- University of York, Archaeology, Post-Docadd
- Science for Conservation and Restoration of Cultural Heritage, Human Evolution, Biomineralization, Geochronology, Protein diagenesis, Bioarchaeology, and 13 moreArchaeological Science, Chemistry, Archaeology of shell middens, Biomineralisation, Archaeology, Climate Change, Material Culture Studies, Middle to Upper Paleolithic Transition, Prehistoric personal ornaments, Amino Acids, Personal Ornaments In Prehistory, Neolithic Archaeology, and Quaternary geochronologyedit
- Biography Beatrice was awarded her MSc in Conservation Science at University of Turin in 2006 and her PhD in Archa... moreBiography
Beatrice was awarded her MSc in Conservation Science at University of Turin in 2006 and her PhD in Archaeology at York in 2009.
Her interests lie in understanding the mechanisms of protein decay in the archaeological and fossil record with specific application to the dating of archaeological and geological Quaternary sites. She is also using ancient proteins to identify biominerals (shells, eggshell) used by humans in the past to make useful objects or personal ornaments.
Her initial work focused upon the use of a wide range of non-destructive analytical techniques to characterise the degradation of both organic and inorganic surfaces from historic buildings and she specifically investigated the impact of chemical and biological deterioration of carbonates. Following the successful award of her Masters (cum laude and Optime prize for the Industrial Union in Turin), she moved to York as a Marie Curie Fellow to explore the potential of marine molluscs as a geochronological tool to date beach deposits and anthropogenic accumulations. This work took her to sites across the UK and around the Mediterranean.
As a NERC Postdoctoral Associate in the Department of Chemistry at York (2009-2013) she specialised in using mass-spectrometric methods to examine the decay of protein in a model system (ostrich eggshells) in order to improve the gechronology of sites in Southern Africa, to establish the beginning of modern human behaviour. Beatrice was also awarded a Marie Curie (Re)Integration Grant for the project mAARiTIME (2010-2013), which aims to build an integrated geochronology for key Quaternary coastal sites around the Mediterranean rim.
Currently she is employed as a Postdoctoral Researcher on the EPSRC project "MIB - The Interface between Materials and Biology" and is developing proteomics approaches to better understand processes of avian eggshell biomineralisation.edit
Rates of peptide bond hydrolysis and other diagenetic reactions are not favourable for Mesozoic protein survival. Proteins hydrolyse into peptide fragments and free amino acids that, in open systems such as bone, can leach from the... more
Rates of peptide bond hydrolysis and other diagenetic reactions are not favourable for Mesozoic protein survival. Proteins hydrolyse into peptide fragments and free amino acids that, in open systems such as bone, can leach from the specimen and be further degraded. However, closed systems are more likely to retain degradation products derived from endogenous proteins. Amino acid racemisation data in experimental and subfossil material suggests that mollusc shell and avian eggshell calcite crystals can demonstrate closed system behaviour, retaining endogenous amino acids. Here, high-performance liquid chromatography reveals that the intra-crystalline fraction of Late Cretaceous (estimated ~80 Ma) titanosaur sauropod eggshell is enriched in some of the most stable amino acids (Glx, Gly, Ala, and possibly Val) and those that racemise are fully racemic, despite being some of the slowest racemising amino acids. These results are consistent with degradation trends deduced from modern, the...
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<p>Results of the classification performed using Learning Vector Quantization. Leave-one-out (L-O-O) classification was used for validation and the results show how the test samples were classified. Each row represents one of the 26... more
<p>Results of the classification performed using Learning Vector Quantization. Leave-one-out (L-O-O) classification was used for validation and the results show how the test samples were classified. Each row represents one of the 26 genera included in the analysis, as indicated on the left of the table together with the number of examples tested. The four-letter codes uniquely identify each genus (full names in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0099839#pone-0099839-t001" target="_blank">Table 1</a>). The columns show the predicted genera. Numerical values are percentages so that the element in column <i>i</i> of row <i>j</i> shows the percentage of genus <i>j</i> that were classified as genus <i>i</i> and the main diagonal shows the percentage of each genus correctly classified. The dotted lines separate Bivalvia from Gastropoda and brackets above the predicted class names group genera within the same order. The grey-scale intensities are related to the numerical values with white corresponding to 100% and the darkest grey to 0% (for which no numerical value is given). Note that rounding may result in rows not summing to 100%.</p
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The realization that ancient biomolecules are preserved in “fossil” samples has revolutionized archaeological science. Protein sequences survive longer than DNA, but their phylogenetic resolution is inferior; therefore, careful assessment... more
The realization that ancient biomolecules are preserved in “fossil” samples has revolutionized archaeological science. Protein sequences survive longer than DNA, but their phylogenetic resolution is inferior; therefore, careful assessment of the research questions is required. Here, we show the potential of ancient proteins preserved in Pleistocene eggshell in addressing a longstanding controversy in human and animal evolution: the identity of the extinct bird that laid large eggs which were exploited by Australia’s indigenous people. The eggs had been originally attributed to the iconic extinct flightless bird Genyornis newtoni (†Dromornithidae, Galloanseres) and were subsequently dated to before 50 ± 5 ka by Miller et al. [ Nat. Commun. 7, 10496 (2016)]. This was taken to represent the likely extinction date for this endemic megafaunal species and thus implied a role of humans in its demise. A contrasting hypothesis, according to which the eggs were laid by a large mound-builder m...
Research Interests: Zoology, Biology, Osteology, Multidisciplinary, Ancient DNA, and 3 moreEggshell, Galliformes, and Taxon
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The extensive use of mollusc shell as a versatile raw material is testament to its importance in prehistoric times. The consistent choice of certain species for different purposes, including the making of ornaments, is a direct... more
The extensive use of mollusc shell as a versatile raw material is testament to its importance in prehistoric times. The consistent choice of certain species for different purposes, including the making of ornaments, is a direct representation of how humans viewed and exploited their environment. The necessary taxonomic information, however, is often impossible to obtain from objects that are small, heavily worked or degraded. Here we propose a novel biogeochemical approach to track the biological origin of prehistoric mollusc shell. We conducted an in-depth study of archaeological ornaments using microstructural, geochemical and biomolecular analyses, including ‘palaeoshellomics’, the first application of palaeoproteomics to mollusc shells (and indeed to any invertebrate calcified tissue). We reveal the consistent use of locally-sourced freshwater mother-of-pearl for the standardized manufacture of ‘double-buttons’. This craft is found throughout Europe between 4200–3800 BCE, highli...
Research Interests: Biochemistry, Evolutionary Biology, Geography, Archaeology, Paleoanthropology, and 15 moreStable Isotope Analysis, Chemical Biology, Biomineralization, Medicine, Prehistory, Craft, Chronology, Shell Ornaments, Ornaments, Pearl, Paleoproteomics, Personal Ornaments In Prehistory, Elife, Mollusc Shells, and Shell buttons
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Structural biominerals are inorganic/organic composites that exhibit remarkable mechanical properties. However, the structure-property relationships of even the simplest building unit-mineral single crystals containing embedded... more
Structural biominerals are inorganic/organic composites that exhibit remarkable mechanical properties. However, the structure-property relationships of even the simplest building unit-mineral single crystals containing embedded macromolecules-remain poorly understood. Here, by means of a model biomineral made from calcite single crystals containing glycine (0-7 mol%) or aspartic acid (0-4 mol%), we elucidate the origin of the superior hardness of biogenic calcite. We analysed lattice distortions in these model crystals by using X-ray diffraction and molecular dynamics simulations, and by means of solid-state nuclear magnetic resonance show that the amino acids are incorporated as individual molecules. We also demonstrate that nanoindentation hardness increased with amino acid content, reaching values equivalent to their biogenic counterparts. A dislocation pinning model reveals that the enhanced hardness is determined by the force required to cut covalent bonds in the molecules.
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Significance Bayesian modeling of AMS radiocarbon dates on the marine mollusk Phorcus turbinatus from Ksâr ‘Akil (Lebanon) indicates that the earliest presence of Upper Paleolithic (UP) modern humans in the Levant predates 45,900 cal B.P.... more
Significance Bayesian modeling of AMS radiocarbon dates on the marine mollusk Phorcus turbinatus from Ksâr ‘Akil (Lebanon) indicates that the earliest presence of Upper Paleolithic (UP) modern humans in the Levant predates 45,900 cal B.P. Similarities in early UP lithic technology and material culture suggest population dispersals between the Levant and Europe around 50,000–40,000 cal B.P. Our data confirm the presence of modern humans carrying a UP toolkit in the Levant prior to any known European modern human fossils and allow rejection of recent claims that European UP modern humans predate those in the Levant. This result, in turn, suggests the Levant served as a corridor for the dispersal of modern humans out of Africa and into Eurasia.
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ABSTRACT DefinitionsAmino acid racemization (AAR): changes in the chirality of amino acids, the building blocks of proteins, resulting from the time-and-temperature-driven breakdown of proteins. AAR is used in the geosciences as a... more
ABSTRACT DefinitionsAmino acid racemization (AAR): changes in the chirality of amino acids, the building blocks of proteins, resulting from the time-and-temperature-driven breakdown of proteins. AAR is used in the geosciences as a relative dating technique, typically comparing the ratio of D/L amino acid enantiomers in biominerals.Paleoclimate: the complex interrelated changes brought upon by temperature shifts caused by orbital forcing of the geosphere, hydrosphere, atmosphere, biosphere, and anthroposphere throughout Earth’s history.IntroductionThe level of racemization in any one sample is in effect a measure of the integrated time/temperature history (thermal age) that accounts for the observed degree of protein diagenesis. Therefore the contribution of amino acid racemization (AAR) to understanding past climate changes is twofold: it can be used either as a geochronological tool, to reconstruct the timing of major climatic events, or (less commonly) as a paleothermometer in the case of sam ...
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Research Interests: Chemical Engineering, Biochemistry, Microbiology, Biophysics, Chemistry, and 15 moreAnalytical Chemistry, Inorganic Chemistry, Immunology, Molecular Biology, Medicine, Presence, Animals, Peptide, Egg Proteins, Amino Acids, Protein Secondary Structure Prediction, Residue, Asparagine, Degradation products, and stereoisomerism
The oldest authenticated peptide sequences to date were reported in 2016 from 3.8 Ma old ostrich eggshell (OES) from the site of Laetoli, Tanzania (Demarchi et al., 2016). Here we demonstrate survival of the same sequences in 6.5-9 Ma OES... more
The oldest authenticated peptide sequences to date were reported in 2016 from 3.8 Ma old ostrich eggshell (OES) from the site of Laetoli, Tanzania (Demarchi et al., 2016). Here we demonstrate survival of the same sequences in 6.5-9 Ma OES recovered from a palaeosteppe setting in northwestern China. The eggshell is thicker than those observed in extant species and consistent with the Liushu Struthio sp. ootaxon. These findings push the preservation of ancient proteins back to the Miocene and highlight their potential for paleontology, paleoecology and evolutionary biology.
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The origins, prevalence and nature of dairying have been long debated by archaeologists. Within the last decade, new advances in high-resolution mass spectrometry have allowed for the direct detection of milk proteins from archaeological... more
The origins, prevalence and nature of dairying have been long debated by archaeologists. Within the last decade, new advances in high-resolution mass spectrometry have allowed for the direct detection of milk proteins from archaeological remains, including ceramic residues, dental calculus, and preserved dairy products. Proteins recovered from archaeological remains are susceptible to post-excavation and laboratory contamination, a particular concern for ancient dairying studies as milk proteins such as beta-lactoglobulin (BLG) and caseins are potential laboratory contaminants. Here, we examine how site-specific rates of deamidation (i.e., deamidation occurring in specific positions in the protein chain) can be used to elucidate patterns of peptide degradation, and authenticate ancient milk proteins. First, we characterize site-specific deamidation patterns in modern milk products and experimental samples, confirming that deamidation occurs primarily at low half-time sites. We then ...
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Bird eggs can become part of the archaeological record either accidentally or as a result of human activities but, in both instances, they can reveal important aspects of the environment at the site, the ways in which people chose to... more
Bird eggs can become part of the archaeological record either accidentally or as a result of human activities but, in both instances, they can reveal important aspects of the environment at the site, the ways in which people chose to exploit it, and even the existence of subtle ecological balances between humans and other animals. This is the case for El Mirόn, one of the most important cave sites in Cantabrian Spain, with occupation levels spanning around 40,000 years, from the late Middle Palaeolithic to the Bronze Age. This mountainous area in Cantabria was an ideal environment for hunting medium-sized game and, as such, supported both human and non-human predators, including birds of prey. Here we use a combination of peptide mass fingerprinting (by MALDI-MS) and protein sequencing (by LC-MS/MS) in order to taxonomically identify ninety-five fragments of eggshells recovered from nineteen archaeological layers. We firmly identify these as diurnal birds of prey (Accipitridae) and suggest that the species might have been bearded vulture, based on previous taphonomic studies that highlighted its presence at the cave. The implication is that both species of diurnal predators, humans and birds, inhabited the cave and used the surrounding environment during different periods of the year.
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In the version of this Perspective originally published, in the third paragraph of the section 'Selection and sampling', the sentence beginning 'Pyrolysis-gas chromatography' should have also referred to high-performance... more
In the version of this Perspective originally published, in the third paragraph of the section 'Selection and sampling', the sentence beginning 'Pyrolysis-gas chromatography' should have also referred to high-performance liquid chromatography; the sentence has now been amended to read 'Pyrolysis-gas chromatography/mass spectrometry (py-GC/MS) and high-performance liquid chromatography (HPLC) can be used to detect the presence of amino acids in any putative proteinaceous sample.'
Palaeoproteomics is an emerging neologism used to describe the application of mass spectrometry-based approaches to the study of ancient proteomes. As with palaeogenomics (the study of ancient DNA), it intersects evolutionary biology,... more
Palaeoproteomics is an emerging neologism used to describe the application of mass spectrometry-based approaches to the study of ancient proteomes. As with palaeogenomics (the study of ancient DNA), it intersects evolutionary biology, archaeology and anthropology, with applications ranging from the phylogenetic reconstruction of extinct species to the investigation of past human diets and ancient diseases. However, there is no explicit consensus at present regarding standards for data reporting, data validation measures or the use of suitable contamination controls in ancient protein studies. Additionally, in contrast to the ancient DNA community, no consolidated guidelines have been proposed by which researchers, reviewers and editors can evaluate palaeoproteomics data, in part due to the novelty of the field. Here we present a series of precautions and standards for ancient protein research that can be implemented at each stage of analysis, from sample selection to data interpreta...
Examples of wetland deposits can be found across the globe and are known for preserving organic archaeological and environmental remains that are vitally important to our understanding of past human–environment interactions. The... more
Examples of wetland deposits can be found across the globe and are known for preserving organic archaeological and environmental remains that are vitally important to our understanding of past human–environment interactions. The Mesolithic site of Star Carr (Yorkshire, United Kingdom) represents one of the most influential archives of human response to the changing climate at the end of the last glacial in Northern Europe. A hallmark of the site since its discovery in 1948 has been the exceptional preservation of its organic remains. Disturbingly, recent excavations have suggested that the geochemistry of the site is no longer conducive to such remarkable survival of organic archaeological and environmental materials. Microcosm (laboratory-based) burial experiments have been undertaken, alongside analysis of artifacts excavated from the site, to assess the effect of these geochemical changes on the remaining archaeological material. By applying a suite of macroscopic and molecular a...
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Mortuary practices in human evolution record cognitive, social changes and technological innovations. The Neolithic Revolution in the Levant was a watershed in this domain that has long fascinated the archaeological community. Plaster... more
Mortuary practices in human evolution record cognitive, social changes and technological innovations. The Neolithic Revolution in the Levant was a watershed in this domain that has long fascinated the archaeological community. Plaster modelled skulls are well known at Jericho and several other Neolithic sites, and in Nahal Hemar cave (Israel, ca. 8200 -7300 cal. BC) excavations yielded six unique human skulls covered with a black organic coating applied in a net pattern evoking a headdress. This small cave was used as storage for paraphernalia in the semi-arid area of the Judean desert and the dry conditions preserved other artefacts such as baskets coated with a similar dark substance. While previous analysis had revealed the presence of amino acids consistent with a collagen signature, in the present report, specific biomarkers were characterised using combined proteomic and lipid approaches. Basket samples yielded collagen and blood proteins of bovine origin (Bos genus) and a lar...
Research Interests: Archaeology, Art, Ancient Greek History, Israel, Humans, and 7 moreCollagen, Fossils, Animals, Skull, Caves, Cattle, and PLANT PROTEINS
Proteins persist longer in the fossil record than DNA, but the longevity, survival mechanisms and substrates remain contested. Here, we demonstrate the role of mineral binding in preserving the protein sequence in ostrich (Struthionidae)... more
Proteins persist longer in the fossil record than DNA, but the longevity, survival mechanisms and substrates remain contested. Here, we demonstrate the role of mineral binding in preserving the protein sequence in ostrich (Struthionidae) eggshell, including from the palaeontological sites of Laetoli (3.8 Ma) and Olduvai Gorge (1.3 Ma) in Tanzania. By tracking protein diagenesis back in time we find consistent patterns of preservation, demonstrating authenticity of the surviving sequences. Molecular dynamics simulations of struthiocalcin-1 and -2, the dominant proteins within the eggshell, reveal that distinct domains bind to the mineral surface. It is the domain with the strongest calculated binding energy to the calcite surface that is selectively preserved. Thermal age calculations demonstrate that the Laetoli and Olduvai peptides are 50 times older than any previously authenticated sequence (equivalent to ~16 Ma at a constant 10°C).
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The extensive use of mollusc shell as a versatile raw material is testament to its importance in prehistoric times. The consistent choice of certain species for different purposes, including the making of ornaments, is a direct... more
The extensive use of mollusc shell as a versatile raw material is testament to its importance in prehistoric times. The consistent choice of certain species for different purposes, including the making of ornaments, is a direct representation of how humans viewed and exploited their environment. The necessary taxonomic information, however, is often impossible to obtain from objects that are small, heavily worked or degraded. Here we propose a novel biogeochemical approach to track the biological origin of prehistoric mollusc shell. We conducted an in-depth study of archaeological ornaments using microstructural, geochemical and biomolecular analyses, including 'palaeoshellomics', the first application of palaeoproteomics to mollusc shells (and indeed to any invertebrate calcified tissue). We reveal the consistent use of locally-sourced freshwater mother-of-pearl for the standardised manufacture of 'double-buttons'. This craft is found throughout Europe between 4200-3800 BCE, highlighting the ornament-makers' profound knowledge of the biogeosphere and the existence of cross-cultural traditions.
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The extensive use of mollusc shell as a versatile raw material is testament to its importance in prehistoric times. The consistent choice of certain species for different purposes, including the making of ornaments, is a direct... more
The extensive use of mollusc shell as a versatile raw material is testament to its importance in prehistoric times. The consistent choice of certain species for different purposes, including the making of ornaments, is a direct representation of how humans viewed and exploited their environment. The necessary taxonomic information, however, is often impossible to obtain from objects that are small, heavily worked or degraded. Here we propose a novel biogeochemical approach to track the biological origin of prehistoric mollusc shell. We conducted an in-depth study of archaeological ornaments using microstructural, geochemical and biomolecular analyses, including 'palaeoshellomics', the first application of palaeoproteomics to mollusc shells (and indeed to any invertebrate calcified tissue). We reveal the consistent use of locally-sourced freshwater mother-of-pearl for the standardized manufacture of 'double-buttons'. This craft is found throughout Europe between 4200 - 3800 BCE, highlighting the ornament-makers' profound knowledge of the biogeosphere and the existence of cross-cultural traditions.
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This study successfully isolates a fraction of intra-crystalline proteins from shells of the marine gastropod Patella vulgata and assesses the suitability of these proteins for IcPD (Intra-crystalline Protein Diagenesis) geochronology. We... more
This study successfully isolates a fraction of intra-crystalline proteins from shells of the marine gastropod Patella vulgata and assesses the suitability of these proteins for IcPD (Intra-crystalline Protein Diagenesis) geochronology. We discuss the mineralogical composition of this gastropod, investigated for the first time by X-ray diffraction mapping, and use the results to inform our sampling strategy. The potential of the calcitic rim and of a bulk sample (containing both apex and rim) of the shell to act as stable repositories for the intra-crystalline proteins during diagenesis is examined. The composition and the diagenetic behaviour of the intra-crystalline proteins isolated from different locations within the shell are compared, highlighting the necessity of targeting consistent sampling positions. We induced artificial diagenesis of both intra-crystalline and whole-shell proteins by conducting high-temperature experiments in hydrous environment; this allowed us to quantify the loss of amino acids by leaching and therefore evaluate the open-or closed-system behaviour of the different fractions of proteins. The results obtained provide further confirmation that patterns of diagenesis vary according to the protein sequence, structure, and location within or outside the intra-crystalline fraction. As Patella is frequently found in the fossil record, both in archaeological and geological contexts, the application of IcPD geochronology to this biomineral opens up the possibility to obtain reliable age information from a range of sites in different areas of the world.
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Available at http://www.catalhoyuk.com/archive_reports/
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Marine faunal remains from Grotta d'Oriente (Favignana Island, NW Sicily) offer invaluable snapshots of human-coastal environment interaction in the central Mediterranean from the Late Pleistocene to the Middle Holocene. The long-term... more
Marine faunal remains from Grotta d'Oriente (Favignana Island, NW Sicily) offer invaluable snapshots of human-coastal environment interaction in the central Mediterranean from the Late Pleistocene to the Middle Holocene. The long-term shellfish and fish records reflect human exploitation of coastal environments undergoing considerable reorganizations during the postglacial sea level rise and the progressive isolation of Favignana from mainland Sicily. We detected an intensification of marine resource exploitation between ∼9.6 ka and ∼7.8 ka BP, which corresponds with the isolation of Favignana Island and, later on, with the introduction of early agro-pastoral economy in this region. We suggest that a higher investment in marine resource exploitation by late foragers and early farmers in NW Sicily was also supported by an increase in marine productivity in the south Tyrrhenian Sea in the Middle Holocene.