About ADαPT

How do aDNA, paleoproteomics, and ZooMS studies work?

Ancient DNA analysis involved the extraction and analysis of genetic material from archaeological or paleontological remains. While early studies focused on the recovery of relatively short fragments of mitochondrial DNA (mtDNA) fragments, the advent of so-called next generation sequencing (NGS) technologies in the mid-2000's allowed billions of genetic sequences to be analyzed in parallel, opening up the world of ancient genomics. NGS technologies can be coupled with hybridization bait-capture methods to enrich degraded DNA allowing for the recovery of high-coverage nuclear, mitochondrial, and bacterial genomes from archaeological and paleontological remains dating back tens of thousands of years, even as far back as the Mid-Pleistocene in permafrost environments. 

The ADαPT Facility specializes in the analysis of aDNA from animal remains, focusing primarily on the use of ancient genetic data to reconstruct past environments and ecosystems, to reconstruct the biodiversity of past ecosystems and explore how humans responded and adapted to natural and anthropogenic environmental changes in the distant past. 

In ‘Zooarchaeology by Mass Spectrometry’ (or ZooMS) method, collagen is extracted from archaeological bone and subjected to enzymatic digestion, which produces a characteristic mixture of peptides. The peptides are analyzed through mass spectrometry, and species can be distinguished by their distinct ‘peptide mass fingerprint’ through comparison with a curated reference database of known species. 

This high-throughput method allows for the rapid taxonomic screening of thousands of bone fragments at a fraction of the time and cost of traditional DNA barcoding approaches. Over the last 10 years, ZooMS has been developed to discriminate among morphologically similar ruminants, marine mammals, rodents, and fish from archaeological contexts in Europe, Asia, and Africa, elucidating diverse archaeological, anthropological, and ecological issues ranging from the identification of late-surviving Neandertal sites in Europe to mapping Medieval Scandinavian trade routes.

In spite of the recent developments and successes of these high-resolution ’omic techniques, there has been comparatively limited application of these methods in Canada. The lab aims to provide new insight into the history of Canada’s natural resources and Indigenous peoples. Furthermore, new collaborations with First Nations communities will enable their access to high-resolution tools to address specific questions concerning past resources management and provide empirical evidence to support their claims to rights and title, and access to resources.

Paleoproteomics is the application of liquid chromatography-tandem mass spectrometry (LC-MS/MS) and has revolutionized ancient protein research by allowing for the detection of fragmented and denatured proteins, providing reliable sequencing of peptides dating back thousands and even millions of years. 

Such ‘shotgun’ proteomic approaches have the potential to characterize and quantify complex mixtures of proteins produced by individual organisms (proteomes) or groups of organisms (metaproteomes). Recent studies have demonstrated that ancient proteins preserve in a remarkable range of archaeological materials, including hard tissues like bone, teeth, and dental tartar,  soft tissues like hair and skin, objects of art including glues, bindings, and paints, and most recently, within the food crusts of archaeological ceramic vessels, demonstrating the power of proteins to provide high-resolution and transformative insight into the diet, cuisine, subsistence, health, disease and cultural heritage of past peoples, and opening up a wealth of new archaeological inquiries.