By recent I mean post-Neolithic, because this genome is only dated to ~4,500 BP. Admittedly though, I am skeptical that all of the Eurasian admixture arrived so late, and await more data points from prehistoric Africa. By the way, this individual belongs to Y-haplogroup E1b1 and mtDNA haplogroup L3. The main text is behind a pay wall, but the supp info is free:
Characterizing genetic diversity in Africa is a crucial step for most analyses reconstructing the evolutionary history of anatomically modern humans. However, historic migrations from Eurasia into Africa have affected many contemporary populations, confounding inferences. Here, we present a 12.5x coverage ancient genome of an Ethiopian male (‘Mota’) who lived approximately 4,500 years ago. We use this genome to demonstrate that the Eurasian backflow into Africa came from a population closely related to Early Neolithic farmers, who had colonized Europe 4,000 years earlier. The extent of this backflow was much greater than previously reported, reaching all the way to Central, West and Southern Africa, affecting even populations such as Yoruba and Mbuti, previously thought to be relatively unadmixed, who harbor 6-7% Eurasian ancestry.
Llorente et al., Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent, Science, Published Online October 8 2015, DOI: 10.1126/science.aad2879
Erratum to Gallego Llorente et al. 2015
The results presented in the Report “Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent“ were affected by a bioinformatics error. A script necessary to convert the input produced by samtools v0.1.19 to be compatible with PLINK was not run when merging the ancient genome, Mota, with the contemporary populations SNP panel, leading to homozygote positions to the human reference genome being dropped as missing data (the analysis of admixture with Neanderthals and Denisovans was not affected). When those positions were included, 255,922 SNP out of 256,540 from the contemporary reference panel could be called in Mota. The conclusion of a large migration into East Africa from Western Eurasia, and more precisely from a source genetically close to the early Neolithic farmers, is not affected. However, the geographic extent of the genetic impact of this migration was overestimated: the Western Eurasian backflow mostly affected East Africa and only a few Sub-Saharan populations; the Yoruba and Mbuti do not show higher levels of Western Eurasian ancestry compared to Mota. We thank Pontus Skoglund and David Reich for letting us know about this problem.