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Ethiopian, Egyptian Genomes Shed Light on Out-of-Africa Route of Eurasian Ancestors

NEW YORK (GenomeWeb) – Ancient humans migrating out of Africa most likely took a northerly route to leave the continent, according to a new genomic analysis.

Researchers from the Wellcome Trust Sanger Center and elsewhere generated genomes from 225 people living in modern-day Ethiopia and Egypt and compared those sequences to those from Eurasians and sub-Saharan Africans to tease out whether Ethiopians or Egyptians shared genetic signatures with modern-day Eurasians, as they reported in the American Journal of Human Genetics today.

"Two geographically plausible routes have been proposed: an exit through the current Egypt and Sinai, which is the northern route, or one through Ethiopia, the Bab el Mandeb strait, and the Arabian Peninsula, which is the southern route," said first author Luca Pagani from the Sanger Center in a statement.

If the ancient forbearers of Eurasians followed the northern route through Egypt and out of Africa, then modern Egyptians should be more genetically similar to modern non-Africans, but if they took the southern route through Ethiopia, then modern Ethiopians should be more genetically similar to modern non-Africans.

Pagani and his colleagues sequenced 100 Egyptians and 125 Ethiopians, representing the Amhara, Oromo, Ethiopian Somali, Wolayta, and Gumuz groups, to a depth of 8x on an Illumina HiSeq machine.

As more modern gene flow has also influenced the genomes of present-day Egyptians and Ethiopians, the researchers sought to first identify and then mask recent non-African ancestry in the two populations.

Through a combination of ADMIXTURE and principal components analysis, they estimated some 80 percent of Egyptian ancestry is non-African, and traced the midpoint of this admixture event to about 750 years ago, or around the time of the Islamic expansion.

Meanwhile, the Ethiopian populations ranged in their percentage of non-African ancestry from some 50 percent in the Amhara and Oromo to just a trace in Gumuz, with these admixture events dating back to between 2,500 years and 3,000 years ago.

Pagani and his colleagues then filtered out these more recent admixture events to unearth more ancient ones. They compared these masked samples to a set of West African genomes and Asian and European — Han Chinese, Toscani in Italy, European in Utah, and South Asian in Texas — genomes.

For their comparison, the researchers focused on some 18,114 genomic regions, spanning some 7.2 megabases, that contained haplotypes shared by Europeans and Asians and thus may pre-date the split that occurred between those populations.

The researchers identified these shared regions by calculating linkage disequilibrium blocks in a set of 457 non-Africans, and then found more than 41,100 haplotypes at these loci within the Egyptian, Ethiopian, and Yoruban samples. They then discarded the haplotypes that were shared by all three African populations to home in on a set of some 6,000 haplotypes.

These haplotypes were then used to try to distinguish between the non-African Chinese and Toscani populations and each of the three African populations.

Egyptian haplotypes, the researchers reported, were enriched in the Chinese and Toscani populations, suggesting that ancient humans followed the northern route out of Africa.

This effect, they added, remained even after the addition of a 10 percent misclassification error to their analysis.

The researchers noted that back-to-Africa migrations could skew their results, but added that such a migration would have had to occur prior to the European-Asian population split some 40,000 years ago. Their masking technique should have removed that effect, they said.

To confirm their finding, Pagani and his colleagues analyzed three Egyptian and five Ethiopian genomes through a multiple sequentially Markovian coalescent approach — both before and after masking — to find that the Egyptian genomes split more recently from both the West African (21,000 years ago) and the non-African (55,000 years ago) genomes than did Ethiopian genomes.

This, the researchers added, indicates higher similarities between non-African and Egyptian genomes than between non-African and Ethiopian genomes, and this further suggested Egypt was on the route the ancestors of Eurasians took on their way out of Africa.

"In our research, we generated the first comprehensive set of unbiased genomic data from Northeast Africans and observed, after controlling for recent migrations, a higher genetic similarity between Egyptians and Eurasians than between Ethiopians and Eurasians," Pagani added.