Preservation of the metaproteome: variability of protein preservation in ancient dental calculus

Use of Proteomics for Dietary Reconstruction: A Case Study Using Animal Teeth from Ancient Mesopotamia

This research examines animal teeth from Early Dynastic (2900-2350 BCE) Mesopotamia (Southern Iraq) to assess animal management practices and identify consumption patterns in animal diets. The objective to answer larger questions about food management and environmental resilience in ancient early complex societies in the Near East was achieved by the use of mass spectrometry-based proteomics for dietary reconstruction. Dietary MS, a revolutionary new methodology applying proteomics techniques to archeological sample sets to reconstruct ancient animal diet. A developed protein extraction technique followed by liquid chromatography tandem mass spectrometry allowed for the identification of the specific plant species consumed in order to highlight variable herd management strategies, resource optimization, for each taxon over time. It also provided information about overall health and indications of disease. This is the first study to apply a full suite of analyses to the region and provides the foundations of a necessary long-term view of human interaction within an environment, through both time and space.

Metaproteomic analysis of King Ghezo tomb wall (Abomey, Benin) confirms 19th century voodoo sacrifices

The palace of King Ghezo in Abomey, capital of the ancient kingdom of Dahomey (present-day Benin), houses two sacred huts which are specific funerary structures. It is claimed that the binder in their walls is made of human blood. In the study presented here, we conceived an original strategy to analyze the proteins present on minute amounts of the cladding sampled from the inner facade of the cenotaph wall and establish their origin. The extracted proteins were proteolyzed and the resulting peptides were characterized by high-resolution tandem mass spectrometry. Over 6397 distinct molecular entities were identified using cascading searches. Starting from without a priori searches of an extended generic database, the peptide repertoire was narrowed down to the most representative organisms-identified by means of taxon-specific peptides. A wide diversity of bacteria, fungi, plants, and animals were detected through the available protein material. This inventory was used to archaeologically reconstruct the voodoo rituals of consecration and maintenance of vitality. Several indicators attested to the presence of traces of human and poultry blood in the material taken. This study shows the essential advantages of paleoproteomics and metaproteomics for the study of ancient residues from archaeological excavations or historical monuments.

Palaeoproteomic investigation of an ancient human skeleton with abnormal deposition of dental calculus

Detailed investigation of extremely severe pathological conditions in ancient human skeletons is important as it could shed light on the breadth of potential interactions between humans and disease etiologies in the past. Here, we applied palaeoproteomics to investigate an ancient human skeletal individual with severe oral pathology, focusing our research on bacterial pathogenic factors and host defense response. This female skeleton, from the Okhotsk period (i.e., fifth to thirteenth century) of Northern Japan, poses relevant amounts of abnormal dental calculus deposition and exhibits oral dysfunction due to severe periodontal disease. A shotgun mass-spectrometry analysis identified 81 human proteins and 15 bacterial proteins from the calculus of the subject. We identified two pathogenic or bioinvasive proteins originating from two of the three "red complex" bacteria, the core species associated with severe periodontal disease in modern humans, as well as two additional bioinvasive proteins of periodontal-associated bacteria. Moreover, we discovered defense response system-associated human proteins, although their proportion was mostly similar to those reported in ancient and modern human individuals with lower calculus deposition. These results suggest that the bacterial etiology was similar and the host defense response was not necessarily more intense in ancient individuals with significant amounts of abnormal dental calculus deposition.

Windows into the past: recent scientific techniques in dental analysis

Teeth are the hardest and most chemically stable tissues in the body, are well-preserved in archaeological remains and, being resistant to decomposition in the soil, survive long after their supporting structures have deteriorated. It has long been recognised that visual and radiographic examination of teeth can provide considerable information relating to the lifestyle of an individual. This paper examines the latest scientific approaches that have become available to investigate recent and ancient teeth. These techniques include DNA analysis, which can be used to determine the sex of an individual, indicate familial relationships, study population movements, provide phylogenetic information and identify the presence of disease pathogens. A stable isotopic approach can shed light on aspects of diet and mobility and even research climate change. Proteomic analysis of ancient dental calculus can reveal specific information about individual diets. Synchrotron microcomputed tomography is a non-invasive technique which can be used to visualise physiological impactful events, such as parturition, menopause and diseases in cementum microstructure - these being displayed as aberrant growth lines.

Extraction Protocol for Parallel Analysis of Proteins and DNA from Ancient Teeth and Dental Calculus

Dental calculus is becoming a crucial material in the study of past populations with increasing interest in its proteomic and genomic content. Here, we suggest further development of a protocol for analysis of ancient proteins and a combined approach for subsequent ancient DNA extraction. We tested the protocol on recent teeth, and the optimized protocol was applied to ancient tooth to limit the destruction of calculus as it is a precious and irreplaceable source of dietary, microbiological, and ecological information in the archeological context. Finally, the applicability of the protocol was demonstrated on samples of the ancient calculus.

Paleoproteomic evidence reveals dairying supported prehistoric occupation of the highland Tibetan Plateau

The extreme environments of the Tibetan Plateau offer considerable challenges to human survival, demanding novel adaptations. While the role of biological and agricultural adaptations in enabling early human colonization of the plateau has been widely discussed, the contribution of pastoralism is less well understood, especially the dairy pastoralism that has historically been central to Tibetan diets. Here, we analyze ancient proteins from the dental calculus (n = 40) of all human individuals with sufficient calculus preservation from the interior plateau. Our paleoproteomic results demonstrate that dairy pastoralism began on the highland plateau by ~3500 years ago. Patterns of milk protein recovery point to the importance of dairy for individuals who lived in agriculturally poor regions above 3700 m above sea level. Our study suggests that dairy was a critical cultural adaptation that supported expansion of early pastoralists into the region's vast, non-arable highlands, opening the Tibetan Plateau up to widespread, permanent human occupation.

Permafrost preservation reveals proteomic evidence for yak milk consumption in the 13th century

Domesticated yaks endure as iconic symbols of high-altitude frozen landscapes, where herding communities depend on their high-fat milk, transport, dung, and natural fibers. While there is established proteomic evidence for ancient consumption of ruminant and horse milk in the mountains and steppes of northern Eurasia, yak dairy products have yet to be detected. Yak domestication and the species' dispersal from Tibet into the mountainous zones to the north are also poorly resolved due to a paucity of zooarchaeological data. To examine the potential of paleoproteomics to shed light on domesticated yak in Mongolia, we analyzed human dental calculus from Mongol era elite individuals recovered from permafrost burials in Khovsgol province, where people continue to herd yak to this day. We report the first evidence for yak dairy consumption, linked to local resource control. In addition, we confirm a large diversity of recovered whey, curd, tissue, and blood proteins, likely reflecting the excellent preservation conditions found at permafrost sites.

Ecological flexibility and adaptation to past climate change in the Middle Nile Valley: A multiproxy investigation of dietary shifts between the Neolithic and Kerma periods at Kadruka 1 and Kadruka 21

Human responses to climate change have long been at the heart of discussions of past economic, social, and political change in the Nile Valley of northeastern Africa. Following the arrival of Neolithic groups in the 6th millennium BCE, the Northern Dongola Reach of Upper Nubia witnessed a cultural florescence manifested through elaborate funerary traditions. However, despite the wealth of archaeological data available from funerary contexts, including evidence for domesticated animals and plants as grave goods, the paucity of stratified habitation contexts hinders interpretation of local subsistence trajectories. While it is recognised archaeologically that, against the backdrop of increasing environmental deterioration, the importance of agriculture based on Southwest Asian winter cereals increased throughout the Kerma period (2500-1450 BCE), the contribution of domesticated cereals to earlier Neolithic herding economies remains unclear. This paper presents direct dietary data from a total of 55 Middle Neolithic and Kerma period individuals from Kadruka 21 and Kadruka 1. Microbotanical data obtained from human dental calculus and grave sediments are integrated with human and faunal stable isotopes to explore changes in dietary breadth over time. The combined results demonstrate the consumption of wild plant species, including C4 wetland adapted grasses, by Middle Neolithic individuals at Kadruka 1. Despite existing evidence for domesticated barley in associated graves, the results obtained in this study provide no clear evidence for the routine consumption of domesticated cereals by Middle Neolithic individuals. Rather, direct microparticle evidence for the consumption of Triticeae cereals is only associated with a single Kerma period individual and corresponds with an isotopic shift indicating a greater contribution of C3-derived resources to diet. These results provide evidence for Neolithic dietary flexibility in Upper Nubia through the persistence of foraging activities and support existing evidence linking increased agricultural reliance to the development of the Kerma culture.

Dental calculus: A repository of bioinformation indicating diseases and human evolution

Dental calculus has long been considered as a vital contributing factor of periodontal diseases. Our review focuses on the role of dental calculus as a repository and discusses the bioinformation recently reported to be concealed in dental calculus from three perspectives: time-varying oral condition, systemic diseases, and anthropology at various times. Molecular information representing an individual's contemporary oral health status could be detected in dental calculus. Additionally, pathogenic factors of systemic diseases were found in dental calculus, including bacteria, viruses and toxic heavy metals. Thus, dental calculus has been proposed to play a role as biological data storage for detection of molecular markers of latent health concerns. Through the study of environmental debris in dental calculus, an overview of an individual's historical dietary habits and information about the environment, individual behaviors and social culture changes can be unveiled. This review summarizes a new role of dental calculus as a repository of bioinformation, with potential use in the prediction of oral diseases, systemic diseases, and even anthropology.

Paleoproteomics

Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human-animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.

Comprehensive Metabolic and Taxonomic Reconstruction of an Ancient Microbial Mat From the McMurdo Ice Shelf (Antarctica) by Integrating Genetic, Metaproteomic and Lipid Biomarker Analyses

Paleobiological reconstructions based on molecular fossils may be limited by degradation processes causing differential preservation of biomolecules, the distinct taxonomic specificity of each biomolecule type, and analytical biases. Here, we combined the analysis of DNA, proteins and lipid biomarkers using 16S and 18S rRNA gene metabarcoding, metaproteomics and lipid analysis to reconstruct the taxonomic composition and metabolisms of a desiccated microbial mat from the McMurdo Ice Shelf (MIS) (Antarctica) dated ~1,000 years BP. The different lability, taxonomic resolution and analytical bias of each biomolecule type led to a distinct microbial community profile. DNA analysis showed selective preservation of DNA remnants from the most resistant taxa (e.g., spore-formers). In contrast, the proteins profile revealed microorganisms missed by DNA sequencing, such as Cyanobacteria, and showed a microbial composition similar to fresh microbial mats in the MIS. Lipid hydrocarbons also confirmed Cyanobacteria and suggested the presence of mosses or vascular plant remnants from a period in Antarctica when the climate was warmer (e.g., Mid-Miocene or Eocene). The combined analysis of the three biomolecule types also revealed diverse metabolisms that operated in the microbial mat before desiccation: oxygenic and anoxygenic photosynthesis, nitrogen fixation, nitrification, denitrification, sulfur reduction and oxidation, and methanogenesis. Therefore, the joint analysis of DNA, proteins and lipids resulted in a powerful approach that improved taxonomic and metabolic reconstructions overcoming information gaps derived from using individual biomolecules types.

Metagenomic analysis of ancient dental calculus reveals unexplored diversity of oral archaeal Methanobrevibacter

BACKGROUND

Dental calculus (mineralised dental plaque) preserves many types of microfossils and biomolecules, including microbial and host DNA, and ancient calculus are thus an important source of information regarding our ancestral human oral microbiome. In this study, we taxonomically characterised the dental calculus microbiome from 20 ancient human skeletal remains originating from Trentino-South Tyrol, Italy, dating from the Neolithic (6000-3500 BCE) to the Early Middle Ages (400-1000 CE).

RESULTS

We found a high abundance of the archaeal genus Methanobrevibacter in the calculus. However, only a fraction of the sequences showed high similarity to Methanobrevibacter oralis, the only described Methanobrevibacter species in the human oral microbiome so far. To further investigate the diversity of this genus, we used de novo metagenome assembly to reconstruct 11 Methanobrevibacter genomes from the ancient calculus samples. Besides the presence of M. oralis in one of the samples, our phylogenetic analysis revealed two hitherto uncharacterised and unnamed oral Methanobrevibacter species that are prevalent in ancient calculus samples sampled from a broad range of geographical locations and time periods.

CONCLUSIONS

We have shown the potential of using de novo metagenomic assembly on ancient samples to explore microbial diversity and evolution. Our study suggests that there has been a possible shift in the human oral microbiome member Methanobrevibacter over the last millennia. Video abstract.

Correlation between the Macronutrient Content of Dental Calculus and the FFQ-Based Nutritional Intake of Obese and Normal-Weight Individuals

The growing epidemic of chronic diseases afflicting both developed and developing countries is related to diet and lifestyle. The current dietary assessment still has many constraints, particularly related to the objectivity of data gathering. Dental calculus, which is usually considered as medical waste in dental treatment, turns out to be a provider of abundant oral information. The objective of this study is to obtain the correlation between the macronutrient content of dental calculus and nutritional intake based on FFQ. This research is an analytic observational study with a case-control study design. Samples consisting of 35 obese individuals and 21 normal-weight individuals were taken using purposive sampling. The nutritional intake data were obtained using FFQ. The macronutrient content of dental calculus was checked using a colorimetric assay. The comparison between obese individuals and normal-weight individuals was tested using the Mann–Whitney test and T-test. The correlation between the macronutrient content of dental calculus and nutritional intake based on FFQ was measured using Spearman's rank-order correlation. The results showed there was a correlation between the macronutrient content of dental calculus and macronutrient intake based on FFQ. However, strong correlation was found only between fat intake with the total lipid content of dental calculus with rs = 0.521 and between carbohydrate intake with the total carbohydrate content of dental calculus with rs = 0.519. It was concluded that carbohydrate, protein, and lipid intake can be assessed using dental calculus. Dental calculus can be an alternative source of noninvasive, inexpensive, and specific dietary biomarkers.

Trends in deamidation across archaeological bones, ceramics and dental calculus

The accumulation of post-translational modifications (PTMs) in proteins throughout the lifecycle has been studied for decades, particularly more so with the advent of soft-ionization mass spectrometry-based proteomic techniques. However, particular PTMs, such as the deamidations of asparagine and glutamine residues, continue to accumulate in proteins that remain into the forensic, archaeological, and palaeontological records. The accurate measurement of these ancient 'molecular timers' has been proposed as a method to not only differentiate between exogenous and endogenous proteins within complex mixtures (i.e., contamination), but also as a method of providing relative age estimations into geological time. In this study we explored the extent to which deamidation varies with chronological age across different proteins in bones, as well as investigated differences between proteins across dental calculus and archaeological ceramics. We also analysed the relationships between the observed extent of deamidation and the protein primary structure. We found that collagen obtained from archaeological bones showed a chronological dependence on the extent of deamidation observed, but only when they were from similar environments, supporting prior suggestions about 'thermal age' being a major influence on the deamidation observed. Our study on non-collagenous proteins (NCPs) in archaeological bones showed that while biglycan, and to a lesser extent chondroadherin, showed positive correlations between geological age and the extent of deamidation, others including fetuin-A and serum albumin did not. However, despite the well-known dependence of deamidation on the three-dimensional structure of the peptides, we were unable to find any clear correlation between the structural motifs of the peptides in archaeological bones and the extent of deamidation observed. Our analysis of a set of food proteins obtained from Neolithic archaeological ceramics in Çatalhöyük also showed similar deamidation levels irrespective of the protein structure. Overall, our results suggest that deamidation in archaeological samples could be useful for obtaining additional information beyond identification of species and tissue type, be that as a measure of protein endogeneity and potential contamination, or a measure of protein degradation, or as an indicator of thermal age and for relative dating; however, further research needs to be undertaken to understand why particular proteins are better for this than others, going beyond simple consideration of their secondary structure.

Assessing the degradation of ancient milk proteins through site-specific deamidation patterns

The origins, prevalence and nature of dairying have been long debated by archaeologists. Within the last decade, new advances in high-resolution mass spectrometry have allowed for the direct detection of milk proteins from archaeological remains, including ceramic residues, dental calculus, and preserved dairy products. Proteins recovered from archaeological remains are susceptible to post-excavation and laboratory contamination, a particular concern for ancient dairying studies as milk proteins such as beta-lactoglobulin (BLG) and caseins are potential laboratory contaminants. Here, we examine how site-specific rates of deamidation (i.e., deamidation occurring in specific positions in the protein chain) can be used to elucidate patterns of peptide degradation, and authenticate ancient milk proteins. First, we characterize site-specific deamidation patterns in modern milk products and experimental samples, confirming that deamidation occurs primarily at low half-time sites. We then compare this to previously published palaeoproteomic data from six studies reporting ancient milk peptides. We confirm that site-specific deamidation rates, on average, are more advanced in BLG  recovered from ancient dental calculus and pottery residues. Nevertheless, deamidation rates displayed a high degree of variability, making it challenging to authenticate samples with relatively few milk peptides. We demonstrate that site-specific deamidation is a useful tool for identifying modern contamination but highlight the need for multiple lines of evidence to authenticate ancient protein data.

Human Bone Proteomes before and after Decomposition: Investigating the Effects of Biological Variation and Taphonomic Alteration on Bone Protein Profiles and the Implications for Forensic Proteomics

Bone proteomic studies using animal proxies and skeletonized human remains have delivered encouraging results in the search for potential biomarkers for precise and accurate post-mortem interval (PMI) and the age-at-death (AAD) estimation in medico-legal investigations. The development of forensic proteomics for PMI and AAD estimation is in critical need of research on human remains throughout decomposition, as currently the effects of both inter-individual biological differences and taphonomic alteration on the survival of human bone protein profiles are unclear. This study investigated the human bone proteome in four human body donors studied throughout decomposition outdoors. The effects of ageing phenomena (in vivo and post-mortem) and intrinsic and extrinsic variables on the variety and abundancy of the bone proteome were assessed. Results indicate that taphonomic and biological variables play a significant role in the survival of proteins in bone. Our findings suggest that inter-individual and inter-skeletal differences in bone mineral density (BMD) are important variables affecting the survival of proteins. Specific proteins survive better within the mineral matrix due to their mineral-binding properties. The mineral matrix likely also protects these proteins by restricting the movement of decomposer microbes. New potential biomarkers for PMI estimation and AAD estimation were identified. Future development of forensic bone proteomics should include standard measurement of BMD and target a combination of different biomarkers.

Comparing the Use of Magnetic Beads with Ultrafiltration for Ancient Dental Calculus Proteomics

Over the past two decades, proteomic analysis has greatly developed in application to the field of biomolecular archaeology, coinciding with advancements in LC-MS/MS instrumentation sensitivity and improvements in sample preparation methods. Recently, human dental calculus has received much attention for its well-preserved proteomes locked in mineralized dental plaque which stores information on human diets and the oral microbiome otherwise invisible to other biomolecular approaches. Maximizing proteome recovery in ancient dental calculus, available only in minute quantities and irreplaceable after destructive analysis, is of paramount importance. Here, we compare the more traditional ultrafiltration-based and acetone precipitation approaches with the newer paramagnetic bead approach in order to test the influence of demineralization acid on recovered proteome complexity obtained from specimens as well as the sequence coverages matched for significant proteins. We found that a protocol utilizing EDTA combined with paramagnetic beads increased proteome complexity, in some cases doubling the number of unique peptides and number of proteins matched, compared to protocols involving the use of HCl and either acetone precipitation or ultrafiltration. Although the increase in the number of proteins was almost exclusively of bacterial origin, a development that has implications for the study of diseases within these ancient populations, an increase in the peptide number for the dairy proteins β-lactoglobulin and casein was also observed reflecting an increase in sequence coverage for these dietary proteins of interest. We also consider structural explanations for the discrepancies observed between these two key dietary proteins preserved in archaeological dental calculus.

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.

Ancient protein analysis in archaeology

The analysis of ancient proteins from paleontological, archeological, and historic materials is revealing insights into past subsistence practices, patterns of health and disease, evolution and phylogeny, and past environments. This review tracks the development of this field, discusses some of the major methodological strategies used, and synthesizes recent developments in archeological applications of ancient protein analysis. Moreover, this review highlights some of the challenges faced by the field and potential future directions, arguing that the development of minimally invasive or nondestructive techniques, strategies for protein authentication, and the integration of ancient protein analysis with other biomolecular techniques are important research strategies as this field grows.

Multi-omic detection of Mycobacterium leprae in archaeological human dental calculus

Mineralized dental plaque (calculus) has proven to be an excellent source of ancient biomolecules. Here we present a Mycobacterium leprae genome (6.6-fold), the causative agent of leprosy, recovered via shotgun sequencing of sixteenth-century human dental calculus from an individual from Trondheim, Norway. When phylogenetically placed, this genome falls in branch 3I among the diversity of other contemporary ancient strains from Northern Europe. Moreover, ancient mycobacterial peptides were retrieved via mass spectrometry-based proteomics, further validating the presence of the pathogen. Mycobacterium leprae can readily be detected in the oral cavity and associated mucosal membranes, which likely contributed to it being incorporated into this individual's dental calculus. This individual showed some possible, but not definitive, evidence of skeletal lesions associated with early-stage leprosy. This study is the first known example of successful multi-omics retrieval of M. leprae from archaeological dental calculus. Furthermore, we offer new insights into dental calculus as an alternative sample source to bones or teeth for detecting and molecularly characterizing M. leprae in individuals from the archaeological record.

This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.

Living off the land: Terrestrial-based diet and dairying in the farming communities of the Neolithic Balkans

The application of biomolecular techniques to archaeological materials from the Balkans is providing valuable new information on the prehistory of the region. This is especially relevant for the study of the neolithisation process in SE Europe, which gradually affected the rest of the continent. Here, to answer questions regarding diet and subsistence practices in early farming societies in the central Balkans, we combine organic residue analyses of archaeological pottery, taxonomic and isotopic study of domestic animal remains and biomolecular analyses of human dental calculus. The results from the analyses of the lipid residues from pottery suggest that milk was processed in ceramic vessels. Dairy products were shown to be part of the subsistence strategies of the earliest Neolithic communities in the region but were of varying importance in different areas of the Balkan. Conversely, milk proteins were not detected within the dental calculus. The molecular and isotopic identification of meat, dairy, plants and beeswax in the pottery lipids also provided insights into the diversity of diet in these early Neolithic communities, mainly based on terrestrial resources. We also present the first compound-specific radiocarbon dates for the region, obtained directly from absorbed organic residues extracted from pottery, identified as dairy lipids.

Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival

While sequencing ancient DNA (aDNA) from archaeological material is now commonplace, very few attempts to sequence ancient transcriptomes have been made, even from typically stable deposition environments such as permafrost. This is presumably due to assumptions that RNA completely degrades relatively quickly, particularly when dealing with autolytic, nuclease-rich mammalian tissues. However, given the recent successes in sequencing ancient RNA (aRNA) from various sources including plants and animals, we suspect that these assumptions may be incorrect or exaggerated. To challenge the underlying dogma, we generated shotgun RNA data from sources that might normally be dismissed for such study. Here, we present aRNA data generated from two historical wolf skins, and permafrost-preserved liver tissue of a 14,300-year-old Pleistocene canid. Not only is the latter the oldest RNA ever to be sequenced, but it also shows evidence of biologically relevant tissue specificity and close similarity to equivalent data derived from modern-day control tissue. Other hallmarks of RNA sequencing (RNA-seq) data such as exon-exon junction presence and high endogenous ribosomal RNA (rRNA) content confirms our data’s authenticity. By performing independent technical library replicates using two high-throughput sequencing platforms, we show not only that aRNA can survive for extended periods in mammalian tissues but also that it has potential for tissue identification. aRNA also has possible further potential, such as identifying in vivo genome activity and adaptation, when sequenced using this technology.

Ancient DNA is known to survive in cold environments for tens of millennia, but it is assumed that ancient RNA could not persist in such a way due to its relative instability. However, this study shows that under permafrost conditions, ancient RNA can survive well enough to show tissue specificity even in mammalian soft tissues.

Fine Endmesolithic fish caviar meal discovered by proteomics in foodcrusts from archaeological site Friesack 4 (Brandenburg, Germany)

The role of aquatic resources in ancient economies and paleodiet is important for understanding the evolution of prehistorical societies. Charred food remains from ancient pottery are valuable molecular evidence of dietary habits in antiquity. However, conventional archaeometric approaches applied in their analysis lack organismal specificity, are affected by abundant environmental contaminants, do not elucidate food processing recipes and are limited in the inland regions where diverse dietary resources are available. We performed proteomics analysis of charred organic deposits adhered on early ceramics from Mesolithic-Neolithic inland site Friesack 4 (Brandenburg, Germany). One of pots—a small coarse bowl radiocarbon dated to the end of the 5^th millennium BC—was attributed to Endmesolithic pottery. Proteomics of foodcrust from this vessel identified fine carp roe meal and revealed details of a prehistorical culinary recipe. Ancient proteins were unequivocally distinguished from contemporary contaminants by computing deamidation ratios of glutamine residues. These data paint a broader picture of the site-specific exploitation of aquatic resources and contribute to better understanding of the dietary context of Neolithic transition in European inland.

Quantitative metaproteomics of medieval dental calculus reveals individual oral health status

The composition of ancient oral microbiomes has recently become accessible owing to advanced biomolecular methods such as metagenomics and metaproteomics, but the utility of metaproteomics for such analyses is less explored. Here, we use quantitative metaproteomics to characterize the dental calculus associated with the remains of 21 humans retrieved during the archeological excavation of the medieval (ca. 1100-1450 CE) cemetery of Tjærby, Denmark. We identify 3671 protein groups, covering 220 bacterial species and 81 genera across all medieval samples. The metaproteome profiles of bacterial and human proteins suggest two distinct groups of archeological remains corresponding to health-predisposed and oral disease-susceptible individuals, which is supported by comparison to the calculus metaproteomes of healthy living individuals. Notably, the groupings identified by metaproteomics are not apparent from the bioarchaeological analysis, illustrating that quantitative metaproteomics has the potential to provide additional levels of molecular information about the oral health status of individuals from archeological contexts.

Ancient proteins from ceramic vessels at Çatalhöyük West reveal the hidden cuisine of early farmers

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.

Proteomic evidence of dietary sources in ancient dental calculus

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.

A guide to ancient protein studies

Palaeoproteomics is an emerging neologism used to describe the application of mass spectrometry-based approaches to the study of ancient proteomes. As with palaeogenomics (the study of ancient DNA), it intersects evolutionary biology, archaeology and anthropology, with applications ranging from the phylogenetic reconstruction of extinct species to the investigation of past human diets and ancient diseases. However, there is no explicit consensus at present regarding standards for data reporting, data validation measures or the use of suitable contamination controls in ancient protein studies. Additionally, in contrast to the ancient DNA community, no consolidated guidelines have been proposed by which researchers, reviewers and editors can evaluate palaeoproteomics data, in part due to the novelty of the field. Here we present a series of precautions and standards for ancient protein research that can be implemented at each stage of analysis, from sample selection to data interpretation. These guidelines are not intended to impose a narrow or rigid list of authentication criteria, but rather to support good practices in the field and to ensure the generation of robust, reproducible results. As the field grows and methodologies change, so too will best practices. It is therefore essential that researchers continue to provide necessary details on how data were generated and authenticated so that the results can be independently and effectively evaluated. We hope that these proposed standards of practice will help to provide a firm foundation for the establishment of palaeoproteomics as a viable and powerful tool for archaeologists, anthropologists and evolutionary biologists.