Haplogroups L3 and E are Asian, not African

The latest evidence suggests that two major haplogroups long considered African actually arose in Asia and then back-migrated to Africa.

The presence of the L haplogroup common in Africa was unexpected given the clustering of the Saudis with Europeans in the phylogenetic tree and suggests some recent African admixture. To examine this further, we performed formal tests for a history of admixture and found no evidence of African admixture in the Saudi after the split. Taken together, these analyses suggest that the L3 haplogroup found in the Saudi were present before the bottleneck 50,000 YBP. Given the TMRCA estimates for the L3 haplogroup of approximately 70,000 YBP and the timing of the Out-of-Africa split, these analyses suggest that L3 haplogroup arose in the Middle East with a subsequent back migration and expansion into Africa over the Horn-of-Africa during the lower sea levels found during the glacial period bottleneck.

Farrell et al. "The Saudi Arabian Genome Reveals a Two Step Out-of-Africa Migration". Am Soc Hum Genet, 2013.

It remained mysterious that how many times the anatomically modern human migrated out of Africa, since that among the three superhaplogrous C, DE and F, Haplogroup F distributes in whole Eurasia, C in Asia and Austronesia, D exclusively in Asia, while D's brother clade E distribute mainly in Africa, so there are two hypotheses, 1) haplogroups D and CF migrated out of Africa separately; 2) the single common ancestor of CF and DE migrated out of Africa followed by a back-migration of E to Africa. From this study, the short interval between CF/DE and C/F divergences weakens the possibility of multiple independent migrations (CF, D, and DE*) out of Africa, and thus supports the latter hypothesis (Fig. S2 a).

Shi Yan et al. "Y Chromosomes of 40% Chinese Are Descendants of Three Neolithic Super-grandfathers". arXiv:1310.3897 [q-bio.PE], 2013.

Related: Eurasian Origin and Back-Migration of L3 and DE