Periodic Reporting for period 1 - NEO (Living in Europe in the late Neolithic: A trans-disciplinary temporal perspective on present-day Europeans) Reporting period: 2018-05-01 to 2020-04-30 Summary of the context and overall objectives of the project Genomic studies on ancient humans have revealed that the process that shaped the population structure of Europe cannot be understood from the analysis of present-day populations only. The Neolithisation process, by which a population of hunter-gatherers shifted to pastoralism and farming, was mainly the result of migrations from Anatolia, starting some ~9,000 years ago, and expanding through both a Danubian and a Mediterranean route. Due to its geographic location, France was also on the way of both routes underlying Neolithic expansions, therefore, French archaeological remains provide a unique opportunity to study both expansion processes within a single country.By the second half of the Vth millennium BC in western Europe, as Neolithisation has completed and social stratification is emerging, Neolithic individuals started to bury their deceased in collective burials, which can host the remains of dozen if not hundreds, of individuals. On present-day France, more than 3,000 of these collective burials have been excavated, each of them potentially representing one community. In the NEO project, ancient DNA extracted from bones and teeth of Neolithic individuals interred in some of these collective burials were investigated to assess their genetic ancestry as well as the diet, health, mobility patterns, residential and funerary rules characterising western European Neolithic societies. Within NEO, a multi-disciplinary approach combining archaeology, physical anthropology and molecular analyses was applied to a rich collection of remains from the late Neolithic, excavated both in northern and southern parts of France, potentially representing the ending points of the Danubian and Mediterranean neolithisation routes, respectively. The general objective of the NEO project was to observe how almost contemporary Neolithic societies developed, with regards to possible regional specificities, in order to advance our knowledge on the building of European populations in prehistory. Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far Within NEO, ancient DNA from a total of 82 individuals interred in collective burials from three different French sites was analysed. This major corpus of data enabled i) to characterize the funerary practices, ii) to track the evolutionary origins of the different groups, assessing mobility patterns and contacts between groups, iii) to reveal important aspects about life in past societies (diet, health status, mating and residential rules, social stratification). This project combines archaeological, anthropological and genomic data from a high number of individuals, highlighting the importance of data management, curation and traceability. The collaborators’ team has published one article presenting an open-source Laboratory Information Management System (LIMS) that can account for the specificities of ancient DNA samples processing and include all sample-related metadata (CASCADE: A Custom-Made Archiving System for the Conservation of Ancient DNA Experimental Data, Dolle et al., Frontiers in Ecology and Evolution, 2020. https://doi.org/10.3389/fevo.2020.00185). Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far) Beyond just focusing on the genome of the individual, it is now possible to characterize the DNA still preserved in ancient dental calculus, providing dietary information but also a snapshot of the oral microbiomes, which have been shown to be influenced by external factors (diet and hygiene) and to be linked to a range of systemic disorders. Characterizing these microbiomes in past European populations holds the potential to advance our knowledge of hygiene and health conditions of Neolithic Europeans, but also to test the extent to which oral microbiomes has shifted in composition following the Neolithic transition from hunter-gathering to farming.In addition, novel approaches in ancient DNA research open for a characterization of the epigenomes of past individuals. The epigenome plays an essential role in regulating gene expression, according to lifestyles and environmental, cultural and social exposure. NEO enables a critical comparison of archaeological, anthropological and molecular (genome-epigenome-microbiome) data, leading to more confident assessments of Neolithic populations in Europe, but also strengthening the contribution of each discipline, paving the way for future similar work in anthropological sciences. Andaine Seguin-Orlando preparing samples in the ancient DNA facility of the AMIS laboratory (UMR5288
