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Marcello Mannino

Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe

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  • Adam B. Rohrlach, Max Planck Institute for the Science of Human History, University of Adelaide
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  • Luka Papac, Max Planck Institute for the Science of Human History
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  • Ainash Childebayeva, Max Planck Institute for the Science of Human History
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  • Maïté Rivollat, Max Planck Institute for the Science of Human History, Universite de Bordeaux
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  • Vanessa Villalba-Mouco, Max Planck Institute for the Science of Human History, Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain.
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  • Gunnar U. Neumann, Max Planck Institute for the Science of Human History
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  • Sandra Penske, Max Planck Institute for the Science of Human History
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  • Eirini Skourtanioti, Max Planck Institute for the Science of Human History
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  • Marieke van de Loosdrecht, Max Planck Institute for the Science of Human History
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  • Murat Akar, Mustafa Kemal University
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  • Kamen Boyadzhiev, Bulgarian Academy of Sciences
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  • Yavor Boyadzhiev, Bulgarian Academy of Sciences
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  • Marie France Deguilloux, Universite de Bordeaux
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  • Miroslav Dobeš, Czech Academy of Sciences
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  • Yilmaz S. Erdal, Hacettepe University
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  • Michal Ernée, Czech Academy of Sciences
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  • Marcella Frangipane, University of Rome La Sapienza
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  • Mirosław Furmanek, University of Wroclaw
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  • Susanne Friederich, State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory
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  • Emmanuel Ghesquière, Inrap Grand Ouest, Universite de Rennes 1
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  • Agata Hałuszko, University of Wroclaw, Archeolodzy.org Foundation
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  • Svend Hansen, German Archaeological Institute
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  • Mario Küßner, Thuringian State Office for Heritage Management and Archeology
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  • Marcello Mannino
  • Rana Özbal, Koc University
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  • Sabine Reinhold, German Protestant Institute of Archaeology in Amman
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  • Stéphane Rottier, Universite de Bordeaux
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  • Domingo Carlos Salazar-García, Ikerbasque Basque Foundation for Science, University of Valencia, University of Cape Town
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  • Jorge Soler Diaz, MARQ Archaeological Museum of Alicante
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  • Philipp W. Stockhammer, Max Planck Institute for the Science of Human History, Ludwig Maximilian University of Munich
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  • Consuelo Roca de Togores Muñoz, MARQ Archaeological Museum of Alicante
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  • K. Aslihan Yener, New York University
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  • Cosimo Posth, Max Planck Institute for the Science of Human History, University of Tübingen
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  • Johannes Krause, Max Planck Institute for the Science of Human History
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  • Alexander Herbig, Max Planck Institute for the Science of Human History
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  • Wolfgang Haak, Max Planck Institute for the Science of Human History, University of Adelaide

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.

Original languageEnglish
Article number15005
JournalScientific Reports
Volume11
ISSN2045-2322
DOIs
Publication statusPublished - Jul 2021

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