Skip to main content
Premium Trial:

Request an Annual Quote

Human Genetic Variation, Population History Gleaned From Hundreds of Diverse Genomes

NEW YORK – A new collection of human genomes from across the world illustrates the genetic diversity of the global human population.

The ancestors of modern humans are thought to have diverged from the ancestors of Neanderthals and Denisovans between 500,000 and 700,000 years ago, with modern humans arising in Africa within the past few 100,000 years. About 50,000 to 70,000 years ago, some humans expanded out of Africa and mixed with more archaic groups in Europe and Asia.

But because many previous studies into the human evolutionary past have relied on limited samples, the full scope of human diversity hasn't been examined yet. As part of the Human Genome Diversity Project, an international team of researchers has now sequenced the genomes of more than 900 individuals from about 50 diverse human populations. As they reported in Science on Thursday, they were able to uncover shared and rare genetic variants in these groups, which suggested a complex population history.

"The detail provided by this study allows us to look deeper into human history, particularly inside Africa where less is currently known about the timescale of human evolution," first author Anders Bergström from the Francis Crick Institute said in a statement. "We find that the ancestors of present-day populations diversified through a gradual and complex process mostly during the last 250,000 years, with large amounts of gene flow between these early lineages. But we also see evidence that small parts of human ancestries trace back to groups that diversified much earlier than this."

Bergström and his colleagues sequenced the genomes of 929 people from 54 geographically, linguistically, and culturally diverse populations to an average 35X coverage. For 26 of these genomes, they also physically resolved the haplotype phase using linked-read sequencing.

Overall, they identified 67.3 million SNPs, 8.8 million indels, and 40,736 CNVs, numbers that include hundreds of thousands of variants that had not previously been uncovered.

In particular, they reported that populations from central and southern Africa as well as from the Americas and Oceania each had hundreds of thousands of common, private variants. At the same time, there was no variant that was found among all samples from one population and not in samples from other geographic locations. While most of these alterations arose as new variants, Oceanians harbored many private mutations derived from Denisovans.

The researchers used these sequences to trace back when various human populations may have split from one another. They estimated that genetic separations arose between human populations during the past 250,000 years, with some of them occurring gradually. For instance, the southern African San split from both the Biaka and Mbuti about 110,000 years ago, though gene flow evidently lingered between the San and Biaka until about 50,000 years ago.

They also tracked population sizes over time to find that most populations expanded during the past 10,000 years, except for hunter-gatherer groups like the Biaka, Mbuti, and San. Isolated groups like Sardinians, Basques, Orkney Islanders, Chinese Lahu, and Siberian Yakut expanded, but to a lesser extent.

The ancestors of Native Americans, meanwhile, may have undergone substantial population growth about 15,000 years ago, which corresponds to their arrival to the Americas. However, the researchers noted this finding needs further study.

By examining this diverse group of samples, the researchers also noticed low diversity among haplotypes originating from Neanderthals. This suggests that there was one major admixture event — though involving multiple individuals — between Neanderthals and modern humans after the out-of-Africa expansion. The Neanderthal genes found in West Africans likely represents genetic backflow from Europeans returning to Africa.

Admixture between Oceanians and Denisovans, though, was more complex, and likely involved at least two mixing events, as there is more variety among the Denisovan-origin haplotypes.

The researchers noted that they are making the new genome sequences freely available.

"Though this resource is just the beginning of many avenues of research, already we can glimpse several tantalizing insights into human history," senior author Chris Tyler-Smith, who recently retired from the Wellcome Sanger Institute, said in a statement.