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Dating ancient human samples using the recombination clock

Priya Moorjani, Sriram Sankararaman, Qiaomei Fu, Molly Przeworski, Nick Patterson, David Reich
doi: https://doi.org/10.1101/023341
Priya Moorjani
1Department of Biological Sciences, Columbia University, New York, NY 10027
2Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142
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  • For correspondence: pm2730@columbia.edu reich@genetics.med.harvard.edu
Sriram Sankararaman
3Department of Genetics, Harvard Medical School, Boston MA 02115
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Qiaomei Fu
3Department of Genetics, Harvard Medical School, Boston MA 02115
4Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China
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Molly Przeworski
1Department of Biological Sciences, Columbia University, New York, NY 10027
5Department of Systems Biology, Columbia University, New York, NY 10027
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Nick Patterson
2Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142
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David Reich
2Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142
3Department of Genetics, Harvard Medical School, Boston MA 02115
6Howard Hughes Medical Institute, Harvard Medical School, Boston MA 02115
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  • For correspondence: pm2730@columbia.edu reich@genetics.med.harvard.edu
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Abstract

The study of human evolution has been revolutionized by inferences from ancient DNA analyses. Key to these is the reliable estimation of the age of ancient specimens. The current best practice is radiocarbon dating, which relies on characterizing the decay of radioactive carbon isotope (14C), and is applicable for dating up to 50,000-year-old samples. Here, we introduce a new genetic method that uses recombination clock for dating. The key idea is that an ancient genome has evolved less than the genomes of extant individuals. Thus, given a molecular clock provided by the steady accumulation of recombination events, one can infer the age of the ancient genome based on the number of missing years of evolution. To implement this idea, we take advantage of the shared history of Neanderthal gene flow into non-Africans that occurred around 50,000 years ago. Using the Neanderthal ancestry decay patterns, we estimate the Neanderthal admixture time for both ancient and extant samples. The difference in these admixture dates then provides an estimate of the age of the ancient genome. We show that our method provides reliable results in simulations. We apply our method to date five ancient Eurasian genomes with radiocarbon dates ranging between 12,000 to 45,000 years and recover consistent age estimates. Our method provides a complementary approach for dating ancient human samples and is applicable to ancient non-African genomes with Neanderthal ancestry. Extensions of this methodology that use older shared events may be able to date ancient genomes that fall beyond the radiocarbon frontier.

Significance We introduce a new genetic method for dating ancient human samples that uses the recombination clock. The main idea relies on the insight that an ancient genome lacks several thousand years of evolution compared to genomes of living individuals. To infer the age of ancient genomes, we take advantage of the shared history of Neanderthal gene flow into non-Africans that occurred around 50,000 years ago. By characterizing the dates of Neanderthal gene flow in ancient and extant genomes and quantifying the difference in these dates, we estimate the age of the ancient specimen. Our method is applicable for dating ancient samples more recent than the Neanderthal mixture event, so on par with radiocarbon dating, providing a complementary approach for dating.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted July 27, 2015.
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Dating ancient human samples using the recombination clock
Priya Moorjani, Sriram Sankararaman, Qiaomei Fu, Molly Przeworski, Nick Patterson, David Reich
bioRxiv 023341; doi: https://doi.org/10.1101/023341
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Dating ancient human samples using the recombination clock
Priya Moorjani, Sriram Sankararaman, Qiaomei Fu, Molly Przeworski, Nick Patterson, David Reich
bioRxiv 023341; doi: https://doi.org/10.1101/023341

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