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91 results for “diet DNA metabarcoding”
Multi-locus DNA metabarcoding of western spotted skunk diet in the McKenzie River Ranger District of the Willamette National Forest from 2017-2019
There are increasing concerns about the declining population trends of small mammalian carnivores around the world. Their conservation and management is often challenging due to limited knowledge about their ecology and natural history. To address one of these deficiencies for western spotted skunks (Spilogale gracilis), we investigated their diet in the Oregon Cascades of the Pacific Northwest during 2017 –2019. We collected 130 spotted skunk scats opportunistically and with detection dog teams and identified prey items using DNA metabarcoding and mechanical sorting. Western spotted skunk diet consisted of invertebrates such as wasps, millipedes, and gastropods, vertebrates such as small mammals, amphibians, and birds, and plants such as Gaultheria, Rubus, and Vaccinium. Diet also consisted of items such as black-tailed deer that were likely scavenged. Comparison in diet by season revealed that spotted skunks consumed more insects during the dry season (June –August), particularly wasps (75% of scats in the dry season), and marginally more mammals during the wet season(September –May). We observed similar diet in areas with no record of human disturbance and areas with a history of logging at most spatial scales, but scats collected in areas with older forest within a skunk’s home range (1 km buffer) were more likely to contain insects. Western spotted skunks provide food web linkages between aquatic, terrestrial, and arboreal systems and serve functional roles of seed dispersal and scavenging. Due to their diverse diet and prey-switching, western spotted skunks may dampen the effects of irruptions of prey, such as wasps during dry springs and summers. By studying the natural history of western spotted skunks in the Pacific Northwest forests while they are still abundant, we provide key information necessary to achieve the conservation goal of keeping this common species common.
DNA metabarcoding and spatial modelling link diet diversification with distribution homogeneity in European bats
<p>Inferences of the interactions between species’ ecological niches and spatial distribution have been historically based on simple metrics such as low-resolution dietary breadth and range size, which might have impeded the identification of meaningful links between niche features and spatial patterns. We analysed the relationship between dietary niche breadth and spatial distribution features of European bats, by combining continent-wide DNA metabarcoding of faecal samples with species distribution modelling. Our results show that while range size is not correlated with dietary features of bats, the homogeneity of the spatial distribution of species exhibits a strong correlation with dietary breadth. We also found that dietary breadth is correlated with bats’ hunting flexibility. However, these two patterns only stand when the phylogenetic relations between prey are accounted for when measuring dietary breadth. Our results suggest that the capacity to exploit different prey types enables species to thrive in more distinct environments and therefore exhibit more homogeneous distributions within their ranges.</p>
Using DNA metabarcoding to explore spatial variation in diet across European Hawfinch populations
<p><span>The investigation of diet in avian species is essential to an understanding of their ecology and local adaptations, as well as long-term conservation. This can be particularly challenging due to the wide distribution and high ecological plasticity of many bird species. Dietary richness and variation are under-studied in woodland bird species, due primarily to challenges in accurately identifying plant and invertebrate taxa consumed. Within Europe, Hawfinch (</span><span><em>Coccothraustes</em> <em>coccothraustes</em></span><span>) have shown variation in population trends, with moderate declines across central and eastern Europe, while western European populations have shown moderate increases. Ecological drivers behind this differing trend are still unknown; one possibility is differences in diet, yet little research has been conducted into Hawfinch diet in mainland Europe or elsewhere. This study aimed to present the first molecular dietary analysis of Hawfinch populations across two European countries. Faecal samples were collected between January and July of 2019 from Hawfinch caught at six artificial feed sites: two in Denmark and four in Germany. DNA was successfully extracted from 80 samples and plant Internal Transcribed Spacer 2 (ITS2) and invertebrate Cytochrome Oxidase Subunit 1 (COI) barcodes were amplified. A total of 35 plant and 37 invertebrate taxa were found across the 80 Hawfinch faecal samples, with plant and insect orders Fagales and Lepidoptera respectively the most frequently detected. Hawfinch dietary composition differed significantly between European countries, suggesting Hawfinch can make use of available food resources which are likely to differ spatially. Our study shows how DNA metabarcoding can be used to provide novel ecological information associated with under-studied bird species, thus providing essential information for future management and conservation of Hawfinch and their habitats. <br></span></p>
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
<p>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 faeces from 300 dead otters across England and Wales between 2007 and 2016, conducting both morphological analysis 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.</p>
Multi‐marker DNA metabarcoding reveals spatial and sexual variation in the diet of a scarce woodland bird
<p>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.</p>
Multi‐marker DNA metabarcoding reveals spatial and sexual variation in the diet of a scarce woodland bird
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Using DNA metabarcoding to explore spatial variation in diet across European Hawfinch populations
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Spatio-temporal variation in diet among age and sex cohorts of a model generalist bird species, the Great Tit Parus major: new insights revealed by DNA metabarcoding
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Comparison of seven DNA metabarcoding sampling methods to assess diet in a large avian predator
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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
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DNA metabarcoding quantifies the relative biomass of arthropod taxa in songbird diets: Validation with camera‐recorded diets
<p class="MsoNormal"><span>Ecological research is often hampered by the inability to quantify animal diets. Diet composition can be tracked through DNA metabarcoding of faecal 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 faeces 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 faeces 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 = 0 .85 (95CI:0.68–0.94) at order level and at R = 0.75 (CI:0.67</span><span>–</span><span>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.</span></p>
DNA metabarcoding sequence data for diet analysis of caribou
<p>Woodland caribou (<em>Rangifer tarandus caribou</em>) are threatened in Canada due to the drastic decline in population size caused primarily by human-induced landscape changes that decrease habitat and increase predation risk. Conservation efforts have largely focused on reducing predators and protecting critical habitat, whereas research on dietary niches and the role of potential food constraints in lichen-poor environments is limited. To improve our understanding of dietary niche variability, we used a next-generation sequencing approach with metabarcoding of DNA extracted from faecal pellets of woodland caribou located on Lake Superior in lichen-rich (mainland) and lichen-poor (island) environments. Amplicon sequencing of fungal ITS2 region revealed lichen-associated fungi as predominant in samples from both populations, but amplification at the chloroplast <em>trnL </em>region, which was only successful on island samples, revealed primary consumption of yew based on relative read abundance (<em>Taxus spp.</em>; 83.68%) with dogwood (<em>Cornus spp</em>.; 9.67%) and maple (<em>Acer spp.</em>; 4.10%) also prevalent. These results suggest that conservation efforts for caribou need to consider the availability of food resources beyond lichen to ensure successful outcomes. More broadly, we provide a reliable methodology for assessing ungulate diet from archived faecal pellets that could reveal important dietary shifts over time in response to climate change.</p>
DNA metabarcoding confirms primary targets and breadth of diet for coral reef butterflyfishes
<p>Understanding species-specific resource requirements is paramount in managing and protecting biodiversity in a world where environmental quality is in decline. Dietary data can inform predator–prey relationships and how changes in prey availability impact different species. However, for many coral reef fishes, prey and predatory events can be difficult to observe and identify, both in situ and within examined stomach samples. Here we applied DNA metabarcoding of stomach content samples for eleven Red Sea butterflyfish species to identify the diversity of dietary components that these primarily benthic feeding fish consume across coral reefs. Detections based on 18S and COI sequences from partially digested stomach contents significantly increased the resolution and diversity of the known diet for this group of fish, which included cryptic prey that are difficult to visually document due to soft parts or morphological ambiguity. In addition to scleractinian corals and other Cnidaria, the obligate corallivore species fed on a wide range of benthic organisms, whereas facultative species displayed a broader diet with crustaceans, tunicates, and worms contributing to samples. While a number of individuals contained DNA that could not be confidently identified using this method, the proportion of unidentifiable sequences was relatively low across butterflyfish species. The COI marker identified the importance of soft corals in the diet for two hard coral specialists; <em>Chaetodon melannotus</em> and <em>Chaetodon</em> <em>semilarvatus</em>, with soft coral detected in over half of the individuals and contributing significantly to the number of DNA sequence reads within their gut. Notably, five prey items identified to the species level were detected that are currently not documented in the Red Sea. Our analysis revealed that the diet of different species of butterflyfish significantly overlaps, with all species deriving most of their diet from the phylum Cnidaria (hard and soft coral, anemones) and symbiotic Symbiodiniaceae algae. Furthermore, accumulation curves suggest that all study species may feed on an even greater fraction of the benthos, likely driven by the availability and diversity of each individual/pair's associated territory. This approach increases the known dietary resolution and diversity of these key reef fishes and further enhances our understanding between butterflyfish and benthic organisms.</p>
Focal vs. faecal: Seasonal variation in the diet of wild vervet monkeys from observational and DNA metabarcoding data
<p>1. Assessing the diet of wild animals reveals valuable information about their ecology and trophic relationships that may help elucidate dynamic interactions in ecosystems and forecast responses to environmental changes.</p> <p>2. Advances in molecular biology provide valuable research tools in this field. However, comparative empirical research is still required to highlight strengths and potential biases of different approaches. Therefore, this study compares environmental DNA and observational methods for the same study population and sampling duration.</p> <p>3. We employed DNA metabarcoding assays targeting plant and arthropod diet items in 823 faecal samples collected over 12 months in a wild population of an omnivorous primate, the vervet monkey (<em>Chlorocebus pygerythrus</em>). DNA metabarcoding data were subsequently compared to direct observations.</p> <p>4. We observed the same seasonal patterns of plant consumption with both methods, however, DNA metabarcoding showed considerably greater taxonomic coverage and resolution compared to observations, mostly due to the construction of a local plant DNA database. We found a strong effect of season on variation in plant consumption largely shaped by the dry and wet seasons. The seasonal effect on arthropod consumption was weaker but feeding on arthropods was more frequent in spring and summer, showing overall that vervets adapt their diet according to available resources. The DNA metabarcoding assay outperformed also direct observations of arthropod consumption in both taxonomic coverage and resolution.</p> <p>5. Combining traditional techniques and DNA metabarcoding data can therefore not only provide enhanced assessments of complex diets or reveal trophic interactions to the benefit of wildlife conservationists and managers but also opens new perspectives for behavioural ecologists studying whether diet variation in social species is induced by environmental differences or might reflect selective foraging behaviours.</p>
Diet DNA metabarcoding data from spiders (Heteropoda venatoria) from Palmyra Atoll (2015-2017) with both individual samples that have and have not been surface sterilized
<p>These are data and code from a study examining the potential for surface contamination to influence diet DNA metabarcoding datasets when DNA is sequenced from full body parts (in this case, the opisthosomas of spider individuals). These datasets include the raw sequencing data, all downstream datasets, and taxonomic assignments collected from database searches on BOLD and GenBank (accessed 2019). The code includes code to reproduce all bioinformatics (merge, filter, match to taxonomies, rarefy, sort) as well as all statistics and figures generated from analyses. Raw data are from DNA extractions of predator gut regions (opisthosomas) and amplification of the CO1 gene using PCR. The predator species is <em>Heteropoda venatoria </em>collected individually with sterilized implements and either the diet sequences from their natural diets were extracted or their diets following feeding spiders in a feeding trial. </p>
Data from: DNA metabarcoding improves the taxonomical resolution of visually determined diet composition of beaked redfish (Sebastes sp.)
<p class="pf0"><span>Beaked r</span><span>edfish, dominated by <em>Sebastes mentella</em>, have recently reached record abundance levels in the Gulf of St. Lawrence (GSL) and knowledge of their diet composition is essential to understand the trophic role that these groundfish play in the ecosystem. The objective of the present study was to compare the performance of the visual examination and DNA metabarcoding of stomach contents of the same individual redfish caught in the estuary and northern Gulf of St. Lawrence. Using a universal metazoan mitochondrial cytochrome c oxidase subunit I (COI) marker, a total of 27 taxonomic sequence matches, 16 at the species level considered as primary prey, were obtained from 185 stomachs with DNA metabarcoding and compared to </span><span>the</span> <span>26 prey types, 16 at genus or species level, obtained with stomach content analysis (SCA). While both techniques pointed to a similar definition of diet composition, our results</span><span> also revealed that the SCA and DNA metabarcoding perform differently among prey categories, both in terms of detectability and taxonomical resolution, as well as in estimated contribution to diet. </span><span>The use of DNA metabarcoding along with SCA improves the taxonomical resolution of visually determined prey,</span><span> which supports the concept that both techniques provide useful complementary information that is best used together to gain a maximum level of information on the predator's diet.</span></p>
Diet of a threatened rattlesnake (eastern massasauga) revealed by DNA metabarcoding
<p>Characterizing the diet of imperiled species using minimally invasive methods is crucial to understanding their ecology and conservation requirements. Here, we apply a DNA metabarcoding approach to study the diet of the eastern massasauga rattlesnake (<em>Sistrurus</em> <em>catenatus</em>), a Federally Threatened snake found throughout the Great Lakes region. Eighty-three fecal samples collected across 10 different massasauga populations located in Michigan, USA, were sequenced, with 70 samples containing prey DNA. We used universal metazoan primers and developed a host-specific oligonucleotide blocker to characterize their diet. We identified at least 12 different prey species, with eastern massasaugas exhibiting opportunistic feeding and a strong preference towards small mammals. Meadow voles (<em>Microtus</em> <em>pennsylvanicus</em>) were the most common prey item (70% of diet) followed by the northern short-tailed shrew (<em>Blarina</em> <em>brevicauda</em>) and masked shrew (<em>Sorex</em> <em>cinereus</em>; 15.7% of diet each), along with occasional bird and snake prey. Adult individuals exhibited a more generalized diet, consuming a larger number of prey taxa on average. Younger snakes consumed a smaller variety of prey items and tended to consume smaller-sized mammals such as masked shrews (<em>Sorex</em> <em>cinereus</em>) and northern short-tailed shrews (<em>Blarina</em> <em>brevicauda</em>). We conclude that small mammals are a crucial part of eastern massasauga rattlesnake diet and recommend this be taken into consideration when conservation strategies are developed. The methods developed in this study can be applied to other reptile species, providing an accurate, minimally invasive, and thorough diet assessment for at-risk reptile species.</p>
Data from: Predator-prey interactions in the Arctic: DNA-metabarcoding reveals that nestling diet of snow buntings reflects arthropod seasonality
<p>Tundra arthropods are of considerable ecological importance as a seasonal food source for many arctic-breeding birds. Dietary composition and food preferences are rarely known, complicating assessments of ecological interactions in a changing environment. In our field study, we investigated nestling diet of snow buntings (<em>Plectrophenax nivalis</em> (L., 1758)) breeding in Svalbard. We collected faecal samples from 8-day-old nestlings and assessed dietary composition by DNA-metabarcoding. Simultaneously, the availability of potential prey arthropods was measured by pitfall-trapping. Molecular analyses of nestling faeces identified 31 arthropod taxa in the diet, whose proportions changed throughout the brood-rearing period. Changes in nestling diet matched varying abundances and emergence patterns of the tundra arthropod community. Snow buntings provisioned their offspring mainly with Diptera (true flies) based on both presence/absence and relative read abundance of diet items. At the beginning of the season in June, Chironomidae (non-biting midges) and the scathophagid fly <em>Scathophaga furcata</em> (Say, 1823) dominated the diet, whereas the muscid fly <em>Spilogona dorsata </em>(Zetterstedt, 1845) dominated the diet later in July. When accounted for availability, muscid flies were selected positively amongst the most often provisioned food taxa. Our study demonstrates the ecological role of the snow bunting as a generalist arthropod predator and highlights DNA-metabarcoding as a non-invasive technique for diet analyses with high taxonomical precision if sufficient DNA-sequence libraries are available.</p>
Data from: DNA metabarcoding reveals rangewide variation in aquatic diet of a riparian avian insectivore, the Prothonotary warbler
<p>Riparian avian insectivores not only depend on terrestrial insect prey but also benefit from the inclusion of aquatic prey during critical life history periods. Diets identified herein show that Prothonotary Warbler (<em>Protonotaria citrea</em>) nestlings were provisioned with aquatic prey throughout the breeding season across their range, but with variation in prey frequency of occurrence and taxonomy. Anthropogenic activity and climate change may impact the trophic link especially between aquatic and riparian habitats by altering the presence, abundance, and timing of prey availability. Thus, we used DNA metabarcoding of fecal samples to quantify the frequency of occurrence of nestling diet items at nine sites across their breeding range that differed in expected aquatic prey consumption. We analyzed spatial and temporal differences in the occurrence and multivariate diet assemblages of each prey source. Lepidoptera was the predominant terrestrial prey occurring in diets across space and time, whereas emergent aquatic insects and freshwater mollusks in aquatic diet exhibited greater variation. The frequency of emergent aquatic prey occurrence in nestling diets ranged from 61-100% across sites and was greater for early-season nestlings. The seasonal decrease in aquatic prey consumption indicates a potential temporal shift in the nutritional landscape from aquatic to terrestrial prey sources and a possible nutritional phenological mismatch for early nestlings as climate change advances the timing of insect emergence. Our findings also suggest that Prothonotary Warblers respond to environmental variability by consuming alternative prey and argue for future research investigating the extent to which shifting diets have nutritional consequences for riparian nestlings.</p>
DNA metabarcoding illuminates the contribution of small and very small prey taxa to the diet of lions
<p><span>Knowledge of food web interactions is essential for understanding the role of carnivores in an ecosystem and designing appropriate conservation and management strategies to preserve them. These interactions can only be understood by studying carnivores' diets and obtaining comprehensive and unbiased diet data. For large carnivores – which typically rely on large herbivores as prey – the role of smaller prey species has not received attention. This study aims to quantify the contribution of small (5–50 kg) and very small (<5 kg) prey taxa in the diet of lions (</span><em><span>Panthera leo melanochaita</span></em><span>)</span><span> in four Kenyan National Parks (NPs). We use DNA metabarcoding to achieve higher-resolution insights into prey composition, which is less biased toward large prey species compared to traditional methods, such as carcass counts. Our study identified 24 prey taxa in a total of 171 lion fecal samples. Small and very small p</span><span>rey taxa together contributed 18.7% out of 278 prey occurrences in all fecal samples. With comparable small prey presence (ranging from 8% to 15%) in the diet for each NP studied. This approach </span><span>proved to be useful in detecting small and very small prey species in the diet of lions and can therefore be used in future research to uncover the diverse diet composition of these large carnivores. The consistent presence of smaller prey species in the diet indicates that lions generally supplement their large prey diet with smaller prey. </span></p>
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