Post-medieval Poverty: An Integrated Investigation

This study stemmed from our contested state of knowledge regarding under- and malnutrition in long-18th century England. The project aims to connect environment, nutrition and health, through the combined approach of osteological, biomolecular and historical research methods, and was motivated by three main research questions: (1) Is the potential scurvy biomarker identified during earlier work a true marker for scurvy in Human Skeletal Remains (HSR)? (2) Can we track potato consumption (a good source of Vitamin C) during this period through evidence of potato starch granules in human dental calculus? (3) Can we use a combination of HSR and historical documentary evidence to trace dietary and social change? A variety of different methods for extracting collagen from HSR were systematically tested, and a new technique has subsequently been established. This was applied to HSR from five post- medieval sites. These extractions - along with those of control samples - were run using MALDI-TOF-MS, and the resulting data analysed to a level of detail that has not previously been carried out, in the search for a scurvy biomarker. These analyses ruled out the potential biomarker, but revealed information that may help with the biomolecular identification of scurvy in the future. Dental calculus samples from individuals buried at one of the sites included here were analysed using light microscopy, but this element of the project was terminated as the data that could be produced was of limited use to the central research questions. Historical documentary evidence related to the sites included here has revealed the complexity of the factors influencing burial ground demographics. All five sites were identified by archaeologists as being linked to ‘poverty’, but this is an oversimplification when historical debate is taken into account. Throughout, this project evidences the benefits of a wider adoption of interdisciplinary approaches to historical research questions

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'

Using combined biomolecular methods to explore whale exploitation and social aggregation in hunter–gatherer–fisher society in Tierra del Fuego

Cetaceans were an important food and raw material resource for the South American hunter–gatherer–fisher (HGF) communities of Tierra del Fuego. Historic ethnographic evidence suggests that relatively mobile HGF groups came together in large numbers to exploit carcasses from individual cetacean stranding events. Substantial accumulations of whale bones within shell middens in the Lanashuaia locality of the Beagle Channel suggests that these social aggregation events may also have occurred in pre-historic periods. The difficulty in assigning taxonomic identifications to the fragmentary whale remains, however, made it difficult to explicitly test this hypothesis. Here, we applied two different biomolecular techniques, collagen peptide mass fingerprinting (ZooMS) and ancient mitochondrial DNA analysis to 42 archeological bone fragments from the Lanashuaia locality to provide accurate species identifications. There was a clear correspondence between ZooMS and DNA results, identifying five different cetacean species (Southern bottlenose, blue, humpback, right, and sei whale) as well as human and sea lion remains. The biomolecular results were not conclusively consistent with HGF social aggregation, revealing an unexpectedly diverse range of cetaceans within the Lanashuaia middens. However, the results could not fully refute the hypothesis that cetacean remains can be used as anthropic markers of aggregation events, as the observed species and haplotypes revealed potential shared exploitation of some whale resources between midden sites

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

Ancient proteins resolve the evolutionary history of Darwin's South American ungulates

No large group of recently extinct placental mammals remains as evolutionarily cryptic as the approximately 280 genera grouped as South American native ungulates'. To Charles Darwin, who first collected their remains, they included perhaps the strangest animal[s] ever discovered'. Today, much like 180 years ago, it is no clearer whether they had one origin or several, arose before or after the Cretaceous/Palaeogene transition 66.2 million years ago, or are more likely to belong with the elephants and sirenians of superorder Afrotheria than with the euungulates (cattle, horses, and allies) of superorder Laurasiatheria. Morphology-based analyses have proved unconvincing because convergences are pervasive among unrelated ungulate-like placentals. Approaches using ancient DNA have also been unsuccessful, probably because of rapid DNA degradation in semitropical and temperate deposits. Here we apply proteomic analysis to screen bone samples of the Late Quaternary South American native ungulate taxa Toxodon (Notoungulata) and Macrauchenia (Litopterna) for phylogenetically informative protein sequences. For each ungulate, we obtain approximately 90% direct sequence coverage of type I collagen α1- and α2-chains, representing approximately 900 of 1,140 amino-acid residues for each subunit. A phylogeny is estimated from an alignment of these fossil sequences with collagen (I) gene transcripts from available mammalian genomes or mass spectrometrically derived sequence data obtained for this study. The resulting consensus tree agrees well with recent higher-level mammalian phylogenies. Toxodon and Macrauchenia form a monophyletic group whose sister taxon is not Afrotheria or any of its constituent clades as recently claimed, but instead crown Perissodactyla (horses, tapirs, and rhinoceroses). These results are consistent with the origin of at least some South American native ungulates from 'condylarths', a paraphyletic assembly of archaic placentals. With ongoing improvements in instrumentation and analytical procedures, proteomics may produce a revolution in systematics such as that achieved by genomics, but with the possibility of reaching much further back in time