Largest genomic study shows Khoe-San people are unique

Sep 20, 2012 by Erna Van Wyk
Traditional San art manufactured by the Khomani people. Credit: Carina Schlebusch

Genetically, culturally and ethically the Khoe-San have something special to add to this world. The importance of this study is to put the Khoe and San heritage in the right place in history and this research will provide a genetic backdrop for future studies - Mattias Jakobsson.

The largest genomic study ever conducted among Khoe and San groups reveals that these groups from southern Africa are descendants of the earliest diversification event in the history of all humans - some 100 000 years ago, well before the 'out-of-Africa' migration of modern humans.

Some 220 individuals from different regions in southern Africa participated in the research that led to the analysis of around 2.3 million DNA variants per individual – the biggest ever.

The research was conducted by a group of , including Professor Himla Soodyall from the Human Genomic Diversity and Disease Research Unit in the Health Faculty at the University of the Witwatersrand in Johannesburg.

Entitled Genomic variation in seven Khoe-San groups reveals adaptation and complex African history, the study has been selected for early online publishing in the renowned scientific journal, Science, on Thursday, September 20, 2012.

"The deepest divergence of all living people occurred some 100 000 years ago, well before modern humans migrated out of Africa and about twice as old as the divergences of central African Pygmies and East African hunter-gatherers and from other African groups," says lead author Dr Carina Schlebusch, a Wits University PhD-graduate now conducting post-doctoral research at Uppsala University in Sweden.

Soodyall, from National Health Laboratory Services in South Africa, has a long standing relationship with Khoe and San communities and said that the findings are a "phenomenal tribute to the indigenous Khoe and San people of southern Africa, and through this magnificent collaboration, we have given the peoples of Africa an opportunity to reclaim their place in the history of the world".

This is a Khomani San settlement near Askham in the Northern Cape Province (SA). Credit: Carina Schlebusch

Besides the publication of the study, the authors will also be visiting the San groups in the Kalahari, in the Askam area in South Africa on the 24th of September 2012 for the country's Heritage Day celebrations. "We are excited that together with some of our colleagues from Uppsala University, we will be able to join in the celebrations with the San groups in the Kalahari who participated in our research and to acknowledge their contribution in making our research possible".

The researchers are now making the genome-wide data freely available: "Genetic information is getting more and more important for medical purposes. In addition to illuminating their history, we hope that this study is a step towards Khoe and San groups also being a part of that revolution," says Schlebusch. Another author, Professor Mike de Jongh from University of South Africa adds, "It is important for us to communicate with the participants prior to the genetic studies, to inform individuals about the nature of our research, and to also go back to not only to share the results with them, but also to explain the significance of the data for recapturing their heritage, to them."

According to Assistant-Professor Mattias Jakobsson from Uppsala University, these deep divergences among African populations have important implications and consequences when the history of all humankind is deciphered.

The deep structure and patterns of genetic variation suggest a complex population history of the peoples of Africa. "The human population has been structured for a long time," says Jakobsson, "and it is possible that modern humans emerged from a non-homogeneous group."

The study also found surprising stratification among Khoe-San groups. For example, the researchers estimate that the San populations from northern Namibia and Angola separated from the Khoe and San populations living in South Africa as early as 25,000 – 40,000 years ago.

"There is astonishing ethnic diversity among the Khoe-San group, and we were able to see many aspects of the colorful history that gave rise to this diversity in their DNA", said Schlebusch.

The study further indicates how pastoralism first spread to southern Africa in combination with the Khoe culture. From archaeological and ethnographic studies it has been suggested that pastoralism was introduced to the Khoe in southern Africa before the arrival of Bantu-speaking farmers, but it has been unclear if this event had any genetic impact.

The Nama, a pastoralist Khoe group from Namibia showed great similarity to 'southern' San groups. "However, we found a small but very distinct genetic component that is shared with East Africans in this group, which may be the result of shared ancestry associated with pastoral communities from East Africa," says Schlebusch.

With the genetic data the researchers could see that the Khoe pastoralists originate from a Southern San group that adopted pastoralism with genetic contributions from an East African group – a group that would have been the first to bring pastoralist practices to southern Africa.

The study also revealed evidence of local adaptation in different Khoe and San groups. For example, the researchers found that there was evidence for selection in genes involved in muscle function, immune response, and UV-light protection in local Khoe and San groups. These could be traits linked with adaptations to the challenging environments in which the ancestors of present-day San and Khoe were exposed to that have been retained in the gene pool of local groups.

The researchers also looked for signals across the genome of ancient adaptations that happened before the historical separation of the Khoe-San lineage from other humans. "Although all humans today carry similar variants in these genes, the early divergence between Khoe-San and other human groups allowed us to zoom-in on genes that have been fast-evolving in the ancestors of all of us living on the planet today," said Pontus Skoglund from Uppsala University.

Among the strongest candidates were genes involved in skeletal development that may have been crucial in determining the characteristics of anatomically .

Explore further: Study shows how epigenetic memory is passed across generations

More information: "Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History," by C.M. Schlebusch et al. Science, 2012.

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Egleton
3.4 / 5 (7) Sep 21, 2012
All non-African people see Africa a a homogeneous mass of black people, and so they miss the amazing variety of types.
I was working with some Englishmen in Zimbabwe when a San walked by. I got excited because I had believed that they were all extinct. The Englishmen did not have a clue what was going on. Why was I so interested in this black when there were so many others?
The San are a completely different people to the aBantu who colonised Southern Africa from West Africa.
I fear for the future of a very special people. Their demise would deprive the world of a great beauty.
ryggesogn2
2 / 5 (4) Sep 21, 2012
I fear for the future of a very special people. Their demise would deprive the world of a great beauty.


I understand the sentiment but do you propose a eugenics law to keep people 'special'?
Egleton
3.7 / 5 (3) Sep 21, 2012
No I propose that we recognise who are the aborigines of Southern Africa and give them the same recognition that other native people demand and receive all over the world.
Other so-called "Natives" are immigrants into their land, albeit a long time ago. And who knows who they displaced.
The San on the other hand are a true indigenous people in that they became human on that very earth.
There is a propensity to consider only whites to be colonisers. A moments reflection will quickly reveal that absurdity.
However the aBantu claim that they are indigenous to Southern Africa. They are not. They are very recent arrivals.
Egleton
3.7 / 5 (3) Sep 21, 2012
The aBantu refuse to acknowledge the existence of the San as a distinct people. They argue that because the San are not a distinct people that means "Blacks" have always existed in Southern Africa.
This is an argument based on skin colour.
The San were hunter-gatherers and the Koi were herders with a very distinct language and culture.
The aBantu are very distinct. It is only if you squint at the skin colour, ignore everything else and use your imagination that you can consider them the same people.
The danger is that if the aBantu are forced to recognise the natives they will kill them all off.
In fact the aBantu are practising what the Australians tried. They are trying to breed the natives into extinction.
jerryd
not rated yet Sep 22, 2012

There are at least 10 different black groups. All you have to do is look at them and understand that. The Bantu, Whoopie Goldberg is an example of their look, is very different from the others from pigmy's to Zulu's, etc. It would take a very dense person to conclude othewrwise.
ryggesogn2
2.3 / 5 (9) Sep 22, 2012
I propose that we recognise who are the aborigines of Southern Africa and give them the same recognition that other native people demand and receive all over the world.

Why?
So they can demand govt welfare?

'Liberals' like to assert Darwinian evolution, except when they want to create a dependent constituency.
Egleton
3.5 / 5 (4) Sep 23, 2012
@Ryqqesong
What government welfare? We are talking about Africa, Numbnut, Not Alabama.
ryggesogn2
2.3 / 5 (6) Sep 23, 2012
@Ryqqesong
What government welfare? We are talking about Africa, Numbnut, Not Alabama.

ecognition that other native people demand and receive all over the world.

To what end? Why do this if they are not granted extra 'rights'?
Torbjorn_Larsson_OM
5 / 5 (3) Sep 23, 2012
"'Liberals' like to assert Darwinian evolution,"

Creationists shouldn't comment on science, it is hilarious to see.

We know and observe evolution to a much better degree than gravity. Would you exit the 10th floor through the window, or damage your adaptive immune system so it can't cope with newly evolving diseases?

And in this case the discussion isn't about the value of new alleles (but they likely are, seeing the selection that evolved them) but how they show the cultural background of some groups.
ryggesogn2
2.3 / 5 (6) Sep 23, 2012
Obviously you missed the point Lars.
It's one thing to analyze genetics and history of peoples, but to what end, science? Great.
If the end result is to classify these these genetic individuals into some special interest group that must be 'protected' for humanity, that is not so great. What if they don't want to be 'protected'? What does 'protected' mean: They must only interbreed in their gene pool? They have the 'right' for the rest of us in the contaminated gene pool to take care of them?

It is the 'liberal' that has the propensity for such 'protection' while claiming they support evolution and natural selection, except for those who the 'liberal' claims to need 'protection' from nature.
Jeweller
3.4 / 5 (5) Sep 23, 2012
Having read the article and the comments, I'm left feeling ill at ease.
It seems like the Koi-San people are still being treated like a Subject to be studied at a University, or "something to be discussed" by intellectuals over drinks in the Gentlemens Club.
We're talking about human beings here, not an alien species.
Oh, and Egleton, you make some sweeping and inaccurate statements which smack of an outdated Colonialist attitude.
Egleton
3 / 5 (2) Sep 23, 2012
Spot on Jewller. I am an out-dated Colonial. I am not impressed by the younger colonialists efforts.

Bob Mugabe is your man. We fought and died to keep him out. You insisted that only he could seize the reigns of power.
And now that Zimbabwe has failed, where are you? In America in Europe?
Sometimes I see one of you making a token effort, getting some happy snaps and bragging rights at home, and then fleeing.
Congratulations, you won. You meddled now it is your problem. Go and fix it and do not leave until the job is done.

And why the outrage if I suggest that the majority aBantu should respect and acknowledge the minority San? Examine your morals.
Jeweller
4 / 5 (2) Sep 23, 2012
Once again, you make some sweeping and inaccurate statements. Also, you seem to be the only "outraged" person here.
I'm a born and bred (white) South African. A patriotic one, still living in Cape Town.
To keep the language clean, I will just say that I dislike Robert Mugabe intensely.
That said, I still feel uncomfortable with the way 'we' discuss the Koi-San people.
Brian Francis Pretorius.
I use the name Jeweller because that is the trade I have been in all my life. As were my Father and Grandfather. In Pretoria.
Egleton
1 / 5 (1) Sep 24, 2012
Good Jeweller.
Then I am not talking to the sublimely ignorant. Since when do morals become "Outdated"? What was wrong a thousand years ago will be wrong in a thousand years time. One does not change ones morals as one changes ones socks.
I hear that you feel uncomfortable discussing the San.
Can nothing be said for them without being paralysed by the fear of being labelled patriarchal? Is this the compromise that you have made with the aBantu so that you can continue to live there? That you will defend them against all criticism? This is a mark of their intolerance.
Is it worth it?
Yes, I am outraged. I shall remember the blood sacrifices we made to Africa until I die. Sit Nomine Digna.
I watch our "Moral Superiors" unravel in Gomorrah.
JGHunter
4 / 5 (3) Sep 24, 2012
All non-African people see Africa a a homogeneous mass of black people, and so they miss the amazing variety of types.


Definitely a sweeping statement. I was aware of the genetic variety in Africa from a young age, but then again I was always good at human geography at school... regardless even just a week in a small area of Kenya further increased my knowledge of the variety. I am not the only one and your idea that all non-Africans are so blind that they think all black people look the same is just straight offensive and incorrect.
ryggesogn2
3.7 / 5 (3) Sep 24, 2012
And why the outrage if I suggest that the majority aBantu should respect and acknowledge the minority San? Examine your morals.


Why aren't all people in Africa respected and acknowledge regardless of majority or minority 'status'?