Reconstructing ancient Southern African mitochondrial genomes at Faraoskop

Abstract Twelve human skeletons, approximately 2000 years old, were recovered from the Faraoskop archaeological site in the Western Cape Province, South Africa (Manhire 1993). Several of the skeletons were well enough preserved to determine the osteological profiles (sex, age and stature etc.). Additionally, paleopathological and traumatic changes were observed on some of these skeletal remains. Given suggested context that these human remains were drawn from a single mortuary event, this paper investigates the possibility of familial relationships between the individuals by establishing maternal profiles from mitochondrial DNA. The mitochondrial DNA analysis resulted in the identification of four full genomes from the Faraoskop (FK) individuals and the two Khoesan pastoralist individuals chosen as reference samples for the analysis. Three other FK individuals provided partial genomes which could be assigned to incomplete haplotypes. Five individuals could not be sequenced due to poor DNA preservation. Molecular sex could be confirmed for five FK and two reference individuals, adding to the sex assessment from osteological data. All but one of the mitochondrial haplotypes were L0d1 or L0d2 which is consistent with mtDNA from living Khoesan populations in southern Africa. One individual (FK1) was L0f1, a haplotype which is not present southern African Khoesan, but is currently centred in Uganda and Tanzania. It is occasionally found amongst southern African Bantu speakers which suggests that the presence of L0f1 is a remnant of an earlier distribution which is now lost. The three L0 mitochondrial haplotypes from the six Faraoskop individuals (L0d1, L0d2, and L0f) suggest a diversity of maternal lineages compatible with the diversity of Khoesan groups but given the simultaneity of the burial, it is tempting to suggest that those with similar maternal haplotypes were closely related.