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Proportion of prey consumed can be determined from faecal DNA using real-time PCR

journal contribution
posted on 2023-05-17, 06:13 authored by Bowles, E, Schulte, PM, Tollit, DJ, Bruce Deagle, Trites, AW
Reconstructing the diets of pinnipeds by visually identifying prey remains recovered in faecal samples is challenging because of differences in digestion and passage rates of hard parts. Analysing the soft-matrix of faecal material using DNA-based techniques is an alternative means to identify prey species consumed, but published techniques are largely nonquantitative, which limits their usefulness for some applications. We further developed and validated a real-time PCR technique using species-specific mitochondrial DNA primers to quantify the proportion of prey in the diets of Steller sea lions (Eumetopias jubatus), a pinniped species thought to be facing significant diet related challenges in the North Pacific. We first demonstrated that the proportions of prey tissue DNA in mixtures of DNA isolated from four prey species could be estimated within a margin of ��12% of the percent in the mix. These prey species included herring Clupea palasii, eula- chon Thaleichthyes pacificus, squid Loligo opalescens and rosethorn rockfish Sebastes helvomaculatus. We then applied real-time PCR to DNA extracted from faecal samples obtained from Steller sea lions in captivity that were fed 11 different combinations of herring, eulachon, squid and Pacific ocean perch rockfish (Sebastes alutus), ranging from 7% to 75% contributions per meal (by wet weight). The difference between the average percentage estimated by real-time PCR and the percentage of prey consumed was generally < 12% for all diets fed. Our findings indicate that real-time PCR of fae- cal DNA can detect the approximate relative quantity of prey consumed for complex diets and prey species, including cephalopods and fish.

History

Publication title

Molecular Ecology Resources

Volume

11

Pagination

530-540

ISSN

1755-098X

Department/School

School of Natural Sciences

Publisher

Wiley-Blackwell Publishing Ltd.

Place of publication

United Kingdom

Rights statement

The definitive published version is available online at: http://onlinelibrary.wiley.com/

Repository Status

  • Restricted

Socio-economic Objectives

Assessment and management of terrestrial ecosystems

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