1) Estimated and calculated centroids location map (Fig. S4 -b)
Note: Centroids are not necessarily indicative of origin, diversity of the lineages in question are a better indicator of origin.
2) Haplogroup A frequency distribution (Fig. S2 -b)
"Haplogroups A and B are the deepest branches in the phylogeny and are essentially restricted to Africa, bolstering the evidence that modern humans first arose there (14, 15). Haplogroup A is mainly found in the Rift Valley from Ethiopia to Cape Town, mostly but not exclusively in some of the oldest hunter-gatherers who still survive and speak Khoikhoi and San languages, proposed by some to be the oldest languages. The interruption of its distribution in the middle of the Rift Valley is possibly the consequence of replacement by Bantu-speaking farmers who settled the region starting in the first millennium of the Christian era."
The "Max" of 11.5% A3b2 (M13) shown above seems a bit low at first glance for East Africa, Semino et. al 2002 and Cruciani et. al 2002 together found 24 A3b2 lineages out of a total of 148 sampled in Ethiopia; Amhara (48), Oromo(78), Beta Israel (22). However, if the results of the Hassan et. al 2008 study of Sudan and the Sanchez et. al 2005 study of Somalia are added to the studies above, the frequency of A3b2 drops from ~16% in just Ethiopia to ~11.5 % (75 / 650) when Sudan and Somalia are included. Also important to note is that the Beta Israel, Dinka, Shiluk, Nuer and Nuba all carry anywhere between 33% and 62% of A3b2 lineages.
3) Haplogroup B frequency distribution (Fig. S1 -a)
"Haplogroup B is found mainly among African Pygmies, who live in the central African forest and are still predominantly hunters-gatherers but speak Bantu languages borrowed from farmers who arrived in the area between 2,000 and 3,000 years ago."
Haplogroup B is found at low levels in Ethiopia, with frequencies varying anywhere between 0 - 2% ( Cruciani et. al 2002, Semino et. al 2002, Moran et. al 2004). The haplogroup is however much more common in Sudan, with frequencies reaching as high as 50% in the Nuer. Generally, frequencies of Haplogroup B are found any where between 8% and 27% in the Sudan among the Nubians, Nuba, Copts, Hausa, Dinka and Shilluk. (Hassan et. al 2008)
4) Haplogroup E frequency distribution (Fig. S1 -b)
"The third predominantly African haplogroup, E, diversified some time afterward, probably descending from the East African population that generated the Out of Africa expansion. The geographic distributions of the major branches of this haplogroup, given in Fig. S1b, suggest that most of the settlement outside of Africa by haplogroup E members involves the later mutant E-M35 varieties like M78, M81, and M123 that extended to Arabia and the northern Mediterranean coast."
5) Haplogroup J frequency distribution (Fig. S5 -a)
Further information on Haplogroup J in Ethiopia can be found in: Semino et. al 2002, Moran et. al 2004, Tofanelli et. al 2009, Chiaroni et. al 2009.
6) Genetic Diversity as a function of Distance from Addis Abeba (Fig. S6 -a)