Supplementary Figure S1: Schematic phylogeny of the African haplogroups found in the 982 individuals of our dataset. The reference sequences RSRS (Behar et al. 2012) and rCRS (corresponding to European haplogroup H, Andrews et al. 1999) are indicated with a black line. Dashed lines indicate nodes with low posterior probability for which the topology could not be resolved. The width of the triangles is proportional to the frequency of a given haplogroup in the dataset. Haplogroups L3d and L3f, in yellow, are described in more detail in Figure S4A and S4B. L0a L0f L0k L0 L0d L1b L1 L1c L2a L2 L2d L2b L2c L2e L3d L3b L3h L3e L3 L3f L4 L5 RSRS rCRS - L0f 0 A B L5 DAM L3d L2a L2e HER 0 L3f 1 1 NEZ 0 1 MBN NYA L2dSUB CHO L0a LUY L1c L2c L3e LOZ L3f TOT GAN L1b SHA FWE NKO TNG HIM L3b L1b L3b 1 L5 L2e L3h TSW MBN GAN L2d KGA NKO L2a L1c LUYKUV L0d CHO L0a LOZ L2b TOT SUB L3e NYA L2 TNG L2c MBK KWA OVM SHO L3d 0 L0k, L0f, L4 East Bantu West Bantu Khoisan L5 MBK L2a SUB 5 L2b LUY GAN KWA L1c LOZ OVM L3e CHO TSW L1b TOT L0a L2d NYA KGA SHO L2c 5 L2 L3d MBN 0 NKO FWE SHA KUV 0 5 0 KGA 1 2 L2 L0f TNG L0d SHO KWA C L3b L3h KUV OVM MBK L2b L0k 2 L2e TSW 5 L3f, L3h 0 Supplementary Figure S3: Haplogroup frequencies of important haplogroups in the populations studied here. A: Haplogroups L0d and L0k. B. Subhaplogroups L3d3a1 and L3f1b4a. The size of the circles is proportional to the sample size. A L0k L0d Others B L3f1b4a L3d3a1 Others Supplementary Figure S4A: Bayesian tree of all African complete mtDNA sequences belonging to haplogroup L3d, and S4B: belonging to haplogroup L3f. The sequences included in these trees are the same as those included in the networks in Figure 4B and D. Branches discussed in the main text are highlighted. The posterior probability associated with major nodes is indicated in red font. Note the different time scale between the two trees. L3d1b A 0.9822 0.2739 0.16610.2212 0.2818 L3d2 1 L3d4 0.0985 0.0001 new! 0.7228 0.3947 L3d3a1 L3d3 0.0021 0.9945 1 0.5498 0.0129 L3d3a1a 1 0.047 0.0456 0.8826 1 0.1025 0.0241 L3d1a 30000 0.9762 25000 1 0.987 0.9983 20000 15000 10000 5000 0 time (years ago) B L3f3 L3f2a1 0.2853 L3f2 1 L3f2b 0.3898 1 L3f1a new! L3f1b4 1 0.998 L3f1b4a L3f1 0.9056 0.9999 0.8427 0.2337 L3f1b L3f1b3 0.3297 1 L3f1b1 L3f1b2 0.3164 60000 50000 40000 30000 time (years ago) 20000 10000 0 Supplementary Figure S5: Bayesian Skyline Plots for the Himba, Herero, Kuvale and Damara. X axis: time in years ago. Y axis: effective population size per generation time. Herero Himba 1.E6 1.E7 1.E6 1.E5 1.E5 1.E4 1.E4 100000 75000 50000 25000 0 1.E3 100000 75000 50000 25000 0 1.E3 Damara Kuvale 1.E7 1.E6 1.E6 1.E5 1.E5 1.E4 1.E4 1.E3 125000 100000 75000 50000 25000 0 1.E3 125000 100000 75000 50000 25000 0
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