History, origin and spread of Agriculture: new evidences from Archaebotany and Paleogenomics – ArkaeoAG

From 65 referenced archaeological sites giving access to 88 assemblages of wheat grains and loaves from 12 taxa and dating from 9,500 B.C.-1,500 A.D., ArkaeoAG offers, through integrated archaeobotanical approaches (investigation on past human-plant interactions) and paleogenomics (analysis of ancient DNA), to provide new insights into the fascinating history of a plant species - wheat - which, from its origin in the Fertile Crescent in the early from the Neolithic era, has spread with human communities on all continents to become the main cereal crop in the world, today comprising several thousand modern varieties adapted to a wide range of environments and human uses. The different centers of origin but also the routes of contact, migration or exchange between founding farmers, independent and scattered in Europe, all these historical events will be traced by archaeological research and ancient DNA on wheat remains covering the last 10,000 years.

Overall, we analyzed in the ArkaeoAG project wheat remains from 19 Neolithic sites for charred samples and 16 Neolithic/Chacolithic sites for cooked dough and bread and 24 archaeological sites for aDNA analyses (WP2), then reaching the initial objectives of the project (i.e 65 archaeological sites - 88 assemblages of remains - 12 taxa - dating to 9500 BC-1500 AD). While a large part of these samples will remain to be analyzed in the coming years, a total of 38 archaeological macro-remains were genetically studied and 21 archaeological wheats were authenticated, including. In general, genetic analyses have made it possible to refine carpological identification, and a Careiron and Pesquier collection has made it possible to uncover dried wheat macro-remains with DNA conservation 10 times higher than conservation in humid environments (waterlogged samples). We compared the genome sequence of the aDNA samples with 287 genotypes representing worldwide extant populations of wild and domesticated wheats based on whole-genome exome capture data. Despite few sample that were genetically identified as barley, the vast majority of past cultivated wheat samples genetically authenticated do not correspond to any of the modern wheats used for pasta (T. durum, only one ancient wheat identified) or bread (T. aestivum, no ancient wheat identified). This unveiled los-past diversity open novel perspective in modern breeding.

We finally integrated all ArkeaoAG’s results in reviews articles in order to present the current state of knowledge on the origins of wheat cultivation, from its domestication during the Holocene to the intensification of its selection and varietal improvement in recent centuries, as a marker of human history as well as offer some perspectives on leveraging this past history to develop the varieties of tomorrow adapted to the new challenges facing agriculture. ArkaeoAG meets a major societal challenge in paving the way to reconstruct past evolutionary trajectories of wheat in response to natural and/or anthropogenic drivers by tracking genomic changes within dated archaeobotanical remains. ArkaeoAG thus proposes a paradigm shift where the adaptation to future climate fluctuations cannot rely only on the modern crop allelic diversity but requires the identification of the ‘hidden’ variability which may no longer be active in modern genomes , but identifiable in ancient DNA.

Pont C. et al., 2019. Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA. Genome Biology, 20 (1): 29

ArkaeoAG aims at tracing the origin and spread of Agriculture during the Holocene as a major process in the socio-economic structuring of modern civilization. To reach this objective ArkaeoAG brings specialists in paleogenomics, evolutionary biology, archaeobotany, carpology and palaeoecology in studying wheat (Triticum spp.) remains preserved in sediments. From 65 referenced archaeological sites delivering access to 88 assemblages of wheat grain and bread remains from 12 taxa and dating to 9500 BC-1500 AD, ArkaeoAG proposes, through archaeobotany (investigating past human-plant interactions, WP1) and paleogenomic (investigating ancient DNA, WP2) data integration (WP3), to provide novel insights into the fascinating history of a plant species - wheat – that, since its origin in the Fertile Crescent in the early Neolithic period, has spread with human communities to all continents to become the main cereal crop worldwide, comprising nowadays several thousand recorded modern varieties adapted to a wide range of environments and human uses. Different centres of origins, contacts, migrations or exchanges between founder farmers and their cultivated wheat species, independent spread over Europe, all these historical events will be recovered in the wheat archaeological and aDNA investigations covering the last 10,000 years. ArkaeoAG is aimed to (i) reconstruct micro-evolutionary steps of wheat domestication (origin and expansion) as the result of human population history (migration, admixture, culture and selection), (ii) characterize intermediate or extinct alleles of trait-related genes delivering a hidden allelic diversity to be utilized to redesign future breeding strategies. The different approaches (archaeology, archaeobotany, paleogenomics) will provide complementary evidence of relatedness between different locations and at different time scales that will be used as proxies to reconstruct the micro-evolutionary history of wheat domestication and assess how much it mirrored that of human population organization. Overall, apart being emblematic of the French patrimony internationally recognized through it breadmaking culture, wheat is a model crop for which the in depth reconstruction of micro-evolutionary steps of domestication inform precisely about Human population history (origins, contacts, movements). ArkaeoAG will finally deliver resources from ancient wheats of major interest to redesign future breeding schemes in the context of sustainable Agriculture. The coordination of the project (WP4) will be managed by a steering committee constituted by one representative of each team involved in the project to organize each step of the work progression regarding the project management and data management during the project lifetime.