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

Di Bernardi, Cecilia and Wikenros, Camilla and Hedmark, Eva and Boitani, Luigi and Ciucci, Paolo and Sand, Håkan and Åkesson, Mikael (2021). Multiple species-specific molecular markers using nanofluidic array as a tool to detect prey DNA from carnivore scats. Ecology and Evolution. 11 , 11739-11748
[Research article]

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Abstract

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.

Authors/Creators:Di Bernardi, Cecilia and Wikenros, Camilla and Hedmark, Eva and Boitani, Luigi and Ciucci, Paolo and Sand, Håkan and Åkesson, Mikael
Title:Multiple species-specific molecular markers using nanofluidic array as a tool to detect prey DNA from carnivore scats
Series Name/Journal:Ecology and Evolution
Year of publishing :2021
Volume:11
Page range:11739-11748
Number of Pages:10
Publisher:WILEY
ISSN:2045-7758
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Ecology
Keywords:Canis lupus, carnivore, cytochrome b gene, diet assessment, prey identification, species detection
URN:NBN:urn:nbn:se:slu:epsilon-p-113287
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-113287
Additional ID:
Type of IDID
DOI10.1002/ece3.7918
Web of Science (WoS)000679912800001
ID Code:25521
Faculty:S - Faculty of Forest Sciences
Department:(NL, NJ) > Dept. of Ecology
(S) > Dept. of Ecology
Deposited By: SLUpub Connector
Deposited On:27 Sep 2021 19:25
Metadata Last Modified:28 Sep 2021 05:01

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