History Alive: DNA & The Rainbow Nation
This research enterprise is to take DNA samples from about 500-1000 South Africans in order to trace their geographical ancestry. It will provide the first national database available in the public domain. The gene pool found in the present-day South African population draws from the indigenous people of Southern Africa, namely the former hunters or San groups, the pastoral Khoikhoi who are thought to have migrated to the Cape in the last 2,000 years introducing sheep and cattle to the region, and people originating from the Niger-Congo area speaking Nguni-languages who migrated south in the last 1,200 years. In addition, sea-borne immigrants from Western Europe (largely from the Netherlands, the United Kingdom, Germany and France ), indentured labourers from India and slaves from the Malaysian Archipelago, Madagascar and other parts of Africa, have also contributed to the gene pool. Varying degrees of gene admixture between the different parental gene pools have resulted in the rich diversity of South Africans and this is evident also from the cultural and linguistic diversity of the ‘Rainbow Nation.’ We wish to provide a DNA map of the genetic heritage adding thereby an additional layer of information to our self-understanding of where we come from and who we are.
Method
Two genetic histories are recovered using mitochondrial DNA (mtDNA) and Y chromosome DNA testing as follows:
Maternal ancestry testing (mtDNA analysis): Females and males
Mitochondrial DNA (mtDNA) is passed on from mothers to both her sons and daughters. However, only her daughters will transmit their mtDNA in successive generations. Both males and females can be tested for mtDNA to trace their maternal ancestry. We sequence a region of about 1000 base-pairs (bp) of the mtDNA control region (also called the hypervariable region of which there are two, HVRI and HVRII). The sequence is then compared to a published reference sequence (also referred to as the Cambridge Reference Sequence, CRS) to identify the positions at which your sequence differs from the CRS. This information is used together with an internationally adopted nomenclature to identify the name of your mtDNA lineage. These lineages are also called haplogroups. Haplogroups are continent specific and subdivisions of these haplogroups have a regional geographic distribution.
Database Matches
After we obtain your mtDNA sequence and deduce the haplogroup, we then compare the sequence to a database of mtDNA sequences in individuals we have examined for our research as well as other published data collected on individuals sampled throughout the world by other researchers. This comparison allows us to find matches or close matches to one’s sequence, to give you information about the distribution of your mtDNA haplogroup, and the most likely region where your mtDNA profile originated.
Y chromosome analysis (only males)
Fathers pass on their Y chromosome to their sons only, who then pass on their Y chromosome to their sons, and so on. We make use of two types of markers on the non-recombining portion of the Y chromosome to resolve the Y chromosome lineages in males. The first type of marker, so-called bi-allelic variants (two states or alleles can be found at one site on the chromosome) is used to classify Y-chromosomes into lineages or haplogroups. These haplogroups, or major branches of the Y chromosome tree, show specific ethnic and/or geographic distribution patterns. The second type of marker, micro satellites or short tandem repeats (STRs) consist of repetitive DNA elements that are tandemly repeated and are highly variable in humans. STRs are used to define haplotypes (like a DNA fingerprint, but on the Y chromosome) within the haplogroups.
Database Matches
After we deduce your Y chromosome haplogroup, we use the STR data to derive your haplotype. We then compare your haplotype to our database and with information from a global database ( www.ystr.charite.de ). This comparison allows us to find matches or close matches to your Y chromosome lineage, to give you information about the distribution of your Y chromosome haplogroup, and the most likely region where your Y haplotype originated.
Limitations of genetic ancestry testing
The limitation of using mtDNA and Y chromosome DNA for genealogical testing is that this DNA will trace only two genetic lines on a family tree in which branches double with each preceding generation. For example, Y chromosome tracing will connect a man to his father but not his mother, and it will connect him to only one of his four grandparents: his paternal grandfather. In the same way it will connect him to one of his eight great grandparents (see figure below). Continue back in this manner for 14 generations and the man will still be connected to only one ancestor in that generation. Y-chromosome DNA testing will not connect him to any of the other 16 383 ancestors in that generation to whom he is also related in equal measure. The same scenario applies when using mtDNA.
Outcomes
• National database of the geographical ancestry of a sample of South Africans;
• Workshop to train journalists and academics to interpret the information and contribute to an edited anthology; Bringing History Alive: DNA and the Rainbow Nation.
• Special website to make ancestry information available for public use and dissemination.
Raj Ramesar is Professor and Head of the Division of Human Genetics at the University of Cape Town. He is also Director of the MRC’s Human Genetics Research Unit. Raj’s interest is in identifying those aspects of the human genome that are worth investigating for their most rapid benefit to our communities in South Africa.
Himla Soodyall is Principal Medical Scientist at the National Health Laboratory Service and holds a joint appointment as an Associate Professor in the Division of Human Genetics at the University of the Witwatersrand. She was appointed Principal Investigator of the Sub-Saharan Africa part of the global Genographic Project, a joint initiative of the National Geographic Society and IBM.
Wilmot James is Chief Executive of the Africa Genome Education Institute and Honorary Professor in the Division of Human Genetics, University of Cape Town. He is also Chairman of the Cape Philharmonic Orchestra, director of Sanlam, Media24 and the Grape Co and Trustee of the Ford Foundation of New York.
Written by: Dr Wilmot James