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The evolutionary history of Neandertal and Denisovan Y chromosomes

View ORCID ProfileMartin Petr, Mateja Hajdinjak, Qiaomei Fu, Elena Essel, Hélène Rougier, Isabelle Crevecoeur, Patrick Semal, Liubov V. Golovanova, Vladimir B. Doronichev, Carles Lalueza-Fox, Marco de la Rasilla, Antonio Rosas, Michael V. Shunkov, Maxim B. Kozlikin, Anatoli P. Derevianko, Benjamin Vernot, Matthias Meyer, Janet Kelso
doi: https://doi.org/10.1101/2020.03.09.983445
Martin Petr
1Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
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  • For correspondence: mp@bodkan.net kelso@eva.mpg.de
Mateja Hajdinjak
1Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
13The Francis Crick Institute, NW1 1AT London, United Kingdom
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Qiaomei Fu
2Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China
3CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China
4University of Chinese Academy of Sciences, Beijing 100049, China
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Elena Essel
1Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
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Hélène Rougier
5Department of Anthropology, California State University Northridge, Northridge, California 91330-8244, USA
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Isabelle Crevecoeur
6Université de Bordeaux, CNRS, UMR 5199-PACEA, 33615 Pessac Cedex, France
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Patrick Semal
7Royal Belgian Institute of Natural Sciences, 1000 Brussels, Belgium
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Liubov V. Golovanova
8ANO Laboratory of Prehistory 14 Linia 3-11, St Petersburg 1990 34, Russia
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Vladimir B. Doronichev
8ANO Laboratory of Prehistory 14 Linia 3-11, St Petersburg 1990 34, Russia
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Carles Lalueza-Fox
9Institute of Evolutionary Biology, Consejo Superior de Investigaciones Científicas, Universitat Pompeu Fabra, 08003 Barcelona, Spain
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Marco de la Rasilla
10Área de Prehistoria, Departamento de Historia, Universidad de Oviedo, 33011 Oviedo, Spain
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Antonio Rosas
11Departamento de Paleobiología, Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
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Michael V. Shunkov
12Institute of Archeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
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Maxim B. Kozlikin
12Institute of Archeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
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Anatoli P. Derevianko
12Institute of Archeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
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Benjamin Vernot
1Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
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Matthias Meyer
1Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
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Janet Kelso
1Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
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  • For correspondence: mp@bodkan.net kelso@eva.mpg.de
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Abstract

Ancient DNA has allowed the study of various aspects of human history in unprecedented detail. However, because the majority of archaic human specimens preserved well enough for genome sequencing have been female, comprehensive studies of Y chromosomes of Denisovans and Neandertals have not yet been possible. Here we present sequences of the first Denisovan Y chromosomes (Denisova 4 and Denisova 8), as well as the Y chromosomes of three late Neandertals (Spy 94a, Mezmaiskaya 2 and El Sidrón 1253). We find that the Denisovan Y chromosomes split around 700 thousand years ago (kya) from a lineage shared by Neandertal and modern human Y chromosomes, which diverged from each other around 370 kya. The phylogenetic relationships of archaic and modern human Y chromosomes therefore differ from population relationships inferred from their autosomal genomes, and mirror the relationships observed on the level of mitochondrial DNA. This provides strong evidence that gene flow from an early lineage related to modern humans resulted in the replacement of both the mitochondrial and Y chromosomal gene pools in late Neandertals. Although unlikely under neutrality, we show that this replacement is plausible if the low effective population size of Neandertals resulted in an increased genetic load in their Y chromosomes and mitochondrial DNA relative to modern humans.

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  • https://www.github.com/bodkan/archaic-ychr

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The evolutionary history of Neandertal and Denisovan Y chromosomes
Martin Petr, Mateja Hajdinjak, Qiaomei Fu, Elena Essel, Hélène Rougier, Isabelle Crevecoeur, Patrick Semal, Liubov V. Golovanova, Vladimir B. Doronichev, Carles Lalueza-Fox, Marco de la Rasilla, Antonio Rosas, Michael V. Shunkov, Maxim B. Kozlikin, Anatoli P. Derevianko, Benjamin Vernot, Matthias Meyer, Janet Kelso
bioRxiv 2020.03.09.983445; doi: https://doi.org/10.1101/2020.03.09.983445
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The evolutionary history of Neandertal and Denisovan Y chromosomes
Martin Petr, Mateja Hajdinjak, Qiaomei Fu, Elena Essel, Hélène Rougier, Isabelle Crevecoeur, Patrick Semal, Liubov V. Golovanova, Vladimir B. Doronichev, Carles Lalueza-Fox, Marco de la Rasilla, Antonio Rosas, Michael V. Shunkov, Maxim B. Kozlikin, Anatoli P. Derevianko, Benjamin Vernot, Matthias Meyer, Janet Kelso
bioRxiv 2020.03.09.983445; doi: https://doi.org/10.1101/2020.03.09.983445

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