Palaeoproteomic analyses of dog palaeofaeces reveal a preserved dietary and host digestive proteome

Abstract

The domestic dog has inhabited the anthropogenic niche for at least 15 000 years, but despite their impact on human strategies, the lives of dogs and their interactions with humans have only recently become a subject of interest to archaeologists. In the Arctic, dogs rely exclusively on humans for food during the winter, and while stable isotope analyses have revealed dietary similarities at some sites, deciphering the details of provisioning strategies have been challenging. In this study, we apply zooarchaeology by mass spectrometry (ZooMS) and liquid chromatography tandem mass spectrometry to dog palaeofaeces to investigate protein preservation in this highly degradable material and obtain information about the diet of domestic dogs at the Nunalleq site, Alaska. We identify a suite of digestive and metabolic proteins from the host species, demonstrating the utility of this material as a novel and viable substrate for the recovery of gastrointestinal proteomes. The recovered proteins revealed that the Nunalleq dogs consumed a range of Pacific salmon species (coho, chum, chinook and sockeye) and that the consumed tissues derived from muscle and bone tissues as well as roe and guts. Overall, the study demonstrated the viability of permafrost-preserved palaeofaeces as a unique source of host and dietary proteomes.

Keywords: Nunalleq Alaska; archaeology; dogs; palaeofaeces; palaeoproteomics; zooms.

Figure 1.

Map showing the location of the Nunalleq site in Alaska and pictures of the palaeofaeces analysed in this study.

Figure 2.

A schematic diagram of a cladogram indicating taxonomic distribution of peptides extracted from palaeofaeces across the five samples analysed from Nunalleq. The size of each bubble is proportional to the number of peptides assigned to each level. Taxonomic distribution was determined using Unipept metaproteome analysis and further interrogated using BLAST against all non-redundant sequences. Keratins and laboratory contaminants are excluded from this schematic. The length of each branch does not represent evolutionary distance.

Figure 3.

Number of identified peptides from each sample, grouped by broad taxonomy. The category carnivore and lower include all peptides assigned to Carnivora, Caniformia, Caninae and Canis lupus familiaris. Other taxa include all detected taxa except for mammals, fishes and bacteria. Peptides belonging to keratins and other intermediate filament (IF) proteins are classified separately, with contaminant keratins denoting those identified in the extraction blank. Post-translational modifications are not included in the peptide counts. (Online version in colour.)