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Genotyping Patterns Hint at Ancient Back-to-Africa Migration

COLD SPRING HARBOR, NY (GenomeWeb) – An ancestral group with genetic ties to present-day populations in Italy migrated into Africa around 3,000 years ago, according to a population study presented at the annual Biology of Genomes meeting this weekend.

Using patterns of admixture and linkage disequilibrium found in genotyping data for thousands of individuals from populations around the world, a team from Harvard Medical School and the Broad Institute delved into the finer-scale migration patterns in sub-Saharan Africa during the past several thousand years, said Harvard's Joseph Pickrell.

The analysis pointed to unappreciated migration events in southern and eastern Africa, including an influx of ancestry from individuals resembling present-day populations in Italy, said Pickrell, who presented findings from the study during a session on population genomic variation on Saturday.

More research is needed understand the details of this apparent back-to-Africa migration, Pickrell noted. For instance, though the team saw signs of European-like ancestry in Jul'hoansi populations in southern Africa, it appears that this admixture reflects indirect contact between the populations.

That could be explained by movement of individuals from outside of Africa — migrating from southern Europe or the Middle East — to eastern Africa, where they met and mixed with populations there. Later on, researchers suspect, eastern African populations may have migrated south, bringing some European-like genetic patterns with them.

As such, results of the analysis "highlight the genomic impact of largely uncharacterized back-to-Africa migrations in human history," Pickrell and co-authors wrote in the abstract accompanying the presentation.

The research group teased apart ancestral sequence information using publicly available genotyping data for more than 3,000 individuals from 100 or more human populations who had been assessed using Affymetrix arrays, Illumina arrays, or both.

"Today, everyone is sort of a mosaic of chunks [of sequence] from different populations," Pickrell said.

And because linkage disequilibrium between various linked SNPs within these sequence chunks breaks down over time, researchers are able to use linkage disequilibrium profiles to not only get clues about past admixtures, but to retrace the timing of these events.

In eastern Africa, for instance, the group found saw signs of ancient mixing between ancestors of the Biaka pygmy population and individuals with closer genetic ties to modern-day Yoruba, Mozabite, or Mandenka populations.

Meanwhile, data from southern Africa suggests that region has been home to multiple migration events, including an apparent migration involving eastern African individuals descended from populations that mixed with migrants from outside of Africa.

The precise nature of the admixture events and populations involved remains to be determined. But based on analyses so far, the team estimated that there was admixture between eastern African populations and mysterious back-to-Africa migrants around 3,000 years ago. Movement by the eastern population into southern Africa is suspected to have occurred around 1,500 years later, Pickrell said.

More generally, those involved in the study argued that the analyses so far highlight the potential of using large-scale genomic datasets to unravel complicated human population patterns from the ancient past.