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01 Sep 2023
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Zooarchaeological investigation of the Hoabinhian exploitation of reptiles and amphibians in Thailand and Cambodia with a focus on the Yellow-headed tortoise (Indotestudo elongata (Blyth, 1854))

A zooarchaeological perspective on testudine bones from Hoabinhian hunter-gatherer archaeological assemblages in Southeast Asia

Recommended by ORCID_LOGO based on reviews by Noel Amano and Iratxe Boneta

The study of the evolution of the human diet has been a central theme in numerous archaeological and paleoanthropological investigations. By reconstructing diets, researchers gain deeper insights into how humans adapted to their environments. The analysis of animal bones plays a crucial role in extracting dietary information. Most studies involving ancient diets rely heavily on zooarchaeological examinations, which, due to their extensive history, have amassed a wealth of data.

During the Pleistocene–Holocene periods, testudine bones have been commonly found in a multitude of sites. The use of turtles and tortoises as food sources appears to stretch back to the Early Pleistocene [1-4]. More importantly, these small animals play a more significant role within a broader debate. The exploitation of tortoises in the Mediterranean Basin has been examined through the lens of optimal foraging theory and diet breadth models (e.g. [5-10]). According to the diet breadth model, resources are incorporated into diets based on their ranking and influenced by factors such as net return, which in turn depends on caloric value and search/handling costs [11]. Within these theoretical frameworks, tortoises hold a significant position. Their small size and sluggish movement require minimal effort and relatively simple technology for procurement and processing. This aligns with optimal foraging models in which the low handling costs of slow-moving prey compensate for their small size [5-6,9]. Tortoises also offer distinct advantages. They can be easily transported and kept alive, thereby maintaining freshness for deferred consumption [12-14]. For example, historical accounts suggest that Mexican traders recognised tortoises as portable and storable sources of protein and water [15]. Furthermore, tortoises provide non-edible resources, such as shells, which can serve as containers. This possibility has been discussed in the context of Kebara Cave [16] and noted in ethnographic and historical records (e.g. [12]). However, despite these advantages, their slow growth rate might have rendered intensive long-term predation unsustainable.

While tortoises are well-documented in the Southeast Asian archaeological record, zooarchaeological analyses in this region have been limited, particularly concerning prehistoric hunter-gatherer populations that may have relied extensively on inland chelonian taxa. With the present paper Bochaton et al. [17] aim to bridge this gap by conducting an exhaustive zooarchaeological analysis of turtle bone specimens from four Hoabinhian hunter-gatherer archaeological assemblages in Thailand and Cambodia. These assemblages span from the Late Pleistocene to the first half of the Holocene. The authors focus on bones attributed to the yellow-headed tortoise (Indotestudo elongata), which is the most prevalent taxon in the assemblages. The research include osteometric equations to estimate carapace size and explore population structures across various sites. The objective is to uncover human tortoise exploitation strategies in the region, and the results reveal consistent subsistence behaviours across diverse locations, even amidst varying environmental conditions. These final proposals suggest the possibility of cultural similarities across different periods and regions in continental Southeast Asia.

In summary, this paper [17] represents a significant advancement in the realm of zooarchaeological investigations of small prey within prehistoric communities in the region. While certain approaches and issues may require further refinement, they serve as a comprehensive and commendable foundation for assessing human hunting adaptations.

 

References

[1] Hartman, G., 2004. Long-term continuity of a freshwater turtle (Mauremys caspica rivulata) population in the northern Jordan Valley and its paleoenvironmental implications. In: Goren-Inbar, N., Speth, J.D. (Eds.), Human Paleoecology in the Levantine Corridor. Oxbow Books, Oxford, pp. 61-74. https://doi.org/10.2307/j.ctvh1dtct.11

[2] Alperson-Afil, N., Sharon, G., Kislev, M., Melamed, Y., Zohar, I., Ashkenazi, R., Biton, R., Werker, E., Hartman, G., Feibel, C., Goren-Inbar, N., 2009. Spatial organization of hominin activities at Gesher Benot Ya'aqov, Israel. Science 326, 1677-1680. https://doi.org/10.1126/science.1180695

[3] Archer, W., Braun, D.R., Harris, J.W., McCoy, J.T., Richmond, B.G., 2014. Early Pleistocene aquatic resource use in the Turkana Basin. J. Hum. Evol. 77, 74-87. https://doi.org/10.1016/j.jhevol.2014.02.012

[4] Blasco, R., Blain, H.A., Rosell, J., Carlos, D.J., Huguet, R., Rodríguez, J., Arsuaga, J.L., Bermúdez de Castro, J.M., Carbonell, E., 2011. Earliest evidence for human consumption of tortoises in the European Early Pleistocene from Sima del Elefante, Sierra de Atapuerca, Spain. J. Hum. Evol. 11, 265-282. https://doi.org/10.1016/j.jhevol.2011.06.002

[5] Stiner, M.C., Munro, N., Surovell, T.A., Tchernov, E., Bar-Yosef, O., 1999. Palaeolithic growth pulses evidenced by small animal exploitation. Science 283, 190-194. https://doi.org/10.1126/science.283.5399.190

[6] Stiner, M.C., Munro, N.D., Surovell, T.A., 2000. The tortoise and the hare: small-game use, the Broad-Spectrum Revolution, and paleolithic demography. Curr. Anthropol. 41, 39-73. https://doi.org/10.1086/300102

[7] Stiner, M.C., 2001. Thirty years on the “Broad Spectrum Revolution” and paleolithic demography. Proc. Natl. Acad. Sci. U. S. A. 98 (13), 6993-6996. https://doi.org/10.1073/pnas.121176198

[8] Stiner, M.C., 2005. The Faunas of Hayonim Cave (Israel): a 200,000-Year Record of Paleolithic Diet. Demography and Society. American School of Prehistoric Research, Bulletin 48. Peabody Museum Press, Harvard University, Cambridge.

[9] Stiner, M.C., Munro, N.D., 2002. Approaches to prehistoric diet breadth, demography, and prey ranking systems in time and space. J. Archaeol. Method Theory 9, 181-214. https://doi.org/10.1023/A:1016530308865

[10] Blasco, R., Cochard, D., Colonese, A.C., Laroulandie, V., Meier, J., Morin, E., Rufà, A., Tassoni, L., Thompson, J.C. 2022. Small animal use by Neanderthals. In Romagnoli, F., Rivals, F., Benazzi, S. (eds.), Updating Neanderthals: Understanding Behavioral Complexity in the Late Middle Palaeolithic. Elsevier Academic Press, pp. 123-143. ISBN 978-0-12-821428-2. https://doi.org/10.1016/C2019-0-03240-2

[11] Winterhalder, B., Smith, E.A., 2000. Analyzing adaptive strategies: human behavioural ecology at twenty-five. Evol. Anthropol. 9, 51-72. https://doi.org/10.1002/(sici)1520-6505(2000)9:2%3C51::aid-evan1%3E3.0.co;2-7

[12] Schneider, J.S., Everson, G.D., 1989. The Desert Tortoise (Xerobates agassizii) in the Prehistory of the Southwestern Great Basin and Adjacent areas. J. Calif. Gt. Basin Anthropol. 11, 175-202. http://www.jstor.org/stable/27825383

[13] Thompson, J.C., Henshilwood, C.S., 2014b. Nutritional values of tortoises relative to ungulates from the Middle Stone Age levels at Blombos Cave, South Africa: implications for foraging and social behaviour. J. Hum. Evol. 67, 33-47. https://doi.org/10.1016/j.jhevol.2013.09.010

[14] Blasco, R., Rosell, J., Smith, K.T., Maul, L.Ch., Sañudo, P., Barkai, R., Gopher, A. 2016. Tortoises as a Dietary Supplement: a view from the Middle Pleistocene site of Qesem Cave, Israel. Quat Sci Rev 133, 165-182. https://doi.org/10.1016/j.quascirev.2015.12.006

[15] Pepper, C., 1963. The truth about the tortoise. Desert Mag. 26, 10-11.

[16] Speth, J.D., Tchernov, E., 2002. Middle Paleolithic tortoise use at Kebara Cave (Israel). J. Archaeol. Sci. 29, 471-483. https://doi.org/10.1006/jasc.2001.0740

[17] Bochaton, C., Chantasri, S., Maneechote, M., Claude, J., Griggo, C., Naksri, W., Forestier, H., Sophady, H., Auertrakulvit, P., Bowonsachoti, J. and Zeitoun, V. (2023) Zooarchaeological investigation of the Hoabinhian exploitation of reptiles and amphibians in Thailand and Cambodia with a focus on the Yellow-headed Tortoise (Indotestudo elongata (Blyth, 1854)), BioRXiv, 2023.04.27.538552 , ver. 3 peer-reviewed and recommended by Peer Community in Archaeology. https://doi.org/10.1101/2023.04.27.538552v3

Zooarchaeological investigation of the Hoabinhian exploitation of reptiles and amphibians in Thailand and Cambodia with a focus on the Yellow-headed tortoise (*Indotestudo elongata* (Blyth, 1854))Corentin Bochaton, Sirikanya Chantasri, Melada Maneechote, Julien Claude, Christophe Griggo, Wilailuck Naksri, Hubert Forestier, Heng Sophady, Prasit Auertrakulvit, Jutinach Bowonsachoti, Valery Zeitoun<p style="text-align: justify;">While non-marine turtles are almost ubiquitous in the archaeological record of Southeast Asia, their zooarchaeological examination has been inadequately pursued within this tropical region. This gap in research hind...Asia, Taphonomy, ZooarchaeologyRuth Blasco Iratxe Boneta, Noel Amano2023-05-02 09:30:50 View
29 Aug 2023
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Designing Stories from the Grave: Reviving the History of a City through Human Remains and Serious Games

AR and VR Gamification as a proof-of-concept

Recommended by ORCID_LOGO based on reviews by Sophie C. Schmidt and Tine Rassalle

Tsaknaki et al. (2023) discuss a work-in-progress project in which the presentation of Cultural Heritage is communicated using Serious Games techniques in a story-centric immersive narration instead of an exhibit-centered presentation with the use of Gamification, Augmented and Virtual Reality technologies. In the introduction the authors present the project called ECHOES, in which knowledge about the past of Thessaloniki, Greece is planned to be processed as an immersive and interactive experience. After presenting related work and the methodology, the authors describe the proposed design of the Serious Game and close the article with a discussion and conclusions.

The paper is interesting because it highlights an ongoing process in the realm of the visualization of Cultural Heritage (see for example Champion 2016). The process described by the authors on how to accomplish this by using Serious Games, Gamification, Augmented and Virtual Reality is promising, although still hypothetical as the project is ongoing. It remains to be seen if the proposed visuals and interactive elements will work in the way intended and offer users an immersive experience after all. A preliminary questionnaire already showed that most of the respondents were not familiar with these technologies (AR, VR) and in my experience these numbers only change slowly. One way to overcome the technological barrier however might be the gamification of the experience, which the authors are planning to implement.

I decided to recommend this article based on the remarks of the two reviewers, which the authors implemented perfectly, as well as my own evaluation of the paper. Although still in progress it seems worthwhile to have this article as a basis for discussion and comparison to similar projects. However, the article did not mention the possible longevity of data and in which ways the usability of the Serious Game will be secured for long-term storage. One eminent problem in these endeavors is, that we can read about these projects, but never find them anywhere to test them ourselves (see for example Gabellone et al. 2016). It is my intention with this review and the recommendation, that the ECHOES project will find a solution for this problem and that we are not only able to read this (and forthcoming) article(s) about the ECHOES project, but also play the Serious Game they are proposing in the near and distant future.

References


Champion, Erik Malcolm. 2016. „Entertaining the Similarities and Distinctions between Serious Games and Virtual Heritage Projects“. Entertainment Computing 14 (Mai): 67–74. https://doi.org/10.1016/j.entcom.2015.11.003

Gabellone, Francesco, Antonio Lanorte, Nicola Masini, und Rosa Lasaponara. 2016. „From Remote Sensing to a Serious Game: Digital Reconstruction of an Abandoned Medieval Village in Southern Italy“. Journal of Cultural Heritage. https://doi.org/10.1016/j.culher.2016.01.012

Tsaknaki, Electra, Anastasovitis, Eleftherios, Georgiou, Georgia, Alagialoglou, Kleopatra, Mavrokostidou, Maria, Kartsiakli, Vasiliki, Aidonis, Asterios, Protopsalti, Tania, Nikolopoulos, Spiros, and Kompatsiaris, Ioannis. (2023). Designing Stories from the Grave: Reviving the History of a City through Human Remains and Serious Games, Zenodo, 7981323, ver. 4 peer-reviewed and recommended by Peer Community in Archaeology. https://doi.org/10.5281/zenodo.7981323

Designing Stories from the Grave: Reviving the History of a City through Human Remains and Serious GamesTsaknaki, Electra; Anastasovitis, Eleftherios; Georgiou, Georgia; Alagialoglou, Kleopatra; Mavrokostidou, Maria; Kartsiakli, Vasiliki; Aidonis, Asterios; Protopsalti, Tania; Nikolopoulos, Spiros; Kompatsiaris, Ioannis<p>The main challenge of the current digital transition is to utilize computing media and cutting-edge technologyin a more meaningful way, which would make the archaeological and anthropological research outcomes relevant to a heterogeneous audien...Bioarchaeology, Computational archaeology, EuropeSebastian Hageneuer2023-05-29 13:19:46 View
14 Mar 2024
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How FAIR is Bioarchaeological Data: with a particular emphasis on making archaeological science data Reusable

FAIR data in bioarchaeology - where are we at?

Recommended by ORCID_LOGO based on reviews by Emma Karoune, Jan Kolar and 2 anonymous reviewers

The increasing reliance on digital and big data in archaeology is pushing the scientific community more and more to reconsider their storing and use [1, 2]. Furthermore, the openness and findability in the way these data are shared represent a key matter for the growth of the discipline, especially in the case of bioarchaeology and archaeological sciences [3]. 

In this paper, [4] the author presents the result of a survey targeted on UK bioarchaeologists and then extended worldwide. The paper maintains the structure of a report as it was intended for the conference it was part of (CAA 2023, Amsterdam) but it represents the first public outcome of an inquiry on the bioarchaeological scientific community. A reflection on ourselves and our own practices. Are all the disciplines adhering to the same policies? Do any bioarchaeologist use the same protocols and formats? Are there any differences in between the domains? Is the Needs Analysis fulfilling the questions?

The results, obtained through an accurate screening to avoid distortions, are creating an intriguing picture on the current state of "fairness" and highlighting how Institutions' rules and policies can and should indicate the correct workflow to follow. In the end, the wide application of the FAIR principles will contribute significantly to the growth of the disciplines and to create an environment where the users are not just contributors, but primary beneficiaries of the system. 

[1] Huggett j. (2020). Is Big Digital Data Different? Towards a New Archaeological Paradigm, Journal of Field Archaeology, 45:sup1, S8-S17. https://doi.org/10.1080/00934690.2020.1713281

[2] Nicholson C., Kansa S., Gupta N. and Fernandez R. (2023). Will It Ever Be FAIR?: Making Archaeological Data Findable, Accessible, Interoperable, and Reusable. Advances in Archaeological Practice 11 (1): 63-75. https://doi.org/10.1017/aap.2022.40

[3] Plomp E., Stantis C., James H.F., Cheung C., Snoeck C., Kootker L., Kharobi A., Borges C., Reynaga D.K.M., Pospieszny Ł., Fulminante, F., Stevens, R., Alaica, A. K., Becker, A., de Rochefort, X. and Salesse, K. (2022). The IsoArcH initiative: Working towards an open and collaborative isotope data culture in bioarchaeology. Data in brief, 45, p.108595. https://doi.org/10.1016/j.dib.2022.108595

[4] Lien-Talks, A. (2024). How FAIR is Bioarchaeological Data: with a particular emphasis on making archaeological science data Reusable. Zenodo, 8139910, ver. 6 peer-reviewed and recommended by Peer Community in Archaeology. https://doi.org/10.5281/zenodo.8139910

How FAIR is Bioarchaeological Data: with a particular emphasis on making archaeological science data ReusableLien-Talks, Alphaeus<p>Bioarchaeology, which encompasses the study of ancient DNA, osteoarchaeology, paleopathology, palaeoproteomics, stable isotopes, and zooarchaeology, is generating an ever-increasing volume of data as a result of advancements in molecular biolog...Bioarchaeology, Computational archaeology, ZooarchaeologyClaudia Speciale2023-07-12 19:12:44 View
02 Mar 2024
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A note on predator-prey dynamics in radiocarbon datasets

A new approach to Predator-prey dynamics

Recommended by ORCID_LOGO based on reviews by Jesús Rodríguez, Miriam Belmaker and 1 anonymous reviewer

Various biological systems have been subjected to mathematical modelling to enhance our understanding of the intricate interactions among different species. Among these models, the predator-prey model holds a significant position. Its relevance stems not only from its application in biology, where it largely governs the coexistence of diverse species in open ecosystems, but also from its utility in other domains. 

Predator-prey dynamics have long been a focal point in population ecology, yet access to real-world data is confined to relatively brief periods, typically less than a century. Studying predator-prey dynamics over extended periods presents challenges due to the limited availability of population data spanning more than a century. The most extensive dataset is the hare-lynx records from the Hudson Bay Company, documenting a century of fur trade [1]. However, other records are considerably shorter, usually spanning decades [2,3]. This constraint hampers our capacity to investigate predator-prey interactions over centennial or millennial scales. 

Marom and Wolkowski [4] propose here that leveraging regional radiocarbon databases offers a solution to this challenge, enabling the reconstruction of predator-prey population dynamics over extensive timeframes. To substantiate this proposition, they draw upon examples from Pleistocene Beringia and the Holocene Judean Desert. This approach is highly relevant and might provide insight into ecological processes occurring at a time scale beyond the limits of current ecological datasets. 

The methodological approach employed in this article proposes that the summed probability distribution (SPD) of predator radiocarbon dates, which reflects changes in population size, will demonstrate either more or less variation than anticipated from random sampling in a homogeneous distribution spanning the same timeframe. A deviation from randomness would imply a covariation between predator and prey populations. This basic hypothesis makes no assumptions about the frequency, mechanism, or cause of predator-prey interactions, as it is assumed that such aspects cannot be adequately tested with the available data. If validated, this hypothesis would offer initial support for the idea that long-term regional radiocarbon data contain signals of predator-prey interactions. This approach could justify the construction of larger datasets to facilitate a more comprehensive exploration of these signal structures.

 

References

[1] Elton, C. and Nicholson, M., 1942. The Ten-Year Cycle in Numbers of the Lynx in Canada. J. Anim. Ecol. 11, 215–244.

[2] Gilg, O., Sittler, B. and Hanski, I., 2009. Climate change and cyclic predator-prey population dynamics in the high Arctic. Glob. Chang. Biol. 15, 2634–2652. https://doi.org/10.1111/j.1365-2486.2009.01927.x

[3] Vucetich, J.A., Hebblewhite, M., Smith, D.W. and Peterson, R.O., 2011. Predicting prey population dynamics from kill rate, predation rate and predator-prey ratios in three wolf-ungulate systems. J. Anim. Ecol. 80, 1236–1245. https://doi.org/10.1111/j.1365-2656.2011.01855.x

[4] Marom, N. and Wolkowski, U. (2024). A note on predator-prey dynamics in radiocarbon datasets, BioRxiv, 566733, ver. 4 peer-reviewed and recommended by Peer Community in Archaeology. https://doi.org/10.1101/2023.11.12.566733

A note on predator-prey dynamics in radiocarbon datasetsNimrod Marom, Uri Wolkowski<p>Predator-prey interactions have been a central theme in population ecology for the past century, but real-world data sets only exist for recent, relatively short (&lt;100 years) time spans. This limits our ability to study centennial/millennial...Bioarchaeology, Environmental archaeology, Palaeontology, Paleoenvironment, ZooarchaeologyRuth Blasco2023-12-12 14:37:22 View
30 Sep 2022
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Parchment Glutamine Index (PQI): A novel method to estimate glutamine deamidation levels in parchment collagen obtained from low-quality MALDI-TOF data

Assessing glutamine deamination in ancient parchment samples

Recommended by based on reviews by Maria Codlin and 3 anonymous reviewers

Data authenticity and approaches to data authentication are crucial issues in ancient protein research. The advent of modern mass spectrometry has enabled the detection of traces of ancient biomolecules contained in fossils, including protein sequences. However, detecting proteins in ancient samples does not equate to demonstrating their endogenous nature: instead, if the mechanisms that drive protein preservation and degradation are understood, then the extent of protein diagenesis can be used for evaluating preservational quality, which in turn may be related to the authenticity of the protein data. 

The post-mortem deamidation of asparaginyl and glutamyl residues is a key degradation reaction, which can be assessed effectively on the basis of mass spectrometry data, and which has accrued a long history of research, both in terms of describing the mechanisms governing the reactions and with regard to the best strategies for assessing and quantifying the extent of glutamine (Gln) and asparagine (Asn) deamidation in ancient samples (Pal Chowdhury et al., 2019; Ramsøe et al., 2021, 2020; Schroeter and Cleland, 2016; Simpson et al., 2016; Solazzo et al., 2014; Welker et al., 2016; Wilson et al., 2012). 

In their paper, Nair and colleagues (2022) build on this wealth of knowledge and present a tool for quantifying the extent of Gln deamidation in parchment. Parchment is a collagen-based material which can yield extraordinary insights into manuscript manufacturing practices in the past, as well as on the daily lives of the people who assembled and used them (“biocodicology”) (Fiddyment et al., 2021, 2019, 2015; Teasdale et al., 2017). Importantly, the extent of deamidation can be directly related to the quality of the parchment produced: rapid direct deamidation of Gln is induced by the liming process, therefore high extents of deamidation are linked to prolonged exposure to the high pH conditions which are typical of liming, thus implying lower-quality parchment.

Nair et al.’s approach focuses on collagen peptides which are typically detected during MALDI-TOF mass spectrometry analyses of parchment and build a simple three-step workflow able to yield an overall index of deamidation for a sample (the parchment glutamine index - PQI) 一 taking into account that different Gln residues degrade at different rates according to their micro-chemical environment. The first step involves pre-processing the MALDI spectra, since Nair et al. are specifically interested in maximising information which can be obtained by low-quality data. The second step builds on well-established methods for quantifying Q → E from MALDI-TOF data by modelling the convoluted isotope distributions (Wilson et al., 2012). Once relative rates of deamidation in selected peptides within a given sample are calculated, the third step uses a mixed effects model to combine the individual deamidation estimates and to obtain an overall estimate of the deamidation for a parchment sample (PQI). 

The PQI can be used effectively for assessing parchment quality, as the authors show for the dataset from Orval Abbey. However, PQI could also have wider applications to the study of processed collagen, which is widely used in the food and pharmaceutical industries. In general, the study by Nair et al. is a welcome addition to a growing body of research on protein diagenesis, which will ultimately improve models for the assessment of the authenticity of biomolecular data in archaeology. 

References

Chowdhury, P.M., Wogelius, R., Manning, P.L., Metz, L., Slimak, L., and Buckley, M. 2019. Collagen deamidation in archaeological bone as an assessment for relative decay rates. Archaeometry 61:1382–1398. https://doi.org/10.1111/arcm.12492

Fiddyment, S., Goodison, N.J., Brenner, E., Signorello, S., Price, K., and Collins, M.J.. 2021. Girding the loins? Direct evidence of the use of a medieval parchment birthing girdle from biomolecular analysis. bioRxiv. https://doi.org/10.1098/rsos.202055

Fiddyment,S., Holsinger, B., Ruzzier, C., Devine, A., Binois, A., Albarella, U., Fischer, R., Nichols, E., Curtis, A., Cheese, E., Teasdale, M.D., Checkley-Scott, C., Milner, S.J., Rudy, K.M., Johnson, E.J., Vnouček, J., Garrison, M., McGrory, S., Bradley, D.G., and Collins, M.J. 2015. Animal origin of 13th-century uterine vellum revealed using noninvasive peptide fingerprinting. Proc Natl Acad Sci U S A 112:15066–15071. https://doi.org/10.1073/pnas.1512264112

Fiddyment, S., Teasdale, M.D., Vnouček, J., Lévêque, É., Binois, A., and Collins, M.J. 2019. So you want to do biocodicology? A field guide to the biological analysis of parchment. Heritage Science 7:35. https://doi.org/10.1186/s40494-019-0278-6

Nair, B., Rodríguez Palomo, I., Markussen, B., Wiuf, C., Fiddyment, S., and Collins, M. Parchment Glutamine Index (PQI): A novel method to estimate glutamine deamidation levels in parchment collagen obtained from low-quality MALDI-TOF data. BiorRxiv, 2022.03.13.483627, ver. 6 peer-reviewed and recommended by Peer community in Archaeology. https://doi.org/10.1101/2022.03.13.483627 

Ramsøe, A., Crispin, M., Mackie, M., McGrath, K., Fischer, R., Demarchi, B., Collins, M.J., Hendy, J., and Speller, C. 2021. Assessing the degradation of ancient milk proteins through site-specific deamidation patterns. Sci Rep 11:7795. https://doi.org/10.1038/s41598-021-87125-x

Ramsøe, A., van Heekeren, V., Ponce, P., Fischer, R., Barnes, I., Speller, C., and Collins, M.J. 2020. DeamiDATE 1.0: Site-specific deamidation as a tool to assess authenticity of members of ancient proteomes. J Archaeol Sci 115:105080. https://doi.org/10.1016/j.jas.2020.105080

Schroeter, E.R., and Cleland, T.P. 2016. Glutamine deamidation: an indicator of antiquity, or preservational quality? Rapid Commun Mass Spectrom 30:251–255. https://doi.org/10.1002/rcm.7445

Simpson, J.P., Penkman, K.E.H., and Demarchi, B. 2016. The effects of demineralisation and sampling point variability on the measurement of glutamine deamidation in type I collagen extracted from bone. J Archaeol Sci 69: 29-38. https://doi.org/10.1016/j.jas.2016.02.002

Solazzo, C., Wilson, J., Dyer, J.M., Clerens, S., Plowman, J.E., von Holstein, I., Walton Rogers, P., Peacock, E.E., and Collins, M.J. 2014. Modeling deamidation in sheep α-keratin peptides and application to archeological wool textiles. Anal Chem 86:567–575. https://doi.org/10.1021/ac4026362

Teasdale, M.D., Fiddyment, S., Vnouček, J., Mattiangeli, V., Speller, C., Binois, A., Carver, M., Dand, C., Newfield, T.P., Webb, C.C., Bradley, D.G., and Collins M.J. 2017. The York Gospels: a 1000-year biological palimpsest. R Soc Open Sci 4:170988. https://doi.org/10.1098/rsos.170988

Welker, F., Soressi, M.A., Roussel, M., van Riemsdijk, I., Hublin, J.-J., and Collins, M.J. 2016. Variations in glutamine deamidation for a Châtelperronian bone assemblage as measured by peptide mass fingerprinting of collagen. STAR: Science & Technology of Archaeological Research 3:15–27. https://doi.org/10.1080/20548923.2016.1258825

Wilson, J., van Doorn, N.L., and Collins, M.J. 2012. Assessing the extent of bone degradation using glutamine deamidation in collagen. Anal Chem 84:9041–9048. https://doi.org/10.1021/ac301333t

Parchment Glutamine Index (PQI): A novel method to estimate glutamine deamidation levels in parchment collagen obtained from low-quality MALDI-TOF dataBharath Nair, Ismael Rodríguez Palomo, Bo Markussen, Carsten Wiuf, Sarah Fiddyment and Matthew Collins<p style="text-align: justify;">Parchment was used as a writing material in the Middle Ages and was made using animal skins by liming them with Ca(OH)<span class="math-tex">\( _2 \)</span>. During liming, collagen peptides containing Glutamine (Q)...Bioarchaeology, Europe, Medieval, ZooarchaeologyBeatrice Demarchi2022-03-22 12:54:10 View
31 Jul 2024
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Palaeoproteomic identification of a whale bone tool from Bronze Age Heiloo, the Netherlands

Prehistoric whaling and tool industry evidenced by advanced proteomic methods

Recommended by based on reviews by 2 anonymous reviewers

Proteomics is an increasingly applied field of study in archaeology. The characterisation of proteins in ancient biomaterials has been used extensively to determine the sex of certain animals (from dental enamel) or to identify species from non-diagnostic bone pieces or fragments of organic materials (glues and residues, for example). Paleoproteomics has been accompanied by methodological developments, in particular to reduce the size of samples affected by destructive analyses and to refine the level of species determination. The article by Joannes Dekker and colleagues (2024) - "Palaeoproteomic identification of a whale bone tool from Bronze Age Heiloo, the Netherlands" - provides a relevant and innovative example, incorporating ZooMS and SPIN techniques as well as the creation of a database of new reference collagens (cetaceans) specific to the site's natural environment (North Sea coast). The interest of this study also lies in the contribution of a use-wear analysis carried out prior to the sampling. This comparison of multidisciplinary data is essential for understanding the links between man and his natural environment and the technical and economic production that is closely linked to it. The tool studied (ca. 1500 BCE) comes from a coastal Bronze Age site in the Netherlands, where the economy was highly diversified, involving the exploitation of wild and domestic animals in both terrestrial and marine environments. The study shows that the bone of a North Atlantic right whale (Eubalaena glacialis) was shaped into a tool that was probably used to process plant fibres. This discovery supports other studies highlighting the intensive and non-opportunistic exploitation of whales in the North Sea since the Pleistocene.

Dekker, J. A. A., Mylopotamitaki, D., Verbaas, A., Sinet-Mathiot, V., Presslee, S., McCarthy, M. L., Olsen, M. T., Olsen, J. V., van den Hurk, Y., Brattinga, J. & Welker, F. (2024) Palaeoproteomic identification of a whale bone tool from Bronze Age Heiloo, the Netherlands. BioRxiv, ver. 2 peer-reviewed and recommended by Peer Community in Archaeology.  https://doi.org/10.1101/2024.04.15.589626

Palaeoproteomic identification of a whale bone tool from Bronze Age Heiloo, the NetherlandsJoannes A. A. Dekker, Dorothea Mylopotamitaki, Annemieke Verbaas, Virginie Sinet-Mathiot, Samantha Presslee, Morgan L. McCarthy, Morten T. Olsen, Jesper V. Olsen, Youri van den Hurk, Joris Brattinga, Frido Welker<p>Identification of the taxonomic origin of bone tools is an important, but often complicated, component of studying past societies. The species used for bone tool production provide insight into what species were exploited, potentially how, and ...Bioarchaeology, Europe, Osseous industry, Raw materialsGwenaëlle GoudeAnonymous, Anonymous2024-04-20 23:30:47 View
23 May 2024
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The contribution of Mediterranean connectivity to morphological variability in Iron Age sheep of the Eastern Mediterranean

Exploring eastern Mediterranean Iron Age coastal connections through sheep astragali using geometric morphometrics

Recommended by ORCID_LOGO based on reviews by 4 anonymous reviewers

It currently seems obvious that the Mediterranean basin is a place of great exchanges of cultures, populations and goods. Although studies have focused quite extensively on the archaeology of maritime exchanges [1–3], it is challenging to assess archaeologically to what extent these networks had an influence on the biology of domesticated animals in the past, or even if animals were part of the trip. The question of past populations establishing extensive connections in the Mediterranean basin during the Iron Age and Persian period and especially, if these population exchange livestock and how these connections contributed to the animals phenotype or morphotype diversity is still difficult to document in the (zoo)archaeological record. These are amongst the questions Harding et al. [4] are making an attempt at documenting. Focusing on archaeological deposits from Cyprus and Israel in the eastern part of the Mediterranean basin, they use sheep astragali as a proxy to explore the potential connections that might have existed between evolution of the animals’ morphology and exchanges through sea travel. Postulating that animals from inland sites should have variant morphology from those of coastal sites due to more intensive exchanges for the latter, mainly because of the incorporation of non-native animals, they conducted geometric morphometrics analyses to make an attempt at documenting the phenomenon. Observing changes in size and shape, but also an increased morphological variability within the assemblages from coastal sites, they nicely discuss and put their results in perspectives with the archaeological record and literature [5,6]. Although, as they acknowledge, their sample size is rather limited to draw any general conclusion, this paper sheds new lights on the influence of maritime transport and its influence over domesticated sheep diversity between Cyprus and the southern Levant, paving the way for future studies.

References
1.     Leidwanger, J. and Knappett, C. (2018). Maritime Networks in the Ancient Mediterranean World. (Cambridge University Press). https://doi.org/10.1017/9781108555685
2.     Leidwanger, J. (2020). Roman Seas: A Maritime Archaeology of Eastern Mediterranean Economies. (Oxford University Press). https://doi.org/10.1093/oso/9780190083656.001.0001
3.     Bernard Knapp, A., Russell, A. and van Dommelen, P. (2022). Cyprus, Sardinia and Sicily: A Maritime Perspective on Interaction, Connectivity and Imagination in Mediterranean Prehistory. Cambridge Archaeological Journal 32, 79–97. https://doi.org/10.1017/S0959774321000330
4.     Harding, S. A., Hadjikoumis, A., Vermeersch, S., Shafir, R. and Marom, N. (2024) The contribution of Mediterranean connectivity to morphological variability in Iron Age sheep of the Eastern Mediterranean. bioRxiv2022.12.24.521859 https://doi.org/10.1101/2022.12.24.521859.
5.     Price, M. D., Perry-Gal, L. and Reshef, H. (2023). The Southern Levantine pig from domestication to Romanization: A biometrical approach. J. Archaeol. Sci. 157, 105828. https://doi.org/10.1016/j.jas.2023.105828
6.     Vigne, J., Zazzo, A., Cucchi, T., Briois, F. and Guilaine, J. (2014). The transportation of mammals to Cyprus shed light on early voyaging and boats in the mediterranean sea. Eurasian Prehistory 10, 157–176.

The contribution of Mediterranean connectivity to morphological variability in Iron Age sheep of the Eastern MediterraneanSierra A. Harding, Angelos Hadjikoumis, Shyama Vermeersch, Nimrod Marom<p>The movement of livestock across the Mediterranean is well-documented in the Neolithic era, but its significance during subsequent periods has received less attention. This study explores potential evidence for maritime connections between shee...Bioarchaeology, Mediterranean, ZooarchaeologyLouise Le MeillourAnonymous2023-12-07 10:10:34 View
03 Nov 2023
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Multiproxy analysis exploring patterns of diet and disease in dental calculus and skeletal remains from a 19th century Dutch population

Detection of plant-derived compounds in XIXth c. Dutch dental calculus

Recommended by ORCID_LOGO based on reviews by Mario Zimmerman and 2 anonymous reviewers

The advent of biomolecular methods has certainly increased our overall comprehension of archaeological societies. One of the materials of choice to perform ancient DNA or proteomics analyses is dental calculus[1,2], a mineralised biofilm formed during the life of one individual. Research conducted in the past few decades has demonstrated the potential of dental calculus to retrieve information about past societies health[3–6], diet[7–11], and more recently, as a putative proxy for isotopic analyses[12]. 


Based on a proof-of-concept previously published by their team[13], Bartholdy and collaborators’ paper presents the identification of compounds and their secondary metabolites derived from consumed plants in individuals from a XIXth century rural Dutch archaeological deposit[14]. Sørensen indeed demonstrated that drug intake is recorded in dental calculus, which are mineralised biofilms that can encapsulate drug compounds long after the latter are no longer detectable in blood. The liquid-chromatography coupled to mass spectrometry (LC-MS/MS)-based method developed showed the potential for archaeological applications[13]. 

Bartholdy et al. utilised the developed LC-MS/MS method to 41 buried individuals, most of them bearing pipe notches on their teeth, from the cemetery of the 19th rural settlement of Middenbeemster, the Netherlands. Along with dental calculus sampling and analysis, they undertook the skeletal and dental examination of all of the specimens in order to assess sex, age-at-death, and pathology on the two tissues. The results obtained on the dental calculus of the sampled individuals show probable consumption of tea, coffee and tobacco indicated by the detection of the various plant compounds and associated metabolites (caffeine, nicotine and salicylic acid, amongst others). 

The authors were able to place their results in perspective and propose several interpretations concerning the ingestion of plant-derived products, their survival in dental calculus and the importance of their findings for our overall comprehension of health and habits of the XIXth c. Dutch population. The paper is well-written and accessible to a non-specialist audience, maximising the impact of their study. I personally really enjoyed handling this manuscript that is not only a good piece of scientific literature but also a pleasant read, the reason why I warmly recommend this paper to be accessible through PCI Archaeology.

References

1.      Fagernäs, Z. and Warinner, C. (2023) Dental Calculus. in Handbook of Archaeological Sciences 575–590. https://doi.org/10.1002/9781119592112.ch28

2.      Wright, S. L., Dobney, K. & Weyrich, L. S. (2021) Advancing and refining archaeological dental calculus research using multiomic frameworks. STAR: Science & Technology of Archaeological Research 7, 13–30. https://doi.org/10.1080/20548923.2021.1882122

3.      Fotakis, A. K. et al. (2020) Multi-omic detection of Mycobacterium leprae in archaeological human dental calculus. Philos. Trans. R. Soc. Lond. B Biol. Sci. 375, 20190584. https://doi.org/10.1098/rstb.2019.0584

4.      Warinner, C. et al. (2014) Pathogens and host immunity in the ancient human oral cavity. Nat. Genet. 46, 336–344. https://doi.org/10.1038/ng.2906

5.      Weyrich, L. S. et al. (2017) Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus. Nature 544, 357–361. https://doi.org/10.1038/nature21674

6.      Jersie-Christensen, R. R. et al. (2018) Quantitative metaproteomics of medieval dental calculus reveals individual oral health status. Nat. Commun. 9, 4744. https://doi.org/10.1038/s41467-018-07148-3

7.      Hendy, J. et al. (2018) Proteomic evidence of dietary sources in ancient dental calculus. Proc. Biol. Sci. 285. https://doi.org/10.1098/rspb.2018.0977

8.      Wilkin, S. et al. (2020) Dairy pastoralism sustained eastern Eurasian steppe populations for 5,000 years. Nat Ecol Evol 4, 346–355. https://doi.org/10.1038/s41559-020-1120-y

9.      Bleasdale, M. et al. (2021) Ancient proteins provide evidence of dairy consumption in eastern Africa. Nat. Commun. 12, 632. https://doi.org/10.1038/s41467-020-20682-3

10.   Warinner, C. et al. (2014) Direct evidence of milk consumption from ancient human dental calculus. Sci. Rep. 4, 7104. https://doi.org/10.1038/srep07104

11.   Buckley, S., Usai, D., Jakob, T., Radini, A. and Hardy, K. (2014) Dental Calculus Reveals Unique Insights into Food Items, Cooking and Plant Processing in Prehistoric Central Sudan. PLoS One 9, e100808. https://doi.org/10.1371/journal.pone.0100808

12.   Salazar-García, D. C., Warinner, C., Eerkens, J. W. and Henry, A. G. (2023) The Potential of Dental Calculus as a Novel Source of Biological Isotopic Data. in Exploring Human Behavior Through Isotope Analysis: Applications in Archaeological Research (eds. Beasley, M. M. & Somerville, A. D.) 125–152. https://doi.org/10.1007/978-3-031-32268-6_6

13.   Sørensen, L. K., Hasselstrøm, J. B., Larsen, L. S. and Bindslev, D. A. (2021) Entrapment of drugs in dental calculus - Detection validation based on test results from post-mortem investigations. Forensic Sci. Int. 319, 110647. https://doi.org/10.1016/j.forsciint.2020.110647

14.   Bartholdy, Bjørn Peare, Hasselstrøm, Jørgen B., Sørensen, Lambert K., Casna, Maia, Hoogland, Menno, Historisch Genootschap Beemster and Henry, Amanda G. (2023) Multiproxy analysis exploring patterns of diet and disease in dental calculus and skeletal remains from a 19th century Dutch population, Zenodo, 7649150, ver. 5 peer-reviewed and recommended by Peer Community in Archaeology. https://doi.org/10.5281/zenodo.7649150

Multiproxy analysis exploring patterns of diet and disease in dental calculus and skeletal remains from a 19th century Dutch populationBartholdy, Bjørn Peare; Hasselstrøm, Jørgen B.; Sørensen, Lambert K.; Casna, Maia; Hoogland, Menno; Historisch Genootschap Beemster; Henry, Amanda G.<p>Dental calculus is an excellent source of information on the dietary patterns of past populations, including consumption of plant-based items. The detection of plant-derived residues such as alkaloids and their metabolites in dental calculus pr...Bioarchaeology, Post-medievalLouise Le Meillour Mario Zimmerman, Anonymous2023-07-31 17:21:40 View
13 Jan 2024
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Dealing with post-excavation data: the Omeka S TiMMA web-database

Managing Archaeological Data with Omeka S

Recommended by ORCID_LOGO based on reviews by Electra Tsaknaki and 1 anonymous reviewer

Managing data in archaeology is a perennial problem. As the adage goes, every day in the field equates to several days in the lab (and beyond). For better or worse, past archaeologists did all their organizing and synthesis manually, by hand, but since the 1970s ways of digitizing data for long term management and analysis have gained increasing attention [1]. It is debatable whether this ever actually made things easier, particularly given the associated problem of sustainable maintenance and accessibility of the data. Many older archaeologists, for instance, still have reels and tapes full of data that now require a new form of archaeology to excavate (see [2] for an unrealized idea on how to solve this).

Today, the options for managing digital archaeological data are limited only by one’s imagination. There are systems built specifically for archaeology, such as Arches [3], Ark [4], Codifi [5], Heurist [6], InTerris Registries [7], OpenAtlas [8], S-Archeo [9], and Wild Note [10], as well as those geared towards museum collections like PastPerfect [11] and CatalogIt [12], among others. There are also mainstream databases that can be adapted to archaeological needs like MS Access [13] and Claris FileMaker [14], as well as various web database apps that function in much the same way (e.g., Caspio [15], dbBee [16], Amazon's Simpledb [17], Sci-Note [18], etc.) — all with their own limitations in size, price, and utility. One could also write the code for specific database needs using pre-built frameworks like those in Ruby-On-Rails [19] or similar languages. And of course, recent advances in machine-learning and AI will undoubtedly bring new solutions in the near future.

But let’s be honest — most archaeologists probably just use Excel. That's partly because, given all the options, it is hard to decide the best tool and whether its worth changing from your current system, especially given few real-world examples in the literature. Bastien Rueff’s new paper [20] is therefore a welcomed presentation on the use of Omeka S [21] to manage data collected for the Timbers in Minoan and Mycenaean Architecture (TiMMA) project. Omeka S is an open-source web-database that is based in PHP and MySQL, and although it was built with the goal of connecting digital cultural heritage collections with other resources online, it has been rarely used in archaeology. Part of the issue is that Omeka Classic was built for use on individual sites, but this has now been scaled-up in Omeka S to accommodate a plurality of sites. 

Some of the strengths of Omeka S include its open-source availability (accessible regardless of budget), the way it links data stored elsewhere on the web (keeping the database itself lean), its ability to import data from common file types, and its multi-lingual support. The latter feature was particularly important to the TiMAA project because it allowed members of the team (ranging from English, Greek, French, and Italian, among others) to enter data into the system in whatever language they felt most comfortable.

However, there are several limitations specific to Omeka S that will limit widespread adoption. Among these, Omeka S apparently lacks the ability to export metadata, auto-fill forms, produce summations or reports, or provide basic statistical analysis. Its internal search capabilities also appear extremely limited. And that is not to mention the barriers typical of any new software, such as onerous technical training, questionable long-term sustainability, or the need for the initial digitization and formatting of data. But given the rather restricted use-case for Omeka S, it appears that this is not a comprehensive tool but one merely for data entry and storage that requires complementary software to carry out common tasks.

As such, Rueff has provided a review of a program that most archaeologists will likely not want or need. But if one was considering adopting Omeka S for a project, then this paper offers critical information for how to go about that. It is a thorough overview of the software package and offers an excellent example of its use in archaeological practice.


NOTES

[1] Doran, J. E., and F. R. Hodson (1975) Mathematics and Computers in Archaeology. Harvard University Press.

[2] Snow, Dean R., Mark Gahegan, C. Lee Giles, Kenneth G. Hirth, George R. Milner, Prasenjit Mitra, and James Z. Wang (2006) Cybertools and Archaeology. Science 311(5763):958–959.

[3] https://www.archesproject.org/

[4] https://ark.lparchaeology.com/

[5] https://codifi.com/

[6] https://heuristnetwork.org/

[7] https://www.interrisreg.org/

[8] https://openatlas.eu/

[9] https://www.skinsoft-lab.com/software/archaelogy-collection-management

[10] https://wildnoteapp.com/

[11] https://museumsoftware.com/

[12] https://www.catalogit.app/

[13] https://www.microsoft.com/en-us/microsoft-365/access

[14] https://www.claris.com/filemaker/

[15] https://www.caspio.com/

[16] https://www.dbbee.com/

[17] https://aws.amazon.com/simpledb/

[18] https://www.scinote.net/

[19] https://rubyonrails.org/

[20] Rueff, Bastien (2023) Dealing with Post-Excavation Data: The Omeka S TiMMA Web-Database. peer-reviewed and recommended by Peer Community in Archaeology. https://zenodo.org/records/7989905

[21] https://omeka.org/

 

Dealing with post-excavation data: the Omeka S TiMMA web-databaseBastien Rueff<p>This paper reports on the creation and use of a web database designed as part of the TiMMA project with the Content Management System Omeka S. Rather than resulting in a technical manual, its goal is to analyze the relevance of using Omeka S in...Buildings archaeology, Computational archaeologyJonathan Hanna2023-05-31 12:16:25 View
02 Feb 2024
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Implementing Digital Documentation Techniques for Archaeological Artifacts to Develop a Virtual Exhibition: the Necropolis of Baley Collection

Out of the storeroom and into the virtual

Recommended by ORCID_LOGO based on reviews by Alicia Walsh and 1 anonymous reviewer

This paper (Raykovska et al. 2023) discusses the digital documentation techniques and development of a virtual exhibition for artefacts retrieved from the necropolis of Baley, Bulgaria. The principal aim of this particular project is a solid one, trying to provide a solution to display artefacts that would otherwise remain hidden in museum storerooms. The paper describes how through a combination of 3D scanning and photogrammetry high quality 3D models have been produced, and provide content for an online virtual exhibition for the scientific community but also the larger public. It is a well-written and concise paper, in which the information on developed methods and techniques are transparently described, and various important aspects of digitization workflows, such as the importance of storing raw data, are addressed.

The paper is a timely discussion on this subject, as strategies to develop digital artefact collections and what to do with those are increasingly being researched. Specifically, it discusses a workflow and its results, both in great detail. Although critical reflection on the process, goals and results from various perspectives would have been a valuable addition to the paper (cf., Jeffra 2020, Paardekoper 2019), it nonetheless provides a good practice example of how to approach the creation of a virtual museum. Those who consider projects concerning digital documentation of archaeological artefacts as well as the creation of virtual spaces to use those in for research, education or valorisation purposes would do well to read this paper carefully.

References

Jeffra, C., Hilditch, J., Waagen, J., Lanjouw, T., Stoffer, M., de Gelder, L., and Kim, M. J. (2020). Blending the Material and the Digital: A Project at the Intersection of Museum Interpretation, Academic Research, and Experimental Archaeology. The EXARC Journal, 2020(4). https://exarc.net/ark:/88735/10541 

Paardekooper, R.P. (2019). Everybody else is doing it, so why can’t we? Low-tech and High-tech approaches in archaeological Open-Air Museums. The EXARC Journal, 2019(4). https://exarc.net/ark:/88735/10457/ 

Raykovska, M., Jones, K., Klecherova, H., Alexandrov, S., Petkov, N., Hristova, T., and Ivanov, G. (2023). Implementing Digital Documentation Techniques for Archaeological Artifacts to Develop a Virtual Exhibition: the Necropolis of Baley Collection. https://doi.org/10.5281/zenodo.10091870

Implementing Digital Documentation Techniques for Archaeological Artifacts to Develop a Virtual Exhibition: the Necropolis of Baley CollectionRaykovska Miglena, Jones Kristen, Klecherova Hristina, Alexandrov Stefan, Petkov Nikolay, Hristova Tanya, Ivanov Georgi<p>Over the past decade, virtual reality has been quickly growing in popularity across disciplines including the field of archaeology and cultural heritage. Despite numerous artifacts being uncovered each year by archaeological excavations around ...Ceramics, Computational archaeology, Conservation/Museum studiesJitte Waagen2023-06-12 14:02:44 View