In September 2007,368 people responded to the invitation extended by the African Genome Education Institute (AGEI) in partnership with Ancestry24 to volunteer a cheek swab sample for genetic ancestry testing. Looking for DNA testing?

Genetic ancestry testing involves the use of specific regions of the human genome, which by virtue of their unique mode of inheritance, have been used widely as tools to shed light on population affinities and human evolution. Mitochondrial DNA (mtDNA), which is inherited exclusively through our matriline (mother, maternal grandmother, maternal great-grandmother, and so on), provides us with the opportunity to trace our maternal ancestry several thousands of years back into the past. Both sons and daughters inherit their mother’s mtDNA, but only the daughters (not sons) will pass their mtDNA to their offspring. All surviving mtDNA lineages ultimately trace back to a common ancestor who lived in Africa approximately 150,000 years ago.
Over time, as humans migrated out of Africa to populate the rest of the world, they took with them a subset of the divergent mtDNA lineages found in Africa which eventually mutated or changed to produce the various lineages found in living people outside of Africa. At the same time, those ancestors who remained in Africa continued to evolve newer lineages. As people migrated and settled throughout the continent, their contact with other groups contributed to gene exchange between groups thereby contributing to shaping the gene pool found in living people.
In the past 20 years or so, researchers have studied several populations throughout the world and have mapped the global patterns of mtDNA variation. There is reasonable concordance between ones geographic region of origin and the mtDNA lineages found in that region. For example, the lineages found in indigenous Africans belong predominantly in haplogroup (or branch) L of the mtDNA tree whereas haplogroup M is found most commonly among Asians from India.
In addition to mtDNA, Y chromosome DNA offers an equivalent tool to trace paternal heritage (father, father’s father, great grandfather, etc) in males. Y chromosome patterns of variation are also highly structured by geographic region. Also, specific Y chromosome changes or mutations have been identified that contribute to the branching pattern of the Y chromosome tree.
In the present study, the Human Genome Diversity and Disease Research Unit at the National Health Laboratory Service and University of the Witwatersrand under the Directorship of Professor Himla Soodyall was invited to conduct the laboratory testing and analysis on the samples collected for this project. The project was conceived with the goal of giving members of the public an opportunity to learn about their ancestry and to engage with scientists on this journey of discovery. Given the rich diversity and history of the people of the Cape, mtDNA and Y chromosome DNA was used to assess how females and males, respectively, have contributed to shaping the gene pool among its inhabitants.

Sample

Of the 368 individuals sampled, we were successful at obtaining results for 365 individuals; the remaining three samples did not yield consistent results and were therefore excluded.

All participants had completed and signed an informed consent form which included among others questions related to the individuals self identified ethnicity, home language and gender. Some of these results are given in Fig. 1.

It should also be stressed that while the sampling was conducted in Cape Town, not all participants were South Africans. In fact, participants cited 48 countries as their home country. Some individuals self identified as Cape Malay (10) while others identified themselves as Coloured. In this sample, all individuals grouped under “Asian” were Indians. Thirty-one individuals chose not to complete the section on identity and we have grouped them under the heading for ethnic group “Unknown/Other” in this analysis.

Mitochondrial DNA (mtDNA) results

The Southern African mtDNA haplogroup (branch) L0 and its sub-haplogroups (sub-branches) altogether made up 19% of mtDNA lineages in the total sample (see Fig. 2). Haplogroup L0 is commonly found in Khoe and San people and their maternal descendants, and can therefore be used as a marker to estimate Khoesan (termed used in reference to the combined group) maternal gene admixture in the other groups (see Fig. 3).

Fig. 2 Schematic diagram showing the branching pattern of mtDNA haplogroups on a tree and their geographic regions of origin (colour circles on tree correspond to geographic region). The pie chart summarizes the apportionment of the mtDNA variation derived from the different geographic regions in the total sample (365 individuals).

At least 1 in 5 people who self identified as Black (predominantly southern Bantu- speakers) have a maternal ancestry linked with Khoesan people (Fig. 3). Also, about 1 in 10 Black people have mtDNA lineages derived from Eurasian (3.0%) and Asian (7.1%) origins. The newly defined haplogroups L4 and L5 that make up the North African mtDNA lineages were only found in the Black sample.

Approximately 1 in 12 individuals who identified as White have mtDNA lineages derived from African sources, of which at least 6% are linked with Khoesan ancestry. Although the Cape Malay and Asian (Indian) sample sizes are small in the present study and therefore does not attain any statistical significance, it is interesting to note that there was no mtDNA contribution from the Khoe and San in the Malay group but there was input into the Indian group (~20% or 1 in 5 people). The Coloured group has mtDNA lineages that traced to a wider geographic region of origin; this is not surprising given the historical context of their origin(s). Those people who chose not to divulge their ethnic identity (which could have been due in part to them not fully understanding what was required in this question or personal reasons) seem to mirror the Coloured sample with respect to their mtDNA gene pool.

For the most part there is good concordance between the self identified ethnic origins indicated by participants and the origins of their mtDNA haplogroups.

Y chromosome DNA results

Y chromosome haplogroup data was obtained for 197 males in the sample. The number of males within each group is given in Fig.4. About one-third of the total sample of males traced their paternal heritage to Y haplogroups that originated in Africa. Given that only 25% of the total sample identified as Black, at least 8% of individuals who identified with another ethnic group traced their heritage to Africa. African derived Y haplogroups accounted for 3% of the Y chromosome pool in Whites and ~20% in the Coloured group (see Fig. 4). The Cape Malay and Asian samples are too small to make any conclusive deductions. Of the 17 males who did not provide an ethnic affiliation, their Y chromosome lineages could be traced to Europe (11.8%), Eurasia (~71%), Asia (~6%), Southern Africa (~5%) and Northern Africa and Mediterranean (~5%) origins.

We have not described the haplotype diversity as deduced from the short tandem repeat analysis in this report. This part of the analysis would be done in the final report after conducting a robust comparative analysis using the data provided from Pietermaritzburg, the other region where sampling was conducted under the auspices of this project.

Report on genetic ancestry testing conducted in Cape Town (September, 2007) by Prof Himla Soodyall

Tags: Ancestors, Bantu, Cape, Coloured, India, Indian, White, Witwatersrand