Fig 1.
Map of study recruitment areas.
Shown is a map of southern Africa depicting United Nations-defined zoned countries. Participants were recruited within the borders of South Africa and Namibia. However, individuals may report place of birth as South Africa, Namibia, Angola, Botswana, or Zimbabwe. Highlighted are geographical distributions and classifications of contemporary populations included in this study. Study participants (n = 182) were defined by place of birth and are broadly classified as San (orange) and Khoe (green) from Namibia, or Khoesan-ancestral (non-Khoesan with a Khoesan contribution), including the Basters (grey) and Southwestern Bantu (maroon) from Namibia and the Coloured (grey) and Southern Bantu (blue) from South Africa. Two Southern Bantu reported Zimbabwe as their place of birth (light blue). Previously published data for the South African #Khomani (purple, n = 32) [25] and Karretjie people (brown, n = 31) [26] has been included and distribution based on reported population densities.
Fig 2.
Phylogeny of 139 complete mitochondrial genomes depicting the earliest diverged maternal lineages.
The 77 novel southern African mitochondrial genomes sequenced in this study included 32 L0d1, 24 L0d2, 9 L0k1, 1 L0g and 11 L0a. Population representations are colour-coded, by tip labels, as defined in Fig. 1. Co-classifications are indicated by asterisks (*) for peoples defined linguistically as Khoe (green) yet practicing clear forager subsistence, including the Naro, Hai//om and Khwe (orange filled green rectangles). Six previously published mtDNA [24] are indicated by hash marks (#) and one ancient L0d2 (StHe) is indicated by orange arrow [6]. All other publicly obtained mtDNA are shown in black. Mitochondrial haplogroups according to PhyloTree Build 16 [32] are labelled in ‘black’, new haplogroups proposed in previous studies are represented in ‘black italic’, and new haplogroups identified in this study are presented in ‘red’, noting that L0d1e could be L0d1c4. Subclades represented by single mtDNA have sample identifiers provided in square brackets ([]). The simplified tree in the inset (red box) shows the phylogeny inferred from the expanded dataset of 603 genomes; individual genomes are collapsed with each triangle representing the relative diversity of the corresponding haplogroups and subclades. Estiimated coalescent times, including their 95% Highest Probability Density, are shown for the major branches.
Table 1.
Southern African distributions of L0 maternal haplogroups from 251 individuals.
Table 2.
Estimated coalescence times for the major southern African L0d/L0k mitochondrial genome haplogroups identified.