Central African Hunter-Gatherer Ancient DNA Is Distinctive

Malawi is along the Great Rift Valley that divides Eastern and Central Africa. 

In 1950, J. Desmond Clark led excavations at a Later Stone Age rockshelter at Hora Mountain, a large inselberg overlooking a modern floodplain in the Mzimba District of northern Malawi. At the Hora 1 site, he recovered two human skeletons, one male and one female, along with a rich—but superficially described and undated—cultural sequence. In 2016, our renewed excavations recovered a wealth of lithic, faunal, and other materials such as mollusk shell beads and ochre. Our reexamination of the skeletons also produced the first ancient DNA from the central African region, which together with previous morphological analysis demonstrates that the LSA foragers of the area cannot be readily fit within the known genetic and phenotypic parameters of living foragers. The significance of the Hora 1 site was made further clear by the relocation of several previously known sites also at the mountain, the discovery of four new rock art sites, and the discovery of four very rich new archaeological sites in the mountains adjacent to the floodplain. Here, we describe our renewed work and how it fits with the original findings to offer unprecedented promise for understanding the lifeways of Holocene foragers in central Africa.

Jessica Thompson, et al., "The Forgotten Significance of the Later Stone Age Sites near Hora Mountain, Mzimba District, Malawi" (Forthcoming, SAA 2017 Conference Paper).

The late stone age site, most notably, precedes Bantu expansion.

This seems to be of a piece with the fact that the substrate population in Mozambique (where Bantu populations have click consonants) likewise does not correspond to any modern African population. As previously noted at this blog in that link:

A 2010 article in the European Journal of Human Genetics found genetic traces of a substrate population in Mozambique that was an ancestral component distinct from any of the other ancestral populations of Africa. As the body text in that open access article explains (citations omitted):

The southeastern Bantu from Mozambique are remarkably differentiated from the western Niger-Congo speaking populations, such as the Mandenka and the Yoruba, and also differentiated from geographically closer Eastern Bantu samples, such as Luhya. 

These results suggest that the Bantu expansion of languages, which started ~5000 years ago at the present day border region of Nigeria and Cameroon, and was probably related to the spread of agriculture and the emergence of iron technology, was not a demographic homogeneous migration with population replacement in the southernmost part of the continent, but acquired more divergence, likely because of the integration of pre-Bantu people. 

The complexity of the expansion of Bantu languages to the south (with an eastern and a western route), might have produced differential degrees of assimilation of previous populations of hunter gatherers. This assimilation has been detected through uniparental markers because of the genetic comparison of nowadays hunter gatherers (Pygmies and Khoisan) with Bantu speaker agriculturalists. 

Nonetheless, the singularity of the southeastern population of Mozambique (poorly related to present Khoisan) could be attributed to a complete assimilation of ancient genetically differentiated populations (presently unknown) by Bantu speakers in southeastern Africa, without leaving any pre-Bantu population in the area to compare with.

In other words, there is genetic evidence that there was an entire "lost race" in Mozambique, distinct from Khoisans, Pygmies, East Africans and West Africans, with no pure blooded remaining members that disappeared when it was subsumed into the population of Bantus expanding into the area.

Those Bantus had a linguistic and cultural legacy from a quite precisely identified small region near the coastal border of Nigeria and Cameroon, but had assimilated a mish mash of Africans peoples into their genetic melting pot, including the ancestral peoples of Mozambique, on their way to Southeast Africa.