Human history writ large in a single genome

The first humans to leave Africa continued to interbreed with Africans for tens of thousands of years.

Ewen Callaway

The genomes of everyone living today contain a record of the history of our species.Scott Hortop Travel/Alamy

 

Stored inside Craig Venter's genome are clues to the history of humankind, including global migrations and population crashes. Researchers have mined the genomics pioneer's publicly available DNA sequence, and those of 6 others, to reveal major milestones in human history.
"You can take a single person's genome and learn an entire population's history from it," says David Reich, a geneticist at Harvard Medical School in Boston, Massachusetts, who was not involved in the study. "This is one of the dreams we've had as a community."

The analysis, published today in Nature¹, suggests that descendants of the first humans to leave Africa dwindled to little more than 1,000 reproductively active individuals before rebounding. The study also suggests that, contrary to assumptions made from archaeological evidence, these early humans continued to breed with sub-Saharan Africans until as recently as 20,000 years ago.

Maternal ties

Geneticists eager to plumb human history have traditionally compared DNA sequences from numerous people around the world to determine how different populations relate to one another and when they might have gone their separate ways. For instance, studies of DNA from maternally inherited cell structures called mitochondria established that all humans can trace their maternal lineage back to one woman — a mitochondrial Eve — who lived in Africa around 200,000 years ago².

But, just as mitochondria can lead us back to a single woman, parts of a person's genome inherited from both their mother and father can also be followed back in time, with individual genes traced back to points before any mutations had developed, when just one version — a common ancestor — of that gene existed. Because of the way a person's maternal and paternal chromosomes shuffle together to create diversity in their sperm or egg cells, some parts of a person's genome inevitably share common ancestors more recently than other parts.

"Each little piece of the genome has its own unique bit of history and goes to a unique ancestor as you go further and further back," explains John Novembre, a population geneticist at the University of California, Los Angeles, who was not involved in the study. "As you look at different parts of the genome, you get access to different parts of history."

On the basis of this principle, Richard Durbin, a genome scientist at the Wellcome Trust Sanger Institute near Cambridge, UK, and his then post-doc Heng Li determined a way to calculate, from the ages of different segments of a single person's genome, changes in the population size of their ancestors.
The genomes of Venter and two others of European ancestry, two Asian men and two West African men all tell the same story up until about 100,000 years ago, when their populations began to split and then plummet in size, probably reflecting the first human migrations out of Africa.

The ancestors of Asians and Europeans dwindled by a factor of ten to roughly 1,200 reproductively active people between 20,000 and 40,000 years ago, Durbin and Li calculate. African populations also crashed, but by nowhere near the same extent, dropping to around 5,700 breeding individuals. Other studies have recorded population crashes at around the same time, Reich says.

In a different analysis, Durbin and Li compared an X chromosome from an African with one from a non-African to determine when their ancestors stopped interbreeding after the first humans left Africa and colonized other parts of the world. Human remains and artefacts unearthed in Europe, Asia and Australia seem to suggest humans rapidly colonized these places by about 40,000 years ago, diminishing the opportunities to interbreed with Africans.

However, Durbin and Li suggest that these groups continued to interbreed until as recently as 20,000 years ago. One possible explanation, Durbin says, is that after the first humans left Africa some 60,000 years ago, successive waves of Africans followed suit, interbreeding with the ancestors of the earlier migrants.

Mix and match

Chris Stringer, a palaeoanthropologist at the Natural History Museum in London, says that human populations outside Africa were probably small and widely dispersed 20,000–50,000 years ago, so regular interbreeding with Africans seems unlikely. "There could have been surges of gene flow at particular times, driven by innovations or environmental change, but it would be surprising if these continued right through that period," he says.

ADVERTISEMENT

Mining individual genomes can't reveal every chapter of human history, notes Reich, who now works with Li at the Broad Institute of Harvard and MIT in Cambridge, Massachusetts. The approach reveals little about upheavals of the last 20,000 years, such as the peopling of the Americas, because few chunks of the genome are young enough. Similarly, Durbin and Li's method can't deduce the history of human ancestors who existed before about 2 million years ago because few regions of the genome are much older.

Despite these limitations, Reich plans to lean heavily on the new approach, not least for work on ancient genomes belonging to Neanderthals³ and a mysterious sister population, known as Denisovans, discovered through DNA recovered from a 30,000–50,000-year-old finger bone found in a Siberian cave⁴. Reich and his colleagues have been unable to determine when Neanderthals and Denisovans stopped breeding with one another, and the new approach has the potential to answer that question. 

• References

  1. Li, H. & Durbin, R. Nature doi:10.1038/nature10231 (2011).
  2. Cann, R. L., Stoneking, M. & Wilson, A. C. Nature 325, 31-36 (1987). | Article | PubMed | ISI | ChemPort |
  3. Green, R. E. et al. Science 328, 710-722 (2010). | Article | PubMed | ISI | ChemPort |
  4. Krause, J. et al. Nature 464, 894-897 (2010). | Article | PubMed | ChemPort |