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Buzan E, Potočnik H, Pokorny B, Potušek S, Iacolina L, Gerič U, Urzi F, Kos I. Molecular analysis of scats revealed diet and prey choice of grey wolves and Eurasian lynx in the contact zone between the Dinaric Mountains and the Alps. Front Zool 2024; 21:9. [PMID: 38500207 PMCID: PMC10949697 DOI: 10.1186/s12983-024-00530-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 03/13/2024] [Indexed: 03/20/2024] Open
Abstract
A comprehensive understanding of the dietary habits of carnivores is essential to get ecological insights into their role in the ecosystem, potential competition with other carnivorous species, and their effect on prey populations. Genetic analysis of non-invasive samples, such as scats, can supplement behavioural or microscopic diet investigations. The objective of this study was to employ DNA metabarcoding to accurately determine the prey species in grey wolf (Canis lupus) and Eurasian lynx (Lynx lynx) scat samples collected in the Julian Alps and the Dinaric Mountains, Slovenia. The primary prey of wolves were red deer (Cervus elaphus) (detected in 96% scat samples), European roe deer (Capreolus capreolus) (68%), and wild boar (Sus scrofa) (45%). A smaller portion of their diet consisted of mesocarnivores, small mammals, and domestic animals. In contrast, the lynx diet mostly consisted of European roe deer (82%) and red deer (64%). However, small mammals and domestic animals were also present in lynx diet, albeit to a lesser extent. Our findings indicate that the dietary habits of wolves and lynx are influenced by geographical location. Snapshot dietary analyses using metabarcoding are valuable for comprehending the behaviour and ecology of predators, and for devising conservation measures aimed at sustainable management of both their natural habitats and prey populations. However, to gain a more detailed understanding of wolf and lynx dietary habits and ecological impact, it would be essential to conduct long-term genetic monitoring of their diet.
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Affiliation(s)
- Elena Buzan
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia
- Faculty of Environmental Protection, Trg mladosti 7, 3320, Velenje, Slovenia
| | - Hubert Potočnik
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Boštjan Pokorny
- Faculty of Environmental Protection, Trg mladosti 7, 3320, Velenje, Slovenia
- Slovenian Forestry Institute, Večna pot 2, 1000, Ljubljana, Slovenia
| | - Sandra Potušek
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia
| | - Laura Iacolina
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia
- Department of Chemistry and Bioscience, Aalborg University, Frederik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Urška Gerič
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia
| | - Felicita Urzi
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia.
| | - Ivan Kos
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
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2
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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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Perry WB. Limited summer palate with no colonic irrigation required: life of a migratory shark through the metabarcoding lens. JOURNAL OF FISH BIOLOGY 2023; 103:1251. [PMID: 38148282 DOI: 10.1111/jfb.15636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
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4
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Alemany I, Pérez-Cembranos A, Pérez-Mellado V, Castro JA, Picornell A, Ramon C, Jurado-Rivera JA. DNA metabarcoding the diet of Podarcis lizards endemic to the Balearic Islands. Curr Zool 2023; 69:514-526. [PMID: 37637311 PMCID: PMC10449427 DOI: 10.1093/cz/zoac073] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 09/06/2022] [Indexed: 08/29/2023] Open
Abstract
Dietary studies are essential to unravel the functioning of ecosystems and ultimately to understand biodiversity. This task, which at first may seem simple, becomes especially complex in those cases of omnivorous species with highly variable diets. In this regard, the emergence of next-generation DNA sequencing methodologies represents a powerful tool to address the problem. Here we implement a high-throughput metabarcoding strategy based on the analysis of four molecular markers aimed at sequencing both mitochondrial (animal prey) and chloroplast (diet plants) genome fragments from fecal samples of two lizard species endemic to the Balearic Archipelago (Podarcis lilfordi and P. pityusensis) obtained through non-invasive methods. The results allowed for the characterization of their diets with a high degree of taxonomic detail and have contributed a large number of new trophic records. The reported diets are based mainly on the consumption of arthropods, mollusks and plants from a diversity of taxonomic orders, as well as carrion and marine subsidies. Our analyses also reveal inter- and intra-specific differences both in terms of seasonality and geographical distribution of the sampled lizard populations. These molecular findings provide new insights into the trophic interactions of these threatened endemic lizards in their unique and isolated ecosystems.
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Affiliation(s)
- Iris Alemany
- Deptartment of Biology, Universitat de les Illes Balears, Ctra. Valldemossa km 7’5, Palma de Mallorca, 07122, Balearic Islands, Spain
| | - Ana Pérez-Cembranos
- Department of Animal Biology, Universidad de Salamanca, Campus Miguel de Unamuno s/n, 37007, Salamanca, Spain
| | - Valentín Pérez-Mellado
- Department of Animal Biology, Universidad de Salamanca, Campus Miguel de Unamuno s/n, 37007, Salamanca, Spain
| | - José Aurelio Castro
- Deptartment of Biology, Universitat de les Illes Balears, Ctra. Valldemossa km 7’5, Palma de Mallorca, 07122, Balearic Islands, Spain
| | - Antònia Picornell
- Deptartment of Biology, Universitat de les Illes Balears, Ctra. Valldemossa km 7’5, Palma de Mallorca, 07122, Balearic Islands, Spain
| | - Cori Ramon
- Deptartment of Biology, Universitat de les Illes Balears, Ctra. Valldemossa km 7’5, Palma de Mallorca, 07122, Balearic Islands, Spain
| | - José A Jurado-Rivera
- Deptartment of Biology, Universitat de les Illes Balears, Ctra. Valldemossa km 7’5, Palma de Mallorca, 07122, Balearic Islands, Spain
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5
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Rijal DP, Hanebrekke T, Arneberg P, Johansen T, Sint D, Traugott M, Skern‐Mauritzen M, Westgaard J. Contaminants reach everywhere: Fish dietary samples should be surface decontaminated prior to molecular diet analysis. Ecol Evol 2023; 13:e10187. [PMID: 37342457 PMCID: PMC10277604 DOI: 10.1002/ece3.10187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 06/23/2023] Open
Abstract
Knowledge of trophic interaction is necessary to understand the dynamics of ecosystems and develop ecosystem-based management. The key data to measure these interactions should come from large-scale diet analyses with good taxonomic resolution. To that end, molecular methods that analyze prey DNA from guts and feces provide high-resolution dietary taxonomic data. However, molecular diet analysis may also produce unreliable results if the samples are contaminated by external sources of DNA. Employing the freshwater European whitefish (Coregonus lavaretus) as a tracer for sample contamination, we studied the possible route of whitefish in beaked redfish (Sebastes mentella) guts sampled in the Barents Sea. We used whitefish-specific COI primers for diagnostic analysis, and fish-specific 12S and metazoa-specific COI primers for metabarcoding analyses of intestine and stomach contents of fish samples that were either not cleaned, water cleaned, or bleach cleaned after being in contact with whitefish. Both the diagnostic and COI metabarcoding revealed clear positive effects of cleaning samples as whitefish were detected in significantly higher numbers of uncleaned samples compared to water or bleach-cleaned samples. Stomachs were more susceptible to contamination than intestines and bleach cleaning reduced the frequency of whitefish contamination. Also, the metabarcoding approach detected significantly more reads of whitefish in the stomach than in intestine samples. The diagnostic analysis and COI metabarcoding detected contaminants in a higher and comparable number of gut samples than the 12S-based approach. Our study underlines thus the importance of surface decontamination of aquatic samples to obtain reliable diet information from molecular data.
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Affiliation(s)
| | | | | | | | - Daniela Sint
- Applied Animal Ecology, Department of ZoologyUniversity of InnsbruckInnsbruckAustria
| | - Michael Traugott
- Applied Animal Ecology, Department of ZoologyUniversity of InnsbruckInnsbruckAustria
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6
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Oelze VM, O'Neal I, Wittig RM, Kupczik K, Schulz-Kornas E, Hohmann G. A skew in poo: Biases in primate fecal isotope analysis and recommendations for standardized sample preparation. Am J Primatol 2023; 85:e23436. [PMID: 36239010 DOI: 10.1002/ajp.23436] [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: 05/09/2022] [Revised: 08/29/2022] [Accepted: 09/05/2022] [Indexed: 01/05/2023]
Abstract
Feces are a treasure trove in the study of animal behavior and ecology. Stable carbon and nitrogen isotope analysis allows to assess the dietary niches of elusive primate species and primate breastfeeding behavior. However, some fecal isotope data may unwillingly be biased toward the isotope ratios of undigested plant matter, requiring more consistent sample preparation protocols. We assess the impact of this potential data skew in 114 fecal samples of wild bonobos (Pan paniscus) by measuring the isotope differences (Δ13 C, Δ15 N) between bulk fecal samples containing larger particles (>1 mm) and filtered samples containing only small particles (<1 mm). We assess the influence of fecal carbon and nitrogen content (ΔC:N) and sample donor age (subadult, adult) on the resulting Δ13 C, Δ15 N values (n = 228). Additionally, we measure the isotope ratios in three systematically sieved fecal samples of chimpanzees (Pan troglodytes verus), with particle sizes ranging from 20 μm to 8 mm (n = 30). We found differences in fecal carbon and nitrogen content, with the smaller fecal fraction containing more nitrogen on average. While the Δ13 C values were small and not affected by age or ΔC:N, the Δ15 N values were significantly influenced by fecal ΔC:N, possibly resulting from the differing proportions of undigested plant macroparticles. Significant relationships between carbon stable isotope ratios (δ13 C) values and %C in large fecal fractions of both age groups corroborated this assessment. Δ15 N values were significantly larger in adults than subadults, which should be of concern in isotope studies comparing adult females with infants to assess breastfeeding. We found a random variation of up to 3.0‰ in δ13 C and 2.0‰ in nitrogen stable isotope ratios within the chimpanzee fecal samples separated by particle sizes. We show that particle size influences isotope ratios and propose a simple, cost-effective filtration method for primate feces to exclude larger undigested food particles from the analysis, which can easily be adopted by labs worldwide.
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Affiliation(s)
- Vicky M Oelze
- Anthropology Department, University of California, Santa Cruz, Santa Cruz, California, USA
| | - Isabella O'Neal
- Anthropology Department, University of California, Santa Cruz, Santa Cruz, California, USA
| | - Roman M Wittig
- Department of Human Behavior, Max Planck Institute for Evolutionary Anthropology, Ecology and Culture, Leipzig, Germany.,Institute for Cognitive Sciences, CNRS UMR5229 University Claude Bernard Lyon 1, Bron, France
| | - Kornelius Kupczik
- Department of Anthropology, Faculty of Social Sciences, University of Chile, Ñuñoa, Santiago de Chile, Chile.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Ellen Schulz-Kornas
- Department of Cariology, Endodontology and Periodontology, University of Leipzig, Leipzig, Germany
| | - Gottfried Hohmann
- Department of Human Behavior, Max Planck Institute for Evolutionary Anthropology, Ecology and Culture, Leipzig, Germany.,Max-Planck-Institute of Animal Behavior, Konstanz, Germany
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7
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“Guess Who’s Coming to Dinner”: Molecular Tools to Reconstruct multilocus Genetic Profiles from Wild Canid Consumption Remains. Animals (Basel) 2022; 12:ani12182428. [PMID: 36139288 PMCID: PMC9495216 DOI: 10.3390/ani12182428] [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: 08/08/2022] [Revised: 09/05/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022] Open
Abstract
Non-invasive genetic sampling is a practical tool to monitor pivotal ecological parameters and population dynamic patterns of endangered species. It can be particularly suitable when applied to elusive carnivores such as the Apennine wolf (Canis lupus italicus) and the European wildcat (Felis silvestris silvestris), which can live in overlapping ecological contexts and sometimes share their habitats with their domestic free-ranging relatives, increasing the risk of anthropogenic hybridisation. In this case study, we exploited all the ecological and genetic information contained in a single biological canid faecal sample, collected in a forested area of central Italy, to detect any sign of trophic interactions between wolves and European wildcats or their domestic counterparts. Firstly, the faecal finding was morphologically examined, showing the presence of felid hair and claw fragment remains. Subsequently, total genomic DNA contained in the hair and claw samples was extracted and genotyped, through a multiple-tube approach, at canid and felid diagnostic panels of microsatellite loci. Finally, the obtained individual multilocus genotypes were analysed with reference wild and domestic canid and felid populations to assess their correct taxonomic status using Bayesian clustering procedures. Assignment analyses classified the genotype obtained from the endothelial cells present on the hair sample as a wolf with slight signals of dog ancestry, showing a qi = 0.954 (C.I. 0.780–1.000) to the wolf cluster, and the genotype obtained from the claw as a domestic cat, showing a qi = 0.996 (95% C.I. = 0.982–1.000) to the domestic cat cluster. Our results clearly show how a non-invasive multidisciplinary approach allows the cost-effective identification of both prey and predator genetic profiles and their taxonomic status, contributing to the improvement of our knowledge about feeding habits, predatory dynamics, and anthropogenic hybridisation risk in threatened species.
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8
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Fonseca ML, Ramírez-Pinzón MA, McNeil KN, Guevara M, Gómez-Gutiérrez LM, Harter K, Mongui A, Stevenson PR. Dietary preferences and feeding strategies of Colombian highland woolly monkeys. Sci Rep 2022; 12:14364. [PMID: 35999220 PMCID: PMC9399098 DOI: 10.1038/s41598-022-17655-5] [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: 02/08/2022] [Accepted: 07/28/2022] [Indexed: 12/02/2022] Open
Abstract
Primates are very selective in the foods they include in their diets with foraging strategies that respond to spatial and temporal changes in resource availability, distribution and quality. Colombian woolly monkeys (Lagothrix lagotricha lugens), one of the largest primate species in the Americas, feed mainly on fruits, but they also eat a high percentage of arthropods. This differs from closely related Atelid species that supplement their diet with leaves. In an 11 month study, we investigated the foraging strategies of this endemic monkey and assessed how resource availability affects dietary selection. Using behavioural, phenological, arthropod sampling and metabarcoding methods, we recorded respectively foraging time, forest productivity, arthropod availability in the forest and arthropod consumption. Scat samples and capturing canopy substrates (i.e. moss, bromeliads, aerial insects) were used for assigning arthropod taxonomy. The most important resource in the diet was fruits (54%), followed by arthropods (28%). Resource availability predicted feeding time for arthropods but not for fruits. Further, there was a positive relationship between feeding time on fruits and arthropods, suggesting that eating both resources during the same periods might work as an optimal strategy to maximize nutrient intake. Woolly monkeys preferred and avoided some fruit and arthropod items available in their home range, choosing a wide variety of arthropods. Geometrid moths (Lepidoptera) were the most important and consistent insects eaten over time. We found no differences in the type of arthropods adults and juveniles ate, but adults invested more time foraging for this resource, especially in moss. Although woolly monkeys are generalist foragers, they do not select their food items randomly or opportunistically.
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Affiliation(s)
- Manuel L Fonseca
- Laboratorio de Ecología de Bosques Tropicales y Primatología (LEBTYP), Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia. .,Comparative Zoology, Institut für Evolution und Ökologie (EvE), Eberhard Karls Universität Tübingen, Tübingen, Germany.
| | - Marcela A Ramírez-Pinzón
- Laboratorio de Zoología y Ecología Acuática (LAZOEA), Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
| | - Kaylie N McNeil
- Department of Anthropology, University of Texas at San Antonio, San Antonio, TX, USA
| | - Michelle Guevara
- Departamento de Ciencias Biológicas, Facultad de Ciencias, Universidad de los Andes, Bogotá, Colombia
| | - Laura M Gómez-Gutiérrez
- Laboratorio de Ecología de Bosques Tropicales y Primatología (LEBTYP), Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
| | - Klaus Harter
- Zentrum für Molekularbiologie der Pflanzen (ZMBP), Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Alvaro Mongui
- Departamento de Ciencias Biológicas, Facultad de Ciencias, Universidad de los Andes, Bogotá, Colombia
| | - Pablo R Stevenson
- Laboratorio de Ecología de Bosques Tropicales y Primatología (LEBTYP), Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
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9
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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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10
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Verkuil YI, Nicolaus M, Ubels R, Dietz MW, Samplonius JM, Galema A, Kiekebos K, de Knijff P, Both C. DNA metabarcoding quantifies the relative biomass of arthropod taxa in songbird diets: Validation with camera‐recorded diets. Ecol Evol 2022; 12:e8881. [PMID: 35571761 PMCID: PMC9077022 DOI: 10.1002/ece3.8881] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/06/2022] [Accepted: 04/15/2022] [Indexed: 11/24/2022] Open
Abstract
Ecological research is often hampered by the inability to quantify animal diets. Diet composition can be tracked through DNA metabarcoding of fecal samples, but whether (complex) diets can be quantitatively determined with metabarcoding is still debated and needs validation using free‐living animals. This study validates that DNA metabarcoding of feces can retrieve actual ingested taxa, and most importantly, that read numbers retrieved from sequencing can also be used to quantify the relative biomass of dietary taxa. Validation was done with the hole‐nesting insectivorous Pied Flycatcher whose diet was quantified using camera footage. Size‐adjusted counts of food items delivered to nestlings were used as a proxy for provided biomass of prey orders and families, and subsequently, nestling feces were assessed through DNA metabarcoding. To explore potential effects of digestion, gizzard and lower intestine samples of freshly collected birds were subjected to DNA metabarcoding. For metabarcoding with Cytochrome Oxidase subunit I (COI), we modified published invertebrate COI primers LCO1490 and HCO1777, which reduced host reads to 0.03%, and amplified Arachnida DNA without significant changing the recovery of other arthropod taxa. DNA metabarcoding retrieved all commonly camera‐recorded taxa. Overall, and in each replicate year (N = 3), the relative scaled biomass of prey taxa and COI read numbers correlated at R = .85 (95CI:0.68–0.94) at order level and at R = .75 (CI:0.67–0.82) at family level. Similarity in arthropod community composition between gizzard and intestines suggested limited digestive bias. This DNA metabarcoding validation demonstrates that quantitative analyses of arthropod diet is possible. We discuss the ecological applications for insectivorous birds.
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Affiliation(s)
- Yvonne I. Verkuil
- Conservation Ecology Group Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen The Netherlands
| | - Marion Nicolaus
- Conservation Ecology Group Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen The Netherlands
| | - Richard Ubels
- Conservation Ecology Group Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen The Netherlands
| | - Maurine W. Dietz
- Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen The Netherlands
| | - Jelmer M. Samplonius
- Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen The Netherlands
| | - Annabet Galema
- Conservation Ecology Group Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen The Netherlands
| | - Kim Kiekebos
- Conservation Ecology Group Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen The Netherlands
| | - Peter de Knijff
- Department of Human Genetics Leiden University Medical Centre Leiden The Netherlands
| | - Christiaan Both
- Conservation Ecology Group Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen The Netherlands
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11
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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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12
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MacAulay KM, Spilker EG, Berg JE, Hebblewhite M, Merrill EH. Beyond the encounter: Predicting multi‐predator risk to elk (
Cervus canadensis
) in summer using predator scats. Ecol Evol 2022; 12:e8589. [PMID: 35222962 PMCID: PMC8843817 DOI: 10.1002/ece3.8589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 12/23/2021] [Accepted: 01/10/2022] [Indexed: 11/08/2022] Open
Affiliation(s)
- Kara M. MacAulay
- Department of Biological Sciences University of Alberta Edmonton Alberta Canada
| | - Eric G. Spilker
- Department of Biological Sciences University of Alberta Edmonton Alberta Canada
| | - Jodi E. Berg
- Department of Biological Sciences University of Alberta Edmonton Alberta Canada
| | - Mark Hebblewhite
- Wildlife Biology Program Department of Ecosystem and Conservation Sciences W. A. Franke College of Forestry and Conservation University of Montana Missoula Montana USA
| | - Evelyn H. Merrill
- Department of Biological Sciences University of Alberta Edmonton Alberta Canada
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13
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Kataoka H, Koita N, Kondo NI, Ito HC, Nakajima M, Momose K, Iima H, Yoshino T, Amano T, Kitazawa T, Endoh D, Nakajima N, Teraoka H. Metabarcoding of feces and intestinal contents to determine carnivorous diets in red-crowned cranes in eastern Hokkaido, Japan. J Vet Med Sci 2022; 84:358-367. [PMID: 35046239 PMCID: PMC8983284 DOI: 10.1292/jvms.21-0516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The red-crowned crane Grus japonensis in Hokkaido, Japan forms a closed population as a residence that is independent of the mainland population. Based on observations of a
limited number of individuals as well as cranes in captivity, red-crowned cranes are omnivores and eat fish, worms, insects and plants in their own territories except in winter, when they
are fed with dent corn that is supplied in eastern Hokkaido. DNA metabarcoding based on high throughput sequencing was carried out using universal primer sets for cytochrome oxidase subunit
I gene. Feces from 27 chicks collected in June and July in the period from 2016 to 2018 and intestinal contents from 33 adult and subadult cranes that were found dead almost throughout year
in 2006–2013 in the field in eastern Hokkaido were used. Although compositions varied considerably in the cranes, both insects and fish were found in adults and subadults to the same
extents, while insects were predominant in chicks. Both insects and fish were detected in all seasons for adults and subadults. Horse flies, scarab beetles and weevils accounted for the most
of the insects regardless of the life stage. Dace, stickleback, flatfish and sculpin were the major fish species in adults, while chicks ate almost only stickleback. The results provide the
first comprehensive data on carnivorous diets in wild red-crowned cranes in eastern Hokkaido as basis for conservation of red-crowned cranes, for which the life style and area continue to
change.
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Affiliation(s)
| | - Nanami Koita
- School of Veterinary Medicine, Rakuno Gakuen University
| | | | - Hiroshi C Ito
- Biodiversity Division, National Institute for Environmental Studies
| | - Momoko Nakajima
- Biodiversity Division, National Institute for Environmental Studies
| | | | | | | | - Tomoko Amano
- College of Agriculture, Food and Environment Sciences, Rakuno Gakuen University
| | | | - Daiji Endoh
- School of Veterinary Medicine, Rakuno Gakuen University
| | | | - Hiroki Teraoka
- School of Veterinary Medicine, Rakuno Gakuen University.,NPO Red-crowned Crane Conservancy
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14
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Hata A, Nakashita R, Fukasawa K, Minami M, Fukue Y, Higuchi N, Uno H, Nakajima Y, Saeki M, Kozakai C, Takada MB. Occurrence patterns of crop-foraging sika deer distribution in an agriculture-forest landscape revealed by nitrogen stable isotopes. Ecol Evol 2021; 11:15303-15311. [PMID: 34765179 PMCID: PMC8571634 DOI: 10.1002/ece3.8216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 09/05/2021] [Accepted: 09/24/2021] [Indexed: 11/09/2022] Open
Abstract
Conflicts arising from the consumption of anthropogenic foods by wildlife are increasing worldwide. Conventional tools for evaluating the spatial distribution pattern of large terrestrial mammals that consume anthropogenic foods have various limitations, despite their importance in management to mitigate conflicts. In this study, we examined the spatial distribution pattern of crop-foraging sika deer by performing nitrogen stable isotope analyses of bone collagen. We evaluated whether crop-foraging deer lived closer to agricultural crop fields during the winter and spring, when crop production decreases. We found that female deer in proximity to agricultural crop fields during the winter and spring were more likely to be crop-foraging individuals. Furthermore, the likelihood of crop consumption by females decreased by half as the distance to agricultural crop fields increased to 5-10 km. We did not detect a significant trend in the spatial distribution of crop-foraging male deer. The findings of spatial distribution patterns of crop-foraging female deer will be useful for the establishment of management areas, such as zonation, for efficient removal of them.
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Affiliation(s)
- Ayaka Hata
- Institute of Livestock and Grassland ScienceNational Agriculture and Food Research Organization (NARO)TsukubaIbarakiJapan
| | - Rumiko Nakashita
- Forestry and Forest Products Research InstituteTsukubaIbarakiJapan
| | - Keita Fukasawa
- Center for Environmental Biology and Ecosystem StudiesNational Institute for Environmental StudiesTsukubaIbarakiJapan
| | - Masato Minami
- School of Veterinary MedicineAzabu UniversitySagamiharaKanagawaJapan
| | - Yuko Fukue
- Insutitute for Biodiversity Research and Education EarthwormKaruizawaNaganoJapan
| | - Naoko Higuchi
- Insutitute for Biodiversity Research and Education EarthwormKaruizawaNaganoJapan
| | - Hikaru Uno
- Advanced Analysis CenterNAROTsukubaIbarakiJapan
| | | | - Midori Saeki
- Institute of Livestock and Grassland ScienceNational Agriculture and Food Research Organization (NARO)TsukubaIbarakiJapan
| | - Chinatsu Kozakai
- Institute of Livestock and Grassland ScienceNational Agriculture and Food Research Organization (NARO)TsukubaIbarakiJapan
| | - Mayura B. Takada
- Faculty of Science and EngineeringChuo UniversityBunkyo‐kuTokyoJapan
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15
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Lazic T, Pierri C, Corriero G, Balech B, Cardone F, Deflorio M, Fosso B, Gissi C, Marzano M, Nonnis Marzano F, Pesole G, Santamaria M, Gristina M. Evaluating the Efficiency of DNA Metabarcoding to Analyze the Diet of Hippocampus guttulatus (Teleostea: Syngnathidae). Life (Basel) 2021; 11:life11100998. [PMID: 34685370 PMCID: PMC8540156 DOI: 10.3390/life11100998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 12/14/2022] Open
Abstract
Seahorses are considered a flagship species for conservation efforts and due to their conservation status, improving knowledge on their dietary composition while applying a non-invasive approach, could be useful. Using Hippocampus guttulatus as a case study, the present study represents pioneering research into investigating the diet of seahorses by NGS-based DNA metabarcoding of fecal samples. The study developed and tested the protocol for fecal DNA metabarcoding during the feeding trials where captive seahorses were fed on a diet of known composition; the process was subsequently applied on fecal samples collected from wild individuals. The analysis of samples collected during the feeding trials indicated the reliability of the applied molecular approach by allowing the characterization of the effectively ingested prey. In the field study, among detected prey species, results revealed that the majority of the seahorse samples contained taxa such as Amphipoda, Decapoda, Isopoda, and Calanoida, while less common prey taxa were Gastropoda and Polyplacophora. As only a small amount of starting fecal material is needed and the sampling procedure is neither invasive nor lethal. The present study indicates DNA metabarcoding as useful for investigating seahorse diet and could help define management and conservation actions.
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Affiliation(s)
- Tamara Lazic
- Department of Biology, University of Bari, 70125 Bari, Italy; (T.L.); (G.C.)
| | - Cataldo Pierri
- Department of Biology, University of Bari, 70125 Bari, Italy; (T.L.); (G.C.)
- Correspondence:
| | - Giuseppe Corriero
- Department of Biology, University of Bari, 70125 Bari, Italy; (T.L.); (G.C.)
| | - Bachir Balech
- Institute of Biomembrane, Bioenergetics and Molecular Biotechnology (IBIOM), National Council of Research (CNR), 70121 Bari, Italy; (B.B.); (B.F.); (C.G.); (M.M.); (G.P.); (M.S.)
| | - Frine Cardone
- Department of Integrated Marine Ecology, Zoological Station Anton Dohrn, 80127 Naples, Italy;
| | - Michele Deflorio
- Department of Veterinary Medicine, University of Bari, 70125 Bari, Italy;
| | - Bruno Fosso
- Institute of Biomembrane, Bioenergetics and Molecular Biotechnology (IBIOM), National Council of Research (CNR), 70121 Bari, Italy; (B.B.); (B.F.); (C.G.); (M.M.); (G.P.); (M.S.)
| | - Carmela Gissi
- Institute of Biomembrane, Bioenergetics and Molecular Biotechnology (IBIOM), National Council of Research (CNR), 70121 Bari, Italy; (B.B.); (B.F.); (C.G.); (M.M.); (G.P.); (M.S.)
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, 70125 Bari, Italy
| | - Marinella Marzano
- Institute of Biomembrane, Bioenergetics and Molecular Biotechnology (IBIOM), National Council of Research (CNR), 70121 Bari, Italy; (B.B.); (B.F.); (C.G.); (M.M.); (G.P.); (M.S.)
| | - Francesco Nonnis Marzano
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43121 Parma, Italy;
| | - Graziano Pesole
- Institute of Biomembrane, Bioenergetics and Molecular Biotechnology (IBIOM), National Council of Research (CNR), 70121 Bari, Italy; (B.B.); (B.F.); (C.G.); (M.M.); (G.P.); (M.S.)
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, 70125 Bari, Italy
| | - Monica Santamaria
- Institute of Biomembrane, Bioenergetics and Molecular Biotechnology (IBIOM), National Council of Research (CNR), 70121 Bari, Italy; (B.B.); (B.F.); (C.G.); (M.M.); (G.P.); (M.S.)
| | - Michele Gristina
- Institute of Anthropic Impacts and Sustainability in Marine Environment (IAS), National Council of Research (CNR), 90100 Palermo, Italy;
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16
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DNA metabarcoding reveals the dietary composition in the endangered black-faced spoonbill. Sci Rep 2021; 11:18773. [PMID: 34548502 PMCID: PMC8455529 DOI: 10.1038/s41598-021-97337-w] [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: 03/10/2021] [Accepted: 08/18/2021] [Indexed: 12/03/2022] Open
Abstract
Extensive loss of natural wetlands caused by changes in land use largely diminishes the food resources essential for the survival of migratory waterbirds. Globally, the decline in waterbird populations in East Asia is the most serious, with 64% of these populations showing a decreasing trend. In this study, we applied DNA metabarcoding to examine the spatiotemporal variations and diversities in the dietary compositions of migratory waterbirds in a natural/artificial wetland complex in Asia. By investigating 110 fecal samples from the endangered black-faced spoonbill (Platalea minor) wintering in the wetland, our results show that P. minor had a broad dietary spectrum. The birds fed on at least 26 species in the classes Actinopterygii and Malacostraca, with Mugiliformes, Cichliformes, and Gobiiformes being the main taxa in their diets. Our results also demonstrated clear patterns of the spatiotemporal variations between the roosting groups and intraspecific variations between the individuals, which potentially reflect some of their feeding habits, and the probable usage of different habitat types in the wetland complex. Using high-throughput sequencing, we were able to elucidate the food resources that are critical to P. minor non-invasively, this method can also be used to provide invaluable information for the conservation of many other waterbird species.
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17
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Tsukada H, Nishikawa Y, Shimada H, Hijikata K, Minami M. A refined method for estimating the number of earthworm chaetae in carnivore feces. Ecol Res 2021. [DOI: 10.1111/1440-1703.12223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hideharu Tsukada
- Laboratory of Wildlife Ecology and Conservation, Department of Animal Science and Biotechnology, School of Veterinary Medicine Azabu University Sagamihara Japan
| | - Yuka Nishikawa
- Laboratory of Wildlife Ecology and Conservation, Department of Animal Science and Biotechnology, School of Veterinary Medicine Azabu University Sagamihara Japan
| | - Haruka Shimada
- Laboratory of Wildlife Ecology and Conservation, Department of Animal Science and Biotechnology, School of Veterinary Medicine Azabu University Sagamihara Japan
| | - Koji Hijikata
- Laboratory of Wildlife Ecology and Conservation, Department of Animal Science and Biotechnology, School of Veterinary Medicine Azabu University Sagamihara Japan
| | - Masato Minami
- Laboratory of Wildlife Ecology and Conservation, Department of Animal Science and Biotechnology, School of Veterinary Medicine Azabu University Sagamihara Japan
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18
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eDNA metabarcoding for biodiversity assessment, generalist predators as sampling assistants. Sci Rep 2021; 11:6820. [PMID: 33767219 PMCID: PMC7994446 DOI: 10.1038/s41598-021-85488-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 02/24/2021] [Indexed: 01/31/2023] Open
Abstract
With an accelerating negative impact of anthropogenic actions on natural ecosystems, non-invasive biodiversity assessments are becoming increasingly crucial. As a consequence, the interest in the application of environmental DNA (eDNA) survey techniques has increased. The use of eDNA extracted from faeces from generalist predators, have recently been described as "biodiversity capsules" and suggested as a complementary tool for improving current biodiversity assessments. In this study, using faecal samples from two generalist omnivore species, the Eurasian badger and the red fox, we evaluated the applicability of eDNA metabarcoding in determining dietary composition, compared to macroscopic diet identification techniques. Subsequently, we used the dietary information obtained to assess its contribution to biodiversity assessments. Compared to classic macroscopic techniques, we found that eDNA metabarcoding detected more taxa, at higher taxonomic resolution, and proved to be an important technique to verify the species identification of the predator from field collected faeces. Furthermore, we showed how dietary analyses complemented field observations in describing biodiversity by identifying consumed flora and fauna that went unnoticed during field observations. While diet analysis approaches could not substitute field observations entirely, we suggest that their integration with other methods might overcome intrinsic limitations of single techniques in future biodiversity surveys.
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19
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Bachiller E, Albo-Puigserver M, Giménez J, Pennino MG, Marí-Mena N, Esteban A, Lloret-Lloret E, Jadaud A, Carro B, Bellido JM, Coll M. A trophic latitudinal gradient revealed in anchovy and sardine from the Western Mediterranean Sea using a multi-proxy approach. Sci Rep 2020; 10:17598. [PMID: 33077761 PMCID: PMC7572414 DOI: 10.1038/s41598-020-74602-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 10/05/2020] [Indexed: 12/21/2022] Open
Abstract
This work combines state-of-the-art methods (DNA metabarcoding) with classic approaches (visual stomach content characterization and stable isotope analyses of nitrogen (δ15N) and carbon (δ13C)) to investigate the trophic ecology of anchovy (Engraulis encrasicolus) and sardine (Sardina pilchardus) at high taxonomic and spatial resolution in the Western Mediterranean Sea. Gut contents observed are in accordance with the dietary plasticity generally described for anchovy and sardine, suggesting a diet related to the opportunistic ingestion of available prey in a certain area and/or time. Genetic tools also showed modest inter-specific differences regarding ingested species. However, inter-specific and intra-specific differences in ingested prey frequencies and prey biomass reflected a latitudinal signal that could indicate a more effective predation on large prey like krill by anchovy versus sardine, as well as a generalized higher large prey ingestion by both species southwards. In fact, both species presented lower δ15N in the northernmost area. This latitudinal gradient indicates changes in the trophic ecology of anchovy and sardine that coincide with previously described better biological conditions for fish in the southern part of the study area as well as higher landings of both species in recent years.
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Affiliation(s)
- Eneko Bachiller
- Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain. .,AZTI, Sustainable Fisheries Management (Data), Basque Research and Technology Alliance (BRTA), Txatxarramendi uhartea z/g, 48395, Sukarrieta, Bizkaia (Basque Country), Spain.
| | - Marta Albo-Puigserver
- Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Joan Giménez
- Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Maria Grazia Pennino
- Instituto Español de Oceanografía, Centro Oceanográfico de Vigo, Subida Radio Faro, 50, 36390, Vigo, Spain
| | - Neus Marí-Mena
- AllGenetics and Biology SL, Edificio CICA, Campus de Elviña, 15008, A Coruña, Spain
| | - Antonio Esteban
- Instituto Español de Oceanografía, Centro Oceanográfico de Murcia, Varadero 1 Apdo 22, 30740, San Pedro del Pinatar, Murcia, Spain
| | - Elena Lloret-Lloret
- Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Angelique Jadaud
- Marine Biodiversity, Exploitation and Conservation (MARBEC), Ifremer, University Montpellier, CNRS, IRD, Sète, France
| | - Belén Carro
- AllGenetics and Biology SL, Edificio CICA, Campus de Elviña, 15008, A Coruña, Spain
| | - José María Bellido
- Instituto Español de Oceanografía, Centro Oceanográfico de Murcia, Varadero 1 Apdo 22, 30740, San Pedro del Pinatar, Murcia, Spain
| | - Marta Coll
- Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
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20
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Olin JA, Shipley ON, Cerrato RM, Nitschke P, Magen C, Frisk MG. Separation of realized ecological niche axes among sympatric tilefishes provides insight into potential drivers of co-occurrence in the NW Atlantic. Ecol Evol 2020; 10:10886-10898. [PMID: 33072303 PMCID: PMC7548204 DOI: 10.1002/ece3.6745] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 08/04/2020] [Accepted: 08/11/2020] [Indexed: 02/01/2023] Open
Abstract
Golden and Blueline Tilefish (Lopholatilus chamaeleonticeps and Caulolatilus microps) are keystone taxa in northwest (NW) Atlantic continental shelf-edge environments due to their biotic (trophic-mediated) and abiotic (ecosystem engineering) functional roles combined with high-value fisheries. Despite this importance, the ecological niche dynamics (i.e., those relating to trophic behavior and food-web interactions) of these sympatric species are poorly understood, knowledge of which may be consequential for maintaining both ecosystem function and fishery sustainability. We used stable isotope ratios of carbon (δ13C) and nitrogen (δ15N) to build realized ecological niche hypervolumes to serve as proxies for diet and production use patterns of L. chamaeleonticeps and C. microps. We hypothesized that: (a) species exhibit ontogenetic shifts in diet and use of production sources; (b) species acquire energy from spatially distinct resource pools that reflect a sedentary life-history and differential use of the continental shelf-edge; and (c) species exhibit differentiation in one or more measured niche axes. We found evidence for ontogenetic shifts in diet (δ15N) but not production source (δ13C) in both species, suggesting a subtle expansion of measured ecological niche axes. Spatial interpolation of stable isotope ratios showed distinct latitudinal gradients; for example, individuals were 13C enriched in northern and 15N enriched in southern regions, supporting the assertion that tilefish species acquire energy from regional resource pools. High isotopic overlap was observed among species (≥82%); however, when hypervolumes included depth and region of capture, overlap among species substantially decreased to overlap estimates of 15%-77%. This suggests that spatial segregation could alleviate potential competition for resources among tilefish species inhabiting continental shelf-edge environments. Importantly, our results question the consensus interpretation of isotopic overlap estimates as representative of direct competition among species for shared resources or habitats, instead identifying habitat segregation as a possible mechanism for coexistence of tilefish species in the NW Atlantic.
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Affiliation(s)
- Jill A Olin
- Great Lakes Research Center Michigan Technological University Houghton Michigan USA
| | - Oliver N Shipley
- School of Marine & Atmospheric Sciences Stony Brook University Stony Brook New York USA
| | - Robert M Cerrato
- School of Marine & Atmospheric Sciences Stony Brook University Stony Brook New York USA
| | - Paul Nitschke
- NOAA-NMFS Northeast Fisheries Science Center Woods Hole Massachusetts USA
| | - Cédric Magen
- Chesapeake Biological Laboratory University of Maryland Solomons Maryland USA
| | - Michael G Frisk
- School of Marine & Atmospheric Sciences Stony Brook University Stony Brook New York USA
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21
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Correction: Food from faeces: Evaluating the efficacy of scat DNA metabarcoding in dietary analyses. PLoS One 2020; 15:e0228950. [PMID: 32023314 PMCID: PMC7001914 DOI: 10.1371/journal.pone.0228950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0225805.].
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22
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Thuo D, Furlan E, Broekhuis F, Kamau J, Macdonald K, Gleeson DM. Food from faeces: Evaluating the efficacy of scat DNA metabarcoding in dietary analyses. PLoS One 2019; 14:e0225805. [PMID: 31851671 PMCID: PMC6980833 DOI: 10.1371/journal.pone.0225805] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 11/12/2019] [Indexed: 02/07/2023] Open
Abstract
Scat DNA metabarcoding is increasingly being used to track the feeding ecology of elusive wildlife species. This approach has greatly increased the resolution and detection success of prey items contained in scats when compared with other classical methods. However, there have been few studies that have systematically tested the applicability and reliability of this approach to study the diet of large felids species in the wild. Here we assessed the effectiveness of this approach in the cheetah Acinonyx jubatus. We tested how scat degradation, meal size, prey species consumed and feeding day (the day a particular prey was consumed) influenced prey DNA detection success in captive cheetahs. We demonstrated that it is possible to obtain diet information from 60-day old scats using genetic approaches, but the efficiency decreased over time. Probability of species-identification was highest for food items consumed one day prior to scat collection and the probability of being able to identify the species consumed increased with the proportion of the prey consumed. Detection success varied among prey species but not by individual cheetah. Identification of prey species using DNA detection methods from a single consumption event worked for samples collected between 8 and 72 hours post-feeding. Our approach confirms the utility of genetic approaches to identify prey species in scats and highlight the need to account for the systematic bias in results to control for possible scat degradation, feeding day, meal size and prey species consumed especially in the wild-collected scats.
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Affiliation(s)
- David Thuo
- Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory, Australia
- Kenya Wildlife Trust, Nairobi, Kenya
- * E-mail:
| | - Elise Furlan
- Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory, Australia
| | - Femke Broekhuis
- Kenya Wildlife Trust, Nairobi, Kenya
- Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Tubney, United Kingdom
| | - Joseph Kamau
- Molecular Biology Laboratory, Institute of Primate Research, Nairobi, Kenya
- Department of Biochemistry, University of Nairobi, Nairobi, Kenya
| | - Kyle Macdonald
- National Zoo and Aquarium, Canberra, Yarralumla, Australian Capital Territory, Australia
| | - Dianne M. Gleeson
- Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory, Australia
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