DNA metabarcoding to assess spotted hyena diet in the Ngorongoro Conservation Area, Tanzania

Methods

Summary

DNA metabarcoding is a non-invasive, high-throughput method that was initially used  to analyse microfauna present in environmental samples (namely soil; Andersen et al., 2012) using Next Generation Sequencing technology. This method has since been applied to sample biodiversity in other similar samples: water (Thomasen et al., 2012; Valentini et al., 2016), flies (Calvignac-Spencer et al., 2013; Hoffman et al., 2018) and leeches (Schnell et al., 2012; Schnell et al., 2015) 

DNA metabarcoding has also been used on faecal samples to determine the dietary preferences in carnivores (Deagle et al., 2009; De Barba et a., 2013; Quéméré et al., 2013; Monterroso et al., 2019). Thus making this an ideal method to non-invasively examine the long-term spatial and temporal dietary preferences of the hyenas, especially during the period of sharp increase in pastoralist and livestock numbers and livestock grazing activity.

However, cost of sequencing 500 samples using two markers (one that will specifically isolate livestock and a second more general vertebrate marker) is expensive. While we have the facilities and expertise to conduct this study, we seek additional funds to cover the cost of DNA extraction kits and downstream processes for 500 samples.

This project combines the expertise of scientists from the Leibniz Institute for Zoo and Wildlife Research (IZW) and The Berlin Center for Genomics in Biodiversity Research (BeGenDiv). The project is being overseen by the IZW’s Ngorongoro Hyena Project (NHP; Hyena-Project.com). NHP scientists have maintained a long-term study on the Ngorongoro Crater’s spotted hyena population; they have been closely monitoring and collecting faecal samples from Crater hyenas since 1996.

Pre Analysis Plan

We have started with the optimization of the markers that we plan to use. We have extracted  DNA from 20 faecal samples and applied them to the 12S mitochondrial DNA marker (12S mtDNA; isolates vertebrates in general). Preliminary results were promising! We were able to identify at least 3 species of prey (zebra wildebeest, gazelle) from these samples, all of which occur in the Crater. 

The next step would be to minimize the amplification of Hyenas using the 12S mtDNA and to optimize the livestock specific marker to the samples as well.

Following this, we would focus on building a reference database. Ideally, we would obtain sequences of animals occurring in and around the crater, from existing databases to which we could compare our data to. Results from this would give us an idea of the feeding behavior of the Hyenas that we have sampled.