Human culture, biology, and health were shaped dramatically by the onset of agriculture ∼12,000 y B.P. This shift is hypothesized to have resulted in increased individual fitness and population growth as evidenced by archaeological and population genomic data alongside a decline in physiological health as inferred from skeletal remains. Here, we consider osteological and ancient DNA data from the same prehistoric individuals to study human stature variation as a proxy for health across a transition to agriculture. Specifically, we compared “predicted” genetic contributions to height from paleogenomic data and “achieved” adult osteological height estimated from long bone measurements for 167 individuals across Europe spanning the Upper Paleolithic to Iron Age (∼38,000 to 2,400 B.P.). We found that individuals from the Neolithic were shorter than expected (given their individual polygenic height scores) by an average of −3.82 cm relative to individuals from the Upper Paleolithic and Mesolithic (P = 0.040) and −2.21 cm shorter relative to post-Neolithic individuals (P = 0.068), with osteological vs. expected stature steadily increasing across the Copper (+1.95 cm relative to the Neolithic), Bronze (+2.70 cm), and Iron (+3.27 cm) Ages. These results were attenuated when we additionally accounted for genome-wide genetic ancestry variation: for example, with Neolithic individuals −2.82 cm shorter than expected on average relative to pre-Neolithic individuals (P = 0.120). We also incorporated observations of paleopathological indicators of nonspecific stress that can persist from childhood to adulthood in skeletal remains into our model. Overall, our work highlights the potential of integrating disparate datasets to explore proxies of health in prehistory.

Archeolodzy org Foundation Wrocław 50 316 Poland

Archeology Center of the University of Lisbon University of Lisbon Lisbon 1600 214 Portugal

Broad Institute of Harvard and Massachusetts Institute of Technology Cambridge MA 02142

Buffalo Human Evolutionary Morphology Lab Department of Anthropology University at Buffalo Buffalo NY 14261 0026

Centre for Applied Bioanthropology Institute for Anthropological Research Zagreb 10000 Croatia

Centre for Functional Ecology Department of Life Sciences University of Coimbra Coimbra 3000 456 Portugal

Departament d'Història i Història de l'Art Universitat Rovira i Virgili Tarragona 43003 Spain

Department of Anatomy Histology and Anthropology Vilnius University Vilnius 01513 Lithuania

Department of Anthropology Hungarian Natural History Museum Budapest 1083 Hungary

Department of Anthropology National Museum Prague 115 79 Czech Republic

Department of Anthropology Ohio State University Columbus OH 43210

Department of Anthropology Pennsylvania State University University Park PA 16802

Department of Archaeology Déri Múzeum Debrecen 4026 Hungary

Department of Archaeology Herman Ottó Museum Miskolc 3530 Hungary

Department of Archaeology Hungarian National Museum Budapest 1088 Hungary

Department of Archaeology István Dobó Castle Museum Eger 3300 Hungary

Department of Archaeology Satu Mare County Museum Satu Mare 440031 Romania

Department of Art Studies and Archaeology Maritime Cultures Research Institute Vrije Univeristeit Brussels Brussels 1050 Belgium

Department of Biological Anthropology Eötvös Loránd University Budapest 1053 Hungary

Department of Biology Pennsylvania State University University Park PA 16802

Department of Chemistry Analytical Environmental and Geo Chemistry Research Unit Vrije Univeristeit Brussels Brussels 1050 Belgium

Department of Evolutionary Anthropology University of Vienna Vienna 1030 Austria

Department of Genetics Harvard Medical School Boston MA 02115

Department of Genetics Human Genetics Institute of New Jersey Rutgers The State University of New Jersey New Brunswick NJ 08854

Department of Human Evolutionary Biology Harvard University Cambridge MA 02138

Department of Physical Anthropology Peter the Great Museum of Anthropology and Ethnography Russian Academy of Sciences St Petersburg 199034 Russia

Department of Prehistory and Archaeology Universidad Autónoma de Madrid Madrid 28049 Spain

Department of Prehistory Universidad Complutense de Madrid Madrid 28040 Spain

Department of Scottish History and Archaeology National Museums Scotland Edinburgh EH1 1JF Scotland

Department of Vegetation Ecology Institute of Botany of the Czech Academy of Sciences Průhonice 252 43 Czech Republic

Deutsche Forschungsgemeinschaft Center for Advanced Studies University of Tübingen Tübingen 72074 Germany

HHMI Harvard Medical School Cambridge MA 02138

Huck Institutes of the Life Sciences Pennsylvania State University University Park PA 16802

Human Evolution and Archaeological Sciences University of Vienna Vienna 1030 Austria

Institut Català de Paleoecologia Humana i Evolució Social Tarragona 43007 Spain

Institute for Research and Learning in Archaeology and Bioarchaeology Columbus OH 43215

Institute for Scientific Archaeology Working Group Palaeoanthropology University of Tübingen Tübingen 72074 Germany

Institute of Archaeology and Museology Masaryk University Brno 602 00 Czech Republic

Institute of Archaeology Research Centre for the Humanities Eötvös Loránd Research Network Budapest 1097 Hungary

Institute of Archaeology University of Wrocław Wrocław 50 139 Poland

Institute of Latvian History University of Latvia Riga 1050 Latvia

Laboratoire d'archéozoologie Université de Neuchâtel Neuchâtel 2000 Switzerland

Olga Necrasov Center for Anthropological Research Romanian Academy Iasi Branch Iasi 700481 Romania

Orheiul Vechi Cultural Natural Reserve Orhei 3506 Republic of Moldova

Professional archaeologist Parla 28980 Spain

Research Centre for Anthropology and Health Department of Life Sciences University of Coimbra Coimbra 3000 456 Portugal

Soprintendenza Archeologia Belle Arti e Paesaggio Rome 00186 Italy

The Max Planck Harvard Research Center for the Archaeoscience of the Ancient Mediterranean Boston MA 02115

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