1
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Cuff JP, Evans DM, Vaughan IP, Wilder SM, Tercel MPTG, Windsor FM. Networking nutrients: How nutrition determines the structure of ecological networks. J Anim Ecol 2024; 93:974-988. [PMID: 38946110 DOI: 10.1111/1365-2656.14124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 05/29/2024] [Indexed: 07/02/2024]
Abstract
Nutrients can shape ecological interactions but remain poorly integrated into ecological networks. Concepts such as nutrient-specific foraging nevertheless have the potential to expose the mechanisms structuring complex ecological systems. Nutrients also present an opportunity to predict dynamic processes, such as interaction rewiring and extinction cascades, and increase the accuracy of network analyses. Here, we propose the concept of nutritional networks. By integrating nutritional data into ecological networks, we envisage significant advances to our understanding of ecological processes from individual to ecosystem scales. We show that networks can be constructed with nutritional data to illuminate how nutrients structure ecological interactions in natural systems through an empirical example. Throughout, we identify fundamental ecological hypotheses that can be explored in a nutritional network context, alongside methods for resolving those networks. Nutrients influence the structure and complexity of ecological networks through mechanistic processes and concepts including nutritional niche differentiation, functional responses, landscape diversity, ecological invasions and ecosystem robustness. Future research on ecological networks should consider nutrients when investigating the drivers of network structure and function.
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Affiliation(s)
- Jordan P Cuff
- 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
| | - Ian P Vaughan
- School of Biosciences, Cardiff University, Cardiff, UK
| | - Shawn M Wilder
- Department of Integrative Biology, 501 Life Sciences West, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Maximillian P T G Tercel
- School of Biosciences, Cardiff University, Cardiff, UK
- Durrell Wildlife Conservation Trust, Trinity, Jersey
| | - Fredric M Windsor
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
- School of Biosciences, Cardiff University, Cardiff, UK
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2
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Meira A, Byers JE, Sousa R. A global synthesis of predation on bivalves. Biol Rev Camb Philos Soc 2024; 99:1015-1057. [PMID: 38294132 DOI: 10.1111/brv.13057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 12/29/2023] [Accepted: 01/16/2024] [Indexed: 02/01/2024]
Abstract
Predation is a dominant structuring force in ecological communities. In aquatic environments, predation on bivalves has long been an important focal interaction for ecological study because bivalves have central roles as ecosystem engineers, basal components of food webs, and commercial commodities. Studies of bivalves are common, not only because of bivalves' central roles, but also due to the relative ease of studying predatory effects on this taxonomic group. To understand patterns in the interactions of bivalves and their predators we synthesised data from 52 years of peer-reviewed studies on bivalve predation. Using a systematic search, we compiled 1334 studies from 75 countries, comprising 61 bivalve families (N = 2259), dominated by Mytilidae (29% of bivalves), Veneridae (14%), Ostreidae (8%), Unionidae (7%), and Dreissenidae and Tellinidae (6% each). A total of 2036 predators were studied, with crustaceans the most studied predator group (34% of predators), followed by fishes (24%), molluscs (17%), echinoderms (10%) and birds (6%). The majority of studies (86%) were conducted in marine systems, in part driven by the high commercial value of marine bivalves. Studies in freshwater ecosystems were dominated by non-native bivalves and non-native predator species, which probably reflects the important role of biological invasions affecting freshwater biodiversity. In fact, while 81% of the studied marine bivalve species were native, only 50% of the freshwater species were native to the system. In terms of approach, most studies used predation trials, visual analysis of digested contents and exclusion experiments to assess the effects of predation. These studies reflect that many factors influence bivalve predation depending on the species studied, including (i) species traits (e.g. behaviour, morphology, defence mechanisms), (ii) other biotic interactions (e.g. presence of competitors, parasites or diseases), and (iii) environmental context (e.g. temperature, current velocity, beach exposure, habitat complexity). There is a lack of research on the effects of bivalve predation at the population and community and ecosystem levels (only 7% and 0.5% of studies respectively examined impacts at these levels). At the population level, the available studies demonstrate that predation can decrease bivalve density through consumption or the reduction of recruitment. At the community and ecosystem level, predation can trigger effects that cascade through trophic levels or effects that alter the ecological functions bivalves perform. Given the conservation and commercial importance of many bivalve species, studies of predation should be pursued in the context of global change, particularly climate change, acidification and biological invasions.
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Affiliation(s)
- Alexandra Meira
- CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus Gualtar, Braga, 4710-057, Portugal
| | - James E Byers
- Odum School of Ecology, University of Georgia, 140 E. Green St, Athens, GA, 30602, USA
| | - Ronaldo Sousa
- CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus Gualtar, Braga, 4710-057, Portugal
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3
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Yoshimura H, Hayakawa T, Kikuchi DM, Zhumabai Uulu K, Qi H, Sugimoto T, Sharma K, Kinoshita K. Metabarcoding analysis provides insight into the link between prey and plant intake in a large alpine cat carnivore, the snow leopard. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240132. [PMID: 39076800 PMCID: PMC11285773 DOI: 10.1098/rsos.240132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 07/31/2024]
Abstract
Species of the family Felidae are thought to be obligate carnivores. However, detection of plants in their faeces raises questions about the role of plants in their diet. This is particularly true for the snow leopard (Panthera uncia). Our study aimed to comprehensively identify the prey and plants consumed by snow leopards. We applied DNA metabarcoding methods on 90 faecal samples of snow leopards collected in Kyrgyzstan, employing one vertebrate and four plant markers. We found that argali (Ovis ammon) was detected only from male snow leopards. Myricaraia sp. was the most consumed among 77 plant operational taxonomic units found in snow leopard samples. It frequently appeared in samples lacking any prey animal DNA, indicating that snow leopards might have consumed this plant especially when their digestive tracts were empty. We also observed differences in the patterns of plant consumption between male and female snow leopards. Our comprehensive overview of prey and plants detected in the faeces of snow leopards and other sympatric mammals will help in formulating hypotheses and guiding future research to understand the adaptive significance of plant-eating behaviour in felids. This knowledge supports the enhancement of their captive environments and the conservation planning of their natural habitats.
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Affiliation(s)
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido, Japan
- Japan Monkey Center, Inuyama, Aichi, Japan
| | - Dale M. Kikuchi
- Department of Bioresource Development, Tokyo University of Agriculture, Kanagawa, Japan
| | | | - Huiyuan Qi
- Wildlife Research Center, Kyoto University, Kyoto, Japan
| | - Taro Sugimoto
- Institute of Natural and Environmental Sciences, University of Hyogo, Tamba, Hyogo, Japan
| | - Koustubh Sharma
- Snow Leopard Foundation in Kyrgyzstan, Bishkek, Kyrgyzstan
- Snow Leopard Trust, Seattle, WA, USA
| | - Kodzue Kinoshita
- Graduate School of Asian and African Area Studies, Kyoto University, Kyoto, Japan
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4
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Velarde-Garcéz DA, Mata VA, Beja P, da Silva LP. DNA metabarcoding, diversity partitioning and null models reveal mechanisms of seasonal trophic specialization in a Mediterranean warbler. Mol Ecol 2024; 33:e17245. [PMID: 38124452 DOI: 10.1111/mec.17245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 11/14/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
Optimal Foraging Theory (OFT) predicts that a population's trophic niche expansion should occur in periods of food scarcity as individuals begin to opportunistically exploit sub-optimal food items. However, the Niche Variation Hypothesis (NVH) posits that niche widening may result from increased among-individual differentiation due to food partitioning to avoid competition. We tested these hypotheses through a DNA metabarcoding study of the Sardinian Warbler (Curruca melanocephala) diet over a year. We used null models and the decomposition of beta diversity on among-individual dietary differentiation to infer the mechanisms driving the population's niche variation. Warblers fed frequently on berries, with a peak in late summer and, to a lesser extent, in autumn. Their diet also included a wide range of arthropods, with their prevalence varying among seasons. Consistent with OFT, the population's niche width was narrower in spring/summer when the population was strongly specialized in berries. In winter, the population's niche expanded, possibly reflecting seasonal declines in food abundance. As predicted by NVH, among-individual differentiation tended to be higher in winter, but this was mainly due to increased differences in dietary richness rather than to the partitioning of resources. Overall, our results suggest that within-individual niche does not increase in lean periods, and instead, individuals adopt either a more opportunistic or more specialized foraging strategy. Increased competition in periods of scarcity may help explain such patterns, but instead of showing increased food partitioning as expected from NVH, it may reflect OFT mechanisms on individuals with differential competitive ability to access better food resources.
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Affiliation(s)
- Daniel A Velarde-Garcéz
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Vanessa A Mata
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Pedro Beja
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Instituto de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Luis P da Silva
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
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5
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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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6
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Drake LE, Cuff JP, Bedmar S, McDonald R, Symondson WOC, Chadwick EA. Otterly delicious: Spatiotemporal variation in the diet of a recovering population of Eurasian otters ( Lutra lutra) revealed through DNA metabarcoding and morphological analysis of prey remains. Ecol Evol 2023; 13:e10038. [PMID: 37181211 PMCID: PMC10170393 DOI: 10.1002/ece3.10038] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/21/2023] [Accepted: 04/03/2023] [Indexed: 05/16/2023] Open
Abstract
Eurasian otters are apex predators of freshwater ecosystems and a recovering species across much of their European range; investigating the dietary variation of this predator over time and space, therefore, provides opportunities to identify changes in freshwater trophic interactions and factors influencing the conservation of otter populations. Here we sampled feces from 300 dead otters across England and Wales between 2007 and 2016, conducting both morphological analyses of prey remains and dietary DNA metabarcoding. Comparison of these methods showed that greater taxonomic resolution and breadth could be achieved using DNA metabarcoding but combining data from both methodologies gave the most comprehensive dietary description. All otter demographics exploited a broad range of taxa and variation likely reflected changes in prey distributions and availability across the landscape. This study provides novel insights into the trophic generalism and adaptability of otters across Britain, which is likely to have aided their recent population recovery, and may increase their resilience to future environmental changes.
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Affiliation(s)
| | - Jordan P. Cuff
- School of BiosciencesCardiff UniversityCardiffUK
- School of Natural and Environmental SciencesNewcastle UniversityNewcastleUK
- Rothamsted Insect Survey, Rothamsted ResearchHarpendenUK
| | - Sergio Bedmar
- School of BiosciencesCardiff UniversityCardiffUK
- Department of Conservation BiologyDoñana Biological Station (EBD‐CSIC)SevillaSpain
| | - Robbie McDonald
- Environment and Sustainability InstituteUniversity of ExeterPenrynUK
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7
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Stenhouse EH, Bellamy P, Kirby W, Vaughan IP, Drake LE, Marchbank A, Workman T, Symondson WOC, Orozco‐terWengel P. Multi-marker DNA metabarcoding reveals spatial and sexual variation in the diet of a scarce woodland bird. Ecol Evol 2023; 13:e10089. [PMID: 37206688 PMCID: PMC10191781 DOI: 10.1002/ece3.10089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 05/21/2023] Open
Abstract
Avian diet can be affected by site-specific variables, such as habitat, as well as intrinsic factors such as sex. This can lead to dietary niche separation, which reduces competition between individuals, as well as impacting how well avian species can adapt to environmental variation. Estimating dietary niche separation is challenging, due largely to difficulties in accurately identifying food taxa consumed. Consequently, there is limited knowledge of the diets of woodland bird species, many of which are undergoing serious population declines. Here, we show the effectiveness of multi-marker fecal metabarcoding to provide in-depth dietary analysis of a declining passerine in the UK, the Hawfinch (Coccothraustes coccothraustes). We collected fecal samples from (n = 262) UK Hawfinches prior to, and during, the breeding seasons in 2016-2019. We detected 49 and 90 plant and invertebrate taxa, respectively. We found Hawfinch diet varied spatially, as well as between sexes, indicating broad dietary plasticity and the ability of Hawfinches to utilize multiple resources within their foraging environments.
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Affiliation(s)
- Ewan H. Stenhouse
- School of BiosciencesCardiff UniversityCardiffUK
- RSPB Centre for Conservation Science, The LodgeSandyUK
| | - Paul Bellamy
- RSPB Centre for Conservation Science, The LodgeSandyUK
| | - Will Kirby
- RSPB Centre for Conservation Science, The LodgeSandyUK
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8
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Tosa MI, Lesmeister DB, Allen JM, Levi T. Multi‐locus
DNA
metabarcoding reveals seasonality of foraging ecology of western spotted skunks in the Pacific Northwest. Ecosphere 2023. [DOI: 10.1002/ecs2.4386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Marie I. Tosa
- Department of Fisheries, Wildlife, and Conservation Sciences Oregon State University Corvallis Oregon USA
| | - Damon B. Lesmeister
- Department of Fisheries, Wildlife, and Conservation Sciences Oregon State University Corvallis Oregon USA
- Pacific Northwest Research Station U.S. Department of Agriculture Forest Service Corvallis Oregon USA
| | - Jennifer M. Allen
- Department of Fisheries, Wildlife, and Conservation Sciences Oregon State University Corvallis Oregon USA
| | - Taal Levi
- Department of Fisheries, Wildlife, and Conservation Sciences Oregon State University Corvallis Oregon USA
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9
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Dietary Variation Is Driven by Landscape Heterogeneity in an Insular Omnivorous Endemic Lizard, Revealed by DNA Metabarcoding. DIVERSITY 2022. [DOI: 10.3390/d14121078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Living on islands entails numerous challenges for animals, among which population density approaching the carrying capacity of trophic resources stands out. To overcome this limitation, many insular lizards can supplement their insectivorous diet with increasing portions of plant material. The Madeira wall lizard, Teira dugesii, is a medium-sized lacertid, endemic to the Madeira and Selvagens archipelagos. As common in this family, adults are sexually dimorphic with males being bigger than females. Previous dietary studies on morphological scatology identified a higher proportion of plant over animal prey items, changing according to the location and sex. Here, we used DNA metabarcoding to examine the diet of this lizard species quantifying it at a higher taxonomical resolution and enhancing the detection of soft-body prey that often go undetected in morphology-based studies. In a sample of 151 faecal samples from eight populations including different habitats and altitudes in Madeira, we identified 289 prey items belonging to eight animal and three plant Classes, encompassing 58 distinct orders and 140 families. Of these, 63 were identified up to the species level. The results support a strong trend towards herbivory in this species with plants representing almost 74% of the diet occurrences in contrast to the 26% of animal prey. Remarkably, the plant fraction of the diet remained stable across localities but varied with size and mass in males. As males grew bigger and heavier, they significantly increased their plant matter intake. Likely, larger bodies and abdomens allowed allocating longer and more complex digestive tracts harbouring intestinal flora to better decompose plant organic compounds. This allowed heavier animals to have a richer diet regime. However, diet richness and composition were not affected by either sex or size, while the locality had a significant effect on both diet components likely in response to local variation in prey availability. By including an increasing plant fraction into a primarily insectivorous diet, this insular lizard has not only enlarged its trophic niche but is also able to exploit more efficiently the highly variable resources provided by insular environments.
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10
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Wanniarachchi S, Swan M, Nevil P, York A. Using eDNA metabarcoding to understand the effect of fire on the diet of small mammals in a woodland ecosystem. Ecol Evol 2022; 12:e9457. [PMID: 36381390 PMCID: PMC9643072 DOI: 10.1002/ece3.9457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/30/2022] [Accepted: 10/05/2022] [Indexed: 11/11/2022] Open
Abstract
Food acquisition is a fundamental process that drives animal distribution and abundance, influencing how species respond to changing environments. Disturbances such as fire create significant shifts in available dietary resources, yet, for many species, we lack basic information about what they eat, let alone how they respond to a changing resource base. In order to create effective management strategies, faunal conservation in flammable landscapes requires a greater understanding of what animals eat and how this change following a fire. What animals eat in postfire environments has received little attention due to the time‐consuming methodologies and low‐resolution identification of food taxa. Recently, molecular techniques have been developed to identify food DNA in scats, making it possible to identify animal diets with enhanced resolution. The primary aim of this study was to utilize eDNA metabarcoding to obtain an improved understanding of the diet of three native Australian small mammal species: yellow‐footed antechinus (Antechinus flavipes), heath mouse (Pseudomys shortridgei), and bush rat (Rattus fuscipes). Specifically, we sought to understand the difference in the overall diet of the three species and how diet changed over time after fire. Yellow‐footed antechinus diets mostly consisted of moths, and plants belonging to myrtles and legume families while bush rats consumed legumes, myrtles, rushes, and beetles. Heath mouse diet was dominated by rushes. All three species shifted their diets over time after fire, with most pronounced shifts in the bush rats and least for heath mice. Identifying critical food resources for native animals will allow conservation managers to consider the effect of fire management actions on these resources and help conserve the species that use them.
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Affiliation(s)
- Saumya Wanniarachchi
- School of Ecosystem and Forest SciencesThe University of MelbourneCreswickVictoriaAustralia
| | - Matthew Swan
- School of Ecosystem and Forest SciencesThe University of MelbourneCreswickVictoriaAustralia
| | - Paul Nevil
- Trace and Environmental DNA Laboratory, School of Life and Molecular SciencesCurtin UniversityPerthWestern AustraliaAustralia
| | - Alan York
- School of Ecosystem and Forest SciencesThe University of MelbourneCreswickVictoriaAustralia
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11
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Tercel MPTG, Cuff JP. The complex epistemological challenge of data curation in dietary metabarcoding: Comment on "The precautionary principle and dietary DNA metabarcoding: Commonly used abundance thresholds change ecological interpretation" by Littleford-Colquhoun et al. (2022). Mol Ecol 2022; 31:5653-5659. [PMID: 35778947 DOI: 10.1111/mec.16576] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 05/30/2022] [Accepted: 06/10/2022] [Indexed: 01/13/2023]
Abstract
In their article, Littleford-Colquhoun et al. (2022) advise against using arbitrary relative read abundance (RRA) thresholds (i.e., minimum sequence copy thresholds) for removing low-abundance sequences since they can increase false negative rates in dietary DNA metabarcoding data sets. The main criticisms presented against these widespread methods are that they (i) are arbitrary, often existing as standard values or defined based on researcher-selected delineations, (ii) are subjective, varying between studies and contexts, and, most problematically, (iii) result in the exclusion of true positives, particularly rarely consumed taxa, to the detriment of ecological insight. We commend the authors for presenting a refreshing and timely perspective on this often neglected topic, which is certainly in need of greater discussion following over a decade of significant advances in dietary metabarcoding. In this complex epistemological problem of false positives versus false negatives, we feel that several of the points raised deserve additional discussion. We address these aspects below, including measured approaches to data filtration and consistent representation of RRAs, and we welcome any further discourse to solidify or refute the concepts therein.
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Affiliation(s)
- Maximillian P T G Tercel
- School of Biosciences, Cardiff University, Cardiff, UK.,Durrell Wildlife Conservation Trust, Trinity, Jersey, Channel Islands
| | - Jordan P Cuff
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
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12
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Brun L, Schneider J, Carrió EM, Dongre P, Taberlet P, Waal VD, Fumagalli L. Focal vs. fecal: Seasonal variation in the diet of wild vervet monkeys from observational and
DNA
metabarcoding data. Ecol Evol 2022; 12:e9358. [PMID: 36203642 PMCID: PMC9526031 DOI: 10.1002/ece3.9358] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 08/12/2022] [Accepted: 09/05/2022] [Indexed: 11/08/2022] Open
Affiliation(s)
- Loïc Brun
- Laboratory for Conservation Biology, Department of Ecology and Evolution, Biophore University of Lausanne Lausanne Switzerland
| | - Judith Schneider
- Laboratory for Conservation Biology, Department of Ecology and Evolution, Biophore University of Lausanne Lausanne Switzerland
| | - Eduard Mas Carrió
- Laboratory for Conservation Biology, Department of Ecology and Evolution, Biophore University of Lausanne Lausanne Switzerland
| | - Pooja Dongre
- Department of Ecology and Evolution, Biophore University of Lausanne Lausanne Switzerland
- Inkawu Vervet Project Mawana Game Reserve, Swart Mfolozi KwaZulu Natal South Africa
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine Université Grenoble Alpes, CNRS Grenoble France
- UiT – The Arctic University of Norway, Tromsø Museum Tromsø Norway
| | - van de Waal
- Department of Ecology and Evolution, Biophore University of Lausanne Lausanne Switzerland
- Inkawu Vervet Project Mawana Game Reserve, Swart Mfolozi KwaZulu Natal South Africa
| | - Luca Fumagalli
- Laboratory for Conservation Biology, Department of Ecology and Evolution, Biophore University of Lausanne Lausanne Switzerland
- Swiss Human Institute of Forensic Taphonomy, University Centre of Legal Medicine Lausanne‐Geneva, Lausanne University Hospital and University of Lausanne Lausanne Switzerland
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13
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Mondino A, Crovadore J, Lefort F, Ursenbacher S. Impact of invading species on biodiversity: Diet study of the green whip snake’s (Hierophis viridiflavus, L. 1789) in Switzerland. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02239] [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
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14
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Henger CS, Hargous E, Nagy CM, Weckel M, Wultsch C, Krampis K, Duncan N, Gormezano L, Munshi-South J. DNA metabarcoding reveals that coyotes in New York City consume wide variety of native prey species and human food. PeerJ 2022; 10:e13788. [PMID: 36164598 PMCID: PMC9508883 DOI: 10.7717/peerj.13788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 07/05/2022] [Indexed: 01/17/2023] Open
Abstract
Carnivores are currently colonizing cities where they were previously absent. These urban environments are novel ecosystems characterized by habitat degradation and fragmentation, availability of human food, and different prey assemblages than surrounding areas. Coyotes (Canis latrans) established a breeding population in New York City (NYC) over the last few decades, but their ecology within NYC is poorly understood. In this study, we used non-invasive scat sampling and DNA metabarcoding to profile vertebrate, invertebrate, and plant dietary items with the goal to compare the diets of urban coyotes to those inhabiting non-urban areas. We found that both urban and non-urban coyotes consumed a variety of plants and animals as well as human food. Raccoons (Procyon lotor) were an important food item for coyotes within and outside NYC. In contrast, white-tailed deer (Odocoileus virginianus) were mainly eaten by coyotes inhabiting non-urban areas. Domestic chicken (Gallus gallus) was the human food item found in most scats from both urban and non-urban coyotes. Domestic cats (Felis catus) were consumed by urban coyotes but were detected in only a small proportion of the scats (<5%), which differs markedly from high rates of cat depredation in some other cities. In addition, we compared our genetic metabarcoding analysis to a morphological analysis of the same scat samples. We found that the detection similarity between the two methods was low and it varied depending on the type of diet item.
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Affiliation(s)
- Carol S. Henger
- Louis Calder Biological Field Station, Fordham University, Armonk, New York, United States
| | - Emily Hargous
- Louis Calder Biological Field Station, Fordham University, Armonk, New York, United States
| | | | - Mark Weckel
- American Museum of Natural History, New York, New York, United States
| | - Claudia Wultsch
- American Museum of Natural History, New York, New York, United States,Bioinformatics and Computational Genomics Laboratory, City University of New York, Hunter College, New York, New York, United States
| | - Konstantinos Krampis
- Bioinformatics and Computational Genomics Laboratory, City University of New York, Hunter College, New York, New York, United States,Department of Biological Sciences, City University of New York, Hunter College, New York, New York, United States,Institute of Computational Biomedicine, Weill Medical College of Cornell University, New York, New York, United States
| | - Neil Duncan
- American Museum of Natural History, New York, New York, United States
| | - Linda Gormezano
- American Museum of Natural History, New York, New York, United States
| | - Jason Munshi-South
- Louis Calder Biological Field Station, Fordham University, Armonk, New York, United States
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15
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Cuff JP, Kitson JJN, Hemprich-Bennett D, Tercel MPTG, Browett SS, Evans DM. The predator problem and PCR primers in molecular dietary analysis: swamped or silenced; depth or breadth? Mol Ecol Resour 2022; 23:41-51. [PMID: 36017818 PMCID: PMC10087656 DOI: 10.1111/1755-0998.13705] [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: 04/28/2022] [Revised: 08/11/2022] [Accepted: 08/24/2022] [Indexed: 11/28/2022]
Abstract
Dietary metabarcoding has vastly improved our ability to analyse the diets of animals, but it is hampered by a plethora of technical limitations including potentially reduced data output due to the disproportionate amplification of the DNA of the focal predator, here termed 'the predator problem'. We review the various methods commonly used to overcome this problem, from deeper sequencing to exclusion of predator DNA during PCR, and how they may interfere with increasingly common multi-predator-taxon studies. We suggest that multi-primer approaches with an emphasis on achieving both depth and breadth of prey detections may overcome the issue to some extent, although multi-taxon studies require further consideration, as highlighted by an empirical example. We also review several alternative methods for reducing the prevalence of predator DNA that are conceptually promising but require additional empirical examination. The predator problem is a key constraint on molecular dietary analyses but, through this synthesis, we hope to guide researchers in overcoming this in an effective and pragmatic way.
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Affiliation(s)
- Jordan P Cuff
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - James J N Kitson
- 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, Les Augrès Manor, La Profonde Rue, Trinity, Jersey, JE3 5BP, Channel Islands
| | - Samuel S Browett
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Darren M Evans
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
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16
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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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17
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Yang T, Song X, Zhong Y, Wang B, Zhou C. Field investigation‐ and dietary metabarcoding‐based screening of arthropods that prey on primary tea pests. Ecol Evol 2022; 12:e9060. [PMID: 35813924 PMCID: PMC9251880 DOI: 10.1002/ece3.9060] [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: 03/23/2022] [Revised: 05/30/2022] [Accepted: 06/10/2022] [Indexed: 11/11/2022] Open
Affiliation(s)
- Tingbang Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
- Institute of Ecology China West Normal University Nanchong China
| | - Xuhao Song
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
- Institute of Ecology China West Normal University Nanchong China
| | - Yang Zhong
- School of Nuclear Technology and Chemistry & Biology Hubei University of Science and Technology Xianning China
- Hubei Engineering Research Center for Fragrant Plants Hubei University of Science and Technology Xianning China
| | - Bin Wang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
- Institute of Ecology China West Normal University Nanchong China
| | - Caiquan Zhou
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
- Institute of Ecology China West Normal University Nanchong China
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18
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Waggershauser CN, Taberlet P, Coissac E, Kortland K, Hambly C, Lambin X. Interspecific coprophagia by wild red foxes:
DNA
metabarcoding reveals a potentially widespread form of commensalism among animals. Ecol Evol 2022; 12:e9029. [PMID: 35795356 PMCID: PMC9251403 DOI: 10.1002/ece3.9029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 05/25/2022] [Accepted: 05/27/2022] [Indexed: 11/07/2022] Open
Abstract
Vertebrate animals are known to consume other species' faeces, yet the role of such coprophagy in species dynamics remains unknown, not least due to the methodological challenges of documenting it. In a large‐scale metabarcoding study of red fox and pine marten scats, we document a high occurrence of domestic dog DNA in red fox scats and investigate if it can be attributed to interspecific coprophagia. We tested whether experimental artifacts or other sources of DNA could account for dog DNA, regressed dog occurrence in the diet of fox against that of the fox’s main prey, short‐tailed field voles, and consider whether predation or scavenging could explain the presence of dog DNA. Additionally, we determined the calorific value of dog faeces through calorimetric explosion. The high occurrence of dog DNA in the diet of fox, the timing of its increase, and the negative relationship between dog and the fox's main prey, point to dog faeces as the source of DNA in fox scats. Dog faeces being highly calorific, we found that foxes, but not pine martens, regularly exploit them, seemingly as an alternative resource to fluctuating prey. Scattered accounts from the literature may suggest that interspecific coprophagia is a potentially frequent and widespread form of interaction among vertebrates. However, further work should address its prevalence in other systems and the implications for ecological communities. Tools such as metabarcoding offer a way forward.
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Affiliation(s)
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine, CNRS Université Grenoble Alpes Saint‐Martin‐d'Heres France
| | - Eric Coissac
- Laboratoire d'Ecologie Alpine, CNRS Université Grenoble Alpes Saint‐Martin‐d'Heres France
| | - Kenny Kortland
- Forestry and Land Scotland Inverness UK
- Cairngorms Connect, Achantoul Aviemore UK
| | - Catherine Hambly
- School of Biological Sciences University of Aberdeen Aberdeen UK
| | - Xavier Lambin
- School of Biological Sciences University of Aberdeen Aberdeen UK
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19
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Stapleton TE, Weinstein SB, Greenhalgh R, Dearing MD. Successes and limitations of quantitative diet metabarcoding in a small, herbivorous mammal. Mol Ecol Resour 2022; 22:2573-2586. [PMID: 35579046 DOI: 10.1111/1755-0998.13643] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 05/11/2022] [Indexed: 12/01/2022]
Abstract
DNA metabarcoding is widely used to determine wild animal diets, however whether this technique provides accurate, quantitative measurements is still under debate. To test our ability to accurately estimate abundance of dietary items using metabarcoding, we fed wild caught desert woodrats (Neotoma lepida) diets comprised of constant amounts of juniper (Juniperus osteosperma, 15%) and varying amounts of creosote (Larrea tridentata, 1-60%), or cactus (Opuntia sp., 0-100%), and commercial chow (0-85%). Using metabarcoding, we compared the representation of items in the original diet samples to that in the fecal samples to test the sensitivity and accuracy of diet metabarcoding, the performance of different bioinformatic pipelines, and our ability to correct sequence counts. Metabarcoding, using standard trnL primers, detected creosote, juniper, and chow. Different pipelines for assigning taxonomy performed similarly. While creosote was detectable at dietary proportions as low as 1%, we failed to detect cactus in most samples, likely due to a primer mismatch. Creosote read counts increased as its proportion in the diet increased, and we could differentiate when creosote was a minor and major component of the diet. However, we found that estimates of juniper and creosote varied. Using previously suggested methods to correct these errors did not improve accuracy estimates of creosote, but did reduce error for juniper and chow. Our results indicate that metabarcoding can provide quantitative information on dietary composition, but may be limited. We suggest that researchers use caution in quantitatively interpreting diet metabarcoding results unless they first experimentally determine the extent of possible biases.
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20
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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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21
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Bodawatta KH, Klečková I, Klečka J, Pužejová K, Koane B, Poulsen M, Jønsson KA, Sam K. Specific gut bacterial responses to natural diets of tropical birds. Sci Rep 2022; 12:713. [PMID: 35027664 PMCID: PMC8758760 DOI: 10.1038/s41598-022-04808-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 12/28/2021] [Indexed: 12/20/2022] Open
Abstract
The composition of gut bacterial communities is strongly influenced by the host diet in many animal taxa. For birds, the effect of diet on the microbiomes has been documented through diet manipulation studies. However, for wild birds, most studies have drawn on literature-based information to decipher the dietary effects, thereby, overlooking individual variation in dietary intake. Here we examine how naturally consumed diets influence the composition of the crop and cloacal microbiomes of twenty-one tropical bird species, using visual and metabarcoding-based identification of consumed diets and bacterial 16S rRNA microbiome sequencing. We show that diet intakes vary markedly between individuals of the same species and that literature-based dietary guilds grossly underestimate intraspecific diet variability. Furthermore, despite an effect of literature-based dietary guild assignment of host taxa, the composition of natural diets does not align with crop and cloacal microbiome similarity. However, host-taxon specific gut bacterial lineages are positively correlated with specific diet items, indicating that certain microbes associate with different diet components in specific avian hosts. Consequently, microbiome composition is not congruent with the overall consumed diet composition of species, but specific components of a consumed diet lead to host-specific effects on gut bacterial taxa.
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Affiliation(s)
- Kasun H Bodawatta
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
| | - Irena Klečková
- Biology Centre of Czech Academy of Sciences, Institute of Entomology, Branisovska 31, 37005, Ceske Budejovice, Czech Republic
| | - Jan Klečka
- Biology Centre of Czech Academy of Sciences, Institute of Entomology, Branisovska 31, 37005, Ceske Budejovice, Czech Republic
| | - Kateřina Pužejová
- Biology Centre of Czech Academy of Sciences, Institute of Entomology, Branisovska 31, 37005, Ceske Budejovice, Czech Republic.,Faculty of Science, University of South Bohemia, Branisovska 1760, 37005, Ceske Budejovice, Czech Republic
| | - Bonny Koane
- New Guinea Binatang Research Centre, Madang, Papua New Guinea
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Knud A Jønsson
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Katerina Sam
- Biology Centre of Czech Academy of Sciences, Institute of Entomology, Branisovska 31, 37005, Ceske Budejovice, Czech Republic.,Faculty of Science, University of South Bohemia, Branisovska 1760, 37005, Ceske Budejovice, Czech Republic
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22
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Tercel MPTG, Moorhouse‐Gann RJ, Cuff JP, Drake LE, Cole NC, Goder M, Mootoocurpen R, Symondson WOC. DNA metabarcoding reveals introduced species predominate in the diet of a threatened endemic omnivore, Telfair's skink ( Leiolopisma telfairii). Ecol Evol 2022; 12:e8484. [PMID: 35127020 PMCID: PMC8794715 DOI: 10.1002/ece3.8484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/31/2021] [Accepted: 09/03/2021] [Indexed: 12/04/2022] Open
Abstract
Introduced species can exert disproportionately negative effects on island ecosystems, but their potential role as food for native consumers is poorly studied. Telfair's skinks are endemic omnivores living on Round Island, Mauritius, a globally significant site of biodiversity conservation. We aimed to determine the dietary diversity and key trophic interactions of Telfair's skinks, whether introduced species are frequently consumed, and if diet composition changes seasonally between male and female skinks. We used DNA metabarcoding of skink fecal samples to identify animals (COI) and plants (ITS2) consumed by skinks. There were 389 dietary presence counts belonging to 77 dietary taxa found across the 73 Telfair's skink fecal samples. Introduced taxa were cumulatively consumed more frequently than other categories, accounting for 49.4% of all detections, compared to cryptogenic (20.6%), native (20.6%), and endemic taxa (9.5%). The most frequently consumed introduced species was the ant, Pheidole megacephala, present in 40% of samples. Blue latan palm, Latania loddigesii, was the most frequently consumed endemic species, present in 33% of samples but was only detected in the dry season, when fruits are produced. We found a strong seasonal difference in diet composition explained by the presence of certain plant species solely or primarily in one season and a marked increase in the consumption of animal prey in the dry season. Male and female skinks consumed several taxa at different frequencies. These results present a valuable perspective on the role of introduced species in the trophic network of their invaded ecosystem. Both native and introduced species provide nutritional resources for skinks, and this may have management implications in the context of species conservation and island restoration.
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Affiliation(s)
| | - Rosemary J. Moorhouse‐Gann
- School of BiosciencesCardiff UniversityCardiffUK
- Durrell Wildlife Conservation TrustTrinityJersey
- Department of Animal & Plant SciencesNERC Biomolecular Analysis FacilitySheffieldUK
| | - Jordan P. Cuff
- School of BiosciencesCardiff UniversityCardiffUK
- Rothamsted Insect Survey, Rothamsted ResearchHarpendenUK
| | | | - Nik C. Cole
- Durrell Wildlife Conservation TrustTrinityJersey
- Mauritian Wildlife FoundationVacoasMauritius
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23
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Moorhouse‐Gann RJ, Vaughan IP, Cole NC, Goder M, Tatayah V, Jones CG, Mike D, Young RP, Bruford MW, Rivers MC, Hipperson H, Russo IM, Stanton DWG, Symondson WOC. Impacts of herbivory by ecological replacements on an island ecosystem. J Appl Ecol 2021. [DOI: 10.1111/1365-2664.14096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Rosemary J. Moorhouse‐Gann
- Durrell Wildlife Conservation Trust Les Augrès Manor Trinity Jersey
- Cardiff University Cardiff UK
- NERC Biomolecular Analysis FacilityDepartment of Animal & Plant Sciences Sheffield UK
| | | | - Nik C. Cole
- Durrell Wildlife Conservation Trust Les Augrès Manor Trinity Jersey
- Mauritian Wildlife Foundation Vacoas Mauritius
| | | | | | - Carl G. Jones
- Durrell Wildlife Conservation Trust Les Augrès Manor Trinity Jersey
- Mauritian Wildlife Foundation Vacoas Mauritius
| | | | - Richard P. Young
- Durrell Wildlife Conservation Trust Les Augrès Manor Trinity Jersey
| | | | | | - Helen Hipperson
- NERC Biomolecular Analysis FacilityDepartment of Animal & Plant Sciences Sheffield UK
| | | | - David W. G. Stanton
- Cardiff University Cardiff UK
- Queen Mary University of London School of Biological and Chemical Sciences London UK
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24
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Urban P, Praebel K, Bhat S, Dierking J, Wangensteen OS. DNA-metabarcoding reveals the importance of gelatinous zooplankton in the diet of Pandalus borealis, a keystone species in the Arctic. Mol Ecol 2021; 31:1562-1576. [PMID: 34936153 DOI: 10.1111/mec.16332] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/02/2021] [Accepted: 12/10/2021] [Indexed: 11/29/2022]
Abstract
Information about the dietary composition of a species is crucial to understanding their position and role in the food web. Increasingly molecular approaches such as DNA-metabarcoding are used in studying trophic relations, not least because they may alleviate problems such as low taxonomic resolution or underestimation of digestible taxa in the diet. Here, we used DNA-metabarcoding with universal primers for cytochrome c oxidase I (COI), to study the diet composition of the Northern shrimp (Pandalus borealis), an Arctic keystone species with large socio-economic importance. Across locations, jellyfish and chaetognaths were the most important components in the diet of P. borealis, jointly accounting for 40-60% of the total read abundance. This dietary importance of gelatinous zooplankton contrasts sharply with published results based on SCA. At the same time, diet composition differed between fjord and shelf locations, pointing to different food webs supporting P. borealis in these two systems. Our study underscores the potential of molecular approaches to provide new insights into the diet of marine invertebrates that are difficult to obtain with traditional methods, and calls for a revision of the role of gelatinous zooplankton in the diet of the key Arctic species P. borealis, and in extension, Arctic food webs.
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Affiliation(s)
- Paulina Urban
- Norwegian College of Fishery Science, UiT the Arctic University of Norway, Tromsø, Norway.,GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
| | - Kim Praebel
- Norwegian College of Fishery Science, UiT the Arctic University of Norway, Tromsø, Norway.,Department of Forestry and Wildlife Management, Inland Norway University of Applied Sciences, Campus Evenstad, Elverum, Norway
| | - Shripathi Bhat
- Norwegian College of Fishery Science, UiT the Arctic University of Norway, Tromsø, Norway
| | - Jan Dierking
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
| | - Owen S Wangensteen
- Norwegian College of Fishery Science, UiT the Arctic University of Norway, Tromsø, Norway
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25
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Drake LE, Cuff JP, Young RE, Marchbank A, Chadwick EA, Symondson WOC. An assessment of minimum sequence copy thresholds for identifying and reducing the prevalence of artefacts in dietary metabarcoding data. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13780] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Jordan P. Cuff
- School of Biosciences Cardiff University Cardiff UK
- Rothamsted Insect Survey, Rothamsted Research West Common Harpenden UK
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26
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Guenay-Greunke Y, Bohan DA, Traugott M, Wallinger C. Handling of targeted amplicon sequencing data focusing on index hopping and demultiplexing using a nested metabarcoding approach in ecology. Sci Rep 2021; 11:19510. [PMID: 34593851 PMCID: PMC8484467 DOI: 10.1038/s41598-021-98018-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 08/30/2021] [Indexed: 01/23/2023] Open
Abstract
High-throughput sequencing platforms are increasingly being used for targeted amplicon sequencing because they enable cost-effective sequencing of large sample sets. For meaningful interpretation of targeted amplicon sequencing data and comparison between studies, it is critical that bioinformatic analyses do not introduce artefacts and rely on detailed protocols to ensure that all methods are properly performed and documented. The analysis of large sample sets and the use of predefined indexes create challenges, such as adjusting the sequencing depth across samples and taking sequencing errors or index hopping into account. However, the potential biases these factors introduce to high-throughput amplicon sequencing data sets and how they may be overcome have rarely been addressed. On the example of a nested metabarcoding analysis of 1920 carabid beetle regurgitates to assess plant feeding, we investigated: (i) the variation in sequencing depth of individually tagged samples and the effect of library preparation on the data output; (ii) the influence of sequencing errors within index regions and its consequences for demultiplexing; and (iii) the effect of index hopping. Our results demonstrate that despite library quantification, large variation in read counts and sequencing depth occurred among samples and that the sequencing error rate in bioinformatic software is essential for accurate adapter/primer trimming and demultiplexing. Moreover, setting an index hopping threshold to avoid incorrect assignment of samples is highly recommended.
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Affiliation(s)
- Yasemin Guenay-Greunke
- Applied Animal Ecology, Department of Zoology, University of Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria. .,Institute of Interdisciplinary Mountain Research, IGF, Austrian Academy of Sciences, Technikerstraße 21a, 6020, Innsbruck, Austria.
| | - David A Bohan
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Michael Traugott
- Applied Animal Ecology, Department of Zoology, University of Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria
| | - Corinna Wallinger
- Applied Animal Ecology, Department of Zoology, University of Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria.,Institute of Interdisciplinary Mountain Research, IGF, Austrian Academy of Sciences, Technikerstraße 21a, 6020, Innsbruck, Austria
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Di Bernardi C, Wikenros C, Hedmark E, Boitani L, Ciucci P, Sand H, Åkesson M. Multiple species-specific molecular markers using nanofluidic array as a tool to detect prey DNA from carnivore scats. Ecol Evol 2021; 11:11739-11748. [PMID: 34522337 PMCID: PMC8427573 DOI: 10.1002/ece3.7918] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 06/29/2021] [Accepted: 07/02/2021] [Indexed: 01/07/2023] Open
Abstract
Large carnivore feeding ecology plays a crucial role for management and conservation for predators and their prey. One of the keys to this kind of research is to identify the species composition in the predator diet, for example, prey determination from scat content. DNA-based methods applied to detect prey in predators' scats are viable alternatives to traditional macroscopic approaches, showing an increased reliability and higher prey detection rate. Here, we developed a molecular method for prey species identification in wolf (Canis lupus) scats using multiple species-specific marker loci on the cytochrome b gene for 18 target species. The final panel consisted of 80 assays, with a minimum of four markers per target species, and that amplified specifically when using a high-throughput Nanofluidic array technology (Fluidigm Inc.). As a practical example, we applied the method to identify target prey species DNA in 80 wolf scats collected in Sweden. Depending on the number of amplifying markers required to obtain a positive species call in a scat, the success in determining at least one prey species from the scats ranged from 44% to 92%. Although we highlight the need to evaluate the optimal number of markers for sensitive target species detection, the developed method is a fast and cost-efficient tool for prey identification in wolf scats and it also has the potential to be further developed and applied to other areas and large carnivores as well.
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Affiliation(s)
- Cecilia Di Bernardi
- Department of Biology and Biotechnologies "Charles Darwin" University of Rome La Sapienza Rome Italy
- Grimsö Wildlife Research Station Department of Ecology Swedish University of Agricultural Sciences Riddarhyttan Sweden
| | - Camilla Wikenros
- Grimsö Wildlife Research Station Department of Ecology Swedish University of Agricultural Sciences Riddarhyttan Sweden
| | - Eva Hedmark
- Grimsö Wildlife Research Station Department of Ecology Swedish University of Agricultural Sciences Riddarhyttan Sweden
| | - Luigi Boitani
- Department of Biology and Biotechnologies "Charles Darwin" University of Rome La Sapienza Rome Italy
| | - Paolo Ciucci
- Department of Biology and Biotechnologies "Charles Darwin" University of Rome La Sapienza Rome Italy
| | - Håkan Sand
- Grimsö Wildlife Research Station Department of Ecology Swedish University of Agricultural Sciences Riddarhyttan Sweden
| | - Mikael Åkesson
- Grimsö Wildlife Research Station Department of Ecology Swedish University of Agricultural Sciences Riddarhyttan Sweden
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Quintero E, Isla J, Jordano P. Methodological overview and data‐merging approaches in the study of plant–frugivore interactions. OIKOS 2021. [DOI: 10.1111/oik.08379] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
| | - Jorge Isla
- Estación Biológica de Doñana, CSIC Sevilla Spain
| | - Pedro Jordano
- Estación Biológica de Doñana, CSIC Sevilla Spain
- Dept Biología Vegetal y Ecología, Univ. de Sevilla Sevilla Spain
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