If bone is considered as a composite of collagen (protein) and bioapatite (mineral),

Current genetic data are equivocal as to whether goat domestication occurred multiple times or was a singular process. We generated genomic data from 83 ancient goats (51 with genome-wide coverage) from Paleolithic to Medieval contexts throughout the Near East. Our findings demonstrate that multiple divergent ancient wild goat sources were domesticated in a dispersed process that resulted in genetically and geographically distinct Neolithic goat populations, echoing contemporaneous human divergence across the region. These early goat populations contributed differently to modern goats in Asia, Africa, and Europe. We also detect early selection for pigmentation, stature, reproduction, milking, and response to dietary change, providing 8000-year-old evidence for human agency in molding genome variation within a partner species.

Gigantopithecus blacki was a giant hominid that inhabited densely forested environments of Southeast Asia during the Pleistocene 1. Its evolutionary relationships to other great ape species, and their divergence during the Middle and Late Miocene (16-5.3 Mya), remains disputed 2,3. Hypotheses regarding relationships between Gigantopithecus and extinct and extant hominids are difficult to substantiate because of its highly derived dentognathic morphology and the absence of cranial and post-cranial remains 1,3-6. Therefore, proposed hypotheses on the phylogenetic position of Gigantopithecus among hominids have been wide-ranging, but none have received independent molecular validation. We retrieved dental enamel proteome sequences from a 1.9 million years (Mya) old Gigantopithecus blacki molar found in Chuifeng Cave, China 7,8. The thermal age of these protein sequences is approximately five times older than any previously published mammalian proteome or genome. We demonstrate that Gigantopithecus is a sister clade to orangutans (genus Pongo) with a common ancestor about 10-12 Mya, implying that the Gigantopithecus divergence from Pongo is part of the Miocene radiation of great apes. Additionally, we hypothesize that the expression of alpha-2-HS-glycoprotein (AHSG), which has not been observed in enamel proteomes previously, had a role in the biomineralization of the thick enamel crowns that characterize the large molars in the genus 9,10. The survival of an Early Pleistocene dental enamel proteome in the subtropics further expands the scope of palaeoproteomic analysis into geographic areas and time periods previously considered incompatible with genetic preservation. Gigantopithecus blacki is an extinct, potentially giant hominid species that once inhabited Asia. It was first discovered and identified by von Koenigswald in 1935 when he described an isolated tooth that he found in a Hong Kong drugstore 11. The entire Gigantopithecus blacki fossil record, dated between the Early Pleistocene (~2.0 Mya) and the late Middle Pleistocene (~0.3 Mya 12), includes thousands of teeth and four partial mandibles from subtropical Southeast Asia 1,13,14. All the known Gigantopithecus blacki localities are situated in southern China, stretching from Longgupo Cave, just south of the Yangtze River, to the Xinchong Cave on Hainan Island, and, possibly, into northern Vietnam and Thailand 15,16. To address the evolutionary relationships between Gigantopithecus and extant hominoids, we performed protein extractions on dentine and enamel samples of a single molar (CF-B-16) found in Chuifeng Cave, China, that is morphologically assigned to Gigantopithecus blacki 7,8. The site is dated using multiple approaches to 1.9±0.2 Mya (Extended Data Figs. 1, 2). Enamel and dentine samples were processed using recently established digestion-free protocols optimized for extremely degraded ancient proteomes 17 (Methods). Enamel demineralization was replicated using two different acids, trifluoroacetic acid (TFA) and hydrochloric acid (HCl). Welker et ...

The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to a revolutionary body of paleogenomic research, yet the dynamics of DNA degradation are still poorly understood. We analyzed 185 paleogenomic datasets and compared DNA survival with environmental variables and sample ages. We find cytosine deamination follows a conventional thermal age model, but we find no correlation between DNA fragmentation and sample age over the timespans analyzed, even when controlling for environmental variables. We propose a model for ancient DNA decay wherein fragmentation rapidly reaches a threshold, then subsequently slows. The observed loss of DNA over time may be due to a bulk diffusion process in many cases, highlighting the importance of tissues and environments creating effectively closed systems for DNA preservation. This model of DNA degradation is largely based on mammal bone samples due to published genomic dataset availability. Continued refinement to the model to reflect diverse biological systems and tissue types will further improve our understanding of ancient DNA breakdown dynamics.

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The analysis of lipids (fats, oils and waxes) absorbed within archaeological pottery has revolutionized the study of past diets and culinary practices. However, this technique can lack taxonomic and tissue specificity and is often unable to disentangle signatures resulting from the mixing of different food products. Here, we extract ancient proteins from ceramic vessels from the West Mound of the key early farming site of Çatalhöyük in Anatolia, revealing that this community processed mixes of cereals, pulses, dairy and meat products, and that particular vessels may have been reserved for specialized foods (e.g., cow milk and milk whey). Moreover, we demonstrate that dietary proteins can persist on archaeological artefacts for at least 8000 years, and that this approach can reveal past culinary practices with more taxonomic and tissue-specific clarity than has been possible with previous biomolecular techniques.

Archaeological dental calculus has emerged as a rich source of ancient biomolecules, including proteins. Previous analyses of proteins extracted from ancient dental calculus revealed the presence of the dietary milk protein β-lactoglobulin, providing direct evidence of dairy consumption in the archaeological record. However, the potential for calculus to preserve other food-related proteins has not yet been systematically explored. Here we analyse shotgun metaproteomic data from 100 archaeological dental calculus samples ranging from the Iron Age to the post-medieval period (eighth century BC to nineteenth century AD) in England, as well as 14 dental calculus samples from contemporary dental patients and recently deceased individuals, to characterize the range and extent of dietary proteins preserved in dental calculus. In addition to milk proteins, we detect proteomic evidence of foodstuffs such as cereals and plant products, as well as the digestive enzyme salivary amylase. We discuss the importance of optimized protein extraction methods, data analysis approaches and authentication strategies in the identification of dietary proteins from archaeological dental calculus. This study demonstrates that proteomic approaches can robustly identify foodstuffs in the archaeological record that are typically under-represented due to their poor macroscopic preservation.

. (2002) 'The taphonomy of cooked bone : characterizing boiling and its physico-chemical eects. ', Archaeometry., 44 (3). pp. 485-494. Further information on publisher's website:http://dx.doi.org/10.1111/1475-4754.t01-1-00080Publisher's copyright statement:Additional information: Use policyThe full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-prot purposes provided that:• a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders.Please consult the full DRO policy for further details. ABSTRACTCooking is perhaps the most common pre-burial taphonomic transformation that occurs to bone, yet it is still one of the least understood. Little progress has been made in determining a method of identifying cooked bone in the archaeological record, despite its import for various branches of archaeology. This paper attempts to describe boiling in terms of its physico-chemical effects on bone, and uses a suite of diagenetic indicators to do this.It is shown that cooking for brief periods of time has little distinguishable effect on bone in the short term, but that increased boiling times can mirror diagenetic effects observed in archaeological bone. The relationship between the loss of collagen and alterations to the bone mineral is explored through heating experiments, and the results compared with archaeological data. The possibility of boiling being used as an analogue for bone diagenesis in future studies is raised, and the key relationship between protein and mineral is once again highlighted as vital to our understanding of bone diagenesis.