Ancient proteins provide evidence of dairy consumption in eastern Africa

Consuming the milk of other species is a unique adaptation of Homo sapiens, with implications for health, birth spacing and evolution. Key questions nonetheless remain regarding the origins of dairying and its relationship to the genetically-determined ability to drink milk into adulthood through lactase persistence (LP). As a major centre of LP diversity, Africa is of significant interest to the evolution of dairying. Here we report proteomic evidence for milk consumption in ancient Africa. Using liquid chromatography tandem mass spectrometry (LC-MS/MS) we identify dairy proteins in human dental calculus from northeastern Africa, directly demonstrating milk consumption at least six millennia ago. Our findings indicate that pastoralist groups were drinking milk as soon as herding spread into eastern Africa, at a time when the genetic adaptation for milk digestion was absent or rare. Our study links LP status in specific ancient individuals with direct evidence for their consumption of dairy products.


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The number of individuals analysed was selected based on the presence of ancient dental calculus deposits and preservation of archaeological bones and teeth. Dental calculus was analysed from humans (n=51, representing 41 individuals) previously excavated from 13 archaeological sites spread across Kenya and Sudan. In addition, archaeological bones (n=13) and teeth (n=21) were sampled from a subset of human individuals for stable carbon (13C), nitrogen (15N) and oxygen (18O) isotope analysis. Enamel and bones were also sampled from associated fauna (including Bos, Cephalophus sp., Ovis, Eudorcas thomosonii, Capra hircus and Dendrohyrax) to create a dietary isotopic baseline. For highly fragmented animal bones (n=8) collagen left over from isotope pretreatment was analysed by Zooarchaeology by Mass Spectrometry (ZooMS) to confirm taxonomic identifications. Five samples (1 bone fragment from petrous portion, 3 teeth and 1 hair sample) from human burials were sent for radiocarbon dating and were split between the Centre for Isotope Research Groningen (CIO, Lab ID: GrM) and Scottish Universities Environmental Research Centre Radiocarbon Laboratory Glasgow (SUERC, Lab ID: GU). Only the hair sample yielded a successful result.
Some dental calculus samples did not have any oral signature after assessment against our Oral Signature Screening Database (OSSD) and were therefore excluded from final data analysis (error-tolerant searches using Mascot and Byonic).
A subset of 10 dental calculus samples were extracted with two different methods (SP3 and FASP). All other calculus samples were extracted with FASP. No replication was performed due to small quantities of starting material.
Samples were run in a randomized order on the LC-MS/MS. A mixture of wild and domestic fauna were analysed for isotope analysis based on the preservation of skeletal elements.
Blinding is not relevant as the experiments performed are based on all available material.