Metabarcoding for parallel identification of species, sex and diet of obligate scavengers: an application to globally-threatened Gyps vultures

Ghosh-Harihar, Mousumi; Gurung, Nehal; Shukla, Harsh; Sinha, Ishani; Pandit, Awadhesh; Prakash, Vibhu; Green, Rhys E.; Ramakrishnan, Uma

doi:10.1007/s12686-020-01171-7

Cited by 7 publications

(6 citation statements)

References 54 publications

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“…The DNA metabarcoding multiplex performed robustly and without negatively affecting the detection of L. nivalis , which means that for a slightly higher cost, one can simultaneously generate arthropod pollinator and plant data. Analogous multiplexes were designed for the identification of species, sex, and diet from the feces of Gyps vultures [ 65 ], and for species, diet, parasites, and genotypes in bats [ 66 ]. The detection of 42 arthropod genera and species corroborates another study showing that arthropod communities can be detected from wildflowers using DNA metabarcoding [ 12 ].…”

Section: Discussionmentioning

confidence: 99%

Endangered Nectar-Feeding Bat Detected by Environmental DNA on Flowers

Walker

Sanchez

Froehlich

et al. 2022

Animals

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Leptonycteris nivalis (the Mexican long-nosed bat) is an endangered nectar-feeding bat species that follows “nectar corridors” as it migrates from Mexico to the southwestern United States. Locating these nectar corridors is key to their conservation and may be possible using environmental DNA (eDNA) from these bats. Hence, we developed and tested DNA metabarcoding and qPCR eDNA assays to determine whether L. nivalis could be detected by sampling the agave flowers on which it feeds. We sampled plants with known bat visitations in the Sierra Madre Oriental in Laguna de Sanchez (LS), Nuevo León, Mexico, and in the Chisos Mountains in Big Bend National Park, Texas, USA (CB). A total of 13 samples included both swabs of agave umbels and cuttings of individual flowers. DNA metabarcoding was performed as a PCR multiplex that targeted bats (SFF-COI), arthropods (ANML-COI), and plants (ITS2 and rbcL). We targeted arthropods and plants in parallel with bats because future metabarcoding studies may wish to examine all the pollinators and plants within the nectar corridor. We developed and tested the sensitivity and specificity of two qPCR assays. We found that both DNA metabarcoding and qPCR were highly successful at detecting L. nivalis (11 of 13 for DNA metabarcoding and 12 of 13 for qPCR). Swabs and flower cuttings and both qPCR assays detected the species over four replicates. We suggest that L. nivalis leaves substantial DNA behind as it forages for nectar. We also suggest that future studies examine the time since sampling to determine its effect on detection success. The DNA metabarcoding multiplex will be useful for parallel questions regarding pollination ecology, while, with further testing, the qPCR assays will be effective for large-scale sampling for the detection of migration corridors and foraging areas. This work may be relevant to other nectar-feeding bat species, which can likely be detected with similar methodologies.

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Section: Discussionmentioning

confidence: 99%

Endangered Nectar-Feeding Bat Detected by Environmental DNA on Flowers

Walker

Sanchez

Froehlich

et al. 2022

Animals

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“…The detailed methods for the diet data generation are described in Ghosh-Harihar et al (2021). We extracted faecal DNA from the field samples following the manufacturer's recommendations using the QIAmp Fast DNA Stool Mini Kit (QIAGEN, Germany).…”

Section: Dietary Data Generationmentioning

confidence: 99%

“…Final libraries (including indexing controls) were sequenced with an Illumina MiSeq (Illumina, USA). We analyzed the HTS data separately for each of the fours metabarcodes following Ghosh-Harihar et al (2021).…”

Section: Dietary Data Generationmentioning

confidence: 99%

“…DNA-based diet analysis presents an alternative to overcome this limitation, and can be more efficient, detect more prey items and distinguish better between prey species (Casper et al, 2007). In a previous study, we developed a standardized diet metabarcoding pipeline to simultaneously identify the Gyps species, its sex and dietary species, which makes the diet analyses both efficient and more reliable (Ghosh-Harihar et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

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Spatial patterns in the diet ofGypsvultures in India and their implications for conservation

Ghosh-Harihar,

Yadav,

Gurung

et al. 2023

Preprint

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Dietary analyses are particularly useful for developing conservation programmes for species threatened by resource depletion, poisoning and environmental pollution.Gypsvultures in South Asia represent one such case, having undergone a population collapse caused by feeding on carcasses of cattle treated with the non-steroidal anti-inflammatory drug diclofenac. Following a ban on the veterinary use of diclofenac, populations of vultures remain low and mostly concentrated near protected areas. Understanding the role of protected areas in the recovery of these critically endangered species requires analyses of spatial variation in their diet. We used faecal metabarcoding to investigate the spatial variation in the diet ofGypsvultures across four landscapes from sites located inside and outside protected areas. We collected faecal 642 samples, of which 419 yielded adequate molecular data to identify the vulture species and 30 molecular operational taxonomic units corresponding to at least 28 diet species. The diet was dominated by large ungulates and varied across landscapes, protection status and vulture species, with the observed variation largely explained by differential intake of wild and domestic species. Domestic livestock was present in >95% of the samples from central, west and north India, but 77% of the samples had only wild species in south India. This variation was explained by livestock density within 100 km radius of the sampling site. Our results imply that protected areas may not offer a respite from possibility of diclofenac-poisoning across most parts of the country and efforts should continue unabated to remove nephrotoxic drugs from veterinary use.

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“…Elucidating the composition of diet can provide basic information on the ecology and evolution of key species ( Symondson 2002 ), as well as define different feeding strategies. In particular, advancing the understanding of the diets of endangered or threatened wildlife is a cornerstone for drafting effective species-specific conservation strategies ( Oehm et al 2011 ; Liu et al 2018 ; Sullins et al 2018 ; Ghosh-Harihar et al 2021; Hacker et al 2021 ).…”

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confidence: 99%

Metabarcoding of fecal DNA reveals the broad and flexible diet of a globally endangered bird

Tang

Wang

et al. 2022

Current Zoology

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Knowing the diet of endangered wild animals is a prerequisite for species-specific conservation and habitat management. The Sichuan partridge Arborophila rufipectus is a globally endangered Galliformes species endemic to the mountains of southwest China. Existing information on the diet of this species is biased and fragmented owing to traditional observation methods. Little is known about their dietary composition or how they respond to temporal variations in food resources throughout the year. In this study, a dietary analysis was performed on 60 fecal samples using DNA Metabarcoding of invertebrates and plants to determine the primary animal and plant components of the diet across three critical periods of adult life history (breeding, post-breeding wandering, and overwintering). Preys from the dipteran order, followed by the lepidopteran and araneaen spp. were the predominant, animal-derived foods. Symplocos, Rubus, Celastrus, Holboellia, and Actinidia spp. supply a large abundance of fruits and seeds for this omnivorous bird. Substantial temporal dietary changes among the three periods and a general shift toward lower dietary diversity during the breeding season was observed, suggesting that the Sichuan partridge can adjust their diet according to the availability of food resources and their own needs. Characterizing the composition and seasonal changes in Sichuan partridge diets informs the habitat management of native flora (the plant taxa that can generate berries and seeds, such as Symplocos, Rubus, Celastrus and Holboellia, which are likely of conservation interest) to achieve full life-cycle conservation.

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Metabarcoding for parallel identification of species, sex and diet of obligate scavengers: an application to globally-threatened Gyps vultures

Cited by 7 publications

References 54 publications

Endangered Nectar-Feeding Bat Detected by Environmental DNA on Flowers

Endangered Nectar-Feeding Bat Detected by Environmental DNA on Flowers

Spatial patterns in the diet ofGypsvultures in India and their implications for conservation

Metabarcoding of fecal DNA reveals the broad and flexible diet of a globally endangered bird

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