Distinguishing African bovids using Zooarchaeology by Mass Spectrometry (ZooMS): New peptide markers and insights into Iron Age economies in Zambia

Abstract

Assessing past foodways, subsistence strategies, and environments depends on the accurate identification of animals in the archaeological record. The high rates of fragmentation and often poor preservation of animal bones at many archaeological sites across sub-Saharan Africa have rendered archaeofaunal specimens unidentifiable beyond broad categories, such as “large mammal” or “medium bovid”. Identification of archaeofaunal specimens through Zooarchaeology by Mass Spectrometry (ZooMS), or peptide mass fingerprinting of bone collagen, offers an avenue for identification of morphologically ambiguous or unidentifiable bone fragments from such assemblages. However, application of ZooMS analysis has been hindered by a lack of complete reference peptide markers for African taxa, particularly bovids. Here we present the complete set of confirmed ZooMS peptide markers for members of all African bovid tribes. We also identify two novel peptide markers that can be used to further distinguish between bovid groups. We demonstrate that nearly all African bovid subfamilies are distinguishable using ZooMS methods, and some differences exist between tribes or sub-tribes, as is the case for Bovina (cattle) vs. Bubalina (African buffalo) within the subfamily Bovinae. We use ZooMS analysis to identify specimens from extremely fragmented faunal assemblages from six Late Holocene archaeological sites in Zambia. ZooMS-based identifications reveal greater taxonomic richness than analyses based solely on morphology, and these new identifications illuminate Iron Age subsistence economies c. 2200–500 cal BP. While the Iron Age in Zambia is associated with the transition from hunting and foraging to the development of farming and herding, our results demonstrate the continued reliance on wild bovids among Iron Age communities in central and southwestern Zambia Iron Age and herding focused primarily on cattle. We also outline further potential applications of ZooMS in African archaeology.

Collagen fingerprinting traces the introduction of caprines to island Eastern Africa

“…Bones that were not included in the stable isotope study were analysed using two published collagen extraction protocols [ 96 , 97 ]. Given known concerns about archaeological collagen preservation in the study region [ 98 ], we wanted to maximize our ability to identify these samples. Both protocols are acid based; the first, referred to here as the ‘acid-insoluble protocol', relies on the demineralization and gelatinization of the bone to extract collagen [ 90 , 99 ], while the second (the acid-soluble protocol) uses the acid-soluble collagen from the initial demineralization [ 100 ].…”

“…Diagnostic peptide markers were identified through the comparison of the resulting spectra with an established reference library [ 98 , 99 , 104 , 105 ] ( table 2 ; electronic supplementary material, data S2). For specimens to achieve a species-level identification of either C. hircus or O. aries , all diagnostic species-specific peaks had to be present, whereas those that were missing peaks at COL1ɑ2 757–789 (G) were only able to be identified as ‘caprine'.…”

“…For specimens to achieve a species-level identification of either C. hircus or O. aries , all diagnostic species-specific peaks had to be present, whereas those that were missing peaks at COL1ɑ2 757–789 (G) were only able to be identified as ‘caprine'. Because wild bovids share many of the same peptide markers, some specimens were only able to be identified to coarser taxonomic groups [ 98 ]. Samples containing high amounts of collagen but where no identification was possible when comparing the peaks to the reference library are reported here as ‘unknowns', which may be identifiable in future with improvements to the reference dataset.…”

“…are present in the LC-MS/MS but are not suitable for species identification with ZooMS (see [ 98 ]). b Cephalophus adersi was used as a representative of Cephalophinae, so may represent more than one species (electronic supplementary material, data S2, [ 98 ]). c markers were predicted from genetic sequences rather than directly from the LC-MS/MS; therefore, species identification is tentative.…”

“… a markers in italics (?) are present in the LC-MS/MS but are not suitable for species identification with ZooMS (see [ 98 ]). b Cephalophus adersi was used as a representative of Cephalophinae, so may represent more than one species (electronic supplementary material, data S2, [ 98 ]).…”