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1. Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history

Author

He Yu, Alexandra Jamieson, Ardern Hulme-Beaman, Chris J. Conroy, Becky Knight, Camilla Speller, Hiba Al-Jarah, Heidi Eager, Alexandra Trinks, Gamini Adikari, Henriette Baron, Beate Böhlendorf-Arslan, Wijerathne Bohingamuwa, Alison Crowther, Thomas Cucchi, Kinie Esser, Jeffrey Fleisher, Louisa Gidney, Elena Gladilina, Pavel Gol’din, Steven M. Goodman, Sheila Hamilton-Dyer, Richard Helm, Jesse C. Hillman, Nabil Kallala, Hanna Kivikero, Zsófia E. Kovács, Günther Karl Kunst, René Kyselý, Anna Linderholm, Bouthéina Maraoui-Telmini, Nemanja Marković, Arturo Morales-Muñiz, Mariana Nabais, Terry O’Connor, Tarek Oueslati, Eréndira M. Quintana Morales, Kerstin Pasda, Jude Perera, Nimal Perera, Silvia Radbauer, Joan Ramon, Eve Rannamäe, Joan Sanmartí Grego, Edward Treasure, Silvia Valenzuela-Lamas, Inge van der Jagt, Wim Van Neer, Jean-Denis Vigne, Thomas Walker, Stephanie Wynne-Jones, Jørn Zeiler, Keith Dobney, Nicole Boivin, Jeremy B. Searle, Ben Krause-Kyora, Johannes Krause, Greger Larson, and David Orton

Subjects
Science
Abstract

‘Archaeogenetic analysis of black rat remains reveals that this species was introduced into temperate Europe twice, in the Roman and medieval periods. This population turnover was likely associated with multiple historical and environmental factors.’

Published
2022
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2. Bones geometric morphometrics illustrate 10th millennium cal. BP domestication of autochthonous Cypriot wild boar (Sus scrofa circeus nov. ssp)

Author

Thomas Cucchi, Auriale Domont, Hugo Harbers, Charlotte Leduc, Aurélie Guidez, Anne Bridault, Hitomi Hongo, Max Price, Joris Peters, François Briois, Jean Guilaine, and Jean-Denis Vigne

Subjects
Medicine, Science
Abstract

Abstract Epipaleolithic hunter-gatherers from the Near East introduced wild boars (Sus scrofa) to Cyprus, with the Early Pre-Pottery Neolithic (PPN) settlers hunting the wild descendants of these boars. However, the geographic origin of the Cypriot boar and how they were integrated into the earliest forms of pig husbandry remain unsolved. Here, we present data on 11,000 to 9000 cal. BP Sus scrofa from the PPN sites of Klimonas and Shillourokambos. We compared them to contemporaneous populations from the Near East and to Neolithic and modern populations in Corsica, exploring their origin and evolution using biosystematic signals from molar teeth and heel bones (calcanei), using 2D and 3D geometric morphometrics. We found that the Cypriot PPN lineage of Sus scrofa originates from the Northern Levant. Yet, their phenotypic idiosyncrasy suggest that they evolved into an insular sub-species that we named Sus scrofa circeus, referring to Circe, the metamorphosis goddess that changed Ulysses companions into pigs. The phenotypic homogeneity among PPNA Klimonas wild boars and managed populations of PPNB Shillourokambos suggests that local domestication has been undertaken on the endemic S. s. circeus, strengthening the idea that Cyprus was integrated into the core region of animal domestication.

Published
2021
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4. The mark of captivity: plastic responses in the ankle bone of a wild ungulate (Sus scrofa)

Author

Hugo Harbers, Dimitri Neaux, Katia Ortiz, Barbara Blanc, Flavie Laurens, Isabelle Baly, Cécile Callou, Renate Schafberg, Ashleigh Haruda, François Lecompte, François Casabianca, Jacqueline Studer, Sabrina Renaud, Raphael Cornette, Yann Locatelli, Jean-Denis Vigne, Anthony Herrel, and Thomas Cucchi

Subjects
domestication, wild boar, phenotypic plasticity, locomotion, geometric morphometrics, experimentation, Science
Abstract

Deciphering the plastic (non-heritable) changes induced by human control over wild animals in the archaeological record is challenging. We hypothesized that changes in locomotor behaviour in a wild ungulate due to mobility control could be quantified in the bone anatomy. To test this, we experimented with the effect of mobility reduction on the skeleton of wild boar (Sus scrofa), using the calcaneus shape as a possible phenotypic marker. We first assessed differences in shape variation and covariation in captive-reared and wild-caught wild boars, taking into account differences in sex, body mass, available space for movement and muscle force. This plastic signal was then contrasted with the phenotypic changes induced by selective breeding in domestic pigs. We found that mobility reduction induces a plastic response beyond the shape variation of wild boars in their natural habitat, associated with a reduction in the range of locomotor behaviours and muscle loads. This plastic signal of captivity in the calcaneus shape differs from the main changes induced by selective breeding for larger muscle and earlier development that impacted the pigs' calcaneus shape in a much greater extent than the mobility reduction during the domestication process of their wild ancestors.

Published
2020
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5. Social Complexification and Pig (Sus scrofa) Husbandry in Ancient China: A Combined Geometric Morphometric and Isotopic Approach.

Author

Thomas Cucchi, Lingling Dai, Marie Balasse, Chunqing Zhao, Jiangtao Gao, Yaowu Hu, Jing Yuan, and Jean-Denis Vigne

Subjects
Medicine, Science
Abstract

Pigs have played a major role in the economic, social and symbolic systems of China since the Early Neolithic more than 8,000 years ago. However, the interaction between the history of pig domestication and transformations in Chinese society since then, have not been fully explored. In this paper, we investigated the co-evolution from the earliest farming communities through to the new political and economic models of state-like societies, up to the Chinese Empire, using 5,000 years of archaeological records from the Xiawanggang (XWG) and Xinzhai (XZ) sites (Henan Province). To trace the changes of pig populations against husbandry practices, we combined the geometric morphometric analysis of dental traits with a study of the stable carbon and nitrogen isotope ratios from bone collagen. The domestication process intensified during the Neolithic Yangshao, prompted by greater selective pressure and/or better herd control against wild introgression. After that, pig farming, in XWG, relied on local livestock and a gradual change of husbandry practices overtime. This was characterized by a gentle increase in millet foddering and animal protein intake, until a complete change over to household management during the Han dynasty. The only rupture in this steady trend of husbandry occurred during the Longshan period, with the appearance of small sized and idiosyncratic pigs with specific feeding practices (relying on millet and household scraps). From three exploratory hypothesis, we explored the possibility of anti-elite pig production in XWG during the Longshan period, as a means to resist incorporation into a new economic model promoting intensified domestic production. This exploratory hypothesis is the most suitable to our dataset; however, numerous areas need to be explored further in order to adequately document the role of pigs in the rise of China's complex societies.

Published
2016
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6. Earliest 'Domestic' Cats in China Identified as Leopard Cat (Prionailurus bengalensis).

Author

Jean-Denis Vigne, Allowen Evin, Thomas Cucchi, Lingling Dai, Chong Yu, Songmei Hu, Nicolas Soulages, Weilin Wang, Zhouyong Sun, Jiangtao Gao, Keith Dobney, and Jing Yuan

Subjects
Medicine, Science
Abstract

The ancestor of all modern domestic cats is the wildcat, Felis silvestris lybica, with archaeological evidence indicating it was domesticated as early as 10,000 years ago in South-West Asia. A recent study, however, claims that cat domestication also occurred in China some 5,000 years ago and involved the same wildcat ancestor (F. silvestris). The application of geometric morphometric analyses to ancient small felid bones from China dating between 5,500 to 4,900 BP, instead reveal these and other remains to be that of the leopard cat (Prionailurus bengalensis). These data clearly indicate that the origins of a human-cat 'domestic' relationship in Neolithic China began independently from South-West Asia and involved a different wild felid species altogether. The leopard cat's 'domestic' status, however, appears to have been short-lived--its apparent subsequent replacement shown by the fact that today all domestic cats in China are genetically related to F. silvestris.

Published
2016
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7. Ancient urban ecology reconstructed from archaeozoological remains of small mammals in the Near East.

Author

Lior Weissbrod, Dan Malkinson, Thomas Cucchi, Yuval Gadot, Israel Finkelstein, and Guy Bar-Oz

Subjects
Medicine, Science
Abstract

Modern rapidly expanding cities generate intricate patterns of species diversity owing to immense complexity in urban spatial structure and current growth trajectories. We propose to identify and uncouple the drivers that give rise to these patterns by looking at the effect of urbanism on species diversity over a previously unexplored long temporal frame that covers early developments in urbanism. To provide this historical perspective we analyzed archaeozoological remains of small mammals from ancient urban and rural sites in the Near East from the 2nd to the 1st millennium BCE, and compared them to observations from modern urban areas. Our data show that ancient urban assemblages consistently comprised two main taxa (Mus musculus domesticus and Crocidura sp.), whereas assemblages of contemporaneous rural sites were significantly richer. Low species diversity also characterizes high-density core areas of modern cities, suggesting that similar ecological drivers have continued to operate in urban areas despite the vast growth in their size and population densities, as well as in the complexity of their technologies and social organization. Research in urban ecology has tended to emphasize the relatively high species diversity observed in low-density areas located on the outskirts of cities, where open and vegetated patches are abundant. The fact that over several millennia urban evolution did not significantly alter species diversity suggests that low diversity is an attribute of densely-populated settlements. The possibility that high diversity in peripheral urban areas arose only recently as a short-term phenomenon in urban ecology merits further research based on long-term data.

Published
2014
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8. A dig into the past mitochondrial diversity of Corsican goats reveals the influence of secular herding practices.

Author

Sandrine Hughes, Helena Fernández, Thomas Cucchi, Marilyne Duffraisse, François Casabianca, Daniel Istria, François Pompanon, Jean-Denis Vigne, Catherine Hänni, and Pierre Taberlet

Subjects
Medicine, Science
Abstract

The goat (Capra hircus) is one of the earliest domesticated species ca. 10,500 years ago in the Middle-East where its wild ancestor, the bezoar (Capra aegagrus), still occurs. During the Neolithic dispersal, the domestic goat was then introduced in Europe, including the main Mediterranean islands. Islands are interesting models as they maintain traces of ancient colonization, historical exchanges or of peculiar systems of husbandry. Here, we compare the mitochondrial genetic diversity of both medieval and extant goats in the Island of Corsica that presents an original and ancient model of breeding with free-ranging animals. We amplified a fragment of the Control Region for 21 medieval and 28 current goats. Most of them belonged to the A haplogroup, the most worldwide spread and frequent today, but the C haplogroup is also detected at low frequency in the current population. Present Corsican goats appeared more similar to medieval goats than to other European goat populations. Moreover, 16 out of the 26 haplotypes observed were endemic to Corsica and the inferred demographic history suggests that the population has remained constant since the Middle Ages. Implications of these results on management and conservation of endangered Corsican goats currently decimated by a disease are addressed.

Published
2012
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9. Telarmachay revisité : nouvelles datations radiocarbone du plus ancien centre de domestication des camélidés andins

Author

Manon Le Neün, Antoine Zazzo, Elise Dufour, Olivier Tombret, François Thil, Jane Wheeler, Thomas CUCCHI, Danièle Lavallée, Nicolas Goepfert, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Instituto de Investigación y Desarrollo de Camélidos Sudamericanos, Av. Reusche M4, Pachacamac, Lima, Peru. (CONOPA), Archéologie des Amériques (ArchAm), Université Paris 1 Panthéon-Sorbonne (UP1)-Centre National de la Recherche Scientifique (CNRS), Région Île-de-France, Domaine d’Intérêt Majeur 'Matériaux anciens et patrimoniaux' (DIM-MAP, AAP 2018-3, project CAMELIDOM), École Doctorale 227 'Sciences de la nature et de l’Homme : évolution et écologie' du Muséum national d’Histoire naturelle et Sorbonne Université (ED227 MNHN-SU, France)., and ANR-15-CE27-0002,CAMELANDES,Les sociétés préhispaniques face à leur environnement : variations spatiales et diachroniques du pastoralisme andin (100-1470 apr. J.-C.)(2015)

Subjects
Holocene, Telarmachay, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Peru, Puna, Radiocarbon AMS dating, Central Andes, South American Camelids
Abstract

International audience; Les archéologues s’accordent pour considérer qu’au sein des camélidés sud-américains (CSA), Les lamas et les alpagas ont été domestiqués à partir de deux espèces sauvages : les guanacos et les vigognes, au cours de la période précéramique. Cependant, documenter les premières étapes de ce processus de domestication reste encore un défi. Le site de Telarmachay (Puna de Junín, Pérou) est un site majeur des Andes précéramiques. Il a apporté les plus anciens indices du processus de domestication des CSA, vers 3000-1800 av. J.-C., soit 2000 ans plus tôt que le reste de la zone andine. Cependant, la longue chronostratigraphie de ce site, entre 7000 à 150 av. J.-C., s’appuie sur 22 datations 14C effectuées avant l’avènement de l’AMS et de surcroit sur des charbons de bois et non des vestiges osseux. C’est pourquoi il était nécessaire de lancer un nouveau programme de datations AMS sur ossements de camélidés. Les résultats montrent ainsi que la chronologie devait être révisée. Nous avons vieilli l’âge du site d’environ 1000 ans et inscrit l’interaction entre les sociétés humaines et les camélidés à Telarmachay sur une période de plus de 4000 ans entre 7152/6510 et 2226/1854 av. J.-C. Enfin, nous avons aussi détecté six outliers que nous avons réattribué à leur couche d’origine. Grâce à cette nouvelle chronologie, il sera possible de retracer l’histoire de l’occupation du site en général et de l’intensification des relations entre les chasseurs-cueilleurs des hautes terres des Andes et les camélidés en particulier.

Published
2022

11. Can growth in captivity alter the calcaneal microanatomy of a wild ungulate?

Author

Romain Cottereau, Katia Ortiz, Yann Locatelli, Alexandra Houssaye, and Thomas Cucchi

Abstract

Reduced mobility associated with captivity induces changes in biomechanical stress on the skeleton of domesticated animals. Due to bone plasticity, bone’s morphology and internal structure can respond to these new biomechanical stresses over individuals’ lifetime. In a context where documenting early process of animal domestication is challenging, this study will test the hypothesis that change in mobility patterns during a wild ungulate’s life will alter the internal structure of its limb bones and provide a proof of concept for the application of this knowledge in Zooarchaeology. Using the calcaneus as a phenotypic marker through qualitative and quantitative 3D microanatomical analyses, we relied on a comparative study across wild boars (Sus scrofa) populations from controlled experimental conditions with different mobility patterns (natural habitat, large pen, and stall) and archaeological specimens collected from middle and late Mesolithic as surrogate for the norm of reaction in European wild boar phenotype before the spread of agriculture and domestic pigs. Results provide evidence for compressive and tensile forces as the main elements affecting the variation in the cortical thickness along the calcaneus. Furthermore, changes in the internal structure of the calcaneus between mobility patterns are observed but their intensity is not directly associated with the degree of mobility restriction and only weakly impacted by the size or weight of the individuals. Despite having greater bone volume, the calcaneus of the Mesolithic wild boars displays a very similar microanatomy compared to the present-day hunted or captive wild boars. These results suggest that calcaneal microanatomy is more affected by population differences than by locomotor variation. For all these reasons, this preliminary study doesn’t support the use of microanatomy of the calcaneus as an indicator of change in locomotor behaviour induced by captivity in the archaeological record.

Published
2022
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12. Bones geometric morphometrics illustrate 10th millennium cal. BP domestication of autochthonous Cypriot wild boar (Sus scrofa circeus nov. ssp)

Author

Jean Guilaine, Hugo Harbers, Roger Alcàntara Fors, Charlotte Leduc, François Briois, Max Price, Aurélie Guidez, Allowen Evin, Jean-Denis Vigne, Joris Peters, Maria Saña, Anne Bridault, Auriale Domont, Hitomi Hongo, Thomas Cucchi, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Archéologies et Sciences de l'Antiquité (ArScAn), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Archéologies environnementales, Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS)-Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Autonomous University of Barcelona, Faculty of Education, Trajectoires - UMR 8215, Université Paris 1 Panthéon-Sorbonne (UP1)-Centre National de la Recherche Scientifique (CNRS), Archéologie et histoire ancienne : Méditerranée - Europe (ARCHIMEDE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS)-Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS), Travaux et recherches archéologiques sur les cultures, les espaces et les sociétés (TRACES), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Collège de France (CdF (institution)), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS)-Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université de Toulouse (UT)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)

Subjects
0106 biological sciences, 0301 basic medicine, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Evolution, Lineage (evolution), [SDE.MCG]Environmental Sciences/Global Changes, Science, Sus scrofa, Zoology, 010603 evolutionary biology, 01 natural sciences, Article, Domestication, 03 medical and health sciences, Wild boar, biology.animal, Animals, Animal Husbandry, Author Correction, History, Ancient, Morphometrics, Multidisciplinary, Epipaleolithic, biology, 030104 developmental biology, Geography, Geographic origin, [SHS.ENVIR]Humanities and Social Sciences/Environmental studies, Medicine, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology
Abstract

Epipaleolithic hunter-gatherers from the Near East introduced wild boars (Sus scrofa) to Cyprus, with the Early Pre-Pottery Neolithic (PPN) settlers hunting the wild descendants of these boars. However, the geographic origin of the Cypriot boar and how they were integrated into the earliest forms of pig husbandry remain unsolved. Here, we present data on 11,000 to 9000 cal. BP Sus scrofa from the PPN sites of Klimonas and Shillourokambos. We compared them to contemporaneous populations from the Near East and to Neolithic and modern populations in Corsica, exploring their origin and evolution using biosystematic signals from molar teeth and heel bones (calcanei), using 2D and 3D geometric morphometrics. We found that the Cypriot PPN lineage of Sus scrofa originates from the Northern Levant. Yet, their phenotypic idiosyncrasy suggest that they evolved into an insular sub-species that we named Sus scrofa circeus, referring to Circe, the metamorphosis goddess that changed Ulysses companions into pigs. The phenotypic homogeneity among PPNA Klimonas wild boars and managed populations of PPNB Shillourokambos suggests that local domestication has been undertaken on the endemic S. s. circeus, strengthening the idea that Cyprus was integrated into the core region of animal domestication.

Published
2021
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13. Exploring the carbonization effect on the interspecific identification of cotton (Gossypium spp.) seeds using classical and 2D geometric morphometrics

Author

Juliette Milon, Charlène Bouchaud, Christopher Viot, Michel Lemoine, and Thomas Cucchi

Subjects
Gossypium arboreum, Identification, Gossypium, Archeology, Morphologie végétale, archéologie, Gossypium hirsutum, F70 - Taxonomie végétale et phytogéographie, Taxonomie, F50 - Anatomie et morphologie des plantes, Gossypium barbadense, Gossypium herbaceum, B50 - Histoire
Abstract

The history of cotton (Gossypium sp), which has become along past millennia a plant of major economic interest, relies on the dried or charred cotton seeds found in archaeobotanical assemblages. Our capacity to document the dispersal routes of cotton, however, is hampered by the lack of taxonomic resolution at specific levels based on current seed anatomic features. In order to explore the taxonomic signal at the interspecific level of cotton seeds, and the impact of carbonization on this signal, we used linear measurements (length, width and thickness) and 2D geometric morphometrics (GM) comparing modern dried cotton seeds of the four domesticates (G. arboreum, G. herbaceum, G. barbadense, G. hirsutum) and experimentally charred seeds. The shape and form (size + shape) of dried and charred cotton seeds were captured using an outline analysis with a sliding semi-landmarks approach and compared after a Generalized Procrustes Superimposition (GPS). The reaction of cotton seeds to charring at 250 °C during 2 h30 was globally characterized by a size reduction but no major shape deformation; this study also shows that the outline form of the seeds rather than their shape provides more stringent taxonomic discriminations than linear measurements. This pilot study emphasizes the relevance of the GM approach while underlying the limit of this method for the taxonomical study of archaeological cotton seeds.

Published
2023
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14. Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history

Author

Ben Krause-Kyora, Jørn Zeiler, Hiba Al-Jarah, Wijerathne Bohingamuwa, Becky Knight, Kinie Esser, Joan Ramon, Chris J. Conroy, Chris Hillman, Beate Böhlendorf-Arslan, Quintana Morales, Tarek Oueslati, Bouthéina Maraoui-Telmini, Jean-Denis Vigne, Nicole Boivin, Jude Perera, Silvia Radbauer, Ardern Hulme-Beaman, G. Adikari, Günther Karl Kunst, Heidi Eager, Sheila Hamilton-Dyer, Jeffrey Fleisher, Thomas Walker, Richard F. Helm, Thomas Cucchi, Terry O'Connor, Alison Crowther, Nimal Perera, Silvia Valenzuela-Lamas, Camilla Speller, Jeremy B. Searle, Arturo Morales-Muñiz, Pavel Gol'din, Anna Linderholm, Nabil Kallala, Alexandra Trinks, Zsófia E. Kovács, He Yu, Johannes Krause, Louisa Gidney, E. V. Gladilina, Wim Van Neer, David Orton, Eréndira M., Alexandra Jamieson, Edward R. Treasure, Joan Sanmartí Grego, Mariana Nabais, Greger Larson, Hanna Kivikero, Inge van der Jagt, Eve Rannamäe, Keith Dobney, Stephanie Wynne-Jones, Henriette Baron, Steven M. Goodman, Kerstin Pasda, René Kyselý, Repositório da Universidade de Lisboa, Yu, He, Jamieson, Alexandra, Hulme-Beaman, Ardern, Conroy, Chris J., Speller, Camilla, Baron, Henriette, Crowther, Alison, Cucchi, Thomas, Fleisher, Jeffrey, Gladilina, Elena, Gol’din, Pavel, Goodman, Steven M., Kunst, Günther Karl, Linderholm, Anna, Morales-Muñiz, Arturo, Nabais, Mariana, Oueslati, Tarek, Quintana Morales, Eréndira M., Rannamäe, Eve, Sanmartí Grego, Joan, Valenzuela-Lamas, Silvia, Neer, Wim Van, Vigne, Jean-Denis, Wynne-Jones, Stephanie, Dobney, Keith, Boivin, Nicole, Searle, Jeremy B., Krause-Kyora, Ben, Krause, Johannes, Larson, Greger, Orton, David, Yu, He [0000-0003-1323-4730], Jamieson, Alexandra [0000-0003-0979-5762], Hulme-Beaman, Ardern [0000-0001-8130-9648], Conroy, Chris J. [0000-0001-7198-9651], Speller, Camilla [0000-0001-7128-9903], Baron, Henriette [0000-0003-4338-3681], Crowther, Alison [0000-0002-2394-1917], Cucchi, Thomas [0000-0001-6021-5001], Fleisher, Jeffrey [0000-0002-6505-9666], Gladilina, Elena [0000-0002-5114-7526], Gol’din, Pavel [0000-0001-6118-1384], Goodman, Steven M. [0000-0001-9318-0570], Kunst, Günther Karl [0000-0002-2175-8641], Linderholm, Anna [0000-0002-1613-9926], Morales-Muñiz, Arturo [0000-0002-9933-6836], Nabais, Mariana [0000-0001-5344-237X], Oueslati, Tarek [0000-0002-2886-085X], Quintana Morales, Eréndira M. [0000-0001-5927-5058], Rannamäe, Eve [0000-0003-1186-5512], Sanmartí Grego, Joan [0000-0002-6635-9249], Valenzuela-Lamas, Silvia [0000-0001-9886-0372], Neer, Wim Van [0000-0003-1710-3623], Vigne, Jean-Denis [0000-0002-7367-7552], Wynne-Jones, Stephanie [0000-0002-3005-8647], Dobney, Keith [0000-0001-9036-4681], Boivin, Nicole [0000-0002-7783-4199], Searle, Jeremy B. [0000-0001-7710-5204], Krause-Kyora, Ben [0000-0001-9435-2872], Krause, Johannes [0000-0001-9144-3920], Larson, Greger [0000-0002-4092-0392], Orton, David [0000-0003-4069-8004], Department of Cultures, Max Planck Institute for the Science of Human History (MPI-SHH), Max-Planck-Gesellschaft, Research Laboratory for Archaeology and the History of Art [Oxford], School of Archaeology [Oxford], University of Oxford-University of Oxford, University of Liverpool, Liverpool John Moores University (LJMU), Museum of Vertebrate Zoology [Berkeley], University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, 07745, Germany, School of Social Science, University of Queensland, University of Queensland [Brisbane], Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Rent a Peasant, National Academy of Sciences of Ukraine (NASU), Field Museum of Natural History [Chicago, USA], Histoire, Archéologie et Littérature des Mondes Anciens - UMR 8164 (HALMA), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture (MC), and Open Access funding enabled and organized by Projekt DEAL

Subjects
0106 biological sciences, Population genetics, [SDV]Life Sciences [q-bio], General Physics and Astronomy, 01 natural sciences, 615 History and Archaeology, [SHS]Humanities and Social Sciences, PHYLOGEOGRAPHY, Max planck institute, PLAGUE, DISPERSAL, 0303 health sciences, Multidisciplinary, humanities, Europe, Multidisciplinary Sciences, ALIGNMENT, Archaeology, 1181 Ecology, evolutionary biology, language, Science & Technology - Other Topics, Christian ministry, Training program, YERSINIA-PESTIS, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, European black rats, Library science, DNA, Mitochondrial, 010603 evolutionary biology, Institutional support, SEQUENCE, General Biochemistry, Genetics and Molecular Biology, Middle East, 03 medical and health sciences, Population history, Classical archaeology, Political science, Animals, Humans, 030304 developmental biology, Plague, National history, Science & Technology, COVID-19, Excavation, General Chemistry, FRAMEWORK, language.human_language, Rats, Coronavirus, MICE, INDIAN-OCEAN, PATTERNS, Catalan
Abstract

The distribution of the black rat (Rattus rattus) has been heavily influenced by its association with humans. The dispersal history of this non-native commensal rodent across Europe, however, remains poorly understood, and different introductions may have occurred during the Roman and medieval periods. Here, in order to reconstruct the population history of European black rats, we generated a de novo genome assembly of the black rat, 67 ancient black rat mitogenomes and 36 ancient nuclear genomes from sites spanning the 1st-17th centuries CE in Europe and North Africa. Analyses of mitochondrial DNA confirm that black rats were introduced into the Mediterranean and Europe from Southwest Asia. Genomic analyses of the ancient rats reveal a population turnover in temperate Europe between the 6th and 10th centuries CE, coincident with an archaeologically attested decline in the black rat population. The near disappearance and re-emergence of black rats in Europe may have been the result of the breakdown of the Roman Empire, the First Plague Pandemic, and/or post-Roman climatic cooling., We thank the wet laboratory teams at MPI-SHH, the PalaeoBARN at the University of Oxford and the University of York. We thank David K. James and Lucia Hui of the Alameda County Vector Control Services District for procuring the rat used for the de novo genome. We are grateful to Sarah Nagel at Max Planck Institute for the Evolutionary Anthropology for the single-stranded library preparation, and Dovetail Genomics for the de novo genome assembly service. We thank Maria Spyrou for her suggestions and comments. We acknowledge Ewan Chipping and Helena England (University of York), Carl Phillips, Veronica Lindholm (Ålands Museum), Christine McDonnell and Nienke van Doorn (York Archaeological Trust), Emile Mittendorf (Gemeente Deventer), Inge Riemersma (Archaeological depot, Provincie Zuid-Holland), the Turkish Ministry of Culture & Tourism, Jan Frolík and Iva Herichová (Institute of Archaeology of the Czech Academy of Sciences, Prague), Franz Humer and Eduard Pollhammer (Archaeological Park Carnuntum), Dorottya B. Nyékhelyi and László Daróczi-Szabó (Budapest History Museum), Institut National du Patrimoine (Tunisia), University of Barcelona, Spanish Ministry of Science and Innovation (Project HUM2006-03432/HIST), Spanish Ministry of Culture (program of archaeological excavations abroad 2009); Spanish Agency of International Cooperation for the Development (2009), Catalan Institute of Classical Archaeology (ICAC), Vujadin Ivanisević, Nemanja Marković and Ivan Bugarski (Archaeological Institute 809 Belgrade), the Field Museum Chicago, the British National History Museum and the American Museum of Natural History for providing materials and support. G.L. and A.J. were supported by the ERC (grant ERC-2013-StG-337574-UNDEAD) and A.J. was supported by the Natural Environment Research Council Doctoral Training Program. D.O. was supported by Wellcome (Small Grant in Humanities and Social Science 209817/Z) and the British Academy / Leverhulme Trust (Small Research Grant SG170938). E.R. was supported by Estonian Research Council grant No PRG29. R.K. was supported by the Czech Academy of Sciences institutional support (RVO:67985912). S.V.-L. was supported by the ERC (grant ERC-StG- 716298 ZooMWest). H.E. was funded by an ERC grant (206148) through the Sealinks Project. A.H.B was funded by the Leverhulme Trust (ECF-2017-315). The de novo genome assembly, population genomics study, and radiocarbon dating were funded by the Max Planck Society.

Published
2022
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15. Investigating Neolithic and Medieval caprine herds mobility in the French island of Corsica

Author

Mélanie Fabre, Hannah James, Vianney Forest, Christophe Ranché, Gilles Giovannangeli, Daniel Istria, Denis Fiorillo, Thomas CUCCHI, D Vigne, J., Christophe Snoeck, Marie Balasse, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Vrije Universiteit Brussel [Bruxelles] (VUB), Institut national de recherches archéologiques préventives (Inrap), Travaux et recherches archéologiques sur les cultures, les espaces et les sociétés (TRACES), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université de Toulouse (UT)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Archéologie Médiévale et Moderne en Méditerranée (LA3M), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Vrije Universiteit Brussel (VUB), ATM MNHN, and TransCorse

Subjects
[SHS]Humanities and Social Sciences
Abstract

International audience

Published
2022

16. How Changes in Functional Demands Associated with Captivity Affect the Skull Shape of a Wild Boar (Sus scrofa)

Author

Anthony Herrel, Jean-Denis Vigne, Ashleigh Haruda, Yann Locatelli, Vincent Debat, Raphaël Cornette, Dimitri Neaux, Cécile Callou, Renate Schafberg, Flavie Laurens, François Lecompte, Barbara Blanc, Gabriele Sansalone, Katia Ortiz, Isabelle Baly, Thomas Cucchi, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de paléontologie, évolution, paléoécosystèmes, paléoprimatologie (PALEVOPRIM ), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Bases de données sur la Biodiversité, Ecologie, Environnement et Sociétés (BBEES), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN), Plate-forme de Chirurgie et Imagerie pour la Recherche et l’Enseignement (CIRE), Institut National de la Recherche Agronomique (INRA), University of New England (UNE), Università degli Studi Roma Tre, Center for Evolutionary Ecology, Martin-Luther-Universität Halle Wittenberg (MLU), Mécanismes Adaptatifs et Evolution (MECADEV), and Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
0106 biological sciences, 0301 basic medicine, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Captivity, Zoology, Mandible, Phenotypic plasticity, Affect (psychology), 010603 evolutionary biology, 01 natural sciences, Domestication, 03 medical and health sciences, Wild boar, biology.animal, medicine, Craniofacial, Ecology, Evolution, Behavior and Systematics, Morphometrics, Pig, biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Masticatory force, Skull, 030104 developmental biology, medicine.anatomical_structure, Cranium
Abstract

International audience; The process of animal domestication is a key evolutionary transition in human history, within which the control of wild populations is considered a crucial first step. Yet, phenotypic changes associated with animal captivity remain challenging to document. Here, we investigated the craniofacial changes in wild boar (Sus scrofa) associated with a lifetime of growth in captivity under conditions of controlled mobility and diet. Using three-dimensional landmark-based geometric morphometrics, we assessed cranial and mandibular size and shape differences between captive and wild-caught wild boar, their link with masticatory forces, and how these plastic changes relate to traits selected in domestic pigs. We observed shape divergence associated with greater masticatory forces in captive wild boar (e.g., wider zygomatic arches, more upright mandibular rami, and reduced gonial angle) corroborating the fundamental role of biomechanical loading and constructional constraints in the skull shape changes associated with captivity. Despite their resemblance with domestic traits, these localised plastic changes follow a different phenotypic trajectory, suggesting that they did not contribute to the setup of the craniofacial morphology of current domestic breeds. A parallel increase of masticatory force in captive wild boars and domestic pigs may explain this phenotypic convergence but needs to be further explored.

Published
2020
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17. The effect of captivity on craniomandibular and calcaneal ontogenetic trajectories in wild boar

Author

Dimitri Neaux, Hugo Harbers, Barbara Blanc, Katia Ortiz, Yann Locatelli, Anthony Herrel, Vincent Debat, and Thomas Cucchi

Subjects
Calcaneus, Swine, Skull, Sus scrofa, Genetics, Molecular Medicine, Humans, Animals, Animal Science and Zoology, Animals, Wild, Plastics, Ecology, Evolution, Behavior and Systematics, Developmental Biology
Abstract

Deciphering the plastic (i.e., nonheritable) changes induced by human control over wild animals in the archeological record is challenging. Previous studies detected morphological markers associated with captivity in the cranium, mandible, and calcaneus of adult wild boar (Sus scrofa) but the developmental trajectories leading up to these changes during ontogeny remain unknown. To assess the impact of growth in a captive environment on morphological structures during postnatal ontogeny, we used an experimental approach focusing on the same three structures and taxon. We investigated the form and size differences of captive-reared and wild-caught wild boar during growth using three-dimensional landmark-based geometric morphometrics. Our results provide evidence of an influence of captivity on the morphology of craniomandibular structures, as wild specimens are smaller than captive individuals at similar ages. The food resources inherent to anthropogenic environments may explain some of the observed differences between captive-reared and wild specimens. The calcaneus presents a different contrasted pattern of plasticity as captive and wild individuals differ in terms of form but not in terms of size. The physically more constrained nature of the calcaneus and the direct influence of mobility reduction on this bone may explain these discrepancies. These results provide new methodological perspectives for bioarchaeological approaches as they imply that the plastic mark of captivity can be observed in juvenile specimens in the same way it has been previously described in adults.

Published
2022

22. Une nouvelle matière, une nouvelle culture : le coton en Arabie antique

Author

Charlène Bouchaud, Thomas CUCCHI, Vladimir Dabrowski, Éric Douville, Juliette Milon, Ryan, Saskia E., Margareta Tengberg, Antoine Zazzo, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Muséum national d'Histoire naturelle (MNHN), Histoire naturelle de l'Homme préhistorique (HNHP), Muséum national d'Histoire naturelle (MNHN)-Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), and Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, [SHS.ENVIR]Humanities and Social Sciences/Environmental studies, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SHS.HIST]Humanities and Social Sciences/History, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2021

23. Reconsidering domestication from a process archaeology perspective

Author

Alexander Weide, Joris Peters, Sarah L. Crowley, Dorian Q. Fuller, Robin Bendrey, Benjamin S. Arbuckle, Tom Gilbert, Elinor K. Karlsson, Fiona Marshall, Robin G. Allaby, Charles Stépanoff, Natalie G. Mueller, Greger Larson, Tim Denham, Thomas Cucchi, Amy Bogaard, Aurelie Manin, Laurent A. F. Frantz, Research Laboratory for Archaeology and the History of Art [Oxford], School of Archaeology [Oxford], University of Oxford-University of Oxford, Santa Fe Institute, University of Warwick [Coventry], University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC), University of Edinburgh, Centre for Geography and Environmental Science (CGES), University of Exeter, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Ludwig Maximilian University [Munich] (LMU), University College of London [London] (UCL), University of Copenhagen = Københavns Universitet (UCPH), University of Oxford, École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL), This work was supported by the European Research Council [ERC-2013-StG-337574-UNDEAD] and the Santa Fe Institute., and European Project: 337574,EC:FP7:ERC,ERC-2013-StG,UNDEAD(2014)

Subjects
Archeology, History, herding, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Process (engineering), Metaphysics, Domestication, 03 medical and health sciences, Hybridity, 0601 history and archaeology, Process philosophy, process, hybridity, SF, 030304 developmental biology, agriculture, 0303 health sciences, QL, 060102 archaeology, Perspective (graphical), Foundation (evidence), Environmental ethics, 06 humanities and the arts, CC, niche, General Earth and Planetary Sciences
Abstract

International audience; Process philosophy offers a metaphysical foundation for domestication studies. This grounding is especially important given the European colonialist origin of 'domestication' as a term and 19th century cultural project. We explore the potential of process archaeology for deep-time investigation of domestication relationships, drawing attention to the variable pace of domestication as an ongoing process within and across taxa; the nature of domestication 'syndromes' and 'pathways' as general hypotheses about process; the importance of cooperation as well as competition among humans and other organisms; the significance of non-human agency; and the ubiquity of hybrid communities that resist the simple wild/domestic dichotomy.

Published
2021
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25. Animal domestication: from distant past to current development and issues

Author

Benjamin S. Arbuckle, Thomas Cucchi, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN), and Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)

Subjects
2. Zero hunger, 0303 health sciences, Introduction, 060102 archaeology, [SDV]Life Sciences [q-bio], Environmental ethics, 06 humanities and the arts, [SHS]Humanities and Social Sciences, 03 medical and health sciences, Geography, Food Animals, [SDE]Environmental Sciences, AcademicSubjects/SCI00960, 0601 history and archaeology, Animal Science and Zoology, Current (fluid), Domestication, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract

International audience; Domestic animals have played an important role in shaping human Evolution and History. After millennia of constructing niches based on hunting, gathering, and foraging, a range of communities in diverse parts of the world embarked on trajectories of food production which in some instances led to the emergence of complex societies, urbanism, and empires, sowing the seeds for our current globalization. Thanks to intensive zooarcheology and genomics research, it is now common knowledge that, apart from dog domestication within hunter-gatherers societies around 23,000 years Before Present (BP) terminus post quem (Perri et al., 2021), the domestication of globally important livestock animals occurred within sedentary communities engaged in early agriculture in three independent cradles. The oldest of these is located in Southwest Asia where cereals (wheat, barley), legumes (pulse, peas, lentils), and fruits (figs) were domesticated between 12,000 and 10,000 BP, followed by sheep, goat, pigs, and cattle between 10,500 and 10,000 BP (Colledge et al., 2013). The second cradle is located in China where domesticated millets and rice were cultivated in the Yellow and Yangtze River valleys by 10,000 BP. This was followed relatively rapidly by pig domestication in the Yellow River valley (Jing and Flad, 2002; Cucchi et al., 2016). The last major center of ungulate domestication is located in the Andes, where agriculture based on imported maize and locally domesticated potato, beans, and squashes emerged between 9000 and 8000 BP along with South American camelids, llamas and alpacas, later followed by Barba's duck and the guinea pig around 4000 BP (Pearsall, 2008; Hardigan et al., 2017). North America, also contributed to global animal domestication with the turkey by 2000 BP (Speller et al., 2010). In the Old World, a later series of animal domestications focused on the use of animal labor, with the domestic forms of donkey, horse, and camel emerging between 5000 and 2000 BP (Clutton-Brock, 2014). These animals revolutionized human

Published
2021
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26. Constraints associated with captivity alter craniomandibular integration in wild boar

Author

Anthony Herrel, Barbara Blanc, Dimitri Neaux, Renate Schafberg, Yann Locatelli, Katia Ortiz, Vincent Debat, Thomas Cucchi, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de paléontologie, évolution, paléoécosystèmes, paléoprimatologie (PALEVOPRIM ), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN), Martin-Luther-University Halle-Wittenberg, Evolutionary Morphology of Vertebrates, Universiteit Gent = Ghent University [Belgium] (UGENT), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), ANR-11-IDEX-0004-02ANR-13-JSH3-0003-01Association Sorbonne UniversiteSU-19-3-EMRG-02, and ANR-10-LABX-0003,BCDiv,Biological and Cultural Diversities : Origins, Evolution, Interactions, Future(2010)

Subjects
0301 basic medicine, Male, skull, Histology, Process (engineering), Sus scrofa, Captivity, Context (language use), morphological integration, 03 medical and health sciences, cranium, domestication, 0302 clinical medicine, Wild boar, biology.animal, Animals, Domestication, geometric morphometrics, Molecular Biology, Ecology, Evolution, Behavior and Systematics, modularity, biology, [SDV.BA]Life Sciences [q-bio]/Animal biology, Cell Biology, Feeding Behavior, 030104 developmental biology, Morphological integration, Evolutionary biology, Female, Anatomy, 030217 neurology & neurosurgery, Developmental Biology
Abstract

International audience; The domestication process is associated with substantial phenotypic changes through time. However, although morphological integration between biological structures is purported to have a major influence on the evolution of new morphologies, little attention has been paid to the influence of domestication on the magnitude of integration. Here, we assessed the influence of constraints associated with captivity, considered as one of the crucial first steps in the domestication process, on the integration of cranial and mandibular structures. We investigated the craniomandibular integration in Western European Sus scrofa using three‐dimensional (3D) landmark‐based geometric morphometrics. Our results suggest that captivity is associated with a lower level of integration between the cranium and the mandible. Plastic responses to captivity can thus affect the magnitude of integration of key functional structures. These findings underline the critical need to develop integration studies in the context of animal domestication to better understand the processes accountable for the set‐up of domestic phenotypes through time.

Published
2021
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27. EvoSheep : The Makeup of Sheep Breeds in the Ancient Near East

Author

Sofiane Bouzid, François Pompanon, Bea De Cupere, Camille Bader, Hossein Davoudi, Philippe Abrahami, Daniel Helmer, Catherine Breniquet, Azadeh Fatemeh Mohaseb, Thomas Cucchi, Rémi Berthon, Moussab Albesso, Oscar Estrada, Lionel Gourichon, Emmanuelle Vila, Marjan Mashkour, Daniel G. Bradley, Manon Vuillien, Jwana Chahoud, Ludovic Orlando, Jacqueline Studer, Wei Huangfu, Cécile Michel, Gilles Escarguel, Joséphine Lesur, Agraw Amane, ARCHEORIENT - Environnements et sociétés de l'Orient ancien (Archéorient), Université Lumière - Lyon 2 (UL2)-Centre National de la Recherche Scientifique (CNRS), Histoire, Archéologie et Littérature des Mondes Anciens - UMR 8164 (HALMA), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture (MC), Addis Ababa University (AAU), International Livestock Research Institute [CGIAR, Ethiopie] (ILRI), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Trinity College Dublin, Centre d'Histoire 'Espaces et Cultures' (CHEC), Université Clermont Auvergne (UCA), Lebanese University [Beirut] (LU), University of Tehran, Royal Belgian Institute of Natural Sciences (RBINS), Équipe 6 - Paléontologie, Paléoécologie, Paléobiogéographie, Évolution (P3E), Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Culture et Environnements, Préhistoire, Antiquité, Moyen-Age (CEPAM), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Maison de l'Orient et de la Méditerranée - Jean Pouilloux (MOM), École normale supérieure de Lyon (ENS de Lyon)-Université Lumière - Lyon 2 (UL2)-Université Jean Moulin - Lyon 3 (UJML), Université de Lyon-Université de Lyon-Aix Marseille Université (AMU)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Archéologies et Sciences de l'Antiquité (ArScAn), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Natural History Museum [Geneva], ANR-17-CE27-0004,EVOSHEEP,Exploration des premières innovations zootechniques dans les sociétés du sud-ouest asiatique (5e-1er millénaires av. J.-C.)(2017), Histoire Archéologie Littérature des Mondes Anciens - UMR 8164 (HALMA), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN), Archaeozoological section, Bioarchaeological laboratory, Directorate Earth & History of Life, Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Department of Archaeozoology, Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Ministère de la Culture (MC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Department of Microbial, Cellular and Molecular Biology, ILRI Ethiopia (ILRI), ILRI, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland, Department of Archaeology, Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA), École normale supérieure - Lyon (ENS Lyon)-Université Lumière - Lyon 2 (UL2)-Université Jean Moulin - Lyon 3 (UJML), Université de Lyon-Université de Lyon-Aix Marseille Université (AMU)-Université Jean Monnet [Saint-Étienne] (UJM)-Centre National de la Recherche Scientifique (CNRS), ARCHEORIENT - Environnements et sociétés de l'Orient ancien [Archéorient], Histoire, Archéologie et Littérature des Mondes Anciens - UMR 8164 [HALMA], Archéozoologie, archéobotanique : sociétés, pratiques et environnements [AASPE], Centre d'Histoire 'Espaces et Cultures' [CHEC], Anthropologie Moléculaire et Imagerie de Synthèse [AMIS], Archéologies et Sciences de l'Antiquité [ArScAn], Laboratoire d'Ecologie Alpine [LECA ], Culture et Environnements, Préhistoire, Antiquité, Moyen-Age [CEPAM], Centre National de la Recherche Scientifique (CNRS)-Université Lumière - Lyon 2 (UL2), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS), and Équipe 6 - Paléontologie, Paléoécologie, Paléobiogéographie, Évolution [P3E]

Subjects
Near East, 010506 paleontology, Archeology, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Textile production, 01 natural sciences, [SHS]Humanities and Social Sciences, 0601 history and archaeology, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Levant, Archaeozoology, 0105 earth and related environmental sciences, 2. Zero hunger, Morphometrics, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, [SDV.GEN]Life Sciences [q-bio]/Genetics, Geometric morphometrics, Middle East, Plateau, geography.geographical_feature_category, Africa, Sheep, 060102 archaeology, General Arts and Humanities, Mesopotamia, 06 humanities and the arts, Archaeology, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Geography, [SDE]Environmental Sciences, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

International audience; The EVOSHEEP project combines archaeozoology, geometric morphometrics and genetics to study archaeo- logical sheep assemblages dating from the sixth to the first millennia BC in eastern Africa, the Levant, the Ana- tolian South Caucasus, the Iranian Plateau and Mesopotamia. The project aims to understand changes in the physical appearance and phenotypic characteristics of sheep and how these related to the appearance of new breeds and the demand for secondary products to supply the textile industry.

Published
2021
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28. Biomechanical constraints associated with captivity modify craniomandibular shape

Author

Dimitri Neaux, Anthony Herrel, Vincent Debat, Thomas Cucchi, Neaux, Dimitri, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Department of Biology, Universiteitsplein 1, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2021

29. Are petrous bones just a repository of ancient biomolecules? Investigating biosystematic signals in sheep petrous bones using 3D geometric morphometrics

Author

Camille Bader, Christophe Mallet, Jwana Chahoud, Agraw Amane, Bea De Cupere, Remi Berthon, Franck Lavenne, Azadeh Mohaseb, Hossein Davoudi, Moussab Albesso, Homa Fathi, Manon Vuillien, Joséphine Lesur, Daniel Helmer, Lionel Gourichon, Olivier Hanotte, Marjan Mashkour, Emmanuelle Vila, and Thomas Cucchi

Subjects
Archeology
Published
2022
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30. Author Correction: Bones geometric morphometrics illustrate 10th millennium cal. BP domestication of autochthonous Cypriot wild boar (Sus scrofa circeus nov. ssp)

Author

Roger Alcàntara Fors, Jean-Denis Vigne, Auriale Domont, Allowen Evin, Aurélie Guidez, François Briois, Joris Peters, Anne Bridault, Maria Saña, Charlotte Leduc, Hitomi Hongo, Jean Guilaine, Hugo Harbers, Max Price, and Thomas Cucchi

Subjects
Morphometrics, Multidisciplinary, Wild boar, biology.animal, Science, Zoology, Medicine, Biology, Domestication
Published
2021

31. Examining the effect of feralization on craniomandibular morphology in pigs, Sus scrofa (Artiodactyla: Suidae)

Author

Renate Schafberg, François Lecompte, Camille Noûs, Ashleigh Haruda, Thomas Cucchi, Dimitri Neaux, Gabriele Sansalone, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de paléontologie, évolution, paléoécosystèmes, paléoprimatologie (PALEVOPRIM ), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Division of Earth Sciences, School of Environmental and Rural Science, University of New England, Armidale, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Martin-Luther-University Halle-Wittenberg

Subjects
0106 biological sciences, 0303 health sciences, biology, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, animal diseases, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Zoology, Morphology (biology), biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Suidae, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract

Feralization is the process by which domestic animals return to the wild and produce self-sustaining populations. It is often considered as a model in understanding the permanence of morphological changes associated with domestication; however, it is still unclear how much the release of anthropogenic selective pressures affects domestic traits. Here, we assessed the influence of feralization on the domestic morphological traits acquired through selective breeding using craniomandibular differences in shape and size between populations of feral pigs, wild boar and domestic pigs, using landmark-based geometric morphometrics. Our results suggest that numerous cranial and mandibular traits associated with domestication still exist in feral specimens, corroborating that domestication-induced changes in the shape of morphological elements are broadly maintained in feral populations. This is not the case for size variations, however, as the cranium is significantly smaller in feral pigs than in domesticated breeds, which could be due to the selective pressures associated with founding events. Our exploratory study, therefore, underlines the complexity of feral population history, the intricate influence of variations in genetic diversity, and novel selection pressures in the morphology of these groups. Future studies will need to expand the sample to take into account the diversity of morphotypes.

Published
2020
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32. Deep learning for species identification of modern and fossil rodent molars

Author

Vincent Miele, Sabrina Renaud, Thomas Cucchi, Gaspard Dussert, Ecologie et évolution des populations, Département écologie évolutive [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), and Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Molar, Morphometrics, 0303 health sciences, Extinction, business.industry, Deep learning, Biodiversity, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], Numerical taxonomy, 03 medical and health sciences, Geography, Species identification, Identification (biology), Artificial intelligence, business, Cartography, 030304 developmental biology
Abstract

Reliable identification of species is a key step to assess biodiversity. In fossil and archaeological contexts, genetic identifications remain often difficult or even impossible and morphological criteria are the only window on past biodiversity. Methods of numerical taxonomy based on geometric morphometric provide reliable identifications at the specific and even intraspecific levels, but they remain relatively time consuming and require expertise on the group under study. Here, we explore an alternative based on computer vision and machine learning. The identification of three rodent species based on pictures of their molar tooth row constituted the case study. We focused on the first upper molar in order to transfer the model elaborated on modern, genetically identified specimens to isolated fossil teeth. A pipeline based on deep neural network automatically cropped the first molar from the pictures, and returned a prediction regarding species identification. The deep-learning approach performed equally good as geometric morphometrics and, provided an extensive reference dataset including fossil teeth, it was able to successfully identify teeth from an archaeological deposit that was not included in the training dataset. This is a proof-of-concept that such methods could allow fast and reliable identification of extensive amounts of fossil remains, often left unstudied in archaeological deposits for lack of time and expertise. Deep-learning methods may thus allow new insights on the biodiversity dynamics across the last 10.000 years, including the role of humans in extinction or recent evolution.

Published
2020

33. Village néolithique de Klimonas (Ayios Tychonas) - 2018

Author

François Briois, Thomas Cucchi, Jean-Denis Vigne, Solange Rigaud, Bernard Gassin, Pantelitsa Mylona, Benoît Devillers, Pierre-Antoin Beauvais, Laurence Astruc, Claire Manen, Jérôme Robitaille, Simon Puaud, Matthieu Lebon, Travaux et recherches archéologiques sur les cultures, les espaces et les sociétés (TRACES), Ministère de la Culture et de la Communication (MCC)-École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J)-Centre National de la Recherche Scientifique (CNRS), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Histoire naturelle de l'Homme préhistorique (HNHP), and Muséum national d'Histoire naturelle (MNHN)-Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS)

Subjects
DEVILLERS (géomorphologue, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, B. GASSIN (Tracéologue), M. LEBON, General Earth and Planetary Sciences, Univ. Montpellier), General Environmental Science
Abstract

Donnees scientifiques produites : Nouvelles donnees sur les debuts du Neolithique a ChypreAgios Tychonas - Klimonas: French Archaeological Mission par le Departement des Antiquites de ChypreMission archeologique francaise de Klimonas par l’Institut francaise de ChypreProgrammes « Ayios Tychonas – Klimonas, le plus ancien village chypriote » par l’AIBLBlog sur Klimonas Rappels des resultats anterieurs Le site de Klimonas, localise sur la commune d’Ayios Thychonas pres de Limassol, a ete decouv...

Published
2020
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34. Village néolithique de Klimonas (Ayios Tychonas) - 2017

Author

Benoît Devillers, Isabelle Carrère, Solange Rigaud, Jean-Denis Vigne, Pantelitsa Mylona, Jean Guilaine, Thomas Cucchi, François Briois, Margareta Tengberg, and Jérôme Robitaille

Subjects
General Earth and Planetary Sciences, General Environmental Science
Abstract

Donnees scientifiques produites : Nouvelles donnees sur les debuts du Neolithique a ChypreAgios Tychonas - Klimonas: French Archaeological Mission par le Departement des Antiquites de ChypreMission archeologique francaise de Klimonas par l’Institut francaise de ChypreProgrammes « Ayios Tychonas – Klimonas, le plus ancien village chypriote » par l’AIBLBlog sur Klimonas Rappels des resultats anterieurs Le site de Klimonas, localise sur la commune d’Ayios Thychonas pres de Limassol, a ete decouv...

Published
2020
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35. Correction for Frantz et al., Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe

Author

Ceiridwen J. Edwards, Anders Götherström, Benjamin S. Arbuckle, Linus Girdland-Flink, Domenico Fulgione, Ross Barnett, Michael J Richards, Katerina Trantalidou, Cristina Valdiosera, M. Thomas P. Gilbert, Joris Peters, Louis du Plessis, Jean-Denis Vigne, Joachim Burger, Dian Boric, Richard P. M. A. Crooijmans, Melinda A. Zeder, Erik Meijaard, Wolfram Schier, Panoraia Alexandri, Jörg Schibler, John Chapman, Adrian Balasescu, Greger Larson, Jörg Orschiedt, Anne Tresset, Simon Stoddart, Keith Dobney, Antonio Tagliacozzo, Thomas H. McGovern, Canan Çakirlar, Bea De Cupere, Caroline Malone, Laurent A. F. Frantz, Vesna Dimitrijević, Sepideh Maziar, Andrea Zeeb-Lanz, Cevdet Merih Erek, Adina Boroneant, Ash Erim-Ozdogan, Hendrik-Jan Megens, Azadeh Fatemeh Mohaseb, Hitomi Hongo, Marjan Mashkour, Amelie Scheu, Evan K. Irving-Pease, Michelle Alexander, David Orton, Richard Sabin, László Bartosiewicz, Nenad Tasić, François-Xavier Ricaut, Anastasia Papathanasiou, Darko Radmanovic, Liora Kolska Horwitz, Christina Geoerg, Clive Bonsall, Anna Linderholm, Peter Rowley-Conwy, Audrey T. Lin, Daniel Helmer, Daniel G. Bradley, Roger Matthews, Ron Pinhasi, Ninna Manaseryan, Shiva Sheikhi, Sophie Van Poucke, Lionel Gourichon, Mike J. Church, Kevin G. Daly, Valentin Dumitraşcu, Joséphine Lesur, Mihai Gligor, Martien A. M. Groenen, Alexander Yanevich, Vincent M. Battista, Cleia Detry, Max Price, Rose-Marie Arbogast, Holley Martlew, Allowen Evin, Elisabeth Stephan, Norbert Benecke, John R. Stewart, Ophélie Lebrasseur, Giedre Motuzaite Matuzeviciute, Gennady F. Baryshnikov, Lucia Sarti, Youri van den Hurk, James Haile, Mike Parker Pearson, Arkadiusz Marciniak, Victoria E. Mullin, Jose-Miguel Carreterow, Kurt J. Gron, Alexandros Triantafyllidis, Thomas Cucchi, Rebecca Miller, Jelena Bulatović, and Anton Ervynck

Subjects
Gene Flow, Multidisciplinary, Swine, Library science, Skin Pigmentation, Biological Sciences, Corrections, DNA, Mitochondrial, Domestication, Europe, Middle East, Anthropology, evolution, Animals, Neolithic, DNA, Ancient, History, Ancient, Phylogeny
Abstract

Significance Archaeological evidence indicates that domestic pigs arrived in Europe, alongside farmers from the Near East ∼8,500 y ago, yet mitochondrial genomes of modern European pigs are derived from European wild boars. To address this conundrum, we obtained mitochondrial and nuclear data from modern and ancient Near Eastern and European pigs. Our analyses indicate that, aside from a coat color gene, most Near Eastern ancestry in the genomes of European domestic pigs disappeared over 3,000 y as a result of interbreeding with local wild boars. This implies that pigs were not domesticated independently in Europe, yet the first 2,500 y of human-mediated selection applied by Near Eastern Neolithic farmers played little role in the development of modern European pigs., Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process.

Published
2020

36. Tracking the Near Eastern origins and European dispersal of the western house mouse

Author

Yannis Hamilakis, Fanis Mavridis, Melinda A. Zeder, François Raymond Valla, François Bonhomme, Régis Debruyne, Fereidoun Biglari, Greger Larson, Emma Jenkins, Cameron A. Petrie, Antoine Zazzo, Adrian Bălășescu, Alireza Sardari, Jean-Christophe Auffray, Roohollah Siahsarvi, Marjan Mashkour, Christiane Denys, Jean-Denis Vigne, Jamshid Darvish, Thomas Cucchi, Alan H. Simmons, Katerina Papayianni, Lloyd Weeks, Sophie Cersoy, Sepideh Maziar, Rémi Berthon, Laetitia Aznar-Cormano, David Orton, Jeremy B. Searle, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Wiener Laboratory, American School of Classical Studies at Athens, Centre de Recherche sur la Conservation (CRC ), Muséum national d'Histoire naturelle (MNHN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Paléontologie - Paris (CR2P), Muséum national d'Histoire naturelle (MNHN)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Direction générale déléguée à la Recherche, à l’Expertise, à la Valorisation et à l’Enseignement-Formation (DGD.REVE), Muséum national d'Histoire naturelle (MNHN), Institute of Archaeology Vasile Parvan, Desert Research Institute (DRI), Archéologies et Sciences de l'Antiquité (ArScAn), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Brown University, Ephorate of Palaeoanthropology–Speleology, Hellenic Ministry of Culture and Sports (YPPO), Ferdowsi University of Mashhad, Center for Paleolithic Research, National Museum of Iran, Department of Archaeology and Anthropology, University of Cambridge, Cambridge, UK, School of Humanities, Arts and Social Sciences, University of New England, Armidale, New South Wales, Australia, Research Institute of Cultural Heritage and Tourism (RICHT), Iranian Center for Archaeological Research (ICAR), Tehran, Iran, Goethe-Universität Frankfurt am Main, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Departments of Archaeology [York] (BioArch), University of York [York, UK], Bournemouth University [Poole] (BU), Smithsonian Institution, National Museum of Natural History, Cornell University [New York], University of Oxford [Oxford], Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, ANR-11-IDEX-0004,SUPER,Sorbonne Universités à Paris pour l'Enseignement et la Recherche(2011), ANR-10-LABX-0003,BCDiv,Biological and Cultural Diversities : Origins, Evolution, Interactions, Future(2010), Petrie, Cameron [0000-0002-2926-7230], Apollo - University of Cambridge Repository, Université Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226, Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS), Ferdowsi University of Mashhad (FUM), University of Oxford, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), University of Cambridge [UK] (CAM), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE)

Subjects
0301 basic medicine, 631/45, Molecular biology, [SDV]Life Sciences [q-bio], lcsh:Medicine, Introduced species, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, Biochemistry, House mouse, law.invention, [SHS]Humanities and Social Sciences, Mice, law, Radiocarbon dating, Europe, Eastern, lcsh:Science, 631/601, ComputingMilieux_MISCELLANEOUS, Multidisciplinary, Middle East, biology, Ecology, article, Mitochondria, Geography, Archaeology, [SDE]Environmental Sciences, 631/337, 010506 paleontology, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, DNA, Mitochondrial, 03 medical and health sciences, Human settlement, Asia, Western, Animals, Humans, Domestication, 0105 earth and related environmental sciences, lcsh:R, Radiometric Dating, Sequence Analysis, DNA, biology.organism_classification, Computational biology and bioinformatics, 030104 developmental biology, Cyprus, Biological dispersal, lcsh:Q, House mice, 631/114, 631/158, Introduced Species, Zoology
Abstract

The house mouse (Mus musculus) represents the extreme of globalization of invasive mammals. However, the timing and basis of its origin and early phases of dispersal remain poorly documented. To track its synanthropisation and subsequent invasive spread during the develoment of complex human societies, we analyzed 829 Mus specimens from 43 archaeological contexts in Southwestern Asia and Southeastern Europe, between 40,000 and 3,000 cal. BP, combining geometric morphometrics numerical taxonomy, ancient mitochondrial DNA and direct radiocarbon dating. We found that large late hunter-gatherer sedentary settlements in the Levant, c. 14,500 cal. BP, promoted the commensal behaviour of the house mouse, which probably led the commensal pathway to cat domestication. House mouse invasive spread was then fostered through the emergence of agriculture throughout the Near East 12,000 years ago. Stowaway transport of house mice to Cyprus can be inferred as early as 10,800 years ago. However, the house mouse invasion of Europe did not happen until the development of proto urbanism and exchange networks — 6,500 years ago in Eastern Europe and 4000 years ago in Southern Europe — which in turn may have driven the first human mediated dispersal of cats in Europe.

Published
2020
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37. Can bone anatomy record behavioral changes induced by the domestication process?

Author

Thomas CUCCHI, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), and Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS, [SHS]Humanities and Social Sciences
Abstract

International audience

Published
2020

38. The mark of captivity: plastic responses in the ankle bone of a wild ungulate ( Sus scrofa )

Author

Raphaël Cornette, François Casabianca, Renate Schafberg, François Lecompte, Anthony Herrel, Yann Locatelli, Cécile Callou, Isabelle Baly, Dimitri Neaux, Ashleigh Haruda, Sabrina Renaud, Barbara Blanc, Flavie Laurens, Thomas Cucchi, Hugo Harbers, Katia Ortiz, Jean-Denis Vigne, Jacqueline Studer, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), Bases de données sur la Biodiversité, Ecologie, Environnement et Sociétés (BBEES), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Centre National de la Recherche Scientifique (CNRS)-Université de Tours-Institut Français du Cheval et de l'Equitation [Saumur]-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA), Museum d'Histoire Naturelle de Genève, Ecologie et évolution des populations, Département écologie évolutive [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Biologie Intégrative des Populations, École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), Evolutionary Morphology of Vertebrates, Ghent University [Belgium] (UGENT), Muséum national d'Histoire naturelle (MNHN), Martin-Luther-Universität Halle Wittenberg (MLU), Chirurgie et Imagerie pour la Recherche et l'Enseignement [Nouzilly] (Plate-forme CIRE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Recherches sur le Développement de l'Elevage (LRDE), Muséum d'Histoire Naturelle de Genève, Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Mécanismes Adaptatifs et Evolution (MECADEV), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Muséum national d'Histoire naturelle (MNHN), Institut International de Paléoprimatologie, Paléontologie Humaine : Evolution et Paléoenvironnement (IPHEP), and Centre National de la Recherche Scientifique (CNRS)-Université de Poitiers

Subjects
0106 biological sciences, Ungulate, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, [SDV]Life Sciences [q-bio], Archaeological record, Captivity, Zoology, Ankle bone, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, phenotypic plasticity, 03 medical and health sciences, domestication, experimentation, Wild boar, biology.animal, medicine, medicine.bone, lcsh:Science, Domestication, geometric morphometrics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Phenotypic plasticity, Multidisciplinary, biology, [SDV.BA]Life Sciences [q-bio]/Animal biology, Human control, biology.organism_classification, locomotion, Organismal and Evolutionary Biology, [SDE]Environmental Sciences, lcsh:Q, wild boar, Research Article
Abstract

International audience; Deciphering the plastic (non-heritable) changes induced by human control over wild animals in the archaeological record is challenging. We hypothesized that changes in locomotor behaviour in a wild ungulate due to mobility control could be quantified in the bone anatomy. To test this, we experimented with the effect of mobility reduction on the skeleton of wild boar (Sus scrofa), using the calcaneus shape as a possible © 2020 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited. phenotypic marker. We first assessed differences in shape variation and covariation in captive-reared and wild-caught wild boars, taking into account differences in sex, body mass, available space for movement and muscle force. This plastic signal was then contrasted with the phenotypic changes induced by selective breeding in domestic pigs. We found that mobility reduction induces a plastic response beyond the shape variation of wild boars in their natural habitat, associated with a reduction in the range of locomotor behaviours and muscle loads. This plastic signal of captivity in the calcaneus shape differs from the main changes induced by selective breeding for larger muscle and earlier development that impacted the pigs' calcaneus shape in a much greater extent than the mobility reduction during the domestication process of their wild ancestors.

Published
2020
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39. First farming in the north-western Mediterranean

Author

Didier Binder, Janet Battentier, Laurent Bouby, Jacques-Élie Brochier, Carré Alain, Thomas CUCCHI, Delhon Claire, Cristina de Stefanis, Léa Drieu, Allowen Evin, Linus Girdland Flink, Gwenaëlle Goude, Lionel Gourichon, Sebastien Guillon, Caroline Hamon, Stéphanie Thiebault, Culture et Environnements, Préhistoire, Antiquité, Moyen-Age (CEPAM), Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)

Subjects
ComputingMilieux_MISCELLANEOUS, [SHS]Humanities and Social Sciences
Abstract

International audience

Published
2020
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41. L’homme facteur d’évolution des faunes mammaliennes à l’Holocène : invasion biologique de la souris commensale et impact de la captivité sur la forme crânienne d’un ongulé sauvage

Author

Thomas CUCCHI, Dimitri Neaux, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), and Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS, [SHS]Humanities and Social Sciences
Abstract

International audience

Published
2019

42. Experimental Domestication: exploring plastic bone markers of captivity

Author

Thomas CUCCHI, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), and Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS, [SHS]Humanities and Social Sciences
Abstract

International audience

Published
2019

43. DOMEXP Exploring bone markers of the domestication process

Author

Thomas CUCCHI, Dimitri Neaux, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), and Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS, [SHS]Humanities and Social Sciences
Abstract

International audience

Published
2019

44. Taxonomic and phylogenetic signals in bovini cheek teeth: Towards new biosystematic markers to explore the history of wild and domestic cattle

Author

Alexandre Hassanin, Barbara Stopp, Renate Schafberg, Jörg Schibler, Thomas Cucchi, Joséphine Lesur, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), University of Basel (Unibas), and Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
2. Zero hunger, 010506 paleontology, Archeology, Bovini, 060102 archaeology, biology, Phylogenetic tree, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Introgression, 06 humanities and the arts, Aurochs, biology.organism_classification, Tribe (biology), Zebu, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, Evolutionary biology, Phylogenetics, 0601 history and archaeology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Domestication, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences
Abstract

Domestic cattle have contributed both to the rise of civilizations and the global loss of biodiversity, but the timing and mechanism of their domestication history remain to be fully understood. Palaeogenetics, which can now explore the target of human selection in the genome, have revolutionized our understanding of cattle domestication. However, biometric approaches of bone remains are still required as a prerequisite for targeted paleogenetic studies to document the taxonomic diversity of wild progenitors and the emergence of domestic morphotypes. But so far, biometric markers of cattle domestication have proven limited in their capacity to disentangle human intentionality from other biotic and abiotic factors. Using a two-dimensional geometric morphometric approach (GMM), we assessed the taxonomic and phylogenetic signals of the enamel folding pattern of occlusal surfaces (EFPOS) in the maxillary and mandibular molars of wild and domestic species of the tribe Bovini, including ancient cattle breeds and archaeological aurochs and domestic cattle. The phylogenetic signal was assessed using a mitochondrial genome phylogeny across 11 wild taxa of the tribe Bovini. We found that EFPOS could accurately identify both the wild and domestic species of the Bovini taxa as well as shape differentiation among aurochs and modern and archaeological cattle. The phylogenetic differentiation among aurochs and both taurine and zebu cattle is strong, but the overall phylogenetic signal among the tribe Bovini is blurred by genetic introgression between wild and domestic Bos species in south-east Asia. These results strongly suggest that the GMM analysis of dental traits are relevant markers that can be used before the implementation of targeted paleogenomic analyses as a mean to document the diversity and distribution of wild progenitors of domestic forms, identify the emergence of the earliest regional morphotype and their trajectory towards modern breeds.

Published
2019
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45. Agricultural economy and the development of cotton cultivation during the Meroitic period (4th c. BC - 5th c. AD) in central Sudan: seed, fruits and morphometric analyses at Mouweis

Author

Juliette Milon, Charlène Bouchaud, Thomas CUCCHI, Marie Millet, Antoine Zazzo, Marie-Pierre Ruas, Muséum national d'Histoire naturelle (MNHN), Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Musée du Louvre, and Bouchaud, Charlène

Subjects
[SHS.ARCHEO] Humanities and Social Sciences/Archaeology and Prehistory, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory
Abstract

International audience; Mouweis (Central Sudan) is located on the bank of the Nile, 50km south from the ancient Meroe. The region is characterized by an arid climate with irregular monsoons. The excavation conducted by the Musée du Louvre and the Sudanese Antiquities since 2007 show that Mouweis is occupied from the 4th c. BC to the 5th c; AD, which correspond to the emergence and decline of the Meroitic kingdom. The site presents all the characteristic structures of a Meroitic town such as a palace, a temple, living/handcraft quarters, etc. Systematic dry-sieving of the excavated sedimenthas been done in order to get botanical macroremains and to define past agricultural dynamics and plant exploitation. The study of archaeobotanical macroremains (1stc. BC to 5thc. AD) highlights the importance of tropical crops growing during summer, such as sorghum (Sorghum bicolor), pearl millet (Pennisetum glaucum) and cotton (Gossypium sp.). Winter crops are less numerous, mostly represented by barley (Hordeum vulgare) and wheat (Triticum cf. turgidum subsp. dicoccon). The presence and diversity of many small Panicoideae suggest that they were exploited for different uses as Human food and feed, forage, medicine. Frequent finds of cotton seeds, radiocarbon dated, highlight the important role of this new textile plant into the Meroitic economy from the 1st c. AD onwards. Geometric morphometric analyses carried out on cotton seeds give new taxonomical information. The results, together with evidence from other Meroitic sites, help us to better define the agricultural economy and figure out the role of tropical crops into the Meroitic society.

Published
2019

46. Domesticación de los camélidos en Telarmachay: nuevas investigaciones zooarqueológicas

Author

Manon Le Neün, Elise Dufour, Nicolas Goepfert, Thomas CUCCHI, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), ANR CAMELANDES- ANR-15-CE27-0002Le Domaine d’intérêt majeur (DIM) Matériaux anciens et patrimoniaux, and Nicolas Goepfert y Élise Dufour

Subjects
[SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019

47. Captivity and cranial development in wild boar (Sus scrofa): exploration of new markers of the process of domestication

Author

Dimitri Neaux, Anthony Herrel, Raphaël Cornette, Vincent Debat, Thomas CUCCHI, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Mécanismes Adaptatifs et Evolution (MECADEV), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), and Cucchi, Thomas

Subjects
[SHS.ARCHEO] Humanities and Social Sciences/Archaeology and Prehistory, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, [SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019

48. Approches combinées pour appréhender l’évolution du cochon domestique en Roumanie : morphométrie géométrique, ADN ancien et analyses isotopiques

Author

Allowen Evin, Marie Balasse, Flink Linus Girdland, Dragomir Popovici, Radian Andreescu, Douglas Bailey, Pavel Mirea, Catalin Lazar, Adina Boroneanţ, Clive Bonsall, Carlos Tornero, Valentin Radu, Denis Fiorillo, Stéphanie Bréhard, Anne Tresset, Thomas CUCCHI, Greger Larson, Keith Dobney, Adrian Bălăşescu, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), MNIR, Musée National d'Histoire de la Roumanie, San Francisco State University (SFSU), Teleorman County Museum, Romanian Academy, University of Edinburgh, Department of Archaeology, Durham University, UK, University of Aberdeen, and Bréhard, Stéphanie

Subjects
[SHS.ARCHEO] Humanities and Social Sciences/Archaeology and Prehistory, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019

49. Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe

Author

Marjan Mashkour, Anastasia Papathanasiou, Joris Peters, John Chapman, Anne Tresset, Simon Stoddart, Antonio Tagliacozzo, Canan Çakirlar, Jörg Schibler, Daniel Helmer, Ceiridwen J. Edwards, Caroline Malone, Vesna Dimitrijević, Andrea Zeeb-Lanz, Christina Geörg, Alexandros Triantafyllidis, Panoraia Alexandri, Ophélie Lebrasseur, Thomas Cucchi, Victoria E. Mullin, Michael P. Richards, James Haile, Laurent A. F. Frantz, Cevdet Merih Erek, John R. Stewart, Joachim Burger, Mihai Gligor, Jörg Orschiedt, Gennady F. Baryshnikov, Lucia Sarti, Rebecca Miller, Youri van den Hurk, Evan K. Irving-Pease, Allowen Evin, Hitomi Hongo, Richard P. M. A. Crooijmans, Jelena Bulatović, Max Price, Keith Dobney, Adina Boroneanţ, Anton Ervynck, Mike Parker Pearson, Joséphine Lesur, Elisabeth Stephan, Holley Martlew, Sepideh Maziar, Kurt J. Gron, Bea De Cupere, Kevin G. Daly, Valentin Dumitraşcu, Anders Götherström, Arkadiusz Marciniak, Azadeh Fatemeh Mohaseb, Richard Sabin, David Orton, Greger Larson, Lionel Gourichon, Cleia Detry, Clive Bonsall, François-Xavier Ricaut, Louis du Plessis, Jean-Denis Vigne, José Miguel Carretero, Benjamin S. Arbuckle, Mike J. Church, Hendrik-Jan Megens, Giedre Motuzaite Matuzeviciute, Linus Girdland-Flink, Domenico Fulgione, Ross Barnett, Ron Pinhasi, Ninna Manaseryan, Liora Kolska Horwitz, Melinda A. Zeder, Peter Rowley-Conwy, Alexander Yanevich, Daniel G. Bradley, Amelie Scheu, László Bartosiewicz, Darko Radmanovic, Shiva Sheikhi, Michelle Alexander, Katerina Trantalidou, Cristina Valdiosera, Adrian Bӑlӑşescu, M. Thomas P. Gilbert, Vincent M. Battista, Anna Linderholm, Norbert Benecke, Aslı Erim-Özdoğan, Rose-Marie Arbogast, Thomas H. McGovern, Audrey T. Lin, Sophie Van Poucke, Roger Matthews, Martien A. M. Groenen, Erik Meijaard, Wolfram Schier, Nenad Tasić, Dusan Boric, Frantz, Laurent A. F., Haile, Jame, Lin, Audrey T., Scheu, Amelie, Geörg, Christina, Benecke, Norbert, Alexander, Michelle, Linderholm, Anna, Mullin, Victoria E., Daly, Kevin G., Battista, Vincent M., Price, Max, Gron, Kurt J., Alexandri, Panoraia, Arbogast, Rose-Marie, Arbuckle, Benjamin, Balaşescu, Adrian, Barnett, Ro, Bartosiewicz, László, Baryshnikov, Gennady, Bonsall, Clive, ̧, Dušan Boric Adina Boroneant, Bulatovic, Jelena, Çakirlar, Canan, Carretero, José-Miguel, Chapman, John, Church, Mike, Crooijmans, Richard, De Cupere, Bea, Detry, Cleia, Dimitrijevic, Vesna, Dumitras ̧cu, Valentin, du Plessis, Loui, Edwards, Ceiridwen J., Merih Erek, Cevdet, ̆an, AslıErim-Özdog, Ervynck, Anton, Fulgione, Domenico, Gligor, Mihai, Götherström, Ander, Gourichon, Lionel, Groenen, Martien A. M., Helmer, Daniel, Hongo, Hitomi, Horwitz, Liora K., Irving-Pease, Evan K., Lebrasseur, Ophélie, Lesur, Joséphine, Malone, Caroline, Manaseryan, Ninna, Marciniak, Arkadiusz, Martlew, Holley, Mashkour, Marjan, Matthews, Roger, Motuzaite Matuzeviciute, Giedre, Maziar, Sepideh, Meijaard, Erik, Mcgovern, Tom, Megens, Hendrik-Jan, Miller, Rebecca, Fatemeh Mohaseb, Azadeh, Orschiedt, Jörg, Orton, David, Papathanasiou, Anastasia, Parker Pearson, Mike, Pinhasi, Ron, Radmanovic, Darko, Ricaut, François-Xavier, Richards, Mike, Sabin, Richard, Sarti, Lucia, Schier, Wolfram, Sheikhi, Shiva, Stephan, Elisabeth, Stewart, John R., Stoddart, Simon, Tagliacozzo, Antonio, Tasic, Nenad, Trantalidou, Katerina, Tresset, Anne, Valdiosera, Cristina, van den Hurk, Youri, Van Poucke, Sophie, Vigne, Jean-Deni, Yanevich, Alexander, Zeeb-Lanz, Andrea, Triantafyllidis, Alexandro, Gilbert, M. Thomas P., Schibler, Jörg, Rowley-Conwy, Peter, Zeder, Melinda, Peters, Jori, Cucchi, Thoma, Bradley, Daniel G., Dobney, Keith, Burger, Joachim, Evin, Allowen, Girdland-Flink, Linu, Larson, Greger, Archaeology of Northwestern Europe, Groningen Institute of Archaeology, Piperno, Dolores R., Repositório da Universidade de Lisboa, Department of Natural Sciences, German Archaeological Institute (DAI), Texas A&M University [College Station], Transplant Research Program [Boston, MA, USA], Boston Children's Hospital, Archéologie et histoire ancienne : Méditerranée - Europe (ARCHIMEDE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Department of Anthropology, Baylor University, Baylor University, University of York [York, UK], Stockholm University, Cardiff School of History, Ancient History, Archaeology and Religion, Cardiff University, Romanian Academy of Sciences, Animal Breeding and Genomics Centre, Wageningen University and Research [Wageningen] (WUR), UNIARQ, Universidade de Lisboa = University of Lisbon (ULISBOA), Department of Structural and Functional Biology, University of Naples Federico II = Università degli studi di Napoli Federico II, Stockholm Univ, Dept Biochem & Biophys, S-10691 Stockholm, Sweden, Gestion des ressources naturelles , environnements et sociétés (GReNES), Culture et Environnements, Préhistoire, Antiquité, Moyen-Age (CEPAM), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), ARCHEORIENT - Environnements et sociétés de l'Orient ancien (Archéorient), Université Lumière - Lyon 2 (UL2)-Centre National de la Recherche Scientifique (CNRS), University of Oxford, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Goethe-Universität Frankfurt am Main, University of Liverpool, HEC Paris - Recherche - Hors Laboratoire, Ecole des Hautes Etudes Commerciales (HEC Paris), School of Archaeology, University College Dublin [Dublin] (UCD), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Department of Human Evolution [Leipzig], Max Planck Institute for Evolutionary Anthropology [Leipzig], Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Connaissance Organisation et Systèmes TECHniques (COSTECH), Université de Technologie de Compiègne (UTC), Department of Archaeology, University of Cambridge [UK] (CAM), Laboratorio di Paleontologia e Archeozoologia, Soprintendenza Speciale al Museo Nazionale Preistorico ed Etnografico 'L. Pigorini', Roma, Museo Nazionale Preistorico Etnografico 'L. Pigorini, Institute of archaeology (UCL), University College of London [London] (UCL), University of Copenhagen = Københavns Universitet (UCPH), University of Basel (Unibas), Institut für Paläoanatomie und Geschichte der Tiermedizin, Ludwig-Maximilians-Universität München (LMU), Department of Archaeology, University of Aberdeen, University of Aberdeen, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Universidade de Lisboa (ULISBOA), Università degli studi di Napoli Federico II, Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), University of Oxford [Oxford], Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), University of Copenhagen = Københavns Universitet (KU), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)

Subjects
0301 basic medicine, Swine, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Skin Pigmentation, [SHS]Humanities and Social Sciences, Gene flow, Domestication, ddc:590, BREEDS, DOMESTIC PIGS, HISTORY, 0601 history and archaeology, Neolithic, History, Ancient, Phylogeny, Multidisciplinary, 060102 archaeology, INTROGRESSION, Europe, pigs, domestication, genomes, WILD, 06 humanities and the arts, Archaeological evidence, SPREAD, Coat, Mitochondrial DNA, Evolution, Zoology, Locus (genetics), Biology, Animal Breeding and Genomics, DNA, Mitochondrial, Middle East, 03 medical and health sciences, Animals, Fokkerij en Genomica, DNA, Ancient, General, ddc:930, Haplotype, DNA, 900 Geschichte und Geografie::930 Geschichte des Altertums (bis ca. 499), Archäologie::930 Geschichte des Altertums bis ca. 499, Archäologie, LONG, SIZE, 030104 developmental biology, domestication evolution gene flow Neolithic, WIAS
Abstract

International audience; Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local Euro-pean wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process. domestication | evolution | gene flow | Neolithic

Published
2019
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