Uniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective. Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture assays such as the 1240 k, ancient DNA studies often fail to utilize the unique perspective that the NRY can yield. Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay), that targets the "mappable" regions of the NRY. We show that compared to low-coverage shotgun sequencing and 1240 k capture, YMCA significantly improves the mean coverage and number of sites covered on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the identification of previously undiscovered variants. To illustrate the power of YMCA, we show that the analysis of ancient Y-chromosome lineages can help to resolve Y-chromosomal haplogroups. As a case study, we focus on H2, a haplogroup associated with a critical event in European human history: the Neolithic transition. By disentangling the evolutionary history of this haplogroup, we further elucidate the two separate paths by which early farmers expanded from Anatolia and the Near East to western Europe.

ARC Centre of Excellence for Mathematical and Statistical Frontiers School of Mathematical Sciences The University of Adelaide Adelaide SA 5005 Australia

Archaeo and Palaeogenetics Group Institute for Archaeological Sciences Eberhard Karls University Tübingen 72070 Tübingen Germany

Archeolodzy org Foundation Wrocław Poland

Departament de Prehistòria Arqueologia i Història Antiga Universitat de València Valencia Spain

Department of Anthropology Hacettepe University 06800 Ankara Turkey

Department of Archaeogenetics Max Planck Institute for the Science of Human History 07745 Jena Germany

Department of Archaeology and History of Art Koç University 34450 Istanbul Turkey

Department of Archaeology Mustafa Kemal University 31060 Alahan Antakya Hatay Turkey

Department of Archaeology School of Culture and Society Aarhus University 8270 Højbjerg Denmark

Department of Classics Sapienza University of Rome 00185 Rome Italy

Department of Geological Sciences University of Cape Town Cape Town South Africa

Department of Prehistory Institute of Archaeology CAS Prague Czech Republic

Eurasia Department German Archaeological Institute Berlin Germany

Grupo de Investigación en Prehistoria IT 1223 19 IKERBASQUE Basque Foundation for Science Vitoria Spain

Inrap Grand Ouest Bourguébus France

Institute for the Study of the Ancient World New York University New York NY 10028 USA

Institute of Archaeology University of Wrocław Wrocław Poland

Institute of Evolutionary Biology CSIC Universitat Pompeu Fabra Barcelona Spain

Ludwig Maximilian University Munich 80799 Munich Germany

MARQ Archaeological Museum of Alicante Alicante Spain

National Institute of Archaeology with Museum Bulgarian Academy of Sciences 1000 Sofia Bulgaria

School of Biological Sciences The University of Adelaide Adelaide SA 5005 Australia

State Office for Heritage Management and Archaeology Saxony Anhalt and State Museum of Prehistory Halle Germany

Thuringian State Office for Heritage Management and Archeology Weimar Germany

Université de Bordeaux CNRS PACEA UMR 5199 33615 Pessac France

Université de Rennes 1 CNRS CReAAH UMR 6566 Rennes France

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Earliest modern human genomes constrain timing of Neanderthal admixture

Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers