Increasing sustainability in palaeoproteomics by optimizing digestion times for large-scale archaeological bone analyses

Palaeoproteomic analysis of skeletal proteomes is used to provide taxonomic identifications for an increasing number of archaeological specimens. The success rate depends on a range of taphonomic factors and differences in the extraction protocols employed. By analyzing 12 archaeological bone specimens from two archaeological sites, we demonstrate that reducing digestion duration from 18 to 3 hours has no measurable impact on the obtained taxonomic identifications. Peptide marker recovery, COL1 sequence coverage, or proteome complexity are also not significantly impacted. Although we observe minor differences in sequence coverage and glutamine deamidation, these are not consistent across our dataset. A 6-fold reduction in digestion time reduces electricity consumption, and therefore CO2 emission intensities. We furthermore demonstrate that working in 96-well plates further reduces electricity consumption by 60%, in comparison to individual microtubes. Reducing digestion time therefore has no impact on the taxonomic identifications, while reducing the environmental impact of palaeoproteomic projects

Contribution de la Paléoprotéomique à l’étude de la diffusion des pratiques d’élevage de caprinés en Afrique de l’Est et Australe

In the absence of wild representatives on the continent, domestic sheep (Ovis aries) and goats (Capra hircus), subfamily Caprinae, were imported from the Levant into Africa around the VIIth millennium before common era (BCE). The archaeological record indicates a very slow diffusion on the continent with an attested presence during the IIIrd millennium BCE in Eastern Africa (Djibouti, Somaliland), Kenya and Tanzania, while the oldest caprines remains are dated only from the Ist century CE in Southern Africa. The introduction of domestic animals into populations subsistence economies is gradually emerging and, after several centuries, become the primary food supply. In archaeological context, the morphological similarities between the two species of caprines and with other small African wild bovids blur zooarchaeological identifications and the fragmentary state of the remains often makes it impossible to propose an identification below the sub-family. The history of the spread of sheep and goats across Africa requires a fine-scale analysis of the remains in order to provide an accurate archaeological interpretation. This doctoral thesis presents the application of palaeoproteomics, the study of ancient proteins preserved in archaeological remains, to various archaeological sites across Eastern and Southern Africa. The type I collagen sequences of nineteen antelope and antelope-like species are proposed, and the resulting phylogenetic analyses discussed. An extraction protocol adapted to remains of arid and semi-arid environments, as well as the palaeoproteomics analyses of 117 remains from 19 archaeological sites are presented. This research has allowed to adapt palaeoproteomics studies to remains from African archaeological contexts, to establish a broad collagen referential of species that can potentially be interpreted as domestic caprines and to note the quasi-systematic association of wild and domestic species within archaeological sites during the Holocene. The results obtained in this study highlighted the importance of multiplying different levels of information and the crucial part that palaeoproteomics has to play concerning the study of caprines herding practices diffusion across Africa.En l’absence de représentants sauvages sur le continent, les moutons (Ovis aries) et les chèvres (Capra hircus) domestiques, sous-famille Caprinae, ont été importés du Levant en Afrique vers le VIIe millénaire avant notre ère (BCE). Le corpus archéologique indique une diffusion très lente sur le continent avec une présence attestée au cours du IIIe millénaire avant notre ère en Afrique de l'Est (Djibouti, Somaliland), au Kenya et en Tanzanie alors que les plus anciens vestiges de caprinés ne sont datés que du Ier siècle de notre ère en Afrique australe. L’introduction d’animaux domestiques dans les économies de subsistance apparait progressivement et, après plusieurs siècles, devient majoritaire. En contexte archéologique, les similitudes morphologiques existant entre les deux espèces de caprinés entre elles et avec d'autres petits bovidés sauvages africains brouillent les identifications et l’état très souvent fragmentaire des restes ne permettent souvent pas de proposer une identification en dessous de la sous-famille. L'histoire de la diffusion des ovins et des caprins à travers l'Afrique nécessite une analyse fine des vestiges afin de fournir une interprétation archéologique précise. Cette thèse de doctorat présente l'application de la paléoprotéomique, l'étude des protéines anciennes conservées dans les vestiges archéologiques, à divers sites archéologiques répartis entre l'Afrique de l’Est et l'Afrique australe. Les séquences de collagène de type I de dix-neuf espèces d'antilopes et assimilées sont proposées et l'analyse phylogénétique qui en résulte est discutée. Un protocole d'extraction adapté aux vestiges des milieux arides et semi-arides, ainsi que les analyses paléoprotéomiques de 117 restes provenant de 19 sites archéologiques sont présentés. Ces recherches ont permis d'adapter les études paléoprotéomiques aux vestiges provenant de contextes archéologiques africains, d'établir un large référentiel d'espèces pouvant potentiellement être interprétées comme des caprinés domestiques et de constater l'association quasi- systématique des espèces sauvages et domestiques au sein des sites archéologiques au cours de l'Holocène. Les résultats obtenus dans cette étude ont mis en évidence l'importance de la multiplication de différents niveaux d’information et le rôle central de la paléoprotéomique dans l’étude de la diffusion des pratiques d’élevage de caprinés domestiques à travers l'Afrique

PR-Skandal in Wikipedia

Zwei enge Mitarbeiter des [englischsprachigen] Projektes sollen ihre Beteiligung genutzt haben, um mit ihrem Engagement für das freie Projekt Geld zu machen, indem sie Änderungen im Interesse zahlender Kunden umsetzten. http://winfuture.de/news,72089.html http://www.zdnet.de/88124110/neuer-streit-wichtige-wikipedia-mitarbeiter-machten-pr http://news.cnet.com/8301-1023_3-57514677-93/corruption-in-wikiland-paid-pr-scandal-erupts-at-wikipedia Wikimedia-UK-Funktionär Roger Bamkin, einer der beide..

Recovering bone and tooth proteins in arid environments using palaeoproteomics -A case study from the Late Stone Age site of Toteng, Botswana Recovering bone and tooth proteins in arid environments using palaeoproteomics

International audienceA case study in the Late Stone Age site of Toteng, Botswana In Africa, the absence of wild ancestors' remains of domestic caprines indicates an exogenous origin of domestic sheep and goat. Archaeological evidences suggest that they were introduced in the Northern part of the continent by the 7 th millenium BCE, but only arrived in the Southern part by the 2 nd century BCE. Moreover, the morphological similarities existing between the two species among them, and with other small wild bovids like antelopes combined with the large amount of highly fragmented remains due to arid environnemental conditions have substantially limited the use of classical comparative anatomy analyses. We report here the use of a promising method, palaeoproteomics, on degraded bone and tooth splinters from the Late Stone Age site of Toteng, Botswana. This study is among the first to focuse on African archaeological remains, strongly degraded by arid burying conditions and diagenesis. The purpose of our work is to both document the presence of domestic caprines at this site, but also to develop a new methodology adapted to archaeological remains from arid environments

Identification of degraded bone and tooth splinters from arid environments using palaeoproteomics

International audienc

The name of the game: palaeoproteomics and radiocarbon dates further refine the presence and dispersal of caprines in eastern and southern Africa

We report the first large-scale palaeoproteomics research on eastern and southern African zooarchaeological samples, thereby refining our understanding of early caprine (sheep and goat) pastoralism in Africa. Assessing caprine introductions is a complicated task because of their skeletal similarity to endemic wild bovid species and the sparse and fragmentary state of relevant archaeological remains. Palaeoproteomics has previously proved effective in clarifying species attributions in African zooarchaeological materials, but few comparative protein sequences of wild bovid species have been available. Using newly generated type I collagen sequences for wild species, as well as previously published sequences, we assess species attributions for elements originally identified as caprine or 'unidentifiable bovid' from 17 eastern and southern African sites that span seven millennia. We identified over 70% of the archaeological remains and the direct radiocarbon dating of domesticate specimens allows refinement of the chronology of caprine presence in both African regions. These results thus confirm earlier occurrences in eastern Africa and the systematic association of domesticated caprines with wild bovids at all archaeological sites. The combined biomolecular approach highlights repeatability and accuracy of the methods for conclusive contribution in species attribution of archaeological remains in dry African environments

The name of the game: palaeoproteomics and radiocarbon dates further refine the presence and dispersal of caprines in eastern and southern Africa

Peer reviewed: TruePublication status: PublishedFunder: Fyssen FoundationFunder: Institut de Recherches Archéologiques et Historiques (IRAH)Funder: Muséum national d'Histoire naturelleFunder: French Ministry of Europe and Foreign AffairsFunder: American Institute for Yemeni Studies; doi: http://dx.doi.org/10.13039/100005283We report the first large-scale palaeoproteomics research on eastern and southern African zooarchaeological samples, thereby refining our understanding of early caprine (sheep and goat) pastoralism in Africa. Assessing caprine introductions is a complicated task because of their skeletal similarity to endemic wild bovid species and the sparse and fragmentary state of relevant archaeological remains. Palaeoproteomics has previously proved effective in clarifying species attributions in African zooarchaeological materials, but few comparative protein sequences of wild bovid species have been available. Using newly generated type I collagen sequences for wild species, as well as previously published sequences, we assess species attributions for elements originally identified as caprine or ‘unidentifiable bovid’ from 17 eastern and southern African sites that span seven millennia. We identified over 70% of the archaeological remains and the direct radiocarbon dating of domesticate specimens allows refinement of the chronology of caprine presence in both African regions. These results thus confirm earlier occurrences in eastern Africa and the systematic association of domesticated caprines with wild bovids at all archaeological sites. The combined biomolecular approach highlights repeatability and accuracy of the methods for conclusive contribution in species attribution of archaeological remains in dry African environments

The name of the game: palaeoproteomics and radiocarbon dates further refine the presence and dispersal of caprines in eastern and southern Africa

Peer reviewed: TruePublication status: PublishedFunder: Fyssen FoundationFunder: Institut de Recherches Archéologiques et Historiques (IRAH)Funder: Muséum national d'Histoire naturelleFunder: French Ministry of Europe and Foreign AffairsFunder: American Institute for Yemeni Studies; doi: http://dx.doi.org/10.13039/100005283We report the first large-scale palaeoproteomics research on eastern and southern African zooarchaeological samples, thereby refining our understanding of early caprine (sheep and goat) pastoralism in Africa. Assessing caprine introductions is a complicated task because of their skeletal similarity to endemic wild bovid species and the sparse and fragmentary state of relevant archaeological remains. Palaeoproteomics has previously proved effective in clarifying species attributions in African zooarchaeological materials, but few comparative protein sequences of wild bovid species have been available. Using newly generated type I collagen sequences for wild species, as well as previously published sequences, we assess species attributions for elements originally identified as caprine or ‘unidentifiable bovid’ from 17 eastern and southern African sites that span seven millennia. We identified over 70% of the archaeological remains and the direct radiocarbon dating of domesticate specimens allows refinement of the chronology of caprine presence in both African regions. These results thus confirm earlier occurrences in eastern Africa and the systematic association of domesticated caprines with wild bovids at all archaeological sites. The combined biomolecular approach highlights repeatability and accuracy of the methods for conclusive contribution in species attribution of archaeological remains in dry African environments.</jats:p