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DNA barcoding in diet assessment

DNA barcoding is broadly used to analyse the diet of both invertebrate and vertebrate organisms (King et al., 2008; Pompanon et al., 2012) and further detect their trophic interactions (Sheppard & Harwood, 2005; Kress et al., 2015).

Mammal diet assessment

General intro on use of DNA barcoding in mammals diet assessment

Methods

2 main approaches depending on previous knowledge on diet: specific or generic markers. Technical details: target regions for mammals (DNA barcodes, cytb); blocking primers of the host (Shehzad et al., 2012; Vestheim & Jarman, 2008; King et al., 2008; Shehzad et al., 2012)

Case studies

bear (De Barba et al., 2014); leopard cat (Shehzad et al., 2012); chamois (Rayé et al., 2011); macaroni penguin (Deagle et al., 2007); seal (Casper et al., 2007; Meheust et al., 2015); red bat (Clare et al., 2009);

Comparison with traditional diet assessment approaches

Casper et al., 2007a-b; Mumma et al., 2015; Shores et al., 2015; Nielsen et al., 2018 review

Potentials and shortcomings

Bird diet assessment

Arthropod diet assessment

Casper, R. M., Jarman, S. N., Deagle, B. E., Gales, N. J., & Hindell, M. A. (2007a). Detecting prey from DNA in predator scats: a comparison with morphological analysis, using Arctocephalus seals fed a known diet. Journal of Experimental Marine Biology and Ecology, 347(1-2), 144-154. Casper, R. M., Jarman, S. N., Gales, N. J., & Hindell, M. A. (2007b). Combining DNA and morphological analyses of faecal samples improves insight into trophic interactions: a case study using a generalist predator. Marine Biology, 152(4), 815-825. Clare, E. L., Fraser, E. E., Braid, H. E., Fenton, M. B., & Hebert, P. D. (2009). Species on the menu of a generalist predator, the eastern red bat (Lasiurus borealis): using a molecular approach to detect arthropod prey. Molecular ecology, 18(11), 2532-2542. De Barba, M., Miquel, C., Boyer, F., Mercier, C., Rioux, D., Coissac, E., & Taberlet, P. (2014). DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet. Molecular Ecology Resources, 14(2), 306-323. Deagle, B. E., Gales, N. J., Evans, K., Jarman, S. N., Robinson, S., Trebilco, R., & Hindell, M. A. (2007). Studying seabird diet through genetic analysis of faeces: a case study on macaroni penguins (Eudyptes chrysolophus). PLoS One, 2(9), e831. Deagle, B. E., Chiaradia, A., McInnes, J., & Jarman, S. N. (2010). Pyrosequencing faecal DNA to determine diet of little penguins: is what goes in what comes out? Conservation genetics, 11(5), 2039-2048. King, R. A., Read, D. S., Traugott, M., & Symondson, W. O. (2008). Molecular analysis of predation: a review of best practice for DNA-based approaches. Molecular Ecology, 17(4), 947-963. doi:10.1111/j.1365-294X.2007.03613.x Mumma, M. A., Adams, J. R., Zieminski, C., Fuller, T. K., Mahoney, S. P., & Waits, L. P. (2015). A comparison of morphological and molecular diet analyses of predator scats. Journal of Mammalogy, 97(1), 112-120. Nielsen, J. M., Clare, E. L., Hayden, B., Brett, M. T., & Kratina, P. (2018). Diet tracing in ecology: Method comparison and selection. Methods in Ecology and Evolution, 9(2), 278-291. Pompanon, F., Deagle, B. E., Symondson, W. O., Brown, D. S., Jarman, S. N., & Taberlet, P. (2012). Who is eating what: diet assessment using next generation sequencing. Molecular ecology, 21(8), 1931-1950. Rayé, G., Miquel, C., Coissac, E., Redjadj, C., Loison, A., & Taberlet, P. (2011). New insights on diet variability revealed by DNA barcoding and high-throughput pyrosequencing: chamois diet in autumn as a case study. Ecological Research, 26(2), 265-276. Sheppard, S. K., & Harwood, J. D. (2005). Advances in molecular ecology: tracking trophic links through predator-prey food-webs. Functional Ecology, 19(5), 751-762. doi:10.1111/j.1365-2435.2005.01041.x Shehzad, W., Riaz, T., Nawaz, M. A., Miquel, C., Poillot, C., Shah, S. A., ... & Taberlet, P. (2012). Carnivore diet analysis based on next‐generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan. Molecular ecology, 21(8), 1951-1965. Shores, C., Mondol, S., & Wasser, S. K. (2015). Comparison of DNA and hair-based approaches to dietary analysis of free-ranging wolves (Canis lupus). Conservation Genetics Resources, 7(4), 871-878. doi:10.1007/s12686-015-0504-9 Symondson, W. O. C. (2002). Molecular identification of prey in predator diets. Molecular Ecology, 11(4), 627-641. doi:10.1046/j.1365-294X.2002.01471.x Valentini, A., Pompanon, F., & Taberlet, P. (2009). DNA barcoding for ecologists. Trends in Ecology & Evolution, 24(2), 110-117. Vestheim, H., & Jarman, S. N. (2008). Blocking primers to enhance PCR amplification of rare sequences in mixed samples–a case study on prey DNA in Antarctic krill stomachs. Frontiers in Zoology, 5(1), 12.