Ancient substructure in early mtDNA lineages of southern Africa

Abstract

Among the deepest-rooting clades in the human mitochondrial DNA (mtDNA) phylogeny are the haplogroups defined as L0d and L0k, which are found primarily in southern Africa. These lineages are typically present at high frequency in the so-called Khoisan populations of hunter-gatherers and herders who speak non-Bantu languages, and the early divergence of these lineages led to the hypothesis of ancient genetic substructure in Africa. Here we update the phylogeny of the basal haplogroups L0d and L0k with 500 full mtDNA genome sequences from 45 southern African Khoisan and Bantu-speaking populations. We find previously unreported subhaplogroups and greatly extend the amount of variation and time-depth of most of the known subhaplogroups. Our major finding is the definition of two ancient sublineages of L0k (L0k1b and L0k2) that are present almost exclusively in Bantu-speaking populations from Zambia; the presence of such relic haplogroups in Bantu speakers is most probably due to contact with ancestral pre-Bantu populations that harbored different lineages than those found in extant Khoisan. We suggest that although these populations went extinct after the immigration of the Bantu-speaking populations, some traces of their haplogroup composition survived through incorporation into the gene pool of the immigrants. Our findings thus provide evidence for deep genetic substructure in southern Africa prior to the Bantu expansion that is not represented in extant Khoisan populations.

Figure 1

Surfer Maps Displaying the Spatial Distribution of Haplogroup Frequencies Dots indicate sample locations. (A) Haplogroup L0d. (B) Haplogroup L0k. Note that the scale in (B) is different from that in (A). (C) Presence of haplogroups L0k1b and L0k2 in southern Africa (large black dots). The actual sampling location of one Topnaar Nama individual with haplogroup L0k1b is shown here; in (A) and (B) this individual was included with the general Nama population sample.

Figure 2

Simplified Tree Topology for the Major Lineages of L0d and L0k, Based on Coding Region Sequences and with Time Scale Indicated Previously undetected branches are labeled in bold font; when a previously reported branch is renamed, the old label is given in brackets. Confidence intervals for the TMRCA of the major nodes are indicated by vertical bars. The red shading highlights the time span that was associated with the deterioration of climate in the central Kalahari area.

Figure 3

MJ-Network of L0k Based on Full Sequences