Modern DNA Reveals Ancient Male Population Explosions

Adapted from a press release prepared by The Wellcome Trust Sanger Institute.

The largest ever study of genetic variation on the human Y chromosome has revealed major male-line population explosions that have occurred between 4,000 and 55,000 years ago. The manuscript, published online today in Nature Genetics and translated into Spanish here, is the final paper from the 1000 Genomes Project.

An international team of 42 scientists compared the Y-chromosome sequences of more than 1,200 men representing 26 populations from around the world. The team was led by corresponding authors Chris Tyler-Smith, Senior Group Leader at the UK-based Wellcome Trust Sanger Institute, and Carlos Bustamante, Professor of Biomedical Data Sciences and of Genetics at Stanford. Lead author David Poznik is a recent graduate from Stanford’s Program in Biomedical Informatics, and co-first author Yali Xue is a Senior Staff Scientist at the Sanger Institute.

Unlike most other chromosomes, the Y chromosome does not have a partner with which to exchange DNA in the cell nucleus. Men transmit their Y chromosomes in whole to their sons, and this phenomenon enables a fine-grained view of how the human male population has developed over the millennia.

The authors identified more than 60,000 single-nucleotide variants (SNVs) and used these sequence differences to build a tree that shows how the 1,244 Y chromosomes are related to one another. All the men in the study descend from a single male ancestor at the root of the tree. This individual, who lived ~190,000 years ago, was certainly not the first man, but he is the only man of his era with male-line descendants in the study; the lineages of most of his contemporaries (possibly all but one) have died out.

The most intriguing finding was that some internal parts of the tree were extremely bush-like, with many branches originating at the same point. These branching patterns indicate that there were explosive increases in the numbers of men carrying certain types of Y chromosomes. The earliest of these rapid increases in male numbers occurred ~50,000 to ~55,000 years ago across Eurasia and ~15,000 years ago in the Americas. The team believes these expansions resulted from the first peopling of vast continents by modern humans.

There were also later expansions, particularly in sub-Saharan Africa, Western Europe, and South Asia, at times between ~4,000 and ~8,000 years ago. The circumstances under which these later expansions took place are not as well-defined. However, the authors speculate that they may have been enabled by advances in technology—such as wheeled transport, metalworking, and organized warfare—that could be controlled by small groups of men. These candidate explanations can now be investigated further, for example using ancient DNA (aDNA).

The SNV data constitute a rich resource for future genealogical, historical, and forensic studies. The authors generated a catalog of diagnostic markers that is particularly valuable for genotyping-array design and for identifying the paternal ancestry of aDNA samples, for which sequencing coverage is often quite limited.

The researchers also discovered and studied thousands of more complex DNA variants. In particular, they leveraged the SNV-based phylogeny to estimate mutation rates for more than 700 polymorphic short tandem repeats (STRs). This work—led by Thomas Willems, a graduate student at MIT, and Yaniv Erlich, Assistant Professor of Computer Science at Columbia University and Member of the New York Genome Center—is described in a companion paper, also published online today, in the American Journal of Human Genetics.

Postdoctoral scholar Fernando Mendez and research associate scientist Peter Underhill, both from Stanford, also contributed to the study.

All data from the 1000 Genomes Project are freely available for use by other scientists and investigators.

David Poznik was supported by the National Science Foundation (NSF) Graduate Research Fellowship under grant number DGE-1147470 and by the National Library of Medicine training grant LM-007033. Fernando Mendez was supported by the National Institutes of Health (NIH) grant number 1R01GM090087, by NSF grant number DMS-1201234, and by a postdoctoral fellowship from the Stanford Center for Computational, Evolutionary and Human Genomics (CEHG). Peter Underhill was supported by SAP grant SP0#115016, and Carlos Bustamante was supported by NIH grant number 5R01HG003229-09.

1000Y

Y-chromosome phylogeny and haplogroup distribution. Branch lengths are drawn proportional to the estimated times between successive splits, with the most ancient division occurring ~190 kya. Colored triangles represent the major clades, and the width of each base is proportional to one less than the corresponding sample size. The authors modeled expansions within eight of the major haplogroups (circled), and dotted triangles represent the ages and sample sizes of the expanding lineages. (Inset) World map indicating, for each of the 26 populations, the geographic source, sample size, and haplogroup distribution.

 

 

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One thought on “Modern DNA Reveals Ancient Male Population Explosions

  1. I’d like to ask a question about the “Y-Chromosome phylogeny and haplogroup distribution” graph. I’ve seen a video from National Geographic in which “genetic adam” is placed at 50,000 years ago. Your graph places him at 190,000 years ago. Why the difference? Why does your
    graph have almost no male-line splits for over 100,00 years and then all of the splits occur within the last 4,000 to 50,000 years?

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