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 ◽  
...  
2019 ◽  
Author(s):  
Yue Shi ◽  
Yves Hoareau ◽  
Ellie Reese ◽  
Samuel K. Wasser

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.


Heredity ◽  
2015 ◽  
Vol 114 (5) ◽  
pp. 525-536 ◽  
Author(s):  
C M Lopes ◽  
M De Barba ◽  
F Boyer ◽  
C Mercier ◽  
P J S da Silva Filho ◽  
...  

2019 ◽  
Vol 2 ◽  
Author(s):  
Lucija Šerić Jelaska ◽  
Barbara Anđelić ◽  
Mišel Jelić ◽  
Tomislav Kos

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.


Author(s):  
Karen L. Bell ◽  
Kathryn L. Batchelor ◽  
Matt Bradford ◽  
Adam McKeown ◽  
Stewart L. Macdonald ◽  
...  

The Auk ◽  
2003 ◽  
Vol 120 (3) ◽  
pp. 680-699
Author(s):  
Robert H. Day ◽  
Alexander K. Prichard ◽  
Debora A. Nigro

Abstract We compared habitat use and niche overlap in the closely related seabirds Kittlitz’s (Brachyramphus brevirostris) and Marbled (B. marmoratus) Murrelets in nearshore waters of Prince William Sound, Alaska, in 1996–1998, and examined the relationship between near shore habitat use and morphology of those two species. Within bays, the distribution of Kittlitz’s Murrelet groups diverged the most from randomness for the variables habitat type (preferring [i.e. using significantly more than what is available] glacial-affected and glacial-stream-affected habitats), distance to shore (preferring areas 51–100 m from shore), and water clarity (preferring highly turbid water), whereas the distribution of Marbled Murrelet groups diverged the most from randomness for the variables habitat type (preferring glacial-unaffected habitats), ice cover (preferring areas of no ice), and sea-surface temperature (SST) (preferring temperatures = 6°C). The probability of a group of birds being Kittlitz’s Murrelets was determined most strongly by water clarity. Kittlitz’s Murrelet groups were more common in the more heavily glaciated College and Harriman fjords than in the other two bays and more common in early and midsummer than in late summer; the reverse was true for Marbled Murrelet groups. Marbled Murrelet groups had the least niche overlap with Kittlitz’s Murrelet groups in water clarity, SST, and site, whereas Kittlitz’s Murrelets had the least overlap with Marbled Murrelets in habitat type and water clarity. Similarly, Kittlitz’s Murrelet groups occurred in water significantly more turbid than did Marbled Murrelet groups in two of four habitat types. Kittlitz’s Murrelets had eyes (as indicated by orbit diameter) that were significantly larger in proportional size than Marbled Murrelets. We propose that these two species are specialized for foraging in different water types, with specialization of the Kittlitz’s Murrelet for turbid water of glacial origin leading to optical specialization.


2018 ◽  
Vol 88 ◽  
pp. 31-42 ◽  
Author(s):  
Maria Buglione ◽  
Valeria Maselli ◽  
Daniela Rippa ◽  
Gabriele de Filippo ◽  
Martina Trapanese ◽  
...  

2021 ◽  
Author(s):  
Melissa R. Ingala ◽  
Nancy B. Simmons ◽  
Claudia Wultsch ◽  
Konstantinos Krampis ◽  
Kaiya L. Provost ◽  
...  

2021 ◽  
Vol 5 ◽  
Author(s):  
Liliane Boukhdoud ◽  
Carole Saliba ◽  
Lillian D. Parker ◽  
Nancy Rotzel McInerney ◽  
Rhea Kahale ◽  
...  

Longevity of species populations depends largely on interactions among animals and plants in an ecosystem. Predation and seed dispersal are among the most important interactions necessary for species conservation and persistence, and diet analysis is a prerequisite tool to evaluate these interactions. Understanding these processes is crucial for identifying conservation targets and for executing efficient reforestation and ecological restoration. In this study, we applied a scat DNA metabarcoding technique using the P6-loop of the trnL (UAA) chloroplastic marker to describe the seasonal plant diet composition of 15 mammal species from a highly biodiverse Lebanese forest in the Eastern Mediterranean. We also recovered plant seeds, when present, from the scats for identification. The mammal species belong to 10 families from 5 different orders. More than 133 plant species from 54 plant families were detected and identified. Species from the Rosaceae, Poaceae, Apiaceae, Fabaceae, Fagaceae and Berberidaceae families were consumed by the majority of the mammals and should be taken into consideration in future reforestation and conservation projects. Our results showed that the DNA metabarcoding approach provides a promising method for tracking the dietary plant components of a wide diversity of mammals, yielding key insights into plant-animal interactions inside Lebanon’s forests.


2020 ◽  
Vol 84 (4) ◽  
pp. 369-384
Author(s):  
Meleppura Rajeeshkumar ◽  
Kannamkulathil Vijayan Aneesh Kumar ◽  
José Luís Otero-Ferrer ◽  
Antoni Lombarte ◽  
Manjebrayakath Hashim ◽  
...  

Anglerfishes are widely distributed from shallow to deep-water habitats occupying different ecological niches. To explain this adaptability, we performed a morpho-functional study on common benthic anglerfishes inhabiting the Indian deep-sea waters. Sensory capabilities of species were examined using the morphology and morphometry of sagitta otoliths (related to detection sound and hearing) and eye size (related to visual communication). We also performed an analysis of the degree of functional niche overlap using fish body traits to understand the coexistence of species. Otoliths showed a morphological pattern similar to that of other anglerfishes: an archaesulcoid sulcus acusticus and variability in the irregularity of the dorsal margin. This last feature affected the allometric relationships between the otolith morphometry and fish length, as well as the otolith relative sizes of each species. The findings suggested that bigger otoliths are associated with the increase of depth distribution of species up to 1000 m, from which it decreases. Our hypothesis is that anglerfishes with irregular otolith shapes could be linked to more nocturnal feeding behaviour because they were characterized by greater eye sizes. The results also indicated interspecific significant differences in functional traits providing a low niche overlap. Therefore, our study supports the hypothesis of an environmental and ecological specialization of benthic anglerfishes.


2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Charlotte E. Hacker ◽  
Brandon D. Hoenig ◽  
Liji Wu ◽  
Wei Cong ◽  
Jingjing Yu ◽  
...  

Abstract Background Diet analysis is essential to understanding the functional role of large bird species in food webs. Morphological analysis of regurgitated bird pellet contents is time intensive and may underestimate biodiversity. DNA metabarcoding has the ability to circumvent these issues, but has yet to be done. Methods We present a pilot study using DNA metabarcoding of MT-RNR1 and MT-CO1 markers to determine the species of origin and prey of 45 pellets collected in Qinghai and Gansu Provinces, China. Results We detected four raptor species [Eurasian Eagle Owl (Bubo bubo), Saker Falcon (Falco cherrug), Steppe Eagle (Aquila nipalensis), and Upland Buzzard (Buteo hemilasius)] and 11 unique prey species across 10 families and 4 classes. Mammals were the greatest detected prey class with Plateau Pika (Ochotona curzoniae) being the most frequent. Observed Shannon’s and Simpson’s diversity for Upland Buzzard were 1.089 and 0.479, respectively, while expected values were 1.312 ± 0.266 and 0.485 ± 0.086. For Eurasian Eagle Owl, observed values were 1.202 and 0.565, while expected values were 1.502 ± 0.340 and 0.580 ± 0.114. Interspecific dietary niche partitioning between the two species was not detected. Conclusions Our results demonstrate successful use of DNA metabarcoding for understanding diet via a novel noninvasive sample type to identify common and uncommon species. More work is needed to understand how raptor diets vary locally, and the mechanisms that enable exploitation of similar dietary resources. This approach has wide ranging applicability to other birds of prey, and demonstrates the power of using DNA metabarcoding to study species noninvasively.


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