Regional Comparison of Snow Leopard (Panthera uncia) Diet using DNA Metabarcoding

Hacker, Charlotte E.; Jevit, Matthew; Hussain, Shafqat; Muhammad, Ghulam; Munkhtsog, Bariushaa; Munkhtsog, Bayaraa; Zhang, Yuguang; Li, Diqiang; Yan-lin, Liu; Farrington, John; Balbakova, Farida; Alamanov, Azat; Kurmanaliev, Omurbek; Chimeddorj, Buyanaa; Bayandonoi, Gantulga; Ochirjav, Munkhtogtokh; Liang, Xinmiao; Bian, Xiaoxing; Weckworth, Byron V.; Jackson, Rodney; Janečka, Jan E.

doi:10.1007/s10531-021-02118-6

Cited by 43 publications

(42 citation statements)

References 55 publications

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“…Our diagnostic method with species‐specific markers adds to the more frequent studies using DNA from carnivore scats to identify prey (Hacker et al., 2021 ; Quéméré et al., 2021 ; Roffler et al., 2021 ; Shi et al., 2021 ; Smith et al., 2018 ; Xiong et al., 2017 ). These studies primarily used DNA metabarcoding, which produces a vast amount of valuable information but sometimes also needs consideration of potential bias sources in key steps in the data handling process, lack of reference databases of barcodes for many prey species, but also intensive laboratory procedures and considerable bioinformatics training (Hacker et al., 2021 ; Tercel et al., 2021 ; Zinger et al., 2019 ). The relatively simple molecular method developed here, applying the nanofluidic array technology to detect prey DNA, represents a promising and valid alternative to other methods.…”

Section: Discussionmentioning

confidence: 99%

Multiple species‐specific molecular markers using nanofluidic array as a tool to detect prey DNA from carnivore scats

Bernardi

Wikenros

Hedmark

et al. 2021

Ecology and Evolution

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Large carnivore feeding ecology plays a crucial role for management and conservation for predators and their prey. One of the keys to this kind of research is to identify the species composition in the predator diet, for example, prey determination from scat content. DNA‐based methods applied to detect prey in predators’ scats are viable alternatives to traditional macroscopic approaches, showing an increased reliability and higher prey detection rate. Here, we developed a molecular method for prey species identification in wolf (Canis lupus) scats using multiple species‐specific marker loci on the cytochrome b gene for 18 target species. The final panel consisted of 80 assays, with a minimum of four markers per target species, and that amplified specifically when using a high‐throughput Nanofluidic array technology (Fluidigm Inc.). As a practical example, we applied the method to identify target prey species DNA in 80 wolf scats collected in Sweden. Depending on the number of amplifying markers required to obtain a positive species call in a scat, the success in determining at least one prey species from the scats ranged from 44% to 92%. Although we highlight the need to evaluate the optimal number of markers for sensitive target species detection, the developed method is a fast and cost‐efficient tool for prey identification in wolf scats and it also has the potential to be further developed and applied to other areas and large carnivores as well.

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Section: Discussionmentioning

confidence: 99%

Multiple species‐specific molecular markers using nanofluidic array as a tool to detect prey DNA from carnivore scats

Bernardi

Wikenros

Hedmark

et al. 2021

Ecology and Evolution

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“…A short segment (~ 100-bp) of MT-RNR1 (primers 12SV5F/12SV5R; Riaz et al 2011) was used to discern all predator and prey species except those belonging to goats and sheep. The primers for MT-CO1 (MT-CO1-379F and MT-CO1-604Rd; Hacker et al 2021) were designed to amplify a gene segment (330-bp) capable of differentiating closely related caprines. Each segment was amplified separately using a PCR reaction containing 1.5 µL of DNA template, 7.94 µL of KAPA HiFi HotStart ReadyMix (2 ×) (Kapa Biosystems, Wilmington, MA, USA), 0.16 µL of 20 µM forward primer, 0.16 µL of 20 µM reverse primer, and 5.2 µL of PCR grade water.…”

Section: Pcr For Species and Diet Analysismentioning

confidence: 99%

“…MT-RNR1 is an RNA gene previously used in studies examining the identity and genetic relationships of animals (Riaz et al 2011). However, MT-RNR1 lacks the genetic diversity to discern wild versus domestic goat (Capra hircus) and sheep species (Shehzad et al 2012;Hacker et al 2021). This is problematic for the discernment of domestic sheep and argali (Ovis ammon), as well as domestic goat and Siberian Ibex (Capra sibirica), in areas where they are sympatric (Reading et al 2020).…”

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confidence: 99%

“…MT-COI is widely used for DNA barcoding as it has both conserved regions and segments with high divergence (Hebert et al 2003). Recent work identified a segment of MT-COI capable of discerning wild and domestic goat and sheep taxa in Central Asia, making it an important addition for diet research of predators and scavengers distributed there (Hacker et al 2021).…”

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confidence: 99%

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Use of DNA metabarcoding of bird pellets in understanding raptor diet on the Qinghai-Tibetan Plateau of China

Hacker

Hoenig

et al. 2021

Avian Res

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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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“…New techniques harnessing the power of Next-Generation Sequencing (NGS) have the ability to reliably discern prey DNA extracted from scat down to multispecies levels [55,56]. This method has been applied to snow leopards previously at local [57] and range-wide scales (Hacker et al; accepted and in review) [58]. One pressing question involves how snow leopard diet may change seasonally, and, thus, we initiated a study to repeatedly sample a site in Dulan County, Qinghai Province, China across seasons beginning in September of 2019.…”

Section: Study 1: Temporal Changes In Snow Leopard Dietmentioning

confidence: 99%

Pastoralism Partnerships: Recognizing the Value of Local Involvement in China’s Snow Leopard Conservation Efforts

Hacker

Janečka

Jackson³

et al. 2020

Sustainability

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Pastoralists are key stakeholders in environmental management decisions in China, thus, their involvement in wildlife conservation and research is imperative for the success of long-term initiatives. Despite the many opportunities for herders to be included in these efforts, biases have hindered knowledge exchange and collaborative outcomes. This is detrimental for species living in quickly changing landscapes reliant on effective conservation, such as that of the snow leopard (Panthera uncia). Pastoralists living in snow leopard habitats on the Qinghai–Tibetan Plateau of China possess a deep and intricate understanding of the environments in which they live, and can serve as strong conservation allies by playing direct roles in scientific endeavors via expert elicitation and engagement. Here, we draw on our own experiences as academically trained scientists to present a framework for broadening opportunities for local community member participation in research efforts on the species. Framework outcomes include better targeting of conservation concerns, increased integration of Western science and local ecological knowledge, additional income to the community, clearer communication and trust between conservation stakeholders, greater flexibility in research, and additional platforms for community-based conservation. We outline avenues of involvement and considerations when working with local community members in snow leopard habitat, and submit this as an example with wide-ranging applicability to other parts of the world where livelihoods are intrinsically tied to the environment.

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Regional Comparison of Snow Leopard (Panthera uncia) Diet using DNA Metabarcoding

Cited by 43 publications

References 55 publications

Multiple species‐specific molecular markers using nanofluidic array as a tool to detect prey DNA from carnivore scats

Multiple species‐specific molecular markers using nanofluidic array as a tool to detect prey DNA from carnivore scats

Use of DNA metabarcoding of bird pellets in understanding raptor diet on the Qinghai-Tibetan Plateau of China

Pastoralism Partnerships: Recognizing the Value of Local Involvement in China’s Snow Leopard Conservation Efforts

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