scholarly journals Prey partitioning between sympatric canid species revealed by DNA metabarcoding

2019 ◽  
Author(s):  
Yue Shi ◽  
Yves Hoareau ◽  
Ellie Reese ◽  
Samuel K. Wasser
Keyword(s):  
Trophic Interactions ◽  
Diet Composition ◽  
Niche Overlap ◽  
Diet Analysis ◽  
Apex Predators ◽  
Fine Grained ◽  
Carnivore Species ◽  
Snowshoe Hares ◽  
Dna Metabarcoding ◽  
Canid Species

AbstractThe recovery of apex predators relies on restoring the full suite of trophic interactions within the ecosystem. Diet analysis with DNA metabarcoding technology can help deliver insights into these trophic interactions with fine-grained resolution. The recovery of wolves in Washington state offers an excellent case to study the trophic cascade impacts of the apex predators on the ecosystem and explore prey partitioning between sympatric canid species. We used DNA metabarcoding technology on scats to characterize the diet composition and its spatiotemporal variations of wolves and coyotes and quantified the diet niche overlap between these two canid species in northeastern Washington. In total, 19 different prey taxa were detected. Frequency of occurrence data showed that wolves primarily preyed upon deer (Odocoileus sp.) (47.47%) and moose (Alces alces) (42.42%). Coyotes also consumed moose (30.10%) and deer (21.36%), but snowshoe hares (Lepus americanus) were the most common prey (61.17%) in their diet. There were significant spatial variations in the wolf diet composition (p = 0.001) with wolves in the Dirty Shirt pack range consuming more moose (71.43%). Coyotes showed significant spatial and temporal dietary variations (season: p = 0.037; pack: p = 0.003; pack:season p = 0.043). Our data suggested that coyotes use ungulate carrion subsidies from wolves as food resources. DNA metabarcoding with fecal DNA provides an excellent noninvasive tool to characterize diet profile at the fine-grained level and can be applied to other carnivore species to help understand the impacts of recovery of apex predators on the local ecosystems.

Ecological specialization and niche overlap of subterranean rodents inferred from DNA metabarcoding diet analysis

2020 ◽  
Vol 29 (16) ◽  
pp. 3143-3153
Author(s):  
Carla Martins Lopes ◽  
Marta De Barba ◽  
Frédéric Boyer ◽  
Céline Mercier ◽  
Daniel Galiano ◽  
...  
Keyword(s):  
Niche Overlap ◽  
Diet Analysis ◽  
Subterranean Rodents ◽  
Ecological Specialization ◽  
Dna Metabarcoding

scholarly journals The food web in a subterranean ecosystem is driven by intraguild predation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Andrea Parimuchová ◽  
Lenka Petráková Dušátková ◽  
Ľubomír Kováč ◽  
Táňa Macháčková ◽  
Ondřej Slabý ◽  
...  
Keyword(s):  
Food Web ◽  
Trophic Interactions ◽  
Intraguild Predation ◽  
Linear Models ◽  
Niche Overlap ◽  
Trophic Niche ◽  
High Availability ◽  
Large Prey ◽  
Arthropod Predators ◽  
Body Sizes

AbstractTrophic interactions of cave arthropods have been understudied. We used molecular methods (NGS) to decipher the food web in the subterranean ecosystem of the Ardovská Cave (Western Carpathians, Slovakia). We collected five arthropod predators of the species Parasitus loricatus (gamasid mites), Eukoenenia spelaea (palpigrades), Quedius mesomelinus (beetles), and Porrhomma profundum and Centromerus cavernarum (both spiders) and prey belonging to several orders. Various arthropod orders were exploited as prey, and trophic interactions differed among the predators. Linear models were used to compare absolute and relative prey body sizes among the predators. Quedius exploited relatively small prey, while Eukoenenia and Parasitus fed on relatively large prey. Exploitation of eggs or cadavers is discussed. In contrast to previous studies, Eukoenenia was found to be carnivorous. A high proportion of intraguild predation was found in all predators. Intraspecific consumption (most likely cannibalism) was detected only in mites and beetles. Using Pianka’s index, the highest trophic niche overlaps were found between Porrhomma and Parasitus and between Centromerus and Eukoenenia, while the lowest niche overlap was found between Parasitus and Quedius. Contrary to what we expected, the high availability of Diptera and Isopoda as a potential prey in the studied system was not corroborated. Our work demonstrates that intraguild diet plays an important role in predators occupying subterranean ecosystems.

scholarly journals MEDITERATRI project - assessing the trophic ecology of predatory arthropods in Mediterranean agriculture via DNA metabarcoding diet analyses

2019 ◽  
Vol 2 ◽  
Author(s):  
Lucija Šerić Jelaska ◽  
Barbara Anđelić ◽  
Mišel Jelić ◽  
Tomislav Kos
Keyword(s):  
Pest Management ◽  
Trophic Ecology ◽  
Arable Land ◽  
Carabid Beetles ◽  
Diet Analysis ◽  
Gut Contents ◽  
Dna Metabarcoding ◽  
Potential Benefits ◽  
Diet Analyses ◽  
Predatory Arthropods

A type of management and the use of pesticides in arable land may negatively affect a range of soil biota and thus their food webs important for ecosystem functioning. By analysing trophic interactions we could reveal the extent of potential benefits that certain organisms can provide in biocontrol and maintaining healthy ecosystems. To evaluate the role of predatory arthropods within olive orchards and vineyards under Integrated Pest Management (IPM) and Ecological Pest Management (EPM) we collected carabid beetles together with other dominant predatory arthropods in the field (e.g. ladybugs, antlions, spiders, centipedes) and subdued the individuals to molecular gut content analyses using NGS. DNA metabarcoding diet analysis approach allowed detecting a wide variety of taxa from gut contents of the predators. In addition, using ICP-MS and LC-MS/MS we quantified Cu, pesticides and its residues in soil and animals representing different trophic guilds. Since concentrations of some toxic compounds detected in carabids body were negatively correlated with those in the soil, we aim to identify a potential vector for possible transfer of toxicants to general predators via predation. The results contribute to the risk assessment of proliferation of detected chemical compounds including copper in the ecosystem and to the knowledge on the overall field sustainability of predatory invertebrates to maximize their role in pest control. The study was conducted under the project activity of HRZZ – Mediteratri.

Species in the faeces: DNA metabarcoding as a method to determine the diet of the endangered yellow-eyed penguin

2020 ◽  
Vol 47 (6) ◽  
pp. 509
Author(s):  
Melanie J. Young ◽  
Ludovic Dutoit ◽  
Fiona Robertson ◽  
Yolanda van Heezik ◽  
Philip J. Seddon ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Diet Composition ◽  
Pcr Primers ◽  
Fish Prey ◽  
Genus Level ◽  
Faecal Samples ◽  
Significant Difference ◽  
Dna Metabarcoding ◽  
Reference Databases ◽  
Diet Assessment

Abstract Context. Diet variability is a significant driver of seabird decline; however, data on seabird diet composition and trends have been affected by changes in precision and resolution owing to the evolution of different sampling methods over time. We investigated the effectiveness of applying a passive molecular diet method using faeces obtained from the endangered yellow-eyed penguin. Aims. To assess the feasibility of applying DNA metabarcoding methods to yellow-eyed penguin faeces to evaluate diet, and to compare the reliability of diet results derived from adults and chicks, and from latrine versus fresh faecal samples. Methods. We collected 313 faecal samples from yellow-eyed penguins resident on the Otago coast of New Zealand from October 2016 to August 2017. We used polymerase chain reaction (PCR) with mitochondrial 16S cephalopod and chordate primers to amplify prey DNA present in the faecal samples, and tested the completeness of our assembled reference databases based on previous diet research. Amplified prey DNA sequences were then assigned to taxa from our reference databases by using QIIME2. Key results. Mitochondrial 16S chordate PCR primers were effective at identifying 29 fish taxa, with 98.3% of amplified sequences being identified to species or genus level in 193 samples (61.7% collected). There was no significant difference in the number, occurrence or proportion of ray-finned fish prey DNA sequences derived from fresh samples or latrines. Mitochondrial 16S cephalopod PCR primers classified 1.98% of amplified DNA sequences as targets, with 96.5% of these target sequences being identified to species or genus level in 48 samples (15.3% collected), and five taxa identified. Conclusions. We recommend the collection of latrine samples to enable long-term monitoring of the diet of yellow-eyed penguins, which will optimise the trade-off between wildlife disturbance and dietary resolution. Further refinement is needed to identify cephalopod dietary components for yellow-eyed penguins, because our cephalopod primers were not as specific as those used for ray-finned fishes, amplifying a large number (>98%) of non-cephalopod species. Implications. DNA metabarcoding offers a robust and comprehensive alternative to other, more intrusive, seabird diet-assessment methods, but still requires parallel studies to provide critical information on prey size, true diet composition and diet quality.

scholarly journals Feeding habits and microhabitat utilization by two syntopic Brazilian Amazonian frogs (Hyla minuta and Pseudopaludicula sp. (gr. falcipes)

1998 ◽  
Vol 58 (4) ◽  
pp. 559-562 ◽  
Author(s):  
M. VAN SLUYS ◽  
C. F. D. ROCHA
Keyword(s):  
Diet Composition ◽  
Niche Breadth ◽  
Feeding Habits ◽  
Niche Overlap ◽  
Microhabitat Use ◽  
Feeding Niche ◽  
Frog Species

We studied the feeding habits and microhabitat use of the Amazonian frogs Hyla minuta and Pseudopaludicula sp. at Serra Norte, Carajás, Brazil. Although living syntopically, the two species differed markedly in both prey types and sizes. Standardized feeding niche breadth of H. minuta (Bst = 0.572) was larger than that of Pseudopaludicula sp. (Bst = 0.149) and their feeding niche overlap was considerably low (10.5%). The two frog species also differed in microhabitat use. When active, Pseudopaludicula sp. were found partially submerged at the lake border whereas H. minuta were found predominantly on Nymphaea sp. leaves. Although we have not evaluated taxonomic effects on diet composition, differences in diet may be partially explained by differences in microhabitat use and frogs' size.

scholarly journals Hammer Chyme: The Russian-Doll Effect Limits Reconstructing Marine Trophic Food Webs

2021 ◽  
Author(s):  
Mark de Bruyn ◽  
Matteo Barbato ◽  
Joseph D. DiBattista ◽  
Matt K. Broadhurst
Keyword(s):  
Trophic Interactions ◽  
Fishing Effort ◽  
Marine Biodiversity ◽  
Carcharhinus Limbatus ◽  
Dietary Preferences ◽  
South Wales ◽  
Eastern Australia ◽  
Dna Metabarcoding ◽  
The Common ◽  
Species Being

Abstract Increasing fishing effort, including bycatch and discard practices, are impacting marine biodiversity, particularly among slow-to-reproduce taxa such as elasmobranchs, and specifically sharks. While some fisheries involving sharks are sustainably managed, collateral mortalities continue, contributing towards >35% of species being threatened with extinction. To effectively manage shark stocks, life-history information, including resource use/feeding ecologies is pivotal, especially among those species with wide-ranging distributions and habitats. Two cosmopolitan sharks bycaught off eastern Australia are the common blacktip shark (Carcharhinus limbatus; globally classified as Near Threatened) and great hammerhead (Sphyrna mokarran; Critically Endangered). We opportunistically sampled the digestive tracts of these two species and also any whole prey; (termed the ‘Russian-doll’ approach) caught in bather-protection gillnets off northern New South Wales to investigate their regional feeding ecologies and the capacity for DNA metabarcoding to delineate trophic interactions. Sphyrna mokkaran fed predominantly on Myliobatiformes and Rajiformes, but also teleosts, while C. limbatus mostly consumed teleosts, with some inter-specific dietary overlap of prey items. Extensive cross-contamination of predator and prey digestive tracts, likely via the predator’s stomach chyme, was evident from the metabarcoding assays limiting the opportunity to delineate trophic interactions from these data. This Russian-doll effect requires further investigation in DNA metabarcoding studies focused on dietary preferences, but implies any outcomes will need to be interpreted concomitant with traditional visual approaches.

scholarly journals Optimisation of a pollen DNA metabarcoding method for diet analysis of flying-foxes (Pteropus spp.)

2021 ◽  
Author(s):  
Karen L. Bell ◽  
Kathryn L. Batchelor ◽  
Matt Bradford ◽  
Adam McKeown ◽  
Stewart L. Macdonald ◽  
...  
Keyword(s):  
Diet Analysis ◽  
Flying Foxes ◽  
Dna Metabarcoding

scholarly journals Diet composition and overlap for 43 fishes in the North Aegean Sea, Greece

2017 ◽  
Vol 58 (1) ◽  
pp. 125-136 ◽  
Author(s):  
Paraskevi K. Karachle
Keyword(s):  
Fish Species ◽  
Plant Material ◽  
Diet Composition ◽  
Aegean Sea ◽  
The Other ◽  
Diet Analysis ◽  
Habitat Segregation ◽  
The North ◽  
North Aegean ◽  
North Aegean Sea

This study presents the diet composition of 43 of some of the most abundant fish species from the North Aegean Sea, Greece. According to the diet analysis and fractional trophic level previously reported in the literature, 20 of the studied species were omnivores with a preference for animals and the other half were carnivores (15 with preference for fish and Cephalopoda, and seven with preference for fish and Decapoda), whereas Parablennius gattorugine was the only recorded omnivore with a preference for plant material. Finally, according to the results of Schoener’s index, diet overlap between species was recorded in a small number of cases (33 out of the 903 pairs examined). Yet, competition among diet-overlapping species may be minimised by either morphological differentiations and/or habitat segregation.

scholarly journals Mesopredators change temporal activity in response to a recolonizing apex predator

2019 ◽  
Vol 30 (5) ◽  
pp. 1324-1335 ◽  
Author(s):  
Carolyn R Shores ◽  
Justin A Dellinger ◽  
Eric S Newkirk ◽  
Shannon M Kachel ◽  
Aaron J Wirsing
Keyword(s):  
Activity Patterns ◽  
Niche Overlap ◽  
Lynx Rufus ◽  
Gray Wolf ◽  
Apex Predator ◽  
Apex Predators ◽  
Anthropogenic Landscapes ◽  
Mediated Effects ◽  
Top Predators ◽  
Temporal Overlap

Abstract Apex predators can influence ecosystems through density and behaviorally mediated effects on herbivores and mesopredators. In many parts of the world, apex predators live in, or are returning to, landscapes that have been modified by people; so, it is important to understand their ecological role in anthropogenic landscapes. We used motion-activated game cameras to compare the activity patterns of humans and 2 mesopredators, coyotes (Canis latrans) and bobcats (Lynx rufus), in areas with and without an apex predator, the gray wolf (Canis lupus), in a multiuse landscape of the northwestern United States. In areas with wolves, there was a significant increase in temporal niche overlap between the mesopredators owing to higher levels of coyote activity at all time periods of the day. Temporal overlap between mesopredators and humans also increased significantly in the presence of wolves. Coyotes exposed to wolves increased their activity during dawn, day, and dusk hours. The increase in coyote activity was greatest during the day, when wolves were least active. The direction of change in bobcat activity in areas with wolves was opposite to coyotes, suggesting a behaviorally mediated cascade between wolves, coyotes, and bobcats, although these findings would need to be confirmed with further research. Our findings suggest that mesopredators in human-dominated systems may perceive humans as less dangerous than apex predators, that humans may be more likely to encounter mesopredators in areas occupied by top predators, and that behaviorally mediated effects of apex predators on mesopredators persist in human-dominated landscapes.

A pilot study on the application of DNA metabarcoding for non-invasive diet analysis in the Italian hare

2018 ◽  
Vol 88 ◽  
pp. 31-42 ◽  
Author(s):  
Maria Buglione ◽  
Valeria Maselli ◽  
Daniela Rippa ◽  
Gabriele de Filippo ◽  
Martina Trapanese ◽  
...  
Keyword(s):  
Pilot Study ◽  
Diet Analysis ◽  
Non Invasive ◽  
Dna Metabarcoding
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