Did you Know?
  • The Lappet-faced Vulture, a regular winter visitor to the DDCR, has a wingspan of 2.5-3 metres (8-10 feet)

Analysis of trophic niche partitioning of desert rodents through diet reconstruction

Project Summary

For this project we want to investigate the trophic niche partitioning of the desert rodents found in the Dubai Desert Conservation Reserve. Currently, the rodent populations and inter-species interactions in the DDCR are relatively unknown. We plan to use next generation sequencing (NGS) on fecal samples from the rodents species found in the DDCR to analyze their diet, gut microbiomes and parasite composition in order to evaluate the presence of trophic niche partitioning and to determine the functional role the gut microbe communities play in host evolution.

Furthermore, we want to evaluate the effects of anthropogenic features in the reserve (i.e. feeding stations and the Al Maha resort) on the rodents’ diets by looking for significant differences in our data from both far and near these features. We want to provide a deeper understanding of UAE desert ecological structures, their dynamics, and mechanisms. This is especially relevant for any future conservation or management action implemented on the area or on the rodents themselves.

Research Objectives

  • Reconstruct the typical diet of the six rodent species using NGS from fecal samples and compare the results for the presence of trophic partitioning.
  • Examine the effects of grazers’ feeding stations on the desert rodents.
  • Investigate if there is a significant anthropogenic effect from the Al Maha resort on the rodents’ diets.


Field study: we plan to deploy approximately 100 baited rodent traps (Sherman traps, life traps) in the DDCR area. The traps will be equally divided amongst the different habitats, as well as close and far from the feeding stations and close and far from the resort. We will conduct three field visits during three different seasons lasting between 2 and 3 days per visit. We expect to obtain 20 feces and tissue samples (obtained via ear punching; for DNA barcoding) per rodent species per season; with a minimum of 5 samples per species per season for sufficient statistical analysis. Additionally, we will collect the available plant species in the different rodent habitats (i.e. the food resource) from the DDCR for DNA barcoding and creation of a reference catalog.

From the samples we will extract the DNA and run 18s and 16s PCR-based amplification. We will do 18s and 16s gene metabarcoding using next generation sequencing. We will analyze the results for presence and absence of organisms and relative abundance in order to check for partitioning of the niche. Furthermore, we will look for significant differences in dietary choices of rodents influenced either by the resort or the feeding stations.

Most statistical analyses will be conducted using Permanova and partial Mantel tests using R software.

Expected Outcomes

  • Using next generation sequencing we will obtain the range of the diet of the desert rodents and whether there is trophic niche partitioning.
  • Analysis of effects of anthropogenic actions on the rodents.