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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). Sentence on DNA tissue collected from the host organism (whole organism, its gut content, its scats)

Symondson 2002 King et al. 2008 Kress et al 2015 Nielsen 2017 Pompanon 2012 Roslin 2019 Valentini 2009

1. Mammal diet assessment General intro on use of Barcoding in mammals diet assessment Methods 2 main approaches depending on 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

2. Bird diet assessment 3. Arthropod diet assessment

References

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.