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Proc Natl Acad Sci U S A. 2016 May 17;113(20):5652-7. doi: 10.1073/pnas.1514696113. Epub 2016 May 2.

A genetic method for dating ancient genomes provides a direct estimate of human generation interval in the last 45,000 years.

Author information

1
Department of Biological Sciences, Columbia University, New York, NY 10027; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142; pm2730@columbia.edu reich@genetics.med.harvard.edu.
2
Department of Genetics, Harvard Medical School, Boston, MA 02115; Department of Computer Science, University of California, Los Angeles, CA 90095; Department of Human Genetics, University of California, Los Angeles, CA 90095;
3
Department of Genetics, Harvard Medical School, Boston, MA 02115; Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China;
4
Department of Biological Sciences, Columbia University, New York, NY 10027; Department of Systems Biology, Columbia University, New York, NY 10027;
5
Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142;
6
Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142; Department of Genetics, Harvard Medical School, Boston, MA 02115; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115 pm2730@columbia.edu reich@genetics.med.harvard.edu.

Abstract

The study of human evolution has been revolutionized by inferences from ancient DNA analyses. Key to these studies is the reliable estimation of the age of ancient specimens. High-resolution age estimates can often be obtained using radiocarbon dating, and, while precise and powerful, this method has some biases, making it of interest to directly use genetic data to infer a date for samples that have been sequenced. Here, we report a genetic method that uses the recombination clock. The idea is that an ancient genome has evolved less than the genomes of present-day individuals and thus has experienced fewer recombination events since the common ancestor. To implement this idea, we take advantage of the insight that all non-Africans have a common heritage of Neanderthal gene flow into their ancestors. Thus, we can estimate the date since Neanderthal admixture for present-day and ancient samples simultaneously and use the difference as a direct estimate of the ancient specimen's age. We apply our method to date five Upper Paleolithic Eurasian genomes with radiocarbon dates between 12,000 and 45,000 y ago and show an excellent correlation of the genetic and (14)C dates. By considering the slope of the correlation between the genetic dates, which are in units of generations, and the (14)C dates, which are in units of years, we infer that the mean generation interval in humans over this period has been 26-30 y. Extensions of this methodology that use older shared events may be applicable for dating beyond the radiocarbon frontier.

KEYWORDS:

ancient DNA; branch shortening; generation interval; molecular clock

PMID:
27140627
PMCID:
PMC4878468
DOI:
10.1073/pnas.1514696113
[Indexed for MEDLINE]
Free PMC Article

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