– The human genome contains a million years worth of population data (io9, Jul 13, 2011):
Our genes don’t just help determine who we are — they also preserve an incredibly ancient record of who our ancestors were. Our genomes can actually reveal human population sizes dating all the way back to before humans even existed.
Richard Durbin of the Wellcome Trust Sanger Institute and Heng Li of the Broad Institute examined the handful of complete human genome sequences. Specifically, they examined how the differences between how particular genes from mothers and fathers were expressed — many differences in gene expression would suggest the family lines diverged a long time ago, while relatively few differences would indicate the two were closely related in the recent past.
Li goes further into just how this all works:
“This elegant tool provides opportunities for further research to enable us to learn more about population history,” says co-author Heng Li, from the Sanger Institute. “Each human genome contains information from the mother and the father, and the differences between these at any place in the genome carry information about its history. Since the genome sequence is so large, we can combine the information from tens of thousands of different places in the genome to build up a composite history of the ancestral contributions to the particular individual who was sequenced.”
Durbin explains some of the more remarkable findings of this genomic archaeology:
“Using this algorithm, we were able to provide new insights into our human history. First, we see an apparent increase in effective human population numbers around the time that modern humans arose in Africa over 100,000 years ago. Second, when we look at non-African individuals from Europe and East Asia, we see a shared history of a dramatic reduction in population, or bottleneck, starting about 60,000 years ago, as others have also observed. But unlike previous studies we also see evidence for continuing genetic exchange with African populations for tens of thousands of years after the initial out-of-Africa bottleneck until 20,000 to 40,000 years ago.
“Previous methods to explore these questions using genetic data have looked at a subset of the human genome. Our new approach uses the whole sequence of single individuals, and relies on fewer assumptions. Using such techniques we will be able to capitalize on the revolution in genome sequencing and analysis from projects such as The 1000 Genomes Project, and, as more people are sequenced, build a progressively finer detail picture of human genetic history.”
Amazingly, the team reconstructed a million years worth of population history from just four male genomes, which came from China, Korea, Europe, and West Africa respectively. It appears that humans remained more or less a single global population until about 60,000 years ago, at which point our numbers in Europe and East Asia crashed to only a tenth of their previous amount.
While versions of this method have been used before, reconstructing populations on this sort of scale using genomics have never before been attempted. Ryan Gutenkunst of the University of Arizona explains why this is such an impressive result:
“The method is really spectacular. Previous methods have taken averages across the genome, but here they are looking at variation from one location to another location and getting good results from even a single individual.”