A test for freckles, disease and identity

How anthropological genetics is rewriting African history

I recently did a DNA test. (I had to do so in Europe as 23andme’s services are not yet available in South Africa.) I learned that I have a 74% chance of little or no back hair (I don’t), a 78% chance my ring finger is longer than my index finger (it is not), and a 77% chance of few, if any, freckles (I don’t). The test is apparently also able to predict that I am more likely to hate chewing sounds (misophonia – I don’t think this is true), just as likely to be bitten by mosquitoes as others (untrue, they love me), and more likely to be able to match a musical pitch (finally some evidence that my primary school choirmaster was wrong).

This is all a little bit silly, of course. But DNA testing is much more than fun and games. 23andme can, for example, identify certain health predispositions, like your risk of type 2 diabetes, Parkinson’s Disease, Late-Onset Alzheimer’s Disease, and Chronic Kidney Disease, to name just a few. It was able to detect a disease risk that I now realise I’ve had all my life but could never identify.

And, of course, it can reveal something about our roots. As an economic historian, this excited me the most: what will my DNA reveal about my ancient ancestors? And at a more fundamental level, how will this new information affect my identity, the story I tell about myself?

As it turns out, my roots are not that surprising. My ancestors are predominantly Western European, from the Netherlands, Germany and France. I have a surprisingly large Scandinavian ancestry. But what is most surprising, given the large number of British immigrants to South Africa in the nineteenth and twentieth centuries, is that there is no British connection. The British Isles are entirely missing from my map.

But my roots are also not exclusively European. 1.2% of my ancestry is Sub-Saharan African, the consequence, as I’ve known, of being a descendant of Krotoa, a Khoe woman who married a Danish surgeon in the seventeenth century. And another 2.2% is Southern Indian and Sri Lankan, with an additional 1.1% East Asian, clear evidence of the Indian Ocean slave network that connected these distant places to the Cape. Despite having a fairly accurate genealogy of my ancestors going back ten generations – based on the work of many amateur genealogists over many decades – there is no evidence of these ancestral linkages in my records.

I predict that within a few years, these DNA tests will become far more mainstream and far more sophisticated. There is the obvious benefit of identifying disease predispositions. Some might argue that they would not want to know about an increased risk of some terrible disease, but scientific advances, I surmise, would not only allow us to know but to do something about it. Disease risks can also often be managed by lifestyle changes.

But I find DNA fascinating not for what it can tell us about the future, but what it can reveal about our past. One of the most exciting scientific fields today is undoubtedly anthropological genetics. These geneticists trace the lineage of human populations back thousands of years to identify where our ancestors lived and when and where they moved around. By comparing the genetic makeup of different human populations, geneticists can understand how humans have adapted to different environments and lifestyles throughout history.

We know, for example, that the domestication of plants and animals, which began around 9000 to 11 000 years ago, was a game-changer for humanity. This shift from hunting-gathering to farming, known as the Neolithic Revolution, boosted population growth, expanded territories, but also increased the spread of diseases. This significant change also led to the growth of various language families, like Bantu, Austronesian, and Indo-European, over large geographical areas.

But what we do not know is which came first. Did migrating farmers bring their culture and languages with them (demic diffusion), or did local hunter-gatherer groups pick up farming and language from neighbouring farmers (cultural diffusion)? And if demic diffusion is the answer, did these farmers replace local hunter-gatherer groups, or were these groups partially incorporated into the expanding farmer populations?

These questions can only be conclusively answered through genetics. By identifying the original farming group’s homeland and establishing their genetic differences from the populations they spread into, genetic studies can reveal the extent of farmer-derived and indigenous ancestry in modern groups.

Take Africa, for example. As discussed in a recent PNAS article by Stoneking et al., around 8000 years ago, domesticated animals from the Middle East made their way into North Africa, gradually moving south. By around 2000 years ago, these animals had entered southern Africa. But even before domesticated animals arrived, or before the first crops were domesticated, Africa was undergoing demographic change. New evidence now shows that North Africans, for example, by 15 000 years ago, not only have sub-Saharan African ancestry but also Near Eastern ancestry. This indicates that the genes from the Near East flowed back into Africa even before farming began. There is much more to learn about these ancient interconnections.

But the democraphic event that most shaped Africa’s present is undoubtedly the Bantu Expansion. The Bantu languages, originating from the border of eastern Nigeria and western Cameroon, are today spoken across a large part of sub-Saharan Africa, or by an estimated 30% of Africans. This expansion, which started around 4000-5000 years ago (2000 to 3000 BCE), was probably the result of the domestication of the yam, an event itself triggered by climate changes that reduced the rainforest in West Central Africa.

But the Bantu Expansion was not a single expansion. And while it may have started in 2000 BCE, it gained momentum over time. Here is how Razib Khan explains it in a recent post (paywalled):

Over the millennium between 500 BC and 500 AD, the Bantu peoples exploded in number, re-sculpting Africa’s whole genomic, ethnolinguistic and ecological landscape. These farmers and herders came to dominate nearly every region south of the Sahel and the Horn of Africa, from coast to coast. In the next millennium, before shiploads of European explorers began to probe Africa’s shores, the Bantu digested what remained of the earlier populations through a process of genetic and cultural assimilation. The world that Europeans presumed represented Africa’s character since time immemorial was ‌a startlingly fresh veneer atop a deep and ancient substrate, a primordial Africa swallowed whole, leaving ancient peoples mostly forgotten, little more trace of their tenure than faint genetic and cultural echoes.

One large new study, led by Mário Vicente and Carina Schlebusch, helps us understand just how it happened. Using the genetic information of over 1700 participants, including nearly 1500 Bantu speakers from across 14 African countries, a team of 30 authors show that as Bantu speakers expanded, they intermingled and shared genetic traits with local groups in those regions. They also found that genetic diversity amongst Bantu-speaking populations decreases the further you go from western Africa, suggesting Zambia and the Democratic Republic of Congo as possible hubs of interaction. The further they went, the more they could incorporate technology like ironworking and several other plant and animal domesticates, including sheep herding.

They were not the first sheep herders, however. Archaeological evidence indicates that pastoralism (sheep-herding) was introduced to southern Africa from eastern Africa around 2,000 years ago, before Bantu-speaking farmers had arrived. Pastoralism probably spread along with the Khoe-Kwadi language family. Genetic studies suggest that eastern African ancestry mixed with Khoisan-related ancestry in southern Africa before the arrival of Bantu-speaking groups; in fact, according to Vicente and Schlebusch, all modern Khoe-San groups ‘have 9–22% admixture from the admixed group of Eurasian-East African ancestry that introduced herding into southern Africa’.

That, perhaps, explains my eastern African heritage; 23andme records my Khoe ancestry as ‘Southern East African’. I asked Marlize Lombard, Research Chair of the Palaeo-Research Institution at the University of Johannesburg and one of the authors of the study on the Bantu Expansion, whether my inference is correct: ‘Yes, your ‘Southern East Africa’-gene represents your Khoe lineage. The Khoe are herders whose pastoral ancestors originate from eastern Africa and then migrated south, mixing with the local San here.’

It is one thing to analyse the DNA of people alive today, but studying the DNA of people who lived hundreds or even thousands of years ago opens up a fascinating window into the past, allowing us to trace ancestry, migration patterns, and even the evolution of diseases. Geneticists, in another study with Lombard,  analysed the DNA of a single person, the Vaalkrans man, who lived about 200 years ago in the southern Cape. She then compared his DNA to that of 10 other people who lived in southern Africa over the past 2000 years. She and her team found that the man from Vaalkrans was mainly related to local San hunter-gatherers, with a more minor part of his ancestry coming from a mix of eastern African and Eurasian people. This mix of DNA is similar to modern Khoe people who live in the Northern Cape and Namibia. The Vaalkrans man’s DNA tells us that Khoe herder groups or individuals were still living in the southern Cape as late as 200 years ago – around 1800 – and that they had not yet mixed with non-African settlers or Bantu-speaking farmers.

It is remarkable that the same genetics that predicts my tendency towards freckle-free skin or mosquito attraction can also reveal the complex migration patterns and societal structures of our ancestors. While many of my traits have been accurately predicted, others have deviated from expectations – perhaps a testament to the ever-evolving nature of our genetic story. But even more thrilling is how this burgeoning science is rewriting history, offering fresh narratives and challenging longstanding theories. As my own genealogy has unveiled unexpected connections, so does the field of anthropological genetics expose hitherto unknown facets of our collective human journey. The science of our past is written in our genes, and as we continue to read these intricate genetic stories, we not only better understand our history but also ourselves.

An edited version of this post appeared (in Afrikaans) in Rapport on 13 August 2023. The image was created using Midjourney v5.2.