The name of the game: Palaeoproteomics and radiocarbon dates further refine the presence and dispersal of caprines in Eastern and Southern Africa

We report the first large-scale palaeoproteomics research on eastern and southern African zooarchaeological samples, thereby refining our understanding of early caprine (sheep and goat) pastoralism in Africa. Assessing caprine introductions is a complicated task because of their skeletal similarity to endemic wild bovid species and the sparse and fragmentary state of relevant archaeological remains. Palaeoproteomics has previously proved effective in clarifying species attributions in African zooarchaeological materials, but few comparative protein sequences of wild bovid species have been available. Using newly generated collagen type I sequences for wild species, as well as previously published sequences, we assess species attributions for elements originally identified as caprine or “unidentifiable bovid” from seventeen eastern and southern African sites that span seven millennia. We identified over 70% of the archaeological remains and the direct radiocarbon dating of domesticate sp..., “Modern” and archaeological samples protein extraction Both reference specimen samples and archaeological samples underwent the same preparation protocol for protein extraction. Briefly, ten to twenty milligrams of bone or tooth powder were sampled using an ethanol clean diamond drill (Supplementary Table 2). The archaeological specimens from Wakarida were mandibles with their teeth and were thus sampled twice to assess the best tissue for sampling. For these, we took one bone sample and another dentine sample, for which organic preservation was assessed using the method described in Lebon et al. (2016). Only the best-preserved sample according to the threshold discussed in Le Meillour et al. (2018) is presented here (Supplementary Table 2). After sampling, bone powders were placed in protein LoBind 2mL tubes (Eppendorf, Germany). We followed the protocol for African remains, which is appropriate for the extraction and characterisation of proteins from remains recovered from arid envir..., MaxQuant 2.3.0 (open source),本研究首次针对东非与南非的动物考古学（zooarchaeological）样本开展大规模古蛋白质组学（palaeoproteomics）研究，借此深化对非洲早期山羊绵羊类（caprine）畜牧史的认知。由于山羊绵羊类的骨骼形态与本土野生牛科物种高度相似，且相关考古遗存多呈零散破碎状态，因此对其传入情况的判定颇具挑战。此前已有研究证实，古蛋白质组学技术可有效厘清非洲动物考古遗存的物种归属，但目前可获取的野生牛科物种对照蛋白质序列仍较为匮乏。本研究结合野生物种的全新I型胶原蛋白（collagen type I）测序结果与已发表的蛋白质序列，对东非与南非17处跨越7000年历史的考古遗址中，最初被判定为山羊绵羊类或"无法鉴定牛科"的遗存开展物种归属分析。本研究已成功鉴定超过70%的考古遗存，并对家养物种（domesticate sp...）开展直接放射性碳定年……"现代"对照样本与考古样本的蛋白质提取。 所有对照样本与考古样本均采用统一的蛋白质提取制备流程。简要而言，研究人员使用经乙醇清洁的金刚石钻头采集10至20毫克骨粉或牙粉样本（补充表2）。瓦卡里达（Wakarida）遗址的考古标本为带牙下颌骨，因此进行了两次采样以确定最优的采样组织类型：本次研究分别采集了骨组织样本与牙本质样本，并参考Lebon等人（2016）提出的方法对样本的有机物质保存状况进行评估。本研究仅呈现依据Le Meillour等人（2018）提出的判定标准筛选出的保存最佳的样本（补充表2）。 采样完成后，骨粉被转移至2mL蛋白质低吸附离心管（LoBind，艾本德Eppendorf，德国）。本研究采用适配非洲干旱环境遗存的蛋白质提取与表征流程……以及开源软件MaxQuant 2.3.0（开源）。