Palaeoproteomic identification of the original binder and modern contaminants in distemper paints from Uvdal stave church, Norway

Two distemper paint samples taken from decorative boards in Uvdal stave church, Norway, were analysed using palaeoproteomics, with an aim of identifying their binder and possible contaminants. The results point at the use of calfskin to produce hide glue as the original paint binder, and are consistent with the instructions of binder production and resource allocation in the historical records of Norway. Although we did not observe any evidence of prior restoration treatments using protein-based materials, we found abundant traces of human saliva proteins, as well as a few oats and barley peptides, likely deposited together on the boards during their discovery in the 1970s. This work illustrates the need to fully consider contamination sources in palaeoproteomics and to inform those working with such objects about the potential for their contamination.

Wheat-Based Glues in Conservation and Cultural Heritage: (Dis)solving the Proteome of Flour and Starch Pastes and Their Adhering Properties

Plant-based adhesives, such as those made from wheat, have been prominently used for books and paper-based objects and are also used as conservation adhesives. Starch paste originates from starch granules, whereas flour paste encompasses the entire wheat endosperm proteome, offering strong adhesive properties due to gluten proteins. From a conservation perspective, understanding the precise nature of the adhesive is vital as the longevity, resilience, and reaction to environmental changes can differ substantially between starch- and flour-based pastes. We devised a proteomics method to discern the protein content of these pastes. Protocols involved extracting soluble proteins using 0.5 M NaCl and 30 mM Tris-HCl solutions and then targeting insoluble proteins, such as gliadins and glutenins, with a buffer containing 7 M urea, 2 M thiourea, 4% CHAPS, 40 mM Tris, and 75 mM DTT. Flour paste's proteome is diverse (1942 proteins across 759 groups), contrasting with starch paste's predominant starch-associated protein makeup (218 proteins in 58 groups). Transformation into pastes reduces proteomes' complexity. Testing on historical bookbindings confirmed the use of flour-based glue, which is rich in gluten and serpins. High levels of deamidation were detected, particularly for glutamine residues, which can impact the solubility and stability of the glue over time. The mass spectrometry proteomics data have been deposited to the ProteomeXchange, Consortium (http://proteomecentral.proteomexchange.org) via the MassIVE partner repository with the data set identifier MSV000093372 (ftp://MSV000093372@massive.ucsd.edu).

Shepherding the past: High-resolution data on Neolithic Southern Iberian livestock management at Cueva de El Toro (Antequera, Málaga)

The feeding strategies of the first domesticated herds had to manage the risks arising from the novelty of livestock practices in territories often distant from the animals' primary habitats. The Iberian Peninsula is characterised by a great diversity of environments, which undoubtedly influenced these dynamics. At the beginning of the Neolithic period these led the possibility to combine diverse livestock farming practices based on different animal feeding habits. This variability is also consistent with the rythms of adoption of domesticated animals, being later on the northern area. In order to address this issue, this work focuses on the dietary regimes of early sheep herds from southern Iberia, an area for which information is currently scarce. This study utilises high-resolution radiocarbon dating and stable isotope data on teeth to investigate sheep husbandry management strategies in Cueva de El Toro (Antequera, Málaga). The radiocarbon dates on the analysed remains evidenced they were deposited at the site over a short period, supporting the recurrent use of the cave. The sequential analysis of oxygen and carbon isotopes in tooth enamel reveals distinct livestock management strategies, reproduction patterns, feeding habits, and mobility during this short period. This variability demonstrates that livestock management practices in the western Mediterranean are more diverse than previously considered. Furthermore, these findings support the hypothesis that early Neolithic communities in the southern Iberian Peninsula were able to adopt different feeding strategies within the same herd, depending on their ecological and productive needs.

Palaeoproteomics and microanalysis reveal techniques of production of animal-based metal threads in medieval textiles

Animal-based metal threads were largely used between the 10th and the fifteenth century, in European, Middle Eastern and Far Eastern textile productions for the decoration of textiles and cloths. They belong to a larger group of metal threads, used either as flat threads or wrapped around a fiber core, that were backed by an organic support (animal or paper). This study focuses on the medieval production of metal threads backed by an animal membrane (e.g. gut membrane), or skin. A total of 91 samples were collected from a corpus of 66 textile fragments belonging to 54 catalogued objects. The relevance and novelty of the present study is represented by the combination of proteomics, cross-section analysis, and scanning electron microscopy (SEM-EDS and SEM-µXRF). The diversity of materials and manufacturing techniques found within each typology of thread, respectively, membrane-based metal threads and skin-based metal threads, hinted at different production technologies. Membrane-based threads were found to be invariably made from cattle gut membrane, coated with gilt-silver leaves. A possible sheep glue adhesive was found in a few samples. Skin-based threads were made from either goat or sheep leather, coated with metal leaves or powder. Within the three different types of coatings identified (silver, gold and gilt-silver), gold coatings were the most represented. Goat leather threads were associated with an egg-white binder, while sturgeon glue was identified as adhesive in all sheep leather threads. Collagen glue from other species (cattle, sheep, horse) was occasionally found in mixed adhesives. In two textiles, the finding of human proteins indicates past contamination due to handling or use. The analytical results show coherence between the fabrication patterns of animal-based metal threads and their probable geographical areas of manufacture, indicating that the study of materials and techniques provide further criteria to classify and group textiles, and trace correlations between manufacturing centers within Eurasian territories.

SpecieScan: semi-automated taxonomic identification of bone collagen peptides from MALDI-ToF-MS

MOTIVATION

Zooarchaeology by Mass Spectrometry (ZooMS) is a palaeoproteomics method for the taxonomic determination of collagen, which traditionally involves challenging manual spectra analysis with limitations in quantitative results. As the ZooMS reference database expands, a faster and reproducible identification tool is necessary. Here we present SpecieScan, an open-access algorithm for automating taxa identification from raw MALDI-ToF mass spectrometry (MS) data.

RESULTS

SpecieScan was developed using R (pre-processing) and Python (automation). The algorithm's output includes identified peptide markers, closest matching taxonomic group (taxon, family, order), correlation scores with the reference databases, and contaminant peaks present in the spectra. Testing on original MS data from bones discovered at Palaeothic archaeological sites, including Denisova Cave in Russia, as well as using publicly-available, externally produced data, we achieved >90% accuracy at the genus-level and ∼92% accuracy at the family-level for mammalian bone collagen previously analysed manually.

AVAILABILITY AND IMPLEMENTATION

The SpecieScan algorithm, along with the raw data used in testing, results, reference database, and common contaminants lists are freely available on Github (https://github.com/mesve/SpecieScan).

Homo sapiens reached the higher latitudes of Europe by 45,000 years ago

The Middle to Upper Palaeolithic transition in Europe is associated with the regional disappearance of Neanderthals and the spread of Homo sapiens. Late Neanderthals persisted in western Europe several millennia after the occurrence of H. sapiens in eastern Europe1. Local hybridization between the two groups occurred2, but not on all occasions3. Archaeological evidence also indicates the presence of several technocomplexes during this transition, complicating our understanding and the association of behavioural adaptations with specific hominin groups4. One such technocomplex for which the makers are unknown is the Lincombian-Ranisian-Jerzmanowician (LRJ), which has been described in northwestern and central Europe5-8. Here we present the morphological and proteomic taxonomic identification, mitochondrial DNA analysis and direct radiocarbon dating of human remains directly associated with an LRJ assemblage at the site Ilsenhöhle in Ranis (Germany). These human remains are among the earliest directly dated Upper Palaeolithic H. sapiens remains in Eurasia. We show that early H. sapiens associated with the LRJ were present in central and northwestern Europe long before the extinction of late Neanderthals in southwestern Europe. Our results strengthen the notion of a patchwork of distinct human populations and technocomplexes present in Europe during this transitional period.

Proteomic Analysis of Collagen: a Mass Spectrometry Approach to Material Identification of Shadow Puppet Cultural Relics

Shadow puppets are a popular art form in various regions, including China, Indonesia, and Turkey, and are rich in cultural significance. However, there is a considerable lack of research on the materials, diseases and conservation techniques related to shadow puppet relics. Material identification is the basis for understanding the production process of ancient shadow puppet relics and evaluating their deterioration degree. The microscopic morphology and infrared spectroscopy results in our experiments showed that the traditional methods of ancient skin identification were not effective in the shadow puppet samples. In order to achieve accurate identification, we used biological mass-spectrometry in proteomics to examine two puppet relics and commercially available modern shadow puppets. The results showed that the above samples could be detected by mass spectrometry with abundant peptides, including peptides specific for bovine skin. These peptides cannot be found in other commonly used materials for making shadow puppets, including the skins of pig, sheep, deer and horse. It is worth mentioning that we have found the peptides specific to yellow cowhide in two ancient shadow puppet relics samples. Therefore, the proteomic evidence shows that the raw materials of the two shadow puppet relics samples are yellow cowhide. Four modern samples also confirmed the reliability of material identification using proteomics. The proteomic evidence shows that the biological mass spectrometry will contribute to the scientific research of shadow puppet relics and other skin and leather cultural relics.

Identification and tentative removal of collagen glue in Palaeolithic worked bone objects: implications for ZooMS and radiocarbon dating

Collagen glue has been used for nearly two centuries to consolidate bone material, although its prevalence in museum collections is only now becoming visible. Identifying and removing collagen glue is crucial before the execution of any geochemical or molecular analyses. Palaeolithic bone objects from old excavations intended for radiocarbon dating were first analysed using ZooMS (Zooarchaeology by Mass Spectrometry) to identify the animal species, however peaks characteristic of both cattle and whale were discovered. Two extraction methods for ZooMS were tested to identify the authentic animal species of these objects, which revealed that these were originally whale bone objects that had been consolidated with cattle collagen glue. This is the first time animal collagen glue has been identified in archaeological remains with ZooMS, illustrating again the incredible versatility of this technique. Another technique, Fourier Transform Infrared Spectroscopy in Attenuated Total Reflectance mode (FTIR-ATR), was also tested if it could rapidly identify the presence of collagen glue in archaeological bone material, which was not the case. Two other cleaning methods were tested to remove bone glue contamination prior to radiocarbon dating, along with two modified collagen extraction methods for ZooMS. These methods were applied to bone blank samples (FmC = 0.0031 ± 0.0002, (n = 219), 47 336 ± 277 yr BP) that were experimentally consolidated with collagen glue and to the Palaeolithic bone material (ca. 15 000 and 12 000 yr BP). The experimental bone blanks produced excellent 14C ages, suggesting the cleaning methods were successful, however the 14C ages for some of the Palaeolithic material remained too young considering their contextual age, suggesting that the collagen glue contamination had most likely cross-linked to the authentic collagen molecule. More research is needed in order to gain a deeper understanding of the occurrence and elimination of cross-linked collagen-based glues in material from museum collections.

ZooMS confirms geometric morphometrics species identification of ancient sheep and goat

Geometric morphometrics can effectively distinguish isolated third lower molars of present-day sheep and goat, but its applicability to archaeological specimens has yet to be established. Using a modern reference collection of 743 sheep and goats and a two-dimensional landmark-based geometric morphometric (GMM) protocol, this study aimed to morphometrically identify 109 archaeological specimens, used as case studies, dating from the Late Neolithic to the modern period/era. These morphometric identifications were then compared to molecular identifications via collagen peptide mass fingerprinting, known as Zooarcheology by Mass Spectrometry (ZooMS). ZooMS confirmed the morphometric identifications for 104 specimens, with the five misidentified specimens all morphometrically identified as goat. Modern sheep and goats have larger teeth and distinct shapes compared to their archaeological counterparts, suggesting strong differences between archaeological and modern specimens potentially linked with recent breed improvement or geographical origin of the specimens. In addition, for both species, some of the archaeological dental morphologies do not match with any of our modern references. This study validates the applicability of geometric morphometrics for identifying isolated archaeological sheep and goat teeth. It represents a stepping stone for future, non-destructive, bioarchaeological studies of the two species.

The prelude to industrial whaling: identifying the targets of ancient European whaling using zooarchaeology and collagen mass-peptide fingerprinting

Taxonomic identification of whale bones found during archaeological excavations is problematic due to their typically fragmented state. This difficulty limits understanding of both the past spatio-temporal distributions of whale populations and of possible early whaling activities. To overcome this challenge, we performed zooarchaeology by mass spectrometry on an unprecedented 719 archaeological and palaeontological specimens of probable whale bone from Atlantic European contexts, predominantly dating from ca 3500 BCE to the eighteenth century CE. The results show high numbers of Balaenidae (many probably North Atlantic right whale (Eubalaena glacialis)) and grey whale (Eschrichtius robustus) specimens, two taxa no longer present in the eastern North Atlantic. This discovery matches expectations regarding the past utilization of North Atlantic right whales, but was unanticipated for grey whales, which have hitherto rarely been identified in the European zooarchaeological record. Many of these specimens derive from contexts associated with mediaeval cultures frequently linked to whaling: the Basques, northern Spaniards, Normans, Flemish, Frisians, Anglo-Saxons and Scandinavians. This association raises the likelihood that early whaling impacted these taxa, contributing to their extirpation and extinction. Much lower numbers of other large cetacean taxa were identified, suggesting that what are now the most depleted whales were once those most frequently used.

The Efficient Extraction Method of Collagen from Deteriorated Leather Artifacts

Collagen is the most crucial component of leather artifacts and analyzing collagen can provide vital information for studying and conserving such artifacts. However, collagen in leather artifacts often faces challenges such as degradation, denaturation, and contamination, which make it difficult to achieve an ideal protein extract using traditional extraction methods. This study aimed to find an efficient collagen extraction strategy for aging leather by comparing and improving commonly used methods. The results of comparing different extraction methods indicated that a NaOH solution was highly effective in extracting collagen from aged leather. To determine the optimal conditions for collagen extraction from the NaOH solution, we conducted orthogonal experiments. The results revealed that a NaOH concentration of 0.05 mol/L, a dissolution temperature of 80 °C, and a dissolution time of 12 h were the most favorable conditions. To validate the effectiveness of this method, we performed SDS-PAGE and biological mass spectrometry tests on collagen extracts from leather samples with varying degrees of aging. All collagen extracts exhibited distinct bands in the gel, and the molecular weight of collagen in each sample exceeded 20 kDa. Furthermore, even with a reduced sample mass of 1 mg (micro-destructive sampling), biological mass spectrometry identified 124 peptides in the protein extract. Notably, four of these peptides were unique to cattle hide collagen and were not present in the collagen of pig, sheep, horse, deer, or human skins. These experimental findings confirm the efficacy of the NaOH solution for extracting collagen from aging leather, suggesting that it can serve as a significant method for collagen identification and analysis in leather artifacts.

Artefact Profiling: Panomics Approaches for Understanding the Materiality of Written Artefacts

This review explains the strategies behind genomics, proteomics, metabolomics, metallomics and isotopolomics approaches and their applicability to written artefacts. The respective sub-chapters give an insight into the analytical procedure and the conclusions drawn from such analyses. A distinction is made between information that can be obtained from the materials used in the respective manuscript and meta-information that cannot be obtained from the manuscript itself, but from residues of organisms such as bacteria or the authors and readers. In addition, various sampling techniques are discussed in particular, which pose a special challenge in manuscripts. The focus is on high-resolution, non-targeted strategies that can be used to extract the maximum amount of information about ancient objects. The combination of the various omics disciplines (panomics) especially offers potential added value in terms of the best possible interpretations of the data received. The information obtained can be used to understand the production of ancient artefacts, to gain impressions of former living conditions, to prove their authenticity, to assess whether there is a toxic hazard in handling the manuscripts, and to be able to determine appropriate measures for their conservation and restoration.

A biological reading of a palimpsest

In the Middle Ages, texts were recorded and preserved on parchment, an animal-derived material. When this resource was scarce, older manuscripts were sometimes recycled to write new manuscripts. In the process, the ancient text was erased, creating what is known as a palimpsest. Here, we explore the potential of peptide mass fingerprinting (PMF), widely applied to identify species, to help reconnect the dispersed leaves of a manuscript and reveal differences in parchment manufacturing. In combination with visual methods, we analyzed a whole palimpsest, the codex AM 795 4to from the Arnamagnæan Collection (Copenhagen, Denmark). We find that both sheep and goat skins were used in this manuscript, and that parchment differed in quality. Notably, the PMF analysis distinguished five groups of folios which match the visual groupings. We conclude that this detailed interrogation of a single mass spectrum can be a promising tool to understand how palimpsest manuscripts were constructed.

Solving the two-decades-old murder case through joint application of ZooMS and ancient DNA approaches

Bones are one of the most common biological types of evidence in forensic cases. Discriminating human bones from irrelevant species is important for the identification of victims; however, the highly degraded bones could be undiagnostic morphologically and difficult to analyze with standard DNA profiling approaches. The same challenge also exists in archaeological studies. Here, we present an initial study of an analytical strategy that involves zooarchaeology by mass spectrometry (ZooMS) and ancient DNA methods. Through the combined strategy, we managed to identify the only biological evidence of a two-decades-old murder case - a small piece of human bone out of 19 bone fragments - and confirmed the kinship between the victim and the putative parents through joint application of next-generation sequencing (NGS) and Sanger sequencing methods. ZooMS effectively screened out the target human bone while ancient DNA methods improve the DNA yields. The combined strategy in this case outperforms the standard DNA profiling approach with shorter time, less cost, as well as higher reliability for the genetic identification results. HIGHLIGHTS: • The first application of zooarchaeology by mass spectrometry technique in the forensic case for screening out human bones from bone fragment mixtures. • Application of ancient DNA technique to recover the highly degraded DNA sequence from the challenging sample that failed standard DNA profiling approaches. • A fast, sensitive, and low-cost strategy that combines the strengths of protein analysis and DNA analysis for kinship identification in forensic research.

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.

Proteins, possibly human, found in World War II concentration camp artifact

Museums displaying artifacts of the human struggle against oppression are often caught in their own internal struggle between presenting factual and unbiased descriptions of their collections, or relying on testament of survivors. Often this quandary is resolved in favor of what can be verified, not what is remembered. However, with improving instrumentation, methods and informatic approaches, science can help uncover evidence able to reconcile memory and facts. Following World War II, thousands of small, cement-like disks with numbers impressed on one side were found at concentration camps throughout Europe. Survivors claimed these disks were made of human cremains; museums erred on the side of caution—without documentation of the claims, was it justifiable to present them as fact? The ability to detect species relevant biological material in these disks could help resolve this question. Proteomic mass spectrometry of five disks revealed all contained proteins, including collagens and hemoglobins, suggesting they were made, at least in part, of animal remains. A new protein/informatics approach to species identification showed that while human was not always identified as the top contributor, human was the most likely explanation for one disk. To our knowledge, this is the first demonstration of protein recovery from cremains. Data are available via ProteomeXchange with identifier PXD035267.

A primer for ZooMS applications in archaeology

Collagen peptide mass fingerprinting by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, also known as zooarchaeology by mass spectrometry (ZooMS), is a rapidly growing analytical technique in the fields of archaeology, ecology, and cultural heritage. Minimally destructive and cost effective, ZooMS enables rapid taxonomic identification of large bone assemblages, cultural heritage objects, and other organic materials of animal origin. As its importance grows as both a research and a conservation tool, it is critical to ensure that its expanding body of users understands its fundamental principles, strengths, and limitations. Here, we outline the basic functionality of ZooMS and provide guidance on interpreting collagen spectra from archaeological bones. We further examine the growing potential of applying ZooMS to nonmammalian assemblages, discuss available options for minimally and nondestructive analyses, and explore the potential for peptide mass fingerprinting to be expanded to noncollagenous proteins. We describe the current limitations of the method regarding accessibility, and we propose solutions for the future. Finally, we review the explosive growth of ZooMS over the past decade and highlight the remarkably diverse applications for which the technique is suited.

Fishing intensification as response to Late Holocene socio-ecological instability in southeastern South America

The emergence of plant-based economies have dominated evolutionary models of Middle and Late Holocene pre-Columbian societies in South America. Comparatively, the use of aquatic resources and the circumstances for intensifying their exploitation have received little attention. Here we reviewed the stable carbon and nitrogen isotope composition of 390 human individuals from Middle and Late Holocene coastal sambaquis, a long-lasting shell mound culture that flourished for nearly 7000 years along the Atlantic Forest coast of Brazil. Using a newly generated faunal isotopic baseline and Bayesian Isotope Mixing Models we quantified the relative contribution of marine resources to the diet of some of these groups. Through the analysis of more than 400 radiocarbon dates we show that fishing sustained large and resilient populations during most of the Late Holocene. A sharp decline was observed in the frequency of sambaqui sites and radiocarbon dates from ca. 2200 years ago, possibly reflecting the dissolution of several nucleated groups into smaller social units, coinciding with substantial changes in coastal environments. The spread of ceramics from ca. 1200 years ago is marked by innovation and intensification of fishing practices, in a context of increasing social and ecological instability in the Late Holocene.

A 41,500 year-old decorated ivory pendant from Stajnia Cave (Poland)

Evidence of mobiliary art and body augmentation are associated with the cultural innovations introduced by Homo sapiens at the beginning of the Upper Paleolithic. Here, we report the discovery of the oldest known human-modified punctate ornament, a decorated ivory pendant from the Paleolithic layers at Stajnia Cave in Poland. We describe the features of this unique piece, as well as the stratigraphic context and the details of its chronometric dating. The Stajnia Cave plate is a personal 'jewellery' object that was created 41,500 calendar years ago (directly radiocarbon dated). It is the oldest known of its kind in Eurasia and it establishes a new starting date for a tradition directly connected to the spread of modern Homo sapiens in Europe.

Neolithic farmers or Neolithic foragers? Organic residue analysis of early pottery from Rakushechny Yar on the Lower Don (Russia)

The emergence of pottery in Europe is associated with two distinct traditions: hunter-gatherers in the east of the continent during the early 6th millennium BC and early agricultural communities in the south-west in the late 7th millennium BC. Here we investigate the function of pottery from the site of Rakushechny Yar, located at the Southern fringe of Eastern Europe, in this putative contact zone between these two economic 'worlds'. To investigate, organic residue analysis was conducted on 120 samples from the Early Neolithic phase (ca. mid-6^th millennium BC) along with microscopic and SEM analysis of associated foodcrusts. The results showed that the earliest phase of pottery use was predominantly used to process riverine resources. Many of the vessels have molecular and isotopic characteristics consistent with migratory fish, such as sturgeon, confirmed by the identification of sturgeon bony structures embedded in the charred surface deposits. There was no evidence of dairy products in any of the vessels, despite the fact these have been routinely identified in coeval sites to the south. Further analysis of some of the mammalian bones using ZooMS failed to demonstrate that domesticated animals were present in the Early Neolithic. Nevertheless, we argue that intensive exploitation of seasonally migratory fish, accompanied by large-scale pottery production, created storable surpluses that led to similar socio-economic outcomes as documented in early agricultural societies.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12520-021-01412-2.

Palaeoproteomic analyses of dog palaeofaeces reveal a preserved dietary and host digestive proteome

The domestic dog has inhabited the anthropogenic niche for at least 15 000 years, but despite their impact on human strategies, the lives of dogs and their interactions with humans have only recently become a subject of interest to archaeologists. In the Arctic, dogs rely exclusively on humans for food during the winter, and while stable isotope analyses have revealed dietary similarities at some sites, deciphering the details of provisioning strategies have been challenging. In this study, we apply zooarchaeology by mass spectrometry (ZooMS) and liquid chromatography tandem mass spectrometry to dog palaeofaeces to investigate protein preservation in this highly degradable material and obtain information about the diet of domestic dogs at the Nunalleq site, Alaska. We identify a suite of digestive and metabolic proteins from the host species, demonstrating the utility of this material as a novel and viable substrate for the recovery of gastrointestinal proteomes. The recovered proteins revealed that the Nunalleq dogs consumed a range of Pacific salmon species (coho, chum, chinook and sockeye) and that the consumed tissues derived from muscle and bone tissues as well as roe and guts. Overall, the study demonstrated the viability of permafrost-preserved palaeofaeces as a unique source of host and dietary proteomes.

Beyond faith: Biomolecular evidence for changing urban economies in multi-faith medieval Portugal

OBJECTIVES

During the Middle Ages, Portugal witnessed unprecedented socioeconomic and religious changes under transitioning religious political rule. The implications of changing ruling powers for urban food systems and individual diets in medieval Portugal is poorly understood. This study aimed to elucidate the dietary impact of the Islamic and Christian conquests.

MATERIALS AND METHODS

Radiocarbon dating, peptide mass fingerprinting (ZooMS) and stable isotope analysis (δ¹³ C, δ¹⁵ N) of animal (n = 59) and human skeletal remains (n = 205) from Muslim and Christian burials were used to characterize the diet of a large historical sample from Portugal. A Bayesian stable isotope mixing model (BSIMM) was used to estimate the contribution of marine protein to human diet.

RESULTS

Early medieval (8-12th century), preconquest urban Muslim populations had mean (±1SD) values of -18.8 ± 0.4 ‰ for δ¹³ C 10.4 ± 1 ‰ for δ¹⁵ N, indicating a predominantly terrestrial diet, while late medieval (12-14th century) postconquest Muslim and Christian populations showed a greater reliance on marine resources with mean (±1SD) values of -17.9 ± 1.3‰ for δ¹³ C and 11.1 ± 1.1‰ for δ¹⁵ N. BSIMM estimation supported a significant increase in the contribution of marine resources to human diet.

DISCUSSION

The results provide the first biomolecular evidence for a dietary revolution that is not evidenced in contemporaneous historical accounts. We find that society transitioned from a largely agro-pastoral economy under Islamic rule to one characterized by a new focus on marine resources under later Christian rule. This economic change led to the naissance of the marine economy that went on to characterize the early-modern period in Portugal and its global expansion.

A predictive model for vertebrate bone identification from collagen using proteomic mass spectrometry

Proteogenomics is an increasingly common method for species identification as it allows for rapid and inexpensive interrogation of an unknown organism’s proteome—even when the proteome is partially degraded. The proteomic method typically uses tandem mass spectrometry to survey all peptides detectable in a sample that frequently contains hundreds or thousands of proteins. Species identification is based on detection of a small numbers of species-specific peptides. Genetic analysis of proteins by mass spectrometry, however, is a developing field, and the bone proteome, typically consisting of only two proteins, pushes the limits of this technology. Nearly 20% of highly confident spectra from modern human bone samples identify non-human species when searched against a vertebrate database—as would be necessary with a fragment of unknown bone. These non-human peptides are often the result of current limitations in mass spectrometry or algorithm interpretation errors. Consequently, it is difficult to know if a “species-specific” peptide used to identify a sample is actually present in that sample. Here we evaluate the causes of peptide sequence errors and propose an unbiased, probabilistic approach to determine the likelihood that a species is correctly identified from bone without relying on species-specific peptides.

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.

Testing the efficacy and comparability of ZooMS protocols on archaeological bone

Collagen peptide mass fingerprinting, best known as Zooarchaeology by Mass Spectrometry (or ZooMS) when applied to archaeology, has become invaluable for the taxonomic identification of archaeological collagenous materials, in particular fragmentary and modified bone remains. Prior to MALDI-based spectrometric analysis, collagen needs to be extracted from the bone's inorganic matrix, isolated and purified. Several protocols are currently employed for ZooMS analysis, however their efficacy and comparability has not been directly tested. Here, we use four different ZooMS protocols to analyze 400 bone samples from seven archaeological sites, dating to between ~500,000-2000 years ago. One of them, single-pot solid-phase-enhance sample preparation (SP3), is used for the first time as a ZooMS protocol. Our results indicate that the least-destructive ZooMS protocol which uses an ammonium bicarbonate buffer as a means of extracting collagen is most suitable for bones with good collagen preservation, whereas the acid-based methodologies can improve success rates for bones with low-to-medium collagen preservation. Since preservation of biomolecules in archaeological bones is highly variable due to age and environmental conditions, we use the percent nitrogen by weight (%N) value as an independent semi-quantitative proxy for assessing collagen content and for predicting which bones will likely result in a successful ZooMS-based identification. We find that 0.26%N as a threshold for screening material could optimize the number of spectra which produce identifications using ZooMS. SIGNIFICANCE STATEMENT: We present a direct comparison of three previously published ZooMS protocols for the analyses of archaeological bones, and the first use of an SP3-based approach to ZooMS analysis. Our results show that the acid-based ZooMS protocols increase the success rate for bones with low-medium collagen preservation. We identify 0.26%N as a threshold for optimizing the number of samples with enough collagen for successful peptide mass fingerprinting.

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.

An integrated analysis of Maglemose bone points reframes the Early Mesolithic of Southern Scandinavia

The extensive peat bogs of Southern Scandinavia have yielded rich Mesolithic archaeological assemblages, with one of the most iconic artefacts being the bone point. Although great in number they remain understudied. Here we present a combined investigation of the typology, protein-based species composition, and absolute chronology of Maglemosian bone points. The majority of the bone points are made from cervids and bovines. However, changes both in species composition and barb morphology can be directly linked to a paucity of finds lasting nearly 600 years in Southern Scandinavia around 10,300 cal BP. We hypothesize that this hiatus was climate-driven and forced hunter-gatherers to abandon the lakes. Furthermore, the marked change in bone points coincides with a change in lithic technology. We, therefore, propose that the Maglemose culture in Southern Scandinavia is fundamentally divided into an Early Complex and a Late Complex.

In Situ Hydrogel Extraction with Dual-Enzyme Digestion of Proteinaceous Binders: the Key for Reliable Mass Spectrometry Investigations of Artworks

A novel strategy based on in situ dual-enzyme digestion of paint layer proteinaceous binders is introduced for faster and more confident identification, resulting in a bottom-up proteomics approach by MALDI-TOF mass spectrometry (MS). In situ sampling/extraction of proteinaceous binders using small pieces of a hydrophilic gel, previously loaded with trypsin and chymotrypsin proteolytic enzymes, was successfully exploited. Along with minimal invasiveness, the synergy of both enzymes was very useful to increase the number of annotated peptide peaks with their corresponding amino acid sequence by database search and subsequent MALDI-TOF/TOF analysis. The protocol was initially aimed at enhancing the identification of egg-based binders and then validated on fresh and aged model pictorial layers; an increased protein coverage was significantly attained regardless of the used painting binders. Optical microscope images and spectrophotocolorimetry analysis evidenced that the painting layers were not damaged or altered because of contact/sampling without leaving hydrogel residues. The proposed protocol was successfully applied on a painted altarpiece "Assumption of the Virgin" dated to the XVI century and on an angel statue of the Nativity crib dated to the XII century, both from Altamura's Cathedral (Apulia, Italy). The occurrence of various protein binders of animal origin was easily and reliably ascertained.

FTIR investigation of the secondary structure of type I collagen: New insight into the amide III band

This work presents a thorough study on the Amide III band in fibrous proteins using Fourier Transformed Infrared Spectroscopy (FTIR). Type I collagen was chosen as a model for this family of proteins, not only because of its important role in mammalian tissues, but also for its involvement in several pathologies. In order to disclose the conformational information contained in the collagen bands, the spectral characteristics of Amide III of type I collagen were related to the ones of Amide I band, performing experiments of thermal denaturation of the protein in acidic solution. Data acquired allowed to observe the protein unfolding and retrieve information about its structural arrangements during the thermal cycle. Taking as guideline the well-known behaviour of the Amide I band, we correlated the structural changes deducible from Amide I analysis with the ones detectable for Amide III band, by exploiting three spectral analysis techniques, namely 2D-correlation analysis, second derivative analysis, and peak-fitting. This approach enabled us to jointly support the obtained results and finally to assign the components of the Amide III of a typical fibrous protein, such as type I collagen, to its characteristic secondary structure.

The biomolecular characterization of a finger ring contextually dated to the emergence of the Early Neolithic from Syltholm, Denmark

We present the analysis of an osseous finger ring from a predominantly early Neolithic context in Denmark. To characterize the artefact and identify the raw material used for its manufacture, we performed micro-computed tomography scanning, zooarchaeology by mass spectrometry (ZooMS) peptide mass fingerprinting, as well as protein sequencing by liquid chromatography tandem mass spectrometry (LC-MS/MS). We conclude that the ring was made from long bone or antler due to the presence of osteons (Haversian canals). Subsequent ZooMS analysis of collagen I and II indicated that it was made from Alces alces or Cervus elaphus material. We then used LC-MS/MS analysis to refine our species identification, confirming that the ring was made from Cervus elaphus, and to examine the rest of the proteome. This study demonstrates the potential of ancient proteomics for species identification of prehistoric artefacts made from osseous material.

Identifying Archaeological Bone via Non-Destructive ZooMS and the Materiality of Symbolic Expression: Examples from Iroquoian Bone Points

Today, practical, functional and symbolic choices inform the selection of raw materials for worked objects. In cases where we can discern the origin of worked bone, tooth, ivory and antler objects in the past, we assume that similar choices are being made. However, morphological species identification of worked objects is often impossible due to the loss of identifying characteristics during manufacture. Here, we describe a novel non-destructive ZooMS (Zooarchaeology by Mass Spectrometry) method which was applied to bone points from Pre-Contact St. Lawrence Iroquoian village sites in southern Quebec, Canada. The traditional ZooMS technique requires destructive analysis of a sample, which can be problematic when dealing with artefacts. Here we instead extracted proteins from the plastic bags in which the points had been stored. ZooMS analysis revealed hitherto unexpected species, notably black bear (Ursus americanus) and human (Homo sapiens sapiens), used in point manufacture. These surprising results (confirmed through genomic sequencing) highlight the importance of advancing biomolecular research in artefact studies. Furthermore, they unexpectedly and exceptionally allow us to identify and explore the tangible, material traces of the symbolic relationship between bears and humans, central to past and present Iroquoian cosmology and mythology.

Radiocarbon dating and isotope analysis on the purported Aurignacian skeletal remains from Fontana Nuova (Ragusa, Italy)

Proving voyaging at sea by Palaeolithic humans is a difficult archaeological task, even for short distances. In the Mediterranean, a commonly accepted sea crossing is that from the Italian Peninsula to Sicily by anatomically modern humans, purportedly of the Aurignacian culture. This claim, however, was only supported by the typological attribution to the Aurignacian of the lithic industries from the insular site of Fontana Nuova. AMS radiocarbon dating undertaken as part of our research shows that the faunal remains, previously considered Aurignacian, actually date to the Holocene. Absolute dating on dentinal collagen also attributes the human teeth from the site to the early Holocene, although we were unable to obtain ancient DNA to evaluate their ancestry. Ten radiocarbon dates on human and other taxa are comprised between 9910–9700 cal. BP and 8600–8480 cal. BP, indicating that Fontana Nuova was occupied by Mesolithic and not Aurignacian hunter-gatherers. Only a new study of the lithic assemblage could establish if the material from Fontana Nuova is a mixed collection that includes both late Upper Palaeolithic (Epigravettian) and Mesolithic artefacts, as can be suggested by taking into account both the results of our study and of the most recent reinterpretation of the lithics. Nevertheless, this research suggests that the notion that Aurignacian groups were present in Sicily should now be revised. Another outcome of our study is that we found that three specimens, attributed on grounds both of morphological and ZooMS identifications to Cervus elaphus, had δ¹³C values significantly higher than any available for such species in Europe.

Recent dating of extinct Atlantic gray whale fossils, (Eschrichtius robustus), Georgia Bight and Florida, western Atlantic Ocean

The Atlantic gray whale (Eschrichtius robustus) presents an interesting case study of climate related dispersal and extinction. While (limited) fossil records confirm its presence in the Atlantic up until the 18th Century, its abundance and distribution within the Eastern and Western basins are still not well understood. The discovery of presumed gray whale fossil remains from the Georgia Bight and the Atlantic coast of Florida, from the mid-1980s to late-2000s, provides a new opportunity to recover additional data regarding their chronology within the Western basin. Here, we apply accelerator mass spectrometry radiocarbon techniques to six fossil whale finds, identifying dates within marine isotope stage 3 (59-24 ka) and the late Holocene, ∼2,000 yr BP. We additionally confirm the taxonomic identification of two fossil bone samples as E. robustus using collagen peptide mass fingerprinting (ZooMS). The obtained dates, when combined with a larger corpus of previously published Atlantic gray whale fossil dates, support the hypothesis for the decline of the Atlantic gray whale in the late Pleistocene and the late Holocene. These new data augment the findings of the Eastern Atlantic Basin and better incorporate the Western Atlantic Basin into a pan-ocean understanding for the species.

Forgotten Mediterranean calving grounds of grey and North Atlantic right whales: evidence from Roman archaeological records

Right whales (Eubalaena glacialis) were extirpated from the eastern North Atlantic by commercial whaling. Grey whales (Eschrichtius robustus) disappeared from the entire North Atlantic in still-mysterious circumstances. Here, we test the hypotheses that both species previously occurred in the Mediterranean Sea, an area not currently considered part of their historical range. We used ancient DNA barcoding and collagen fingerprinting methods to taxonomically identify a rare set of 10 presumed whale bones from Roman and pre-Roman archaeological sites in the Strait of Gibraltar region, plus an additional bone from the Asturian coast. We identified three right whales, and three grey whales, demonstrating that the ranges of both of these species historically encompassed the Gibraltar region, probably including the Mediterranean Sea as calving grounds. Our results significantly extend the known range of the Atlantic grey whale, and suggest that 2000 years ago, right and grey whales were common when compared with other whale species. The disappearance of right and grey whales from the Mediterranean region is likely to have been accompanied by broader ecosystem impacts, including the disappearance of their predators (killer whales) and a reduction in marine primary productivity. The evidence that these two coastal and highly accessible species were present along the shores of the Roman Empire raises the hypothesis that they may have formed the basis of a forgotten whaling industry.

Melding the Old with the New: Trends in Methods Used to Identify, Monitor, and Control Microorganisms on Cultural Heritage Materials

Microbial activity has an important impact on the maintenance of cultural heritage materials, owing to the key role of microorganisms in many deterioration processes. In order to minimize such deleterious effects, there is a need to fine-tune methods that detect and characterize microorganisms. Trends in microbiology indicate that this need can be met by incorporating modern techniques. All of the methods considered in this review paper are employed in the identification, surveillance, and control of microorganisms, and they have two points in common: They are currently used in microbial ecology (only literature from 2009 to 2015 is included), and they are often applied in the cultural heritage sector. More than 75 peer-reviewed journal articles addressing three different approaches were considered: molecular, sensory and morphological, and biocontrol methods. The goal of this review is to highlight the usefulness of the traditional as well as the modern methods. The general theme in the literature cited suggests using an integrated approach.

Accelerated Ageing of Parchment: Investigation of a Photo Catalysed, Low-Heat Approach

Accelerated ageing is an often-used tool in conservation research, yet difficult to apply to parchment due to the materials inherent heat sensitivity. The complexity of this organic material makes the analysis of its deterioration especially challenging. An attempt to develop a non-heat ageing protocol for parchment is described in this paper. The work was performed within the scope of a MA-thesis at the State Academy of Art and Design Stuttgart. Samples of a modern new limed goat parchment and pieces of reconstituted parchment made from bovine hide powder were subjected to a combination of light ageing and dynamic ageing at moderate temperatures. All samples were analysed with the goal to observe degradation on as many structural levels as possible: colour measurement via VIS spectrometry and light-microscopic observation of fibre damage were employed to assess visible changes. Shrinkage temperature (Ts) was measured as an indicator for the amount of intact intrafibrillar bonds and the determination of the maximum moisture absorption capacity gave an impression on the parchments overall level of hygroscopy. In addition, PMF (Peptid Mass Fingerprinting) via MALDI/MS TOF was performed on extracts from unaged and light aged goat parchment. The results of the different types of analysis showed significant degradation on different structural levels of the parchment, indicating that accelerated ageing of parchment that uses a combination of light and dynamic ageing may be a viable alternative to the more commonly applied thermal ageing.

Analyzing the Heterogeneous Hierarchy of Cultural Heritage Materials: Analytical Imaging

Objects of cultural heritage significance are created using a wide variety of materials, or mixtures of materials, and often exhibit heterogeneity on multiple length scales. The effective study of these complex constructions thus requires the use of a suite of complementary analytical technologies. Moreover, because of the importance and irreplaceability of most cultural heritage objects, researchers favor analytical techniques that can be employed noninvasively, i.e., without having to remove any material for analysis. As such, analytical imaging has emerged as an important approach for the study of cultural heritage. Imaging technologies commonly employed, from the macroscale through the micro- to nanoscale, are discussed with respect to how the information obtained helps us understand artists' materials and methods, the cultures in which the objects were created, how the objects may have changed over time, and importantly, how we may develop strategies for their preservation.

Scientific investigation of the lacquered wooden coffin of Xiang Fei excavated from Eastern Royal Tombs of the Qing Dynasty

The composition, structure, and lacquering craft used to manufacture the coffin of Xiang Fei were analyzed using multiple analytical methods.

Barcoding the largest animals on Earth: ongoing challenges and molecular solutions in the taxonomic identification of ancient cetaceans

Over the last few centuries, many cetacean species have witnessed dramatic global declines due to industrial overharvesting and other anthropogenic influences, and thus are key targets for conservation. Whale bones recovered from archaeological and palaeontological contexts can provide essential baseline information on the past geographical distribution and abundance of species required for developing informed conservation policies. Here we review the challenges with identifying whale bones through traditional anatomical methods, as well as the opportunities provided by new molecular analyses. Through a case study focused on the North Sea, we demonstrate how the utility of this (pre)historic data is currently limited by a lack of accurate taxonomic information for the majority of ancient cetacean remains. We then discuss current opportunities presented by molecular identification methods such as DNA barcoding and collagen peptide mass fingerprinting (zooarchaeology by mass spectrometry), and highlight the importance of molecular identifications in assessing ancient species' distributions through a case study focused on the Mediterranean. We conclude by considering high-throughput molecular approaches such as hybridization capture followed by next-generation sequencing as cost-effective approaches for enhancing the ecological informativeness of these ancient sample sets.This article is part of the themed issue 'From DNA barcodes to biomes'.

Direct radiocarbon dating and genetic analyses on the purported Neanderthal mandible from the Monti Lessini (Italy)

Anatomically modern humans replaced Neanderthals in Europe around 40,000 years ago. The demise of the Neanderthals and the nature of the possible relationship with anatomically modern humans has captured our imagination and stimulated research for more than a century now. Recent chronological studies suggest a possible overlap between Neanderthals and anatomically modern humans of more than 5,000 years. Analyses of ancient genome sequences from both groups have shown that they interbred multiple times, including in Europe. A potential place of interbreeding is the notable Palaeolithic site of Riparo Mezzena in Northern Italy. In order to improve our understanding of prehistoric occupation at Mezzena, we analysed the human mandible and several cranial fragments from the site using radiocarbon dating, ancient DNA, ZooMS and isotope analyses. We also performed a more detailed investigation of the lithic assemblage of layer I. Surprisingly we found that the Riparo Mezzena mandible is not from a Neanderthal but belonged to an anatomically modern human. Furthermore, we found no evidence for the presence of Neanderthal remains among 11 of the 13 cranial and post-cranial fragments re-investigated in this study.

Animal origin of 13th-century uterine vellum revealed using noninvasive peptide fingerprinting

Tissue-thin parchment made it possible to produce the first pocket Bibles: Thousands were made in the 13th century. The source of this parchment, often called "uterine vellum," has been a long-standing controversy in codicology. Use of the Latin term abortivum in many sources has led some scholars to suggest that the skin of fetal calves or sheep was used. Others have argued that it would not be possible to sustain herds if so many pocket Bibles were produced from fetal skins, arguing instead for unexpected alternatives, such as rabbit. Here, we report a simple and objective technique using standard conservation treatments to identify the animal origin of parchment. The noninvasive method is a variant on zooarchaeology by mass spectrometry (ZooMS) peptide mass fingerprinting but extracts protein from the parchment surface by using an electrostatic charge generated by gentle rubbing of a PVC eraser on the membrane surface. Using this method, we analyzed 72 pocket Bibles originating in France, England, and Italy and 293 additional parchment samples that bracket this period. We found no evidence for the use of unexpected animals; however, we did identify the use of more than one mammal species in a single manuscript, consistent with the local availability of hides. These results suggest that ultrafine vellum does not necessarily derive from the use of abortive or newborn animals with ultrathin hides, but could equally well reflect a production process that allowed the skins of maturing animals of several species to be rendered into vellum of equal quality and fineness.