The Demeter project. Eight millennia of agrobiodiversity changes in the northwest Mediterranean basin

The development of agricultural societies is closely entangled with that of domestic animals and plants. Local and traditional domestic breeds and varieties are the result of millennia of selection by farmers. DEMETER (2020-2025) is an international project which is aiming to characterize the changes in animal and plant agrobiodiversity (pigs, sheep, goats, and barley) in relation with environmental and socioeconomic factors in the northwestern Mediterranean basin since the beginnings of agriculture. The project is based on a combination of approaches including phenomics (through geometric morphometrics), databasing, zooarchaeology, archaeobotany, climate modeling, paleoproteins (ZooMs) and statistical analyses. Several hundreds of archaeological sites from the South of France and Catalonia will be studied, covering the maximum environmental, societal and cultural diversity of context over the course of the last eight millennia

Approches croisées de l’agrobiodiversité animale et végétale exploitée en Méditerranée nord-occidentale médiévale : le projet DEMETER

La domestication des plantes et des animaux marque une transition majeure dans l'histoire humaine et constitue un élément clé du développement des sociétés modernes. Les races et variétés domestiques locales et traditionnelles sont en effet le résultat de millénaires de sélection par les agriculteurs. Cependant, nous vivons aujourd'hui une crise majeure, avec une perte drastique de la diversité des systèmes de production alimentaire et la disparition progressive des pratiques traditionnelles. La sauvegarde de la diversité des espèces, des variétés et des races cultivées est ainsi menacée. Dans ce contexte, l'objectif du projet ERC DEMETER est de retracer comment, au cours des huit derniers millénaires, les sociétés ont influencé l'évolution des espèces domestiques sous différents régimes agricoles, environnementaux et socio-économiques, en se concentrant principalement sur le bassin nord-ouest de la Méditerranée (France méditerranéenne, Catalogne). Au cœur du projet, le Moyen Âge occupe une place importante. Il s’agit en effet d’une période qui connait des changements importants, tant du point de vue socio-économique (évolutions multiples de l’occupation et de la gestion des campagnes, vagues migratoires, essor démographique, urbanisation galopante) que climatique (optimum, péjoration), ayant eu des conséquences, documentées par l’archéologie, sur les productions et pratiques agropastorales. Elle constitue également une des dernières phases précédant l’intensification des sélections par l’homme, qui se produit au cours de la période contemporaine.Pour la période médiévale, la zone géographique investie par le projet a été particulièrement bien documentée par la carpologie et l’archéozoologie au cours des dernières décennies, en raison notamment de l’essor de l’archéologie préventive et d’une sensibilisation des opérateurs aux problématiques et méthodes de la bioarchéologie. La quantité de sites et d’échantillons disponibles est ainsi remarquable par rapport aux périodes pré- et protohistoriques. Notre approche ciblée sur certains taxons (cochon, mouton, chèvre, orge) nous permet de qualifier la diversité ancienne de ces espèces domestiques, et d’appréhender en finesse leur évolution au cours du temps. Pour qualifier cette diversité et ses évolutions, le projet s'appuie sur une combinaison d'approches incluant la phénomique (par la morphométrie géométrique), les bases de données, l'archéozoologie, la carpologie, la modélisation climatique, les paléoprotéines (ZooMs) et les analyses statistiques. Dans le cadre de cette présentation, nous aborderons en particulier l’émerge des races et variétés actuelles, ainsi que les liens possibles entre l’agrobiodiversité médiévale et l’actuelle

Approches croisées de l’agrobiodiversité animale et végétale exploitée en Méditerranée nord-occidentale médiévale : le projet DEMETER

La domestication des plantes et des animaux marque une transition majeure dans l'histoire humaine et constitue un élément clé du développement des sociétés modernes. Les races et variétés domestiques locales et traditionnelles sont en effet le résultat de millénaires de sélection par les agriculteurs. Cependant, nous vivons aujourd'hui une crise majeure, avec une perte drastique de la diversité des systèmes de production alimentaire et la disparition progressive des pratiques traditionnelles. La sauvegarde de la diversité des espèces, des variétés et des races cultivées est ainsi menacée. Dans ce contexte, l'objectif du projet ERC DEMETER est de retracer comment, au cours des huit derniers millénaires, les sociétés ont influencé l'évolution des espèces domestiques sous différents régimes agricoles, environnementaux et socio-économiques, en se concentrant principalement sur le bassin nord-ouest de la Méditerranée (France méditerranéenne, Catalogne). Au cœur du projet, le Moyen Âge occupe une place importante. Il s’agit en effet d’une période qui connait des changements importants, tant du point de vue socio-économique (évolutions multiples de l’occupation et de la gestion des campagnes, vagues migratoires, essor démographique, urbanisation galopante) que climatique (optimum, péjoration), ayant eu des conséquences, documentées par l’archéologie, sur les productions et pratiques agropastorales. Elle constitue également une des dernières phases précédant l’intensification des sélections par l’homme, qui se produit au cours de la période contemporaine.Pour la période médiévale, la zone géographique investie par le projet a été particulièrement bien documentée par la carpologie et l’archéozoologie au cours des dernières décennies, en raison notamment de l’essor de l’archéologie préventive et d’une sensibilisation des opérateurs aux problématiques et méthodes de la bioarchéologie. La quantité de sites et d’échantillons disponibles est ainsi remarquable par rapport aux périodes pré- et protohistoriques. Notre approche ciblée sur certains taxons (cochon, mouton, chèvre, orge) nous permet de qualifier la diversité ancienne de ces espèces domestiques, et d’appréhender en finesse leur évolution au cours du temps. Pour qualifier cette diversité et ses évolutions, le projet s'appuie sur une combinaison d'approches incluant la phénomique (par la morphométrie géométrique), les bases de données, l'archéozoologie, la carpologie, la modélisation climatique, les paléoprotéines (ZooMs) et les analyses statistiques. Dans le cadre de cette présentation, nous aborderons en particulier l’émerge des races et variétés actuelles, ainsi que les liens possibles entre l’agrobiodiversité médiévale et l’actuelle

Archaeophenomics of ancient domestic plants and animals using geometric morphometrics : a review

International audienceGeometric morphometrics revolutionized domestication studies through the precise quantification of the phenotype of ancient plant and animal remains. Geometric morphometrics allow for an increasingly detailed understanding of the past agrobiodiversity and our ability to characterize large scale ancient phenotypes has led to what can be named archaeophenomics : the large scale phenotyping of ancient remains. This review describes advances in the bioarchaeological study of domesticated species and their wild relatives where their phenomes are quantified through geometric morphometrics. The two main questions addressed by archaeophenomics are i) taxonomic identification, including domestication signature, and ii) the inference of the spatio-temporal agrobiodiversity dynamics. Archaeophenomics is a growing field in bioarchaeology of domestic species that will benefit in the near future from advances in artificial intelligence and from an increasing interest in multiproxy approaches combining morphometric data with e.g. isotopes or archaeogenomics

La variation phénotypique documente la diversité moderne de l’orge : une application de la morphométrie géométrique à l’étude de la forme des graines

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Studying the current diversity of barley using geometric morphometrics on modern seeds: protocol and first results

International audienceGeometric morphometrics is a powerful method to explore intraspecies variation in cultivated plants (Terral et al., 2012 ; Bonhomme et al., 2017). Barley (Hordeum vulgare L.) is one of the staple crop of the Mediterranean since the Neolithic (Zohary et al., 2012). While morphological discrete characters are available to distinguish two-rowed from six-rowed barley, and naked from hulled barley (Jacomet et al. 2006), quantitative approaches still need to be developed at a large scale. The aim of this study is to explore the morphometric grain variation between barley varieties, six- and two-rowed types, naked and hulled types and spring and winter varieties. Size and shape of 2950 modern barley seeds from 84 current varieties provided by the Small grain cereals Biological Resources Centre (INRAE, Clermont Ferrand, France) were quantified using Elliptic Fourier Transforms (EFT) applied to gain outlines 2D coordinates. Results open interesting perspectives for investigating archaeological barley seeds and trace barley evolution in the western occidental Mediterranean basin since the Neolithic. This perspective will be realized in the framework of the ERC project DEMETER (grant agreement No. 852573)

Barley systematics and taxonomy foreseen by seed morphometric variation.

Since its Neolithic domestication in the Fertile Crescent, barley has spread to all continents and represents a major cereal in many modern agrarian systems. Current barley diversity includes thousands of varieties divided into four main categories corresponding to 2-row and 6-row subspecies and naked and hulled types, each of them with winter and spring varieties. This diversity is associated to different uses and allow cultivation in diverse environments. We used a large dataset of 58 varieties of French origin, (1) to assess the taxonomic signal in barley grain measurements comparing 2-row and 6-row subspecies, and naked and hulled types; (2) to test the impact of the sowing period and interannual variation on the grains size and shape; (3) to investigate the existence of morphological differences between winter and spring types; and finally (4) to contrast the relationship between the morphometric and genetic proximity. Size and shape of 1980 modern barley caryopses were quantified through elliptic Fourier Transforms and traditional size measurements. Our results indicate that barley grains record morphological diversity of the ear (89.3% classification accuracy between 2-row/6-row subspecies; 85.2% between hulled and naked type), sowing time of the grains (from 65.6% to 73.3% within barley groups), and environmental conditions during its cultivation and varietal diversity. This study opens perspectives for studying archaeological barley seeds and tracing the barley diversity and evolution since the Neolithic

Identification of archaeological barley grains using geometric morphometrics and experimental charring

International audienceBarley is one of the main cereals found in archaeological sites in the north-western Mediterranean basin, over the last 8 millennia. Grains are preserved in archaeological sediments by charring after or before dehusking. Morphological criteria for distinguishing 2-row from 6-row barley, but also hulled barley from naked barley, can be affected by charring and this can complicate identification of barley subgroups. In the last decade, geometric morphometrics applied to uncharred barley grains has shown the possibility of identifying barley subgroups, but its applicability to archaeological remains still needs to be ascertained. We used 3985 raw and charred grains of 113 current varieties to (1) assess charring effects on the shape of barley caryopses, depending on their subgroup and whether they were charred husked or dehusked and (2) select the best dataset for identifying barley subgroups. We also used 700 archaeological grains, from the Neolithic period to the end of the Middle Ages, to (3) compare the morphometric taxonomic assignment of the grains with their carpological identification based on discrete anatomical features in a series of 7 archaeological samples. Our results indicate size and shape differences between barley grains when charredhusked or dehusked. Although the charring process results in greater morphometric homogeneity, it allows subgroups of barley to be identified. For the 2-row vs. 6-row identification, more than 71% of the charred modern grains can be correctly identified. For the hulled vs. naked identification, the correct cross-validation percentages range from 70 to 73%. Finally, the good correlation between carpological and morphometric identifications of archaeological grains suggests that it is possible to identify archaeobotanical samples in the future

Agricultural Dynamics in Southwestern Mediterranean France from the End of the Iron Age to the Early Middle Ages

International audienceIn the northwestern Mediterranean, the rural world underwent major economic, social and cultural changes between the end of the Iron Age and the beginning of the Middle Ages, with a decisive impact on the evolution of agricultural production, practices and landscapes. Roman expansion first led to the spread of villae during the 2 nd and 1 st c. BC, leading to a new structuration of rural areas and the development of a speculative agriculture, which strongly favoured wine production. By the end of the Roman period, new changes are observed: while certain Roman villae are still occupied, the appearance of a new network of rural settlements reveals the emergence of a new form of rural economy. Although these changes are increasingly well documented by archaeology, their impact on the agrarian production and practices remains little explored. The multiplication of archaeobotanical investigations in southwestern Mediterranean France allows us to present a first review of farming practices and their evolution during this key period. The study of 30 rural sites provides new data concerning local agriculture between the 2 nd c. BC and the 8 th c. AD (cultivated plants, prevalence of certain species, associated farming practices, exploited landscapes) and attempts to detect potential specificities / evolutions over time such as changes in staple crops, diversification, exploitation of new "terroirs"

Deep learning<i>versus</i>geometric morphometrics for archaeobotanical domestication study and subspecific identification

Taxonomical identification of archaeological fruit and seed is of prime importance for any archaeobotanical studies. We compared the relative performance of deep learning and geometric morphometrics at identifying pairs of plant taxa. We used their seeds and fruit stones that are the most abundant recovered organs in archaeobotanical assemblages, and whose morphological identification, chiefly between wild and domesticated types, allow to document their domestication and biogeographical history. We used existing modern datasets of four plant taxa (date palm, barley, olive and grapevine) corresponding to photographs of two orthogonal views of their seeds that were analysed separately to offer a larger spectrum of shape diversity. On these eight datasets, we compared the performance of a deep learning approach, here convolutional neural networks (CNN), to that of a geometric morphometric approach, here outline analyses using elliptical Fourier transforms (EFT). Sample sizes were at minimum eight hundred seeds in each class, which is quite small when training deep learning models but of typical magnitude for archaeobotanical studies. Our objectives were twofold: i) to test whether deep learning can beat geometric morphometrics in taxonomic identification and if so, ii) to test which minimal sample size is required. We ran simulations on the full datasets and also on subsets, starting from 50 images in each binary class. For CNN networks, we deliberately used a candid approach relying on pre-parameterised VGG16 network. For EFT, we used a state-of-the art morphometrical pipeline. The main difference rests in the data used by each model: CNN used bare photographs where EFT used (x, y) outline coordinates. This "pre-distilled" geometrical description of seed outlines is often the most time-consuming part of morphometric studies. Results show that CNN beats EFT in most cases, even for very small datasets. We finally discuss the potential of CNN for archaeobotany, why outline analyses and morphometrics have not yet said their last word by providing quantitative descriptions, and how bioarchaeological studies could embrace both approaches, used in a complementary way, to better assess and understand the past history of species