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)

Understanding Spatiotemporal Dynamics of a Desert Gecko Community. Insights From Diet, Microbiome, and Parasitic Composition

Project Summary

Understanding trophic interactions and the ways in which they influence niche partitioning remain at the core of ecology, and may have strong implications for conservation biology. Unfortunately, the dynamics of trophic interactions within communities of desert species remain largely undescribed. An example reflecting this claim is a community of nocturnal geckos inhabiting sandy sheets of the United Arab Emirates, which consists of three species - Stenodactylus arabicus, Stenodactylus doriae and Bunopus tuberculatus. A single study investigating basic ecology of the desert lizards of Arabia characterized the aforementioned geckos as insectivores. However, the exact way in which the partitioning of the dietary niche occurs within this community remains unknown.

A similar lack of understanding occurs within a system of two species inhabiting gravel plains. Stenodactylus slevini and Stenodactylus leptocosymbotes are two closely related nocturnal sepcies characterized by comparable morphological traits. Interestingly, field surveys revealed lack of overlap in the occurrence ranges, indicating that these two gecko species may exclude each other. An explanation of this phenomenon may be a potential overlap in dietary prefrences, however, this claim has never been investigated.

Diet is also known to influence microbial and parasitic composition. The vast majority of microorganisms associated with vertebrates can be found in the digestive system. These microorganisms have been shown to influence the host's physiology, development, and immune system. Until today, it remains a major goal to determine the functional role these microbe communities play in host evolution.

Excessive grazing of captive camels has been recognized as the single greatest threat to the desert ecosystems of the UAE. However, the effect of this phenomenon on small vertebrate (i.e lizard) communities remains unknown. Even though in most cases a direct prey competition between these animals and camels does not occur, there may be a strong indirect effect exerted by the grazers (decrease in number of prey animals who are dependent on substantial vegetation cover, reduction of hiding places, increase in terrestrial temperatures, etc). Hence, it remains of uttermost importance to understand how the results of overgrazing affect the dynamics of small vertebrate communities in order to establish appropriate conservational measures.

The proposed study aims at identifying the dietary preferences, microbial and parasitic compositions of the gecko species across different seasons and locations with varying grazing pressure. For this, stool samples of S. arabicus, S. doriae and B. tuberculatus will be collected over three seasons (fall, winter, summer) and contents will be analyzed using next-generation sequencing. In addition, prey availability and selection will be analyzed using pitfall trapping of arthropods and selective sequencing for barcoding purposes. Sampling will be conducted in two distinct locations - the DDCR and the Arabian Nights Village Road (Abu Dhabi Emirate), which differ significantly in the extent of vegetation cover. The project will potentially be extended to include S. slevini and S. leptocosymbotes from the gravel plains to determine reasons for mutual exclusion.

The results from next-generation sequencing will be analyzed using Permanova and partial Mantel tests to detect significant differences in diet, microbial and parasite compositions between the study species.

Research Objectives

  • To identify the dietary preferences of the three gecko species inhabiting the sandy sheets (B. tuberculatus, S. doriae, S. arabicus) across seasons.
  • To determine the effect of dietary preference on niche partitioning of S. slevini and S. leptocosymbotes.
  • To identify the effect of vegetation cover on the dietary preferences, microbiome and parasitic composition of the gecko species.


Individuals from the chosen gecko species will be collected at night in order to obtain their fecal samples. The fresh stool will be transferred to sterile tubes and stored in liquid nitrogen immediately. The sampled geckos will be individually marked in order to avoid repetitions. Additionally, the sampling locations will be surveyed for insects, which will be captured, identified and euthanized in order to obtain 18s sequences.

Upon return to the laboratory, DNA from the feces will be extracted using Qiagen Stool Kit. Then, genetic markers 16s and 18s will be amplified using PCR-based protocol. The PRC products will be sequenced using next-generation sequencing. The sequences retrieved from the facility will be annotated, cleaned and compared with the ones available in the datasets. In such a way, species-specific information about dietary preferences, microbial and parasitic composition will be obtained and used to answer the questions at the community level.

Expected Outcomes

  • We expect that closely related, syntopic, and nocturnal gecko species from the sandy sheets will segregate and dietary niche to allow for co-existence (avoidance of competitive exclusion); in case of the two species inhabiting gravel plains, we expect that they will have highly similar diets (competitive exclusion).
  • We expect that overgrazing will have strong negative effects on gecko species composition, abundance, as well as effects (positive, neutral or negative) on dietary, microbial and parasite composition.