The figure to the left comes from a short paper in The American Journal of Human Genetics, A Revised Root for the Human Y Chromosomal Phylogenetic Tree: The Origin of Patrilineal Diversity in Africa. The paper is interesting because of two factors: 1) they sequenced more of the Y chromosome 2) their African data set of individuals was very large, in excess of 2,000. The weird thing about the results is that it upends one of the truisms in human phylogenetics: that African Pygmies and Khoisan are basal to other human lineages. By this, I mean that they “split off” first (this is why people say these are the “oldest” human populations). This is not what these researchers found. Rather, the basal Y chromosomal haplogroups were concentrated in Central West Africa and Northwest Africa! The map below shows the distributions of the two most divergent Y chromosomal lineages, red being the outgroup, and green being the second most divergent:

A second major point in this paper is that they recalculated the coalescence back to the last common ancestor ...