A guide to ancient protein studies

ProAlanase is an Effective Alternative to Trypsin for Proteomics Applications and Disulfide Bond Mapping

Trypsin is the protease of choice in bottom-up proteomics. However, its application can be limited by the amino acid composition of target proteins and the pH of the digestion solution. In this study we characterize ProAlanase, a protease from the fungus Aspergillus niger that cleaves primarily on the C-terminal side of proline and alanine residues. ProAlanase achieves high proteolytic activity and specificity when digestion is carried out at acidic pH (1.5) for relatively short (2 h) time periods. To elucidate the potential of ProAlanase in proteomics applications, we conducted a series of investigations comprising comparative multi-enzymatic profiling of a human cell line proteome, histone PTM analysis, ancient bone protein identification, phosphosite mapping and de novo sequencing of a proline-rich protein and disulfide bond mapping in mAb. The results demonstrate that ProAlanase is highly suitable for proteomics analysis of the arginine- and lysine-rich histones, enabling high sequence coverage of multiple histone family members. It also facilitates an efficient digestion of bone collagen thanks to the cleavage at the C terminus of hydroxyproline which is highly prevalent in collagen. This allows to identify complementary proteins in ProAlanase- and trypsin-digested ancient bone samples, as well as to increase sequence coverage of noncollagenous proteins. Moreover, digestion with ProAlanase improves protein sequence coverage and phosphosite localization for the proline-rich protein Notch3 intracellular domain (N3ICD). Furthermore, we achieve a nearly complete coverage of N3ICD protein by de novo sequencing using the combination of ProAlanase and tryptic peptides. Finally, we demonstrate that ProAlanase is efficient in disulfide bond mapping, showing high coverage of disulfide-containing regions in a nonreduced mAb.

First sequencing of ancient coral skeletal proteins

Here we report the first recovery, sequencing, and identification of fossil biomineral proteins from a Pleistocene fossil invertebrate, the stony coral Orbicella annularis. This fossil retains total hydrolysable amino acids of a roughly similar composition to extracts from modern O. annularis skeletons, with the amino acid data rich in Asx (Asp + Asn) and Glx (Glu + Gln) typical of invertebrate skeletal proteins. It also retains several proteins, including a highly acidic protein, also known from modern coral skeletal proteomes that we sequenced by LC-MS/MS over multiple trials in the best-preserved fossil coral specimen. A combination of degradation or amino acid racemization inhibition of trypsin digestion appears to limit greater recovery. Nevertheless, our workflow determines optimal samples for effective sequencing of fossil coral proteins, allowing comparison of modern and fossil invertebrate protein sequences, and will likely lead to further improvements of the methods. Sequencing of endogenous organic molecules in fossil invertebrate biominerals provides an ancient record of composition, potentially clarifying evolutionary changes and biotic responses to paleoenvironments.

On the standardization of ZooMS nomenclature

Zooarchaeology by Mass Spectrometry (ZooMS) is rapidly becoming a staple in archaeological and cultural heritage science. Developed a decade ago, this peptide mass fingerprinting technique is expanding from a small group of researchers mainly involved in method development to a broader group of scientists using it as another tool in their toolboxes. With new researchers beginning to use the method, it is imperative that a user-friendly, standardized approach be established. A major barrier has been the often haphazard and changing nomenclature used to label peptide markers necessary for taxonomic identification. Consistent, reliable, and easy-to-understand nomenclature is key to the growth of ZooMS, particularly as the reference library continues to expand. We propose a new set of standardized guidelines for peptide markers based on their position in the type I collagen sequence from the beginning of the highly conserved, helical region. Since this region has no insertions or deletions over a wide range of taxonomic groups, the proposed nomenclature system can be used reliably and consistently across all vertebrate taxa. We propose to label ZooMS peptide markers with the gene, followed by the position of the first and last amino acid of the marker from the start of the helical region. SIGNIFICANCE STATEMENT: We propose a standardized nomenclature system for ZooMS peptide markers that provides consistent labels across multiple, broad taxonomic groups. This system unambiguously locates the marker peptides in the type I collagen sequence, avoids duplication of marker names, and facilitates the creation of large ZooMS databases which can include all vertebrates.

Untangling the fibre ball: Proteomic characterization of South American camelid hair fibres by untargeted multivariate analysis and molecular networking

The proteomic analysis of hairs, yarns or textiles has emerged as a powerful method to determine species of origin, mainly used in archaeozoological research and fraud control. Differentiation between the South American camelid (SAC) species (the wild guanaco and vicuña and their respective domesticates the llama and alpaca) is particularly challenging due to poor database information and significant hybridization between species. In this study, we analysed 41 modern and 4 archaeological samples from the four SACs species. Despite strong similarities with Old World Camelidae, we identified 7 peptides specific to SACs assigned to keratin K86 and the keratin-associated proteins KAP13-1 and KAP11-1. Untargeted multivariate analysis of the LC-MS data permitted to distinguish SAC species and propose discriminant features. MS/MS-based molecular networking combined with database-assisted de novo sequencing permitted to identify 5 new taxonomic peptides assigned to K33a, K81 and/or K83 keratins and KAP19-1. These peptides differentiate the two wild species, guanaco and vicuña. These results show the value of combining database search and untargeted metabolomic approaches for paleoproteomics, and reveal for the first time the potential of molecular networks to highlight deamidation related to diagenesis and cluster highly similar peptides related to interchain homologies or intra- or inter-specific polymorphism. SIGNIFICANCE: This study used an innovative approach combining multivariate analysis of LC-MS data together with molecular networking and database-assisted de novo sequencing to identify taxonomic peptides in palaeoproteomics. It constitutes the first attempt to differentiate between hair fibres from the four South American camelids (SACs) based on proteomic analysis of modern and archaeological samples. It provides different proteomic signatures for each of the four SAC species and proposes new SAC taxonomic peptides of interest in archaeozoology and fraud control. SACs have been extensively exploited since human colonization of South America but have not been studied to the extent of their economic, cultural and heritage importance. Applied to the analysis of ancient Andean textiles, our results should permit a better understanding of cultural and pastoral practices in South America. The wild SACs are endangered by poaching and black-market sale of their fibre. For the first time, our results provide discriminant features for the determination of species of origin of contraband fibre.

A versatile and user-friendly approach for the analysis of proteins in ancient and historical objects

Identification and characterization of ancient proteins still require technical developments towards non-invasiveness, sensitivity, versatility and ease of use of the analyses. We report that the enzyme functionalized films, described in Cicatiello et al. (2018), can be used efficiently on the surface of different objects ranging from fixative-coated paper to canvas to the coating on an albumen photograph, as well as the much harder surfaces of ivory objects and the proteinaceous binders in the decoration of a wooden Egyptian coffin. The mixture of digested peptides that are efficiently captured on the functionalized surface are also amenable to LC-MS/MS analysis, which is necessary to confidently identify chemical modifications induced upon degradation, in order to characterize the conservation state of proteins. Moreover, in a two-step procedure, we have combined the trypsin functionalized film with a PNGaseF functionalized film, which adds a deglycosylation pretreatment allowing improved detection of glycosylated proteins. SIGNIFICANCE: User friendly trypsin functionalized films were implemented to expand their potential as versatile, modular tools that can be widely exploited in the world of diagnosis of cultural heritage objects, ancient proteins, and palaeoproteomics: a procedure that could be carried out by conservators or archaeologists first on-site and later analysed with standard MS techniques.

Child murder in the Early Bronze Age: proteomic sex identification of a cold case from Schleinbach, Austria

The identification of sex-specific peptides in human tooth enamel by nanoflow liquid chromatography-tandem mass spectrometry (nanoLC-MS/MS) represents a quantum leap for the study of childhood and social relations more generally. Determining sex-related differences in prehistoric child rearing and mortality has been hampered by the insufficient accuracy in determining the biological sex of juveniles. We conducted mass spectrometric analysis to identify sex-specific peptides in the dental enamel of a child from a settlement pit of the Early Bronze Age settlement of Schleinbach, Austria (c. 1950-1850 bc). Four perimortal impression fractures on the skull of a 5-6-year-old child indicate an intentional killing, with a co-buried loom weight as possible murder weapon. Proteomic analysis, conducted for the first time on prehistoric teeth in Austria, determined the child's sex as male. While we cannot conclusively determine whether the child was the victim of conflicts between village groups or was slain by members of his own community, we suggest that contextual evidence points to the latter. A possible trigger of violence was the follow-on effects of an uncontrolled middle ear infection revealed by an osteological analysis. The boy from Schleinbach highlights the potential for further investigation of gender-biased violence, infanticide and child murder based on the recently developed method of proteomic sex identification.

Palaeoproteomic analysis of Pleistocene cave hyenas from east Asia

The spotted hyena (Crocuta crocuta) is the only extant species of the genus Crocuta, which once occupied a much wider range during the Pliocene and Pleistocene. However, its origin and evolutionary history is somewhat contentious due to discordances between morphological, nuclear, and mitochondrial data. Due to the limited molecular data from east Asian Crocuta, also known as cave hyena, and the difficulty of extracting ancient DNA from this area, here we present proteomic analysis of cave hyenas from three locations in northern China. This marks the first proteomic data generated from cave hyenas, adding new molecular data to the east Asian populations. Phylogenetic analysis based on these protein sequences reveals two different groups of cave hyenas in east Asia, one of which could not be distinguished from modern spotted hyenas from northern Africa, tentatively the result of previously suggested gene flow between these lineages. With developments of instrumentation and analytical methods, proteomics holds promising potential for molecular phylogenetic reconstructions of ancient fauna previously thought to be unreachable using ancient DNA.

Palaeoproteomics gives new insight into early southern African pastoralism

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 north-eastern 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.

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.

Present-Day DNA Contamination in Ancient DNA Datasets

Present-day contamination can lead to false conclusions in ancient DNA studies. A number of methods are available to estimate contamination, which use a variety of signals and are appropriate for different types of data. Here an overview of currently available methods highlighting their strengths and weaknesses is provided, and a classification based on the signals used to estimate contamination is proposed. This overview aims at enabling researchers to choose the most appropriate methods for their dataset. Based on this classification, potential avenues for the further development of methods are discussed.

Non-destructive ZooMS identification reveals strategic bone tool raw material selection by Neandertals

Five nearly identical fragments of specialized bone tools, interpreted as lissoirs (French for “smoothers”), have been found at two Middle Paleolithic sites in southwest France. The finds span three separate archaeological deposits, suggesting continuity in the behavior of late Neandertals. Using standard morphological assessments, we determined that the lissoirs were produced on ribs of medium-sized ungulates. However, since these bones are highly fragmented and anthropogenically modified, species determinations were challenging. Also, conservative curation policy recommends minimizing destructive sampling of rare, fragile, or small artifacts for molecular identification methods. To better understand raw material selection for these five lissoirs, we reassess their taxonomy using a non-destructive ZooMS methodology based on triboelectric capture of collagen. We sampled four storage containers and obtained identifiable MALDI-TOF MS collagen fingerprints, all indicative of the same taxonomic clade, which includes aurochs and bison (Bos sp. and Bison sp.). The fifth specimen, which was stored in a plastic bag, provided no useful MALDI-TOF MS spectra. We show that the choice of large bovid ribs in an archaeological layer dominated by reindeer (Rangifer tarandus) demonstrates strategic selection by these Neandertals. Furthermore, our results highlight the value of a promising technique for the non-destructive analysis of bone artifacts.

Protein aggregate formation permits millennium-old brain preservation

Human proteins have not been reported to survive in free nature, at ambient temperature, for long periods. Particularly, the human brain rapidly dissolves after death due to auto-proteolysis and putrefaction. The here presented discovery of 2600-year-old brain proteins from a radiocarbon dated human brain provides new evidence for extraordinary long-term stability of non-amyloid protein aggregates. Immunoelectron microscopy confirmed the preservation of neurocytoarchitecture in the ancient brain, which appeared shrunken and compact compared to a modern brain. Resolution of intermediate filaments (IFs) from protein aggregates took 2-12 months. Immunoassays on micro-dissected brain tissue homogenates revealed the preservation of the known protein topography for grey and white matter for type III (glial fibrillary acidic protein, GFAP) and IV (neurofilaments, Nfs) IFs. Mass spectrometry data could be matched to a number of peptide sequences, notably for GFAP and Nfs. Preserved immunogenicity of the prehistoric human brain proteins was demonstrated by antibody generation (GFAP, Nfs, myelin basic protein). Unlike brain proteins, DNA was of poor quality preventing reliable sequencing. These long-term data from a unique ancient human brain demonstrate that aggregate formation permits for the preservation of brain proteins for millennia.

Enamel proteome shows that Gigantopithecus was an early diverging pongine

Gigantopithecus blacki was a giant hominid that inhabited densely forested environments of Southeast Asia during the Pleistocene¹. 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.

The dynamics of Early Celtic consumption practices: A case study of the pottery from the Heuneburg

The Early Celtic site of the Heuneburg (Baden-Wuerttemberg, Germany) has long been understood as a hallmark of early urbanization in Central Europe. The rich collection of Mediterranean imports recovered from the settlement, the elite burials in its surroundings and the Mediterranean-inspired mudbrick fortification wall further point to the importance of intercultural connections with the Mediterranean as a crucial factor in the transformation of Early Iron Age societies. We describe a new facet of this process by studying the transformation of consumption practices, especially drinking habits, brought about by intercultural encounters from the late 7^th to the 5^th century BC through the analysis of organic remains in 133 ceramic vessels found at the Heuneburg using Organic Residue Analysis (ORA). During the Ha D1 phase, fermented beverages, including Mediterranean grape wine, were identified in and appear to have been consumed from local handmade ceramics. The latter were recovered from different status-related contexts within the Heuneburg, suggesting an early and well-established trade/exchange system of this Mediterranean product. This contrasts with the results obtained for the drinking and serving vessels from the Ha D3 phase that were studied. The consumption of fermented beverages (wine and especially bacteriofermented products) appears to have been concentrated on the plateau. The ORA analyses presented here seem to indicate that during this time, grape wine was consumed primarily from imported vessels, and more rarely from local prestigious fine wheel-made vessels. In addition to imported wine, we demonstrate the consumption of a wide variety of foodstuffs, such as animal fats (especially dairy products), millet, plant oils and waxy plants, fruit and beehive products as well as one or several other fermented beverage(s) that were probably locally produced. Through this diachronic study of vessel function from different intra-site contexts, we inform on changing and status-related practices of food processing and consumption.

Analysis of 5000 year-old human teeth using optimized large-scale and targeted proteomics approaches for detection of sex-specific peptides

The study demonstrates the high potential of MS-based proteomics coupled to an iterative database search strategy for the in-depth investigation of ancient proteomes. An efficient targeted PRM MS-based approach, although limited to the detection of a single pair of sex-specific amelogenin peptides, allowed confirming the sex of individuals in ancient dental remains, an essential information for paleoanthropologists facing the issue of sex determination and dimorphism.

Not a limitless resource: ethics and guidelines for destructive sampling of archaeofaunal remains

With the advent of ancient DNA, as well as other methods such as isotope analysis, destructive sampling of archaeofaunal remains has increased much faster than the effort to collect and curate them. While there has been considerable discussion regarding the ethics of destructive sampling and analysis of human remains, this dialogue has not extended to archaeofaunal material. Here we address this gap and discuss the ethical challenges surrounding destructive sampling of materials from archaeofaunal collections. We suggest ways of mitigating the negative aspects of destructive sampling and present step-by-step guidelines aimed at relevant stakeholders, including scientists, holding institutions and scientific journals. Our suggestions are in most cases easily implemented without significant increases in project costs, but with clear long-term benefits in the preservation and use of zooarchaeological material.

Relief food subsistence revealed by microparticle and proteomic analyses of dental calculus from victims of the Great Irish Famine

Food and diet were class markers in 19th-century Ireland, which became evident as nearly 1 million people, primarily the poor and destitute, died as a consequence of the notorious Great Famine of 1845 to 1852. Famine took hold after a blight (Phytophthora infestans) destroyed virtually the only means of subsistence-the potato crop-for a significant proportion of the population. This study seeks to elucidate the variability of diet in mid-19th-century Ireland through microparticle and proteomic analysis of human dental calculus samples (n = 42) from victims of the famine. The samples derive from remains of people who died between August 1847 and March 1851 while receiving poor relief as inmates in the union workhouse in the city of Kilkenny (52°39' N, -7°15' W). The results corroborate the historical accounts of food provisions before and during the famine, with evidence of corn (maize), potato, and cereal starch granules from the microparticle analysis and milk protein from the proteomic analysis. Unexpectedly, there is also evidence of egg protein-a food source generally reserved only for export and the better-off social classes-which highlights the variability of the prefamine experience for those who died. Through historical contextualization, this study shows how the notoriously monotonous potato diet of the poor was opportunistically supplemented by other foodstuffs. While the Great Irish Famine was one of the worst subsistence crises in history, it was foremost a social disaster induced by the lack of access to food and not the lack of food availability.

Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny

Ancient DNA (aDNA) sequencing has enabled reconstruction of speciation, migration, and admixture events for extinct taxa¹. Outside the permafrost, however, irreversible aDNA post-mortem degradation² has so far limited aDNA recovery to the past ~0.5 million years (Ma)³. Contrarily, tandem mass spectrometry (MS) allowed sequencing ~1.5 million year (Ma) old collagen type I (COL1)⁴ and suggested the presence of protein residues in Cretaceous fossil remains⁵, although with limited phylogenetic use⁶. In the absence of molecular evidence, the speciation of several Early and Middle Pleistocene extinct species remain contentious. In this study, we address the phylogenetic relationships of the Eurasian Pleistocene Rhinocerotidae^7–9 using a ~1.77 Ma old dental enamel proteome of a Stephanorhinus specimen from the Dmanisi archaeological site in Georgia (South Caucasus)¹⁰. Molecular phylogenetic analyses place the Dmanisi Stephanorhinus as a sister group to the woolly (Coelodonta antiquitatis) and Merck’s rhinoceros (S. kirchbergensis) clade. We show that Coelodonta evolved from an early Stephanorhinus lineage and that the latter includes at least two distinct evolutionary lines. As such, the genus Stephanorhinus is currently paraphyletic and its systematic revision is therefore needed. We demonstrate that Early Pleistocene dental enamel proteome sequencing overcomes the limits of ancient collagen- and aDNA-based phylogenetic inference. It also provides additional information about the sex and taxonomic assignment of the specimens analysed. Dental enamel, the hardest tissue in vertebrates¹¹, is highly abundant in the fossil record. Our findings reveal that palaeoproteomic investigation of this material can push biomolecular investigation further back into the Early Pleistocene.

Unlocking the potential of ancient fish DNA in the genomic era

Fish are the most diverse group of vertebrates, fulfil important ecological functions and are of significant economic interest for aquaculture and wild fisheries. Advances in DNA extraction methods, sequencing technologies and bioinformatic applications have advanced genomic research for nonmodel organisms, allowing the field of fish ancient DNA (aDNA) to move into the genomics era. This move is enabling researchers to investigate a multitude of new questions in evolutionary ecology that could not, until now, be addressed. In many cases, these new fields of research have relevance to evolutionary applications, such as the sustainable management of fisheries resources and the conservation of aquatic animals. Here, we focus on the application of fish aDNA to (a) highlight new research questions, (b) outline methodological advances and current challenges, (c) discuss how our understanding of fish ecology and evolution can benefit from aDNA applications and (d) provide a future perspective on how the field will help answer key questions in conservation and management. We conclude that the power of fish aDNA will be unlocked through the application of continually improving genomic resources and methods to well-chosen taxonomic groups represented by well-dated archaeological samples that can provide temporally and/or spatially extensive data sets.

Paleoproteomics of Mesozoic Dinosaurs and Other Mesozoic Fossils

Molecular studies have contributed greatly to our understanding of evolutionary processes that act upon virtually every aspect of living organisms. However, these studies are limited with regard to extinct organisms, particularly those from the Mesozoic because fossils pose unique challenges to molecular workflows, and because prevailing wisdom suggests no endogenous molecular components can persist into deep time. Here, the power and potential of a molecular approach to Mesozoic fossils is discussed. Molecular methods that have been applied to Mesozoic fossils-including iconic, non-avian dinosaurs- and the challenges inherent in such analyses, are compared and evaluated. Taphonomic processes resulting in the transition of living organisms from the biosphere into the fossil record are reviewed, and the possible effects of taphonomic alteration on downstream analyses that can be problematic for very old material (e.g., molecular modifications, limitations of on comparative databases) are addressed. Molecular studies applied to ancient remains are placed in historical context, and past and current studies are evaluated with respect to producing phylogenetically and/or evolutionarily significant data. Finally, some criteria for assessing the presence of endogenous biomolecules in very ancient fossil remains are suggested as a starting framework for such studies.

A new home for microbes

Modern microorganisms growing in fossils provide major challenges for researchers trying to detect ancient molecules in the same fossils.

Cretaceous dinosaur bone contains recent organic material and provides an environment conducive to microbial communities

Fossils were thought to lack original organic molecules, but chemical analyses show that some can survive. Dinosaur bone has been proposed to preserve collagen, osteocytes, and blood vessels. However, proteins and labile lipids are diagenetically unstable, and bone is a porous open system, allowing microbial/molecular flux. These 'soft tissues' have been reinterpreted as biofilms. Organic preservation versus contamination of dinosaur bone was examined by freshly excavating, with aseptic protocols, fossils and sedimentary matrix, and chemically/biologically analyzing them. Fossil 'soft tissues' differed from collagen chemically and structurally; while degradation would be expected, the patterns observed did not support this. 16S rRNA amplicon sequencing revealed that dinosaur bone hosted an abundant microbial community different from lesser abundant communities of surrounding sediment. Subsurface dinosaur bone is a relatively fertile habitat, attracting microbes that likely utilize inorganic nutrients and complicate identification of original organic material. There exists potential post-burial taphonomic roles for subsurface microorganisms.

Mawangdui-Type Ancient Human Cadavers in China and Strategies for Their Long-Term Preservation

Ancient human remains may exist as intact cadavers in various forms, including mummies as well as humid or soft corpses. These valuable human depositories have been increasingly investigated with modern molecular biological approaches, delivering breakthrough discoveries in the field of paleoanthropology. Many ancient remains are also preserved in museums for public education of the history of human civilization. The Mawangdui tomb No. 1 cadaver was unearthed in 1972 in Changsha, China, and is a well-preserved humid-type corpse of a deceased woman who lived in the Western Han Dynasty (206BC-24AD). During the past few decades, a number of other similar cadavers have been discovered in China. The Mawangdui cadaver thus appears to represent an archetype of the humid corpses that are commonly unearthed from buried coffins, but show a great extent of anatomical and histological integrity at the time of excavation. Long-term protection of these cadavers is important with regard to scientific investigation and heritage conservation, while challenges exist to develop effective preservation protocols. In this perspective article, we describe the overall features of the humid cadavers found in China, and discuss the factors that potentially contributed to their preservation before excavation. We also introduce the efforts taken for, and experience learned from, postexcavation preservation of the Mawangdui cadaver during the past four decades. Finally, we propose that research into the mechanism governing the breakdown of macromolecules may provide potential solutions for extended protection of these valuable ancient human remains.

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.

Bronze Age population dynamics and the rise of dairy pastoralism on the eastern Eurasian steppe

Since the Bronze Age, pastoralism has been a dominant subsistence mode on the Western steppe, but the origins of this tradition on the Eastern steppe are poorly understood. Here we investigate a putative early pastoralist population in northern Mongolia and find that dairy production was established on the Eastern steppe by 1300 BCE. Milk proteins preserved in dental calculus indicate an early focus on Western domesticated ruminants rather than local species, but genetic ancestry analysis indicates minimal admixture with Western steppe herders, suggesting that dairy pastoralism was introduced through adoption by local hunter-gatherers rather than population replacement.

Recent paleogenomic studies have shown that migrations of Western steppe herders (WSH) beginning in the Eneolithic (ca. 3300–2700 BCE) profoundly transformed the genes and cultures of Europe and central Asia. Compared with Europe, however, the eastern extent of this WSH expansion is not well defined. Here we present genomic and proteomic data from 22 directly dated Late Bronze Age burials putatively associated with early pastoralism in northern Mongolia (ca. 1380–975 BCE). Genome-wide analysis reveals that they are largely descended from a population represented by Early Bronze Age hunter-gatherers in the Baikal region, with only a limited contribution (∼7%) of WSH ancestry. At the same time, however, mass spectrometry analysis of dental calculus provides direct protein evidence of bovine, sheep, and goat milk consumption in seven of nine individuals. No individuals showed molecular evidence of lactase persistence, and only one individual exhibited evidence of >10% WSH ancestry, despite the presence of WSH populations in the nearby Altai-Sayan region for more than a millennium. Unlike the spread of Neolithic farming in Europe and the expansion of Bronze Age pastoralism on the Western steppe, our results indicate that ruminant dairy pastoralism was adopted on the Eastern steppe by local hunter-gatherers through a process of cultural transmission and minimal genetic exchange with outside groups.

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.