Article
Multidisciplinary Sciences
Sara Silvestrini, Federico Lugli, Matteo Romandini, Cristina Real, Eduardo Sommella, Emanuela Salviati, Simona Arrighi, Eugenio Bortolini, Carla Figus, Owen Alexander Higgins, Giulia Marciani, Gregorio Oxilia, Davide Delpiano, Antonino Vazzana, Marcello Piperno, Carlo Crescenzi, Pietro Campiglia, Carmine Collina, Marco Peresani, Enza Elena Spinapolice, Stefano Benazzi
Summary: This study combines traditional zooarchaeology and proteomic identification to explore the potential of morphologically non-diagnostic bone fragments. The results provide a more complete understanding of the faunal assemblage and paleoenvironment during the Middle-Upper Palaeolithic transition in Italy.
Article
Multidisciplinary Sciences
F. Di Gianvincenzo, D. Peggie, M. Mackie, C. Granzotto, C. Higgitt, E. Cappellini
Summary: Undertaking the conservation of artworks informed by molecular analyses, particularly mass spectrometry-based proteomics, has become increasingly important. This study successfully applied a palaeoproteomic workflow to identify protein-based binders and their origin in a 15th-century panel painting. The approach proved to be accurate, sensitive, and applicable in the cultural heritage field with limited starting material.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Samantha Brown, Naihui Wang, Annette Oertle, Maxim B. Kozlikin, Michael Shunkov, Anatoly P. Derevianko, Daniel Comeskey, Blair Jope-Street, Virginia L. Harvey, Manasij Pal Chowdhury, Michael Buckley, Thomas Higham, Katerina Douka
Summary: Denisova Cave in the Altai Mountains of Russian Siberia has provided significant fossil evidence for the Pleistocene in Northern Asia. Through ZooMS analysis of bone fragments, trends related to climate variability and patterns of bone fragmentation have been identified, indicating a cyclical pattern involving human-induced and carnivore-related fragmentation.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Abigail Ramsoe, Mia Crispin, Meaghan Mackie, Krista McGrath, Roman Fischer, Beatrice Demarchi, Matthew J. Collins, Jessica Hendy, Camilla Speller
Summary: This study examines the use of site-specific deamidation rates in identifying modern contamination and authenticating ancient milk proteins, showing its potential but also highlighting the challenges posed by the high variability of deamidation rates in ancient milk peptides. Multiple lines of evidence are needed to authenticate ancient protein data due to this variability.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Kristine Korzow Richter, Maria C. Codlin, Melina Seabrook, Christina Warinner
Summary: Collagen peptide mass fingerprinting by MALDI-TOF-MS, also known as ZooMS, is a rapidly growing analytical technique in the fields of archaeology, ecology, and cultural heritage. It enables rapid taxonomic identification of large bone assemblages and cultural heritage objects. However, there are limitations that need to be addressed for future advancements.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Analytical
Fabrice Bray, Isabelle Fabrizi, Stephanie Flament, Jean-Luc Locht, Pierre Antoine, Patrick Auguste, Christian Rolando
Summary: Peptide mass fingerprinting (PMF) using MALDI-TOF mass spectrometry is used for identifying bone species based on their type I collagen sequence. In the field of archaeology and paleontology, PMF is referred to as zooarchaeology mass spectrometry (ZooMS) and is widely used for identifying markers for various species, including extinct ones. The method also enables dating estimation through measuring the deamidation value of specific peptides. Several enhancements have been made to the classical ZooMS technique, including reduced sample amount requirement, improved deamidation value calculation, and high-resolution PMF using MALDI-FTICR analysis. These improvements allow for reliable species identification and provide valuable information in specific contexts.
ANALYTICAL CHEMISTRY
(2023)
Article
Anthropology
Michael Buckley, Virginia L. Harvey, David Petiffer, Hannah Russ, Wim Wouters, Wim Van Neer
Summary: This study explores the potential of collagen peptide mass fingerprinting (ZooMS) for identifying fish remains from the Medieval Newport shipwreck. Through the inclusion of over 50 reference taxa, the archaeologists identified nine distinct taxonomic groups, dominated by ling. However, the inability to identify all taxonomic groups accurately highlights the need for a larger reference collection or collagen sequences.
ARCHAEOLOGICAL AND ANTHROPOLOGICAL SCIENCES
(2022)
Article
Chemistry, Applied
Kristin D. Mattice, Alejandro G. Marangoni
Summary: This study investigated potential improvements to the physical properties of brittle, self-assembled zein networks through microbial transglutaminase crosslinking. Although crosslinked heteropolymers were observed, they were not found in multiprotein networks with zein, resulting in a weaker structure. The observed behavior was mainly attributed to glutamine deamidation by microbial transglutaminase, changing the hydrophobicity of the protein and modifying non-covalent bonding within the network.
Article
Multidisciplinary Sciences
Georgia Ntasi, Ismael Rodriguez Palomo, Gennaro Marino, Fabrizio Dal Piaz, Francesco Sirano, Enrico Cappellini, Leila Birolo, Pierpaolo Petrone
Summary: Proteomic analysis of human bones from the victims of the AD 79 eruption in Pompeii revealed that the bone proteomes from Pompeii were more degraded compared to those from Herculaneum, despite the latter being exposed to higher temperatures. The slow decomposition of victims' soft tissues in Pompeii, due to the natural dry-wet hydrogeological soil cycles, damaged their bone proteome more than the intense heat experienced at Herculaneum in a waterlogged burial context.
SCIENTIFIC REPORTS
(2022)
Article
Biochemical Research Methods
Manasij Pal Chowdhury, Michael Buckley
Summary: This study investigates the correlation between deamidation and protein age, as well as differences in various proteins found in bones, dental calculus, and archaeological ceramics. The results show that collagen in archaeological bones exhibits a chronological dependence on deamidation, and that the extent of deamidation varies across different proteins. However, the correlation between the structural motifs of peptides and deamidation was not clear. Overall, deamidation in archaeological samples can provide additional information beyond species and tissue type identification, serving as a measure of protein endogeneity, degradation, or thermal age for relative dating.
Article
Geochemistry & Geophysics
Ella Sokol, Maxim B. Kozlikin, Svetlana N. Kokh, Anna Nekipelova, Natalya A. Kulik, Viktoria A. Danilovsky, Pavel Khvorov, Michael Shunkov
Summary: The distribution of authigenic phosphates in Denisova Cave provides important archaeological implications, indicating alternating occupations by humans and insectivorous bats during the Late Pleistocene-Early Holocene. The formation of phosphates follows the biodegradation pathway of organic matter, and the depth profile of authigenic phosphates reflects changes in pH conditions of the sedimentary environment.
Article
Chemistry, Physical
Katherine E. Lawson, Megan N. Evans, Joseph K. Dekle, Andrew J. Adamczyk
Summary: This study analyzed the thermochemical and kinetic properties of Gln and Asn deamidation reactions using density functional theory. The results showed that Gln deamidation has a more significant impact on physiological proteins, while Asn deamidation is associated with both pharmaceutical and physiological proteins.
JOURNAL OF PHYSICAL CHEMISTRY A
(2022)
Review
Geosciences, Multidisciplinary
Ana Garcia-vazquez, Ana Cristina Pinto-llona, Julia Maroto, Trinidad Torres, Aurora Grandal-d'anglade
Summary: The identification of bone fragments using peptide mass fingerprinting or mass spectrometry is becoming a powerful tool in Quaternary palaeontology. The use of mass spectrometry allows for the studying of variations in amino acid sequences in bone collagen, which can be used for taxonomic purposes. However, no peptide fingerprint taxonomic study has specifically focused on the cave bear species. This study investigates the bone collagen of cave and brown bear samples using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI TOF) and in-silico analysis.
EARTH AND ENVIRONMENTAL SCIENCE TRANSACTIONS OF THE ROYAL SOCIETY OF EDINBURGH
(2023)
Article
Geography, Physical
Jeffrey S. Munroe
Summary: This report introduces Winter Wonderland Cave on the southern slope of the Uinta Mountains in Utah, USA, discussing the temperature differences inside and outside the cave, distribution of ice layers, age and origin of the ice, as well as results from stable isotope and glaciochemistry analyses. Liquid water appearing in the cave in recent years could indicate a changing cave environment.
Article
Anthropology
Roshan Paladugu, Kristine Korzow Richter, Maria Joao Valente, Sonia Gabriel, Cleia Detry, Christina Warinner, Cristina Barrocas Dias
Summary: A novel peptide marker has been discovered to reliably distinguish between horse and donkey skeletal remains. This method has the potential to enhance our understanding of the relative importance of these two species in past human societies and facilitate the collection of morphological data for studying equids in Iberia and throughout Eurasia and Africa.
JOURNAL OF ARCHAEOLOGICAL SCIENCE
(2023)
Article
Biochemical Research Methods
Samantha Brown, Katerina Douka, Matthew J. Collins, Kristine Korzow Richter
Summary: ZooMS, a peptide mass fingerprinting technique, is increasingly utilized in archaeological and cultural heritage science, but faces challenges due to inconsistent nomenclature for peptide markers. Standardized guidelines proposed here aim to provide a reliable and consistent naming system, supporting the growth of ZooMS across diverse vertebrate taxa.
JOURNAL OF PROTEOMICS
(2021)
Article
Biochemical Research Methods
Wang Naihui, Brown Samantha, Ditchfield Peter, Hebestreit Sandra, Kozilikin Maxim, Luu Sindy, Wedage Oshan, Grimaldi Stefano, Chazan Michael, Horwitz Kolska Liora, Spriggs Matthew, Summerhayes Glenn, Shunkov Michael, Richter Korzow Kristine, Douka Katerina
Summary: This study compares three different ZooMS protocols and finds that acid-based methods can improve success rates for bones with low to medium collagen preservation, while the least-destructive protocol using ammonium bicarbonate buffer is suitable for well-preserved bones. By utilizing 0.26% N as a threshold, the number of samples with enough collagen for successful peptide mass fingerprinting can be optimized.
JOURNAL OF PROTEOMICS
(2021)
Article
Multidisciplinary Sciences
Maria Martinon-Torres, Francesco d'Errico, Elena Santos, Ana Alvaro Gallo, Noel Amano, William Archer, Simon J. Armitage, Juan Luis Arsuaga, Jose Maria Bermudez de Castro, James Blinkhorn, Alison Crowther, Katerina Douka, Stephan Dubernet, Patrick Faulkner, Pilar Fernandez-Colon, Nikos Kourampas, Jorge Gonzalez Garcia, David Larreina, Francois-Xavier Le Bourdonnec, George MacLeod, Laura Martin-Frances, Diyendo Massilani, Julio Mercader, Jennifer M. Miller, Emmanuel Ndiema, Belen Notario, Africa Pitarch Marti, Mary E. Prendergast, Alain Queffelec, Solange Rigaud, Patrick Roberts, Mohammad Javad Shoaee, Ceri Shipton, Ian Simpson, Nicole Boivin, Michael D. Petraglia
Summary: This study describes the partial skeleton of a roughly 2.5- to 3.0-year-old child dating to 78,000 years ago found in the Middle Stone Age (MSA) layers of Panga ya Saidi (PYS) in Kenya. The discovery sheds light on how MSA populations interacted with the dead, providing insight into early human burial practices in Africa.
Article
Multidisciplinary Sciences
Anneke Janzen, Kristine Korzow Richter, Ogeto Mwebi, Samantha Brown, Veronicah Onduso, Filia Gatwiri, Emmanuel Ndiema, Maggie Katongo, Steven T. Goldstein, Katerina Douka, Nicole Boivin
Summary: This study provides a complete set of ZooMS peptide markers for African bovid tribes and identifies two novel peptide markers for further distinguishing between bovid groups. The results demonstrate that nearly all African bovid subfamilies can be distinguished using ZooMS methods, revealing greater taxonomic richness than morphology-based analyses.
Article
Geochemistry & Geophysics
Rob Dinnis, Alexander A. Bessudnov, Natasha Reynolds, Gennady A. Khlopachev, Mikhail Sablin, Andrei Sinitsyn, Thomas Higham, Katerina Douka
Summary: The new radiocarbon dates presented in this study for the Kostenki sites confirm short-term accumulation of archaeological layers at Kostenki 15 and Kostenki 1, supporting the view that many Kostenki assemblages are chronologically distinct. The results provide important insights into the tempo of Upper Paleolithic cultural change in Eastern Europe.
Article
Geochemistry & Geophysics
Esteban Alvarez-Fernandez, Jesus F. Jorda Pardo, Pablo Arias, Julian Becares, Sergio Martin-Jarque, Rodrigo Portero, Luis Teira, Katerina Douka
Summary: Four excavations have been conducted at the archaeological site of Cova Rosa in Cantabrian Spain, revealing occupations during the Last Glacial period, Solutrean, Magdalenian, and early Holocene. Stratigraphic correlation and new radiocarbon dates have helped compare these occupations with other sites in Cantabrian Spain and Asturias specifically.
Article
Multidisciplinary Sciences
Courtney Culley, Anneke Janzen, Samantha Brown, Mary E. Prendergast, Jesse Wolfhagen, Bourhane Abderemane, Abdallah K. Ali, Othman Haji, Mark C. Horton, Ceri Shipton, Jillian Swift, Tabibou A. Tabibou, Henry T. Wright, Nicole Boivin, Alison Crowther
Summary: This study utilized ZooMS technology to analyze archaeological remains from eight Iron Age sites in eastern Africa's islands, revealing a wider distribution of caprines than previously known. The results indicate that goats were introduced to island eastern Africa from at least the seventh century CE, while sheep arrived one-two centuries later. Goats may have been preferred due to their better adaptation to the islands' environments as browsers.
ROYAL SOCIETY OPEN SCIENCE
(2021)
Article
Ecology
Samantha Brown, Diyendo Massilani, Maxim B. Kozlikin, Michael V. Shunkov, Anatoly P. Derevianko, Alexander Stoessel, Blair Jope-Street, Matthias Meyer, Janet Kelso, Svante Paeaebo, Thomas Higham, Katerina Douka
Summary: Through collagen peptide mass fingerprinting analysis of thousands of non-diagnostic bone fragments, five new hominin bones were discovered in Denisova Cave, Siberia, Russia, with three identified as Denisovan and one as Neanderthal based on mitochondrial DNA analysis. These bones, dating back to 200 ka, provide valuable insights into the material culture, behavior, and environmental adaptations of these early hominins, and have significantly expanded our understanding of Denisovan and Neanderthal interactions and archaeological signatures.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Fa-Gang Wang, Shi-Xia Yang, Jun-Yi Ge, Andreu Olle, Ke-Liang Zhao, Jian-Ping Yue, Daniela Eugenia Rosso, Katerina Douka, Ying Guan, Wen-Yan Li, Hai-Yong Yang, Lian-Qiang Liu, Fei Xie, Zheng-Tang Guo, Ri-Xiang Zhu, Cheng-Long Deng, Francesco D'Errico, Michael Petraglia
Summary: The study describes a well-preserved archaeological site, Xiamabei, in northern China, which reveals the earliest known ochre-processing feature and unique cultural traits in East Asia. These traits do not correspond with those found in other archaeological sites inhabited by archaic populations or associated with the expansion of Homo sapiens, suggesting a process of technological innovation and cultural diversification during a period of hominin hybridization and admixture.
Article
Biology
Patrick Roberts, Katerina Douka, Monica Tromp, Stuart Bedford, Stuart Hawkins, Laurie Bouffandeau, Jana Ilgner, Mary Lucas, Sara Marzo, Rebecca Hamilton, Wallace Ambrose, David Bulbeck, Sindy Luu, Richard Shing, Chris Gosden, Glenn Summerhayes, Matthew Spriggs
Summary: This study explores the chronology and diets of the earliest human remains found in Near and Remote Oceania. The oldest human fossil outside of mainland New Guinea-Aru area dates back to approximately 11,800 years ago. It also shows that early sea-faring populations in Bismarck Archipelago and Vanuatu relied heavily on interior tropical forest resources. This finding suggests that local tropical habitats should be emphasized when discussing human diets and cultural practices in this region.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Multidisciplinary Sciences
L. Gatti, Federico Lugli, Giorgia Sciutto, M. Zangheri, S. Prati, M. Mirasoli, S. Silvestrini, S. Benazzi, T. Tuetken, K. Douka, C. Collina, F. Boschin, M. Romandini, P. Iacumin, M. Guardigli, A. Roda, R. Mazzeo
Summary: A study found that mutual protection between biomineral and organic fractions in bones and teeth helps promote the preservation of the organic fraction, and investigated the correlation between elemental variations and collagen distribution. By combining two methods, it was discovered that collagen had an uneven distribution in highly degraded samples, and there was a correlation between the presence of uranium and rare earth elements with collagen content.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Ludovic Slimak, Clement Zanolli, Tom Higham, Marine Frouin, Jean-Luc Schwenninger, Lee J. Arnold, Martina Demuro, Katerina Douka, Norbert Mercier, Gilles Guerin, Helene Valladas, Pascale Yvorra, Yves Giraud, Andaine Seguin-Orlando, Ludovic Orlando, Jason E. Lewis, Xavier Muth, Hubert Camus, Segolene Vandevelde, Mike Buckley, Carolina Mallol, Chris Stringer, Laure Metz
Summary: The discovery of human fossils in Grotte Mandrin, France, suggests the presence of early modern humans in Europe between 56,800 and 51,700 years ago. This indicates alternating occupations between Neanderthals and modern humans, with the latter using unique technologies from Africa or the Levant.
Article
Ecology
Ben Shaw, Stuart Hawkins, Lorena Becerra-Valdivia, Chris S. M. Turney, Simon Coxe, Vincent Kewibu, Jemina Haro, Kenneth Miamba, Mathieu Leclerc, Matthew Spriggs, Karen Privat, Simon Haberle, Felicitas Hopf, Emily Hull, Alana Pengilley, Samantha Brown, Christopher E. Marjo, Geraldine Jacobsen
Summary: Excavation in Island New Guinea has provided evidence for the spread of Lapita culture in the Pacific and its origins. The study reveals the earliest evidence for Lapita-introduced animals, turtle bone technology, and obsidian import, which occurred alongside indigenous technologies, suggesting a multicultural influence on population diversity. It also suggests that initial Lapita expansion in New Guinea was more extensive than previously thought, with indigenous contact influencing migration pathways and island-hopping strategies.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Elena Essel, Elena I. Zavala, Ellen Schulz-Kornas, Maxim B. Kozlikin, Helen Fewlass, Benjamin Vernot, Michael V. Shunkov, Anatoly P. Derevianko, Katerina Douka, Ian Barnes, Marie-Cecile Soulier, Anna Schmidt, Merlin Szymanski, Tsenka Tsanova, Nikolay Sirakov, Elena Endarova, Shannon P. McPherron, Jean-Jacques Hublin, Janet Kelso, Svante Paeaebo, Mateja Hajdinjak, Marie Soressi, Matthias Meyer
Summary: Artefacts made from stones, bones and teeth are important for understanding human subsistence strategies and culture in the Pleistocene. However, it is difficult to associate these artefacts with specific individuals, unless they are found within burials. A non-destructive method has been developed to extract DNA from ancient bone and tooth artefacts, and analysis revealed that a female individual made the pendant.
Article
Anthropology
Julia Becher, Alex Schoeman, Gavin Whitelaw, Stephen Buckley, Jean-Pierre Celliers, Sara Cafisso, Matthias Belser, Maxime Rageot, Cynthianne Spiteri
Summary: This study represents the first application of Organic Residue Analysis (ORA) to southern African early farming pottery to gain a deeper understanding of past human behavior and subsistence patterns. The study found evidence of dairy processing and multi-purpose functionality of the ceramics. It also discovered potential medicinal use and the involvement of dung in pottery sealing and mending.
JOURNAL OF ARCHAEOLOGICAL SCIENCE
(2024)
Article
Anthropology
Jon Clindaniel, Matthew Magnani
Summary: Large sources of digital trace data have become important in the study of material culture. The authors introduce a computational method to observe digital formation processes and highlight the importance of accounting for these processes in studies utilizing digital trace data.
JOURNAL OF ARCHAEOLOGICAL SCIENCE
(2024)
Article
Anthropology
Rebecca A. G. Reid, Miranda M. E. Jans, Lesley A. Chesson, Rebecca J. Taylor, Gregory E. Berg
Summary: Chemical treatment of skeletal remains can reduce overall DNA quality and quantity but has no significant impact on stable isotope ratio analysis. Examination of treated and untreated human remains through histological and stable isotope analysis reveals that treated remains exhibit better preservation compared to untreated remains. Stable isotope ratio analysis is viable for both treated and untreated remains, regardless of their origin.
JOURNAL OF ARCHAEOLOGICAL SCIENCE
(2024)
Article
Anthropology
Laura Tome, Eneko Iriartec, Antonio Blanco-Gonzalez, Margarita Jambrina-Enriquez, Natalia Eguez, Antonio V. Herrera-Herrera, Carolina Mallola
Summary: This paper presents the outcomes of a microcontextual geoarchaeological study conducted on earthen dwellings from the Early Iron Age village of Cerro de San Vicente. The study employed soil micromorphology, lipid biomarker analysis, XRD, and XRF analyses to investigate various aspects of the dwellings, including construction materials, site formation processes, and daily life practices. The results have shed light on the construction layers, floor use, maintenance, repaving, periods of abandonment and decay, and the presence of lipid biomarkers associated with dwelling functionality. The study significantly contributes to our understanding of ancient construction practices and the utilization of domestic spaces during the Early Iron Age.
JOURNAL OF ARCHAEOLOGICAL SCIENCE
(2024)
