so far been neglected as it usually contains only a few morphologically identifiable hard parts of prey. Molecular approaches have the potential to retrieve dietary information from the gut, although this has not yet been verified. As well as identifying the prey, it is important to estimate any secondary predation to avoid food web errors in dietary analyses. The assignment of accidentally consumed prey is notoriously difficult regardless of the prey identification approach used. In the present study, morphological and molecular analyses were, for the first time, combined to maximize the dietary information retrievable from the complete digestive tract of Great Cormorants Phalacrocorax carbo sinensis. Moreover, a novel approach based on predator-prey size ratios was applied to these piscivorous birds to minimize the number of samples that might contain secondarily predated prey. The stomach contents of the examined birds were found to provide the most dietary information when morphological and molecular analyses were used in combination. However, compared with the morphological approach, the molecular analysis increased the number of fish species detected by 39%. The molecular approach also permitted the identification of fish DNA in the Cormorant guts. Predator-prey size ratios derived from morphological analysis of fish hard parts can reduce the incidence of potential confounding influence of secondarily predated prey by 80%. Our findings demonstrate that a combination of morphological and molecular approaches maximizes the trophic information retrievable from bird carcasses.
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Affiliation(s)
- Johannes Oehm
- Institute of Ecology University of Innsbruck Technikerstraße 25 6020 Innsbruck Austria
| | - Bettina Thalinger
- Institute of Ecology University of Innsbruck Technikerstraße 25 6020 Innsbruck Austria
| | - Hannes Mayr
- Institute of Ecology University of Innsbruck Technikerstraße 25 6020 Innsbruck Austria
| | - Michael Traugott
- Institute of Ecology University of Innsbruck Technikerstraße 25 6020 Innsbruck Austria
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