Species identification using ZooMS, with reference to the exploitation of animal resources in the medieval town of Odense

Cervidae antlers exploited to manufacture prehistoric tools and hunting implements as a reliable source of ancient DNA

Antler is one of the primary animal raw materials exploited for technical purposes by the hunter-gatherer groups of the Eurasian Upper Palaeolithic (UP) all over the ecological range of deers, and beyond. It was exhaustively employed to produce one of the most critical tools for the survival of the UP societies: hunting weapons. However, antler implements can be made from diverse deer taxa, with different ecological requirements and ethological behaviours. Identifying the antler's origin at a taxonomic level is thus essential in improving our knowledge of humans' functional, practical and symbolic choices, as well as the human-animal interface during Prehistoric times. Nevertheless, palaeogenetics analyses have focused mainly on bone and teeth, with genetic studies of antler generally focused on modern deer conservation. Here we present the results of the first whole mitochondrial genome ancient DNA (aDNA) analysis by means of in-solution hybridisation capture of antlers from pre-Holocene archaeological contexts. We analysed a set of 50 Palaeolithic and Neolithic (c. 34-8ka) antler and osseous objects from South-Western Europe, Central Europe, South-Western Asia and the Caucasus. We successfully obtained aDNA, allowing us to identify the exploited taxa and demonstrate the archaeological relevance of those finds. Moreover, as most of the antlers were sampled using a minimally-invasive method, further analyses (morphometric, technical, genetic, radiometric and more) remain possible on these objects.

Touching the (almost) untouchable: a minimally invasive workflow for microbiological and biomolecular analyses of cultural heritage objects

Microbiological and biomolecular approaches to cultural heritage research have expanded the established research horizon from the prevalent focus on the cultural objects' conservation and human health protection to the relatively recent applications to provenance inquiry and assessment of environmental impacts in a global context of a changing climate. Standard microbiology and molecular biology methods developed for other materials, specimens, and contexts could, in principle, be applied to cultural heritage research. However, given certain characteristics common to several heritage objects-such as uniqueness, fragility, high value, and restricted access, tailored approaches are required. In addition, samples of heritage objects may yield low microbial biomass, rendering them highly susceptible to cross-contamination. Therefore, dedicated methodology addressing these limitations and operational hurdles is needed. Here, we review the main experimental challenges and propose a standardized workflow to study the microbiome of cultural heritage objects, illustrated by the exploration of bacterial taxa. The methodology was developed targeting the challenging side of the spectrum of cultural heritage objects, such as the delicate written record, while retaining flexibility to adapt and/or upscale it to heritage artifacts of a more robust constitution or larger dimensions. We hope this tailored review and workflow will facilitate the interdisciplinary inquiry and interactions among the cultural heritage research community.

Peptide mass fingerprinting of preserved collagen in archaeological fish bones for the identification of flatfish in European waters

Bones of Pleuronectiformes (flatfish) are often not identified to species due to the lack of diagnostic features on bones that allow adequate distinction between taxa. This hinders in-depth understanding of archaeological fish assemblages and particularly flatfish fisheries throughout history. This is especially true for the North Sea region, where several commercially significant species have been exploited for centuries, yet their archaeological remains continue to be understudied. In this research, eight peptide biomarkers for 18 different species of Pleuronectiformes from European waters are described using MALDI-TOF MS and liquid chromatography tandem mass spectrometry data obtained from modern reference specimens. Bone samples (n = 202) from three archaeological sites in the UK and France dating to the medieval period (ca seventh-sixteenth century CE) were analysed using zooarchaeology by mass spectrometry (ZooMS). Of the 201 that produced good quality spectra, 196 were identified as flatfish species, revealing a switch in targeted species through time and indicating that ZooMS offers a more reliable and informative approach for species identification than osteological methods alone. We recommend this approach for future studies of archaeological flatfish remains as the precise species uncovered from a site can tell much about the origin of the fish, where people fished and whether they traded between regions.

Archaeological occurrences of terrestrial herpetofauna in the insular Caribbean: cultural and biological significance

Although the importance of the archaeological record for addressing questions of biodiversity is gaining ground, its relevance for describing past faunal communities is still under-exploited, particularly for the most under-documented areas and species. Among the most poorly documented taxa are reptiles and amphibians, which are rarely studied in detail in the archaeological record, even in tropical areas where most of these species occur today. Here I evaluate the archaeological and paleontological significance of reptiles and amphibians from the Indigenous archaeological record of the insular Caribbean. Quantitative (bone counts) and qualitative (taxonomic identification) analyses allow researchers to discuss the role of herpetofauna in the subsistence strategies of Indigenous populations as well as their interest for assessing past insular biodiversity. This overview sheds light on both the poor representation of herpetofaunal taxa in Caribbean archaeological deposits and trends in the potential exploitation of reptiles and amphibians by Indigenous populations. In terms of paleoecology, the presented results reveal strong regional differences in the quality and density of data as well as the inadequacy of available archaeofaunal data for addressing questions of past biodiversity.

The effect of eraser sampling for proteomic analysis on Palaeolithic bone surface microtopography

Bone surface modifications are crucial for understanding human subsistence and dietary behaviour, and can inform about the techniques employed in the production and use of bone tools. Permission to destructively sample such unique artefacts is not always granted. The recent development of non-destructive proteomic extraction techniques has provided some alternatives for the analysis of rare and culturally significant artefacts, including bone tools and personal ornaments. The Eraser Extraction Method (EEM), first developed for ZooMS analysis of parchment, has recently been applied to bone and ivory specimens. To test the potential impact of the EEM on ancient bone surfaces, we analyse six anthropogenically modified Palaeolithic bone specimens from Bacho Kiro Cave (Bulgaria) through a controlled sampling experiment using qualitative and 3D quantitative microscopy. Although the overall bone topography is generally preserved, our findings demonstrate a slight flattening of the microtopography alongside the formation of micro-striations associated with the use of the eraser for all bone specimens. Such modifications are similar to ancient use-wear traces. We therefore consider the EEM a destructive sampling approach for Palaeolithic bone surfaces. Together with low ZooMS success rates in some of the reported studies, the EEM might not be a suitable approach to taxonomically identify Pleistocene bone specimens.

Distinguishing African bovids using Zooarchaeology by Mass Spectrometry (ZooMS): New peptide markers and insights into Iron Age economies in Zambia

Assessing past foodways, subsistence strategies, and environments depends on the accurate identification of animals in the archaeological record. The high rates of fragmentation and often poor preservation of animal bones at many archaeological sites across sub-Saharan Africa have rendered archaeofaunal specimens unidentifiable beyond broad categories, such as “large mammal” or “medium bovid”. Identification of archaeofaunal specimens through Zooarchaeology by Mass Spectrometry (ZooMS), or peptide mass fingerprinting of bone collagen, offers an avenue for identification of morphologically ambiguous or unidentifiable bone fragments from such assemblages. However, application of ZooMS analysis has been hindered by a lack of complete reference peptide markers for African taxa, particularly bovids. Here we present the complete set of confirmed ZooMS peptide markers for members of all African bovid tribes. We also identify two novel peptide markers that can be used to further distinguish between bovid groups. We demonstrate that nearly all African bovid subfamilies are distinguishable using ZooMS methods, and some differences exist between tribes or sub-tribes, as is the case for Bovina (cattle) vs. Bubalina (African buffalo) within the subfamily Bovinae. We use ZooMS analysis to identify specimens from extremely fragmented faunal assemblages from six Late Holocene archaeological sites in Zambia. ZooMS-based identifications reveal greater taxonomic richness than analyses based solely on morphology, and these new identifications illuminate Iron Age subsistence economies c. 2200–500 cal BP. While the Iron Age in Zambia is associated with the transition from hunting and foraging to the development of farming and herding, our results demonstrate the continued reliance on wild bovids among Iron Age communities in central and southwestern Zambia Iron Age and herding focused primarily on cattle. We also outline further potential applications of ZooMS in African archaeology.

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.

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.

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.

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.

Combining ZooMS and zooarchaeology to study Late Pleistocene hominin behaviour at Fumane (Italy)

Collagen type I fingerprinting (ZooMS) has recently been used to provide either palaeoenvironmental data or to identify additional hominin specimens in Pleistocene contexts, where faunal assemblages are normally highly fragmented. However, its potential to elucidate hominin subsistence behaviour has been unexplored. Here, ZooMS and zooarchaeology have been employed in a complementary approach to investigate bone assemblages from Final Mousterian and Uluzzian contexts at Fumane cave (Italy). Both approaches produced analogous species composition, but differ significantly in species abundance, particularly highlighted by a six fold-increase in the quantity of Bos/Bison remains in the molecularly identified component. Traditional zooarchaeological methods would therefore underestimate the proportion of Bos/Bison in these levels to a considerable extent. We suggest that this difference is potentially due to percussion-based carcass fragmentation of large Bos/Bison bone diaphyses. Finally, our data demonstrates high variability in species assignment to body size classes based on bone cortical thickness and fragment size. Thus, combining biomolecular and traditional zooarchaeological methods allows us to refine our understanding of bone assemblage composition associated with hominin occupation at Fumane.