University of Pennsylvania ScholarlyCommons Department of Anthropology Papers Department of Anthropology 5-29-2013 Uniparental Markers in Italy Reveal a Sex-Biased Genetic Structure and Different Historical Strata Alessio Boattini Begoña Martinez-Cruz Stefania Sarno Christine Harmant Antonella Useli See next page for additional authors Follow this and additional works at: https://repository.upenn.edu/anthro_papers Part of the Anthropology Commons, and the Genetics and Genomics Commons Recommended Citation Boattini, A., Martinez-Cruz, B., Sarno, S., Harmant, C., Useli, A., Sanz, P., Yang-Yao, D., Manry, J., Ciani, G., Luiselli, D., Quintana-Murci, L., Comas, D., Pettener, D., Genographic Consortium, & Schurr, T. G. (2013). Uniparental Markers in Italy Reveal a Sex-Biased Genetic Structure and Different Historical Strata. PLoS ONE, 8 (5), e65441. https://doi.org/10.1371/journal.pone.0065441 Theodore G. Schurr is not listed as an individual author on this paper but is part of the Genographic Consortium. A full list of Genographic Consortium members for this paper can be found in the Acknowledgements. This paper is posted at ScholarlyCommons. https://repository.upenn.edu/anthro_papers/41 For more information, please contact [email protected]. Uniparental Markers in Italy Reveal a Sex-Biased Genetic Structure and Different Historical Strata Abstract Located in the center of the Mediterranean landscape and with an extensive coastal line, the territory of what is today Italy has played an important role in the history of human settlements and movements of Southern Europe and the Mediterranean Basin. Populated since Paleolithic times, the complexity of human movements during the Neolithic, the Metal Ages and the most recent history of the two last millennia (involving the overlapping of different cultural and demic strata) has shaped the pattern of the modern Italian genetic structure. With the aim of disentangling this pattern and understanding which processes more importantly shaped the distribution of diversity, we have analyzed the uniparentally- inherited markers in ~900 individuals from an extensive sampling across the Italian peninsula, Sardinia and Sicily. Spatial PCAs and DAPCs revealed a sex-biased pattern indicating different demographic histories for males and females. Besides the genetic outlier position of Sardinians, a North West–South East Y-chromosome structure is found in continental Italy. Such structure is in agreement with recent archeological syntheses indicating two independent and parallel processes of Neolithisation. In addition, date estimates pinpoint the importance of the cultural and demographic events during the late Neolithic and Metal Ages. On the other hand, mitochondrial diversity is distributed more homogeneously in agreement with older population events that might be related to the presence of an Italian Refugium during the last glacial period in Europe. Keywords Bolivia, haplogroups, haplotypes, mitochondrial DNA, Peru, Phylogeography, population genetics, Quechuas Disciplines Anthropology | Genetics and Genomics | Social and Behavioral Sciences Comments Theodore G. Schurr is not listed as an individual author on this paper but is part of the Genographic Consortium. A full list of Genographic Consortium members for this paper can be found in the Acknowledgements. Author(s) Alessio Boattini, Begoña Martinez-Cruz, Stefania Sarno, Christine Harmant, Antonella Useli, Paula Sanz, Daniele Yang-Yao, Jeremy Manry, Graziella Ciani, Donata Luiselli, Lluis Quintana-Murci, David Comas, Davide Pettener, Genographic Consortium, and Theodore G. Schurr This journal article is available at ScholarlyCommons: https://repository.upenn.edu/anthro_papers/41 Uniparental Markers in Italy Reveal a Sex-Biased Genetic Structure and Different Historical Strata Alessio Boattini1., Begon˜ a Martinez-Cruz2., Stefania Sarno1, Christine Harmant3,4, Antonella Useli5, Paula Sanz2, Daniele Yang-Yao1, Jeremy Manry3,4, Graziella Ciani1, Donata Luiselli1, Lluis Quintana- Murci3,4, David Comas2* , Davide Pettener1* , the Genographic Consortium" 1 Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Universita` di Bologna, Bologna, Italy, 2 Institut de Biologia Evolutiva (CSIC-UPF), Departament de Cie`ncies de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona, Spain, 3 Institut Pasteur, Human Evolutionary Genetics Unit, Department of Genomes and Genetics, Paris, France, 4 Centre National de la Recherche Scientifique, Paris, France, 5 Dipartimento di Scienze della Natura e del Territorio, Universita` di Sassari, Sassari, Italy Abstract Located in the center of the Mediterranean landscape and with an extensive coastal line, the territory of what is today Italy has played an important role in the history of human settlements and movements of Southern Europe and the Mediterranean Basin. Populated since Paleolithic times, the complexity of human movements during the Neolithic, the Metal Ages and the most recent history of the two last millennia (involving the overlapping of different cultural and demic strata) has shaped the pattern of the modern Italian genetic structure. With the aim of disentangling this pattern and understanding which processes more importantly shaped the distribution of diversity, we have analyzed the uniparentally- inherited markers in ,900 individuals from an extensive sampling across the Italian peninsula, Sardinia and Sicily. Spatial PCAs and DAPCs revealed a sex-biased pattern indicating different demographic histories for males and females. Besides the genetic outlier position of Sardinians, a North West–South East Y-chromosome structure is found in continental Italy. Such structure is in agreement with recent archeological syntheses indicating two independent and parallel processes of Neolithisation. In addition, date estimates pinpoint the importance of the cultural and demographic events during the late Neolithic and Metal Ages. On the other hand, mitochondrial diversity is distributed more homogeneously in agreement with older population events that might be related to the presence of an Italian Refugium during the last glacial period in Europe. Citation: Boattini A, Martinez-Cruz B, Sarno S, Harmant C, Useli A, et al. (2013) Uniparental Markers in Italy Reveal a Sex-Biased Genetic Structure and Different Historical Strata. PLoS ONE 8(5): e65441. doi:10.1371/journal.pone.0065441 Editor: David Caramelli, University of Florence, Italy Received January 8, 2013; Accepted April 24, 2013; Published May 29, 2013 Copyright: ß 2013 Boattini et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This study was supported by Strategic Project 2006-09 from the University of Bologna to DP and from MIUR PRIN 2007 and 2009 Grants to DP. The project was also supported by the Spanish Government grant CGL2010-14944/BOS. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: [email protected] (DC); [email protected] (DP) . These authors contributed equally to this work. " Membership of the Genographic Consortium is provided in the Acknowledgments. Introduction and an area of expansion during the different major migratory events following the early Paleolithic colonization. Due to its central position and to the extension of its coastal line The most recent archaeological syntheses [10] describe the early (,7,460 Km), the modern Republic of Italy – e.g. the Italian Neolithisation of Italy as the result of two independent and parallel Peninsula and the two major islands of Sicily and Sardinia – has processes, involving respectively the Adriatic and the Tyrrhenian been one of the focal points in the settlement history of Southern coasts and dating as early as 8,100 YBP (Apulia, South-Eastern Europe and the Mediterranean Basin. Italy) and 7,900 YBP (Liguria, North-Western Italy). Populated by early modern humans since approximately Italian Late Neolithic and the Metal Ages revealed to be a 30,000–40,000 years before present (YBP) [1] during the LGM complicated tapestry of different cultural strata, potentially (,25,000 YBP) it was involved in the southward contraction of associated with population movements. During the first millenni- human groups from Central Europe that rapidly retreated to the um BC, Italy hosted a vast set of different peoples whose origins in Mediterranean coastlines, occupying refuge areas, such as in the some cases remain unknown (e.g. Etruscans, Ligurians, Veneti), well-known cases of Iberia and the Balkans [2–5]. After while in other cases are the result of specific migration processes contributing to the substantial re-shaping of the early Paleolithic (Celts in North-Western Italy; Greeks in Southern Italy and Sicily) genetic composition of glacial Refugia, northward re-peopling [11]. processes started approximately 16,000–13,000 YBP [3], [6–9]. In addition, independent and/or intersecting subsequent Subsequently Italy has received the passage of multiple human historic events (related with the trade and expansion of different groups in prehistoric and historic times, acting both as a step point populations in our era: Phoenician, Greek, Carthaginian, Roman, PLOS ONE | www.plosone.org