Palaeoproteomics gives new insight into early southern African pastoralism

Abstract

The advent of domestication is a major step that transformed the subsistence strategies of past human societies. In Africa, domestic caprines (sheep and goat) were introduced in the northeastern part of the continent from the Near East more than 9000 years ago. However, their diffusion southwards was slow. They are thought to have made their first appearance in the southern part of the continent ca. 2000 years ago, at a few Later Stone Age sites, including Leopard Cave (Erongo region, Namibia), which provided the oldest directly dated remains assigned to sheep or goat on the basis of morphology of bones and teeth. However, similarities in morphology, not only between these two domesticated caprine species, but also between them and the small wild antelopes, raised questions about the morphological species attribution of these remains. Additionally, the high fragmentation of the site's osteological remains makes it difficult to achieve species-level taxonomic identification by comparative anatomy. In this paper, we report molecular species identification of the Leopard Cave remains using palaeoproteomics, a method that uses protein markers in bone and tooth collagen to achieve taxonomic identification of archaeological remains. We also report new direct radiocarbon dates. Wild antelope remains from museum collections were used to enrich the available protein record and propose de novo type I collagen sequences. Our results demonstrate that the remains morphologically described as domesticates actually belong to a wild antelope species and that domestic caprines first appeared at Leopard Cave 1500 years later than previously thought. This study illustrates that the use of palaeoproteomics coupled with direct radiocarbon dates is particularly suited to complement classic zooarchaeological studies, in this case concerning the arrival of the first herding practices in arid environments. Understanding how past human populations interacted with their environment, and particularly with other animals, allows understanding large parts of societies, their organisation and their economy. Climatic change is one of the factors that may have pressured human populations to adapt their subsistence strategy and diet. With Saharan and Sahelian aridification starting at the end of the African Humid Period (ca. 14,800-5500 years before present [BP] 1), Africa experienced its last major climatic change 2 and humans had to adapt to new environments 3. Thus, the inception of domestication may have been constrained by fewer food resources and their increased unpredictability 4. Given that they have no wild representatives on the continent, it is now commonly accepted that domestic sheep (Ovis aries) and goat (Capra hircus) were introduced from the Near East 5,6. The first archaeozoological evidence of these species dates from the end of the 9th and the beginning of the 8th millennium BP, in the eastern part of the Sahara 7-13. Yet, their diffusion across the continent was slow: the first

Palaeoproteomics confirm earliest domesticated sheep in southern Africa ca. 2000 BP

“…The consensus springbok collagen sequences that we present differ from those shown in supplementary Fig. S1 of Le Meillour et al (2020) 24 . That figure shows the GE P GP V GAVGPAGAVGPR (corresponding caprine ortholog of the m/z 1532 marker) as present in springbok alpha 2 chain of collagen type 1.…”

“…Recent biomolecular studies at other archaeological sites in this part of the world have shown that some putative early domesticates are actually wild species 24 ; see also 16 – 18 . The winter rainfall climate of south-western Africa precluded the spread of African grain crops (principally sorghum and millets) into the region, so that agriculture was practised only after European colonisation in the seventeenth century CE.…”

“…All those mentioned above have been identified only by their morphology, and confusion with several similar-sized species of wild bovids is possible, as highlighted by the mismatch between morphological and ancient DNA (aDNA) identifications of putative early domesticates at the site of Blydefontein in central South Africa 15 – 19 , at Sehonghong in Lesotho 20 – 22 and elsewhere 23 . Several teeth from Leopard’s Cave in Namibia, dated to just over 2000 BP and originally thought to be from domesticated caprines (sheep and/or goat), have since been shown by Le Meillour et al (2020) to derive from wild springbok 24 . This study, like Le Meillour et al (2020), uses proteomic analysis to distinguish species based on species-specific protein sequences.…”

“…A number of recent studies have utilised ancient protein (or palaeoproteomic) techniques to identify archaeological bone and ivory remains in sub-Saharan Africa. Le Meillour et al developed a protocol for the identification of degraded bone fragments and applied it to the identification of remains from Toteng 32 and from Leopard’s Cave in Namibia 24 . Zooarchaeology by Mass Spectrometry (ZooMS) has been used to identify animal species from which bone was selected to fashion into artefacts 33 , to distinguish East African sheep and goats 2 , to identify Asian fauna moving into eastern Africa 30 , and to investigate early farmers’ choice of elephant or hippo ivory in south-eastern Africa 34 .…”

Collagen fingerprinting traces the introduction of caprines to island Eastern Africa

“…These issues often render their bones indistinguishable from one another, and from other similar-sized wild bovids (e.g. [ 39 , 40 ]). To address this issue, this paper uses the biomolecular method of collagen fingerprinting to identify caprines to species level at eight archaeological sites across island eastern Africa.…”