When considering the amount of existing material, the molecular based studies for investigating ancient Egyptian mummies, especially within the context of animal cults, is minuscule to say the least; pairing this aspect with a commonly minute number of specimens, which in turn is procured from museum collections lacking the archaeological context, puts the scope of the number of studies that could be produced in perspective. The primary dataset, that makes up the core of this PhD project is comparatively large (specimen (N)=125) and contains multiple sample-types, originating from a well documented archaeological site, located in the North of Saqqara, a known hub for cultic activity. And while this dataset was to, hypothetically provide a rich source of insight into animal cult activity, the overwhelming obstacle of diminished sample preservation faced in this thesis, enforced a course correction. This led to the consideration of non-standard approaches such as enamel dating, optimisation of existing aDNA laboratory protocols for efficient amplification of the DNA and finally utilising ancient metagenomics for an exploratory study.

Chapter 1 provides a brief archaeological background to the dog catacomb, and the work carried out by the catacomb of Anubis’ project team on the site.

Chapter 2 will focus on the utility of teeth enamel as dating material, despite being geared towards pre-quaternary studies, which is much older than the dog datacomb.This dating material proves to be quite interesting, as it has increased robustness, compared to bone material (from the roots of the teeth for example), yet it is less accurate. Due to the preservation conditions in the catacomb, this approach is however seemingly well-suited. Thus, approximately 19 enamel dates were produced, along with two root (bone-portion of the teeth) dates, with the latter providing consistent points of reference to assess overall robustness of the models. Alas, the roadblocks do not end here, as the calibration of the dates’ placement along certain plateaus on the carbon calibration curve, impedes an accurate inference for the span of activity of the catacomb. To resolve this, varied types of modelling were utilised, estimating an upper limit of the activity span of ≈420 years. Additionally, this catacomb, even at the latest estimated time period of its use, shows that its activity did not continue into the Roman occupation of Egypt.

Chapter 3 examines the lack of endogenous aDNA in the petrous bone dataset used in this project, impeding the original goals of the project from being pursued. This is followed by an inspection of both the molecular roadblocks that plague mummified Egyptian samples, such as inhibitory substance to optimal PCR amplification of the aDNA, and the protocol adjustments applied to improve said recovery of the aDNA molecules.

Chapter 4 presents a small comparative pilot study, utilising the variation in the Egyptian mummified sample set, containing varying degrees of inhibition, to assess the efficacy of possible inhibition removal protocols to diminish the overall inhibition associated with Egyptian mummified samples.

Chapter 5 will take a metagenomics approach to the shotgun sequencing generated throughout the thesis, including the specimens excavated from the Dog Catacombs from Saqqara encompassing all the sample types collected, as well as supplementary specimens/datasets of similar context. Through the use of computational pipelines geared towards ancient metagenomics, the primary objective will be to inspect the variation in the microbial profile of these specimens, how it relates to the Catacombs environment and the possibility of uncovering a pattern in the long term necrobiome of Egyptian mummies.

Finally, a Closing thoughts section to reflect on the considerations, that should be accounted for, when constructing a study plan involving Egyptian mummified remains, And what future directions could be carried out to push the envelope of what could be done with this unique sample type.