DNA-based diet analysis

Overview

This topic was the focus of my PhD thesis  (University of Tasmania - completed 2006). At that time DNA diet studies were uncommon, but the field had a major transformation in 2009 when high-throughput DNA sequencing methods were first applied. The approach is now commonly used to look at diet in all sorts of animals. For some examples, see papers in the 2019 special issue of Molecular Ecology on "Species interactions, ecological networks and community dynamics"

My work in this area has primarily focused on evaluating how useful the prey DNA present in seal and penguin faecal samples will be for studying their diet. In several studies we've examined scats from captive animals with known diets to test the approach. I've also applied the methods in field-based studies of macaroni penguins, Australian fur seals, Adelie penguins and other species.

One of the goals in developing DNA-based diet methods in the Australian Antarctic Program was to produce standardised the methodology that could be integrating into a long-term Southern Ocean monitoring program (CCAMLR - CEMP).

Example publications

Deagle BE, Thomas AC, McInnes JC, Clarke LJ, Vesterinen EJ, Clare EL, Kartzinel TR, Eveson JP (2019) Counting with DNA in metabarcoding studies: how should we convert sequence reads to dietary data? Molecular Ecology 28:391-406 (PDF)

Deagle B, McInnes J , Emmerson L, Dunn M, Adlard S , Waluda C (  2018) Adélie penguin diet: a pilot study directly comparing data from stomach flushing with faecal DNA analysis. Working Group Paper for Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR) WG-EMM-18/29

Thomas AC, Deagle BE, Eveson JP, Harsch CH, Trites AW (2016) Quantitative DNA metabarcoding: improved estimates of species proportional biomass using correction factors derived from control material. Molecular Ecology Resources 16: 714–726 (PDF)

Pompanon F, Deagle BE, Symondson WOC, Brown DS, Jarman SN, Taberlet P (2012) Who is eating what: diet assessment using next generation sequencing. Molecular Ecology, 21: 1931–1950 (PDF)

Deagle BE, Kirkwood R, Jarman SN (2009) Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces. Molecular Ecology 18: 2022–2038 (PDF)

Deagle BE, Gales NJ, Evans K, Jarman SN, Trebilco R, Robinson S, Hindell MA (2007) Studying seabird diet through genetic analysis of faeces: a case study on macaroni penguins (Eudyptes chrysolophus). PLOS ONE 2: e831 (PDF)

Deagle BE, Tollit DJ, Jarman SN, Hindell MA, Trites AW, Gales NJ (2005) Molecular scatology as a tool to study diet: analysis of prey DNA in scats from captive Steller sea lions. Molecular Ecology 14: 1831–1842 (PDF)

Collaborators

Norman Ratcliffe, Claire Waluda and Michael Dunn (British Antarctic Survey, UK)

Julie McInnes (University of Tasmania, Australia)

Andre Chiaradia and Cathy Cavallo (Phillip Island Nature Parks, Australia)

Austen Thomas (Smith-Root, Vancouver, Washington, USA)

Simon Jarman (University of Western Australia, CSIRO Environomics, Australia)

Andrew Trites, Dom Tollit, Ella Bowles (University of British Columbia, Canada)

Mark Hindell (University of Tasmania, Australia)