Understanding the microbial biogeography of ancient human dentitions to guide study design and interpretation

The oral cavity is a heterogeneous environment, varying in factors such as pH, oxygen levels, and salivary flow. These factors affect the microbial community composition and distribution of species in dental plaque, but it is not known how well these patterns are reflected in archaeological dental calculus. Inmost archaeological studies, a single sample of dental calculus is studied per individual and is assumed to represent the entire oral cavity. However, it is not known if this sampling strategy introduces biases into studies of the ancient oral microbiome. Here, we present the results of a shotgun metagenomic study of a dense sampling of dental calculus from four Chalcolithic individuals from the southeast Iberian peninsula (ca. 4500-5000 BP). Interindividual differences in microbial composition are found to be much larger than intraindividual differences, indicating that a single sample can indeed represent an individual in most cases. However, there are minor spatial patterns in species distribution within the oral cavity that should be taken into account when designing a study or interpreting results. Finally, we show that plant DNA identified in the samples is likely of postmortem origin, demonstrating the importance of including environmental controls or additional lines of biomolecular evidence in dietary interpretations

Genomic transformation and social organization during the Copper Age–Bronze Age transition in southern Iberia

The emerging Bronze Age (BA) of southeastern Iberia saw marked social changes. Late Copper Age (CA) settlements were abandoned in favor of hilltop sites, and collective graves were largely replaced by single or double burials with often distinctive grave goods indirectly reflecting a hierarchical social organization, as exemplified by the BA El Argar group. We explored this transition from a genomic viewpoint by tripling the amount of data available for this period. Concomitant with the rise of El Argar starting ~2200 cal BCE, we observe a complete turnover of Y-chromosome lineages along with the arrival of steppe-related ancestry. This pattern is consistent with a founder effect in male lineages, supported by our finding that males shared more relatives at sites than females. However, simple two-source models do not find support in some El Argar groups, suggesting additional genetic contributions from the Mediterranean that could predate the BA.Introduction Results - Genetic substructure in the Iberian CA - Genetic turnover in the southern Iberian BA and the rise of El Argar - Mediterranean and central European ancestries shaped the genetic profile of southeastern BA groups in Iberia - A late Argar genetic outlier makes links to North Africa and the central Mediterranean - Insights into phenotypic variation, demography, and social correlates of CA and EBA El Argar societies Discussion Material and method

Assesing use and suitability of scanning electron microscopy in the analysis of micro remains in dental calculus

Dental calculus is increasingly recognized as a major reservoir of dietary information. Palaeodietary studies using plant and animal micro remains (e.g. phytoliths, pollen, sponge spicules, and starch grains) trapped in calculus have the potential to revise our knowledge of the dietary role of plants in past populations. The conventional methods used to isolate and identify these micro remains rely on removing them from their microenvironment in the calculus, thus the microenvironment that traps and preserves micro remains is not understood. By using scanning electron microscopy and energy dispersive X-ray spectroscopy (SEMeEDX) on modern chimpanzee calculus from the Taï Forest, Côte d¿Ivoire, and human calculus from the Chalcolithic site of Camino del Molino, Spain, we present the first reported observations on characteristics of the matrix setting that are conducive to the survival of starch in dental calculus. We also assess the potential for SEMeEDX to detect starch and differentiate it from structurally and molecularly similar substrates. We demonstrate that SEMeEDX may offer a nondestructive technique for studying micro remains in certain contexts. Finally, we compare traditional optical analytical techniques (OM) with less invasive electron microscopy. The results indicate that SEM-EDX and OM are both effective for observing micro remains in calculus, but differ in their analytical resolution to identify different micro remains, and we therefore recommend a sequential use of both techniques

Genomic transformation and social organization during the Copper Age-Bronze Age transition in southern Iberia

The emerging Bronze Age (BA) of southeastern Iberia saw marked social changes. Late Copper Age (CA) settlements were abandoned in favor of hilltop sites, and collective graves were largely replaced by single or double burials with often distinctive grave goods indirectly reflecting a hierarchical social organization, as exemplified by the BA El Argar group. We explored this transition from a genomic viewpoint by tripling the amount of data available for this period. Concomitant with the rise of El Argar starting ~2200 cal BCE, we observe a complete turnover of Y-chromosome lineages along with the arrival of steppe-related ancestry. This pattern is consistent with a founder effect in male lineages, supported by our finding that males shared more relatives at sites than females. However, simple two-source models do not find support in some El Argar groups, suggesting additional genetic contributions from the Mediterranean that could predate the BA

The Beaker phenomenon and the genomic transformation of northwest Europe

From around 2750 to 2500 bc, Bell Beaker pottery became widespread across western and central Europe, before it disappeared between 2200 and 1800 bc. The forces that propelled its expansion are a matter of long-standing debate, and there is support for both cultural diffusion and migration having a role in this process. Here we present genome-wide data from 400 Neolithic, Copper Age and Bronze Age Europeans, including 226 individuals associated with Beaker-complex artefacts. We detected limited genetic affinity between Beaker-complex-associated individuals from Iberia and central Europe, and thus exclude migration as an important mechanism of spread between these two regions. However, migration had a key role in the further dissemination of the Beaker complex. We document this phenomenon most clearly in Britain, where the spread of the Beaker complex introduced high levels of steppe-related ancestry and was associated with the replacement of approximately 90% of Britain’s gene pool within a few hundred years, continuing the east-to-west expansion that had brought steppe-related ancestry into central and northern Europe over the previous centuries

From Tthe “Quincallería” to the late antiquity burial at 6 Selgas Street, Lorca (Murcia)

©. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/ This document is the Published, version of a Published Work that appeared in final form in [Alberca]La excavación del solar de la calle Selgas núm. 6 ha permitido aportar más indicios al devenir histórico del lugar de la ciudad de Lorca. Por un lado, ha corroborado la información que se tenía en los archivos de este lugar, además de dejar a la vista que los vertederos de los alfares almohades del barrio de alfareros llegaban hasta la misma ladera de la medina, al exterior de la muralla. Además, se ha constatado la presencia de enterramientos posiblemente de un momento tardoantiguo que con un estudio antropológico completo podrían acercarnos más a la vida cotidiana de los antiguos pobladores de Eliocroca.The excavation of the lot at 6 Selgas St. has allowed providing more indications of the historical evolution of Lorca city. On the one hand, it has corroborated the information that was located in the Archives of this specific place, in addition to showing that the dumps of the Almohad potteries of the Potters Quarter reached the very slope of the Medina, outside the city wall. Furthermore, the presence of burials, possibly from the Late Roman period, has been confirmed, that with a complete anthropological study could bring us closer to the daily life of some of the ancient inhabitants of Eliocroca

Fire in the Early Palaeolithic: Evidence from burnt small mammal bones at Cueva Negra del Estrecho del Río Quípar, Murcia, Spain

The development of pyrotechnology is a hallmark of human history, providing our ancestors with warmth, security and cooked food. Evidence for fire use before 400 thousand years ago (kya) remains contentious due largely to the taphonomically fragile nature of charcoal and ash. As such, it is imperative to the study of prehistoric fire that we develop techniques and methodologies for identifying anthropogenic fire use via more robust materials. A new methodology described by Fernández-Jalvo and Avery (2015) based on small mammal taphonomy to identify high intensity fire events from the distant past is replicated herein. When we applied this method to assemblages from Cueva Negra del Estrecho del Río Quípar, an upland rock-shelter in southeastern Spain, dated to between 780 kya and 980 kya, we recognized a spatial relationship between highly heat modified micromammal specimens and a previously reported delineated feature of thermally altered and carbonate rich sediment which also includes heat-fractured chert and calcined bone (the fire feature). The proportion of heavily heat-modified specimens (charred and/or calcined specimens) identified within the stratigraphic context associated with the fire feature proved statistically significant (x2 = 169.18, p < 0.001) when compared with the proportion of similarly modified specimens from overlying deposits (within other stratigraphic layers). The degree of discolouration seen on the micromammal remains within the fire feature has been linked to temperatures exceeding 600 °C (Shipman et al., 1984), and as such supports claims that the fire feature may have an anthropogenic origin. Environmental scanning electron microscopy and energy dispersive spectroscopy (SEM-EDS) of bone specimens confirms that this discolouration is due to burning rather than post-depositional mineral staining. This confirms that methodology, which represents a novel line of evidence for identifying pyrotechnical events at early Palaeolithic sites, can be used to identify potentially anthropogenic fire events from the distant past when alternative scenarios are excluded. Furthermore, studies of this type showcase the value of including detailed taphonomic studies of microfauna assemblages within multidisciplinary research projects.This research was funded by the Social Sciences and Humanities Research Council of Canada (SSHRC), the University of Toronto Department of Anthropology and the University of Toronto Faculty of Arts and Science Germany/Europe Research Travel Fund. Special thanks to the Murcian Association for the Study of Palaeoanthropology and the Quaternary, MUPANTQUAT, for granting access to the materials and laboratory space and to Ángel Tomás Buitrago-López and Azucena Avilés-Fernández for the general assistance.Peer Reviewe

Planificación y metodología de campo para una investigación interdisciplinar en la maqbara islámica del conjunto arqueológico de San Esteban (Murcia)

©. This manuscript version is made available under the CC-BY 4.0 license http://creativecommons.org/licenses/by/4.0/ This document is the Published Manuscript version of a Published Work that appeared in final form in ArkeoGazte.El yacimiento de San Esteban constituye el mejor conjunto arqueológico documentado hasta la fecha del arrabal medieval de la Arrixaca, que fue una parte muy importante de la ciudad andalusí de Mursiya, cuya evolución es bien conocida tanto por las intervenciones arqueológicas como por la documentación escrita árabe y bajomedieval castellana. La investigación se realizó en el seno de equipo interdisciplinar de arqueólogos, antropólogos físicos y bioarqueólogos. Los protocolos establecidos fueron claros y estrictos en el proceso de recuperación y análisis de restos. La instalación de una máquina de fotación de circuito cerrado favoreció el incremento en número de la recuperación de los restos de reducidas dimensiones, incluyendo el registro arqueobotánico y arqueozoológico. Los resultados de los muestreos en los sedimentos de los distntos enterramientos (paleoparasitología) y en los propios restos humanos (ADN mitocondrial, análisis de isótopos, C14) son imprescindibles para la aproximación a la población allí enterrada entre los siglos XI y XIII

Understanding the microbial biogeography of ancient human dentitions to guide study design and interpretation

The oral cavity is a heterogeneous environment, varying in factors such as pH, oxygen levels, and salivary flow. These factors affect the microbial community composition and distribution of species in dental plaque, but it is not known how well these patterns are reflected in archaeological dental calculus. In most archaeological studies, a single sample of dental calculus is studied per individual and is assumed to represent the entire oral cavity. However, it is not known if this sampling strategy introduces biases into studies of the ancient oral microbiome. Here, we present the results of a shotgun metagenomic study of a dense sampling of dental calculus from four Chalcolithic individuals from the southeast Iberian peninsula (ca. 4500–5000 BP). Interindividual differences in microbial composition are found to be much larger than intraindividual differences, indicating that a single sample can indeed represent an individual in most cases. However, there are minor spatial patterns in species distribution within the oral cavity that should be taken into account when designing a study or interpreting results. Finally, we show that plant DNA identified in the samples is likely of postmortem origin, demonstrating the importance of including environmental controls or additional lines of biomolecular evidence in dietary interpretations.Horizon 2020(H2020)StG- 677576Bioarchaeolog