Human Y chromosome diversity and the peopling of the “Green Sahara” during the Holocene humid phase

In Africa, the human population dynamics have been heavily influenced by the Sahara desert, as suggested by the strong Y haplogroup differentiation between northern and sub-Saharan Africa. During the Holocene, the climatic changes of the “African humid period” led to the replacement of the desert with a fertile environment (the “Green Sahara”), which allowed human settlements as indicated by archeological and paleoanthropological evidences. To evaluate the extent and trajectories of human movements across the Sahara, we analyzed by NGS about 3.3 Mb of the X-degenerate portion of the Y chromosome in 104 subjects, focusing on haplogroups currently found both in northern Africa and in the sub-Saharan area. We identified 7,544 polymorphisms, which were used to reconstruct the phylogeny and to estimate the coalescence age of nodes. Informative markers were further analyzed in a wider set of about 5,000 Y chromosomes. Combining phylogeography and age estimates, we found that northern African and sub-Saharan lineages only coalesced within a 5-12 kya time frame, suggesting extensive human movements across the “Green Sahara” and subsequent isolation after the desertification.