Comparing DNA metabarcoding with faecal analysis for diet determination of the Eurasian otter (Lutra lutra) in Vejlerne, Denmark

Woo

et al. 2022

Sci Rep

The Korean water deer (Hydropotes inermis argyropus) is considered a vermin in Korea because it damages crops, but also listed as a vulnerable species on the IUCN’s red list. Therefore, it is indispensable to manage them appropriately by understanding the ecology such as food habits. Here, we aimed to apply high-throughput sequencing (HTS), a sensitive and objective method, to investigate the dietary composition of the Korean water deer inhabiting the lowland and forest areas in summer and winter. We targeted the internal transcribed spacer 2 (ITS2) region for plant identification. From a total of 40 fecal samples analyzed, 63 plant genera were identified, with Morus being the most abundant, and some of the plant taxa identified by HTS were detected for the first time as the diets of Korean water deer. By type, woody plants (68.6%) were the most predominant, followed by forbs (7.0%) and graminoids (0.7%). We found that the deer in the forest area ate more woody plants (84.6%) than those in the lowland area (52.7%). It was also found that the type of woody plants that the deer ate changed by season. Overall, our results indicate that the Korean water deer is a browser that is seasonally adaptable and feeds on a wide variety of woody plants. We expect that the results and genetics methods reported here, by parallelly investigating their habitat range and reproductive behavior in the future, will help the management and conservation of the Korean water deer, which is in contradictory situations.

Section: Discussionsupporting

confidence: 92%

Using high-throughput sequencing to investigate the dietary composition of the Korean water deer (Hydropotes inermis argyropus): a spatiotemporal comparison

Woo

et al. 2022

Sci Rep

“…This problem can be overcome by using a blocking oligonucleotide, designed specifically to prevent amplification of the host DNA (Vestheim & Jarman, 2008). Blocking oligonucleotide have successfully inhibited host DNA amplification and improved the amplification of nonhost taxa in several species including the Eurasian otter ( Lutra lutra ; Pertoldi et al, 2021) and wild pig ( Sus scrofau ; Robeson et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

DNA metabarcoding reveals a broad dietary range for Tasmanian devils introduced to a naive ecosystem

McLennan

Wise²,

Lee³

et al. 2022

Ecology and Evolution

Top carnivores are essential for maintaining ecosystem stability and biodiversity. Yet, carnivores are declining globally and current in situ threat mitigations cannot halt population declines. As such, translocations of carnivores to historic sites or those outside the species' native range are becoming increasingly common. As carnivores are likely to impact herbivore and small predator populations, understanding how carnivores interact within an ecosystem following translocation is necessary to inform potential remedial management and future translocations. Dietary analyses provide a preliminary assessment of the direct influence of translocated carnivores on a recipient ecosystem. We used a metabarcoding approach to quantify the diet of Tasmanian devils introduced to Maria Island, Tasmania, a site outside the species' native range. We extracted DNA from 96 scats and used a universal primer set targeting the vertebrate 12S rRNA gene to identify diet items. Tasmanian devils on Maria Island had an eclectic diet, with 63 consumed taxa identified. Cat DNA was detected in 14% of scats, providing the first instance of cats appearing as part of Tasmanian devil diets either via predation or scavenging. Short-tail shearwaters and little penguins were commonly consumed, corresponding with previous surveys showing sharp population declines in these species since the introduction of Tasmanian devils. Our results indicate that the introduction of carnivores to novel ecosystems can be very successful for the focal species, but that commonly consumed species should be closely monitored to identify any vulnerable species in need of remedial management.

“…The advancement of molecular HTS in providing the ability to effectively identify prey consumed at lowest taxonomic resolution is making it possible to overcome the limitations of these techniques ( Nielsen et al 2018 ). HTS approach provides rapid dietary screening of the numerous prey taxa present in a single sample and can act as a noninvasive tool to obtain dietary information of a wide range of animals ( Kolkert et al 2020 ; Hacker et al 2021 ; Johnson et al 2021 ; Pertoldi et al 2021 ), including birds ( Sullins et al 2018 ; Chan et al 2019 ; da Silva et al 2020 ; Evens et al 2020 ; Mansor et al 2020a ). As the technology has spread and costs reduced, ecologists have rapidly turned to this powerful, novel tool for ecological studies, including dietary analysis.…”

mentioning

confidence: 99%

High-throughput sequencing reveals dietary segregation in Malaysian babblers

et al. 2021

The coexistence of numerous species within a community results from how those species use available resources. Babblers are one of the major groups of Malaysian insectivorous birds, which frequently forage in dense vegetation cover and have a high level of sympatry. Therefore, examining the diet, prey selection and niche segregation of babblers can be challenging. In this study, we used high-throughput sequencing to investigate potential dietary overlap or segregation among 10 babbler species of the four genera of the family Pellorneidae and Timaliidae: Pellorneum, Malacopteron, Stachyris and Cyanoderma in central peninsular Malaysia. We tested the hypothesis that trophically similar species may differ in resource use to avoid competitive exclusion. We identified 81 distinct arthropod taxa from fecal samples, belonging to 71 families representing 13 orders, which were predominantly from 16 dipteran, 13 lepidopteran and 10 coleopteran families. Of all the prey taxa consumed, 45% were found to be distinct across the 10 babbler species, and less than 35% were shared simultaneously by three or more babbler species, indicating minimal dietary overlap. The black-throated babbler Stachyris nigricollis and moustached babbler Malacopteron magnirostre had the most generalist tendencies because they consumed a greater variety of prey taxa. Small dietary overlap values (Ojk) and a relatively wide range of food resources suggest that dietary segregation occurred among the studied babblers. The great diversity of prey consumed revealed the presence of dietary flexibility among the sympatric insectivorous birds, thus reducing any active dietary competition and facilitating the coexistence through niche partitioning.