Digging Deep: Ancient DNA discovered in Africa reveals human migration insights

A new study in Nature reports on the DNA recovered from six individuals from southeastern Africa who lived between 18-5 kya (thousand years ago). A notable finding, the study is one of the few to have reported on ancient DNA from the continent, where hot and humid conditions are not conducive to the preservation of genetic material.
Lipson et al. (2022) reported the entire genetic sequence, along with the radiocarbon dates, of three Late Pleocene (125-12 kya) and three early-mid Holocene (11-5 kya) individuals (a total of six-four infants, two adults). These six individuals were spread across five sites in eastern and southern-central Africa: Tanzania, Malawi and Zambia, to be precise. These individuals range from 18 to 5 kya, ‘doubling the time depth of aDNA reported from sub-Saharan Africa.’ The exercise was supplemented previously published studies.
The DNA was sourced from the petrous bone of the inner ear. The petrous is one of the hardest and most dense bones in the body and preserves genetic material better than any other. A 2015 study even reported over 100 times more DNA yield from the bone than any other. Ancient DNA yielded from the petrous has helped shed light on the first farmers in Turkey, ancestry in Oceania and diaspora in Tanzania, among other things.
The researchers tapped into the insights offered uniparental markers i.e. those components of an individual’s genetic material that come from only one parent. Uniparental markers are passed down ‘as is’ from one generation to the next ie the set of traits are passed down together as a single ‘haplotype.’ Uniparental markers are, therefore, extremely useful in reconstructing lineages through deep time. Two of the most commonly studied uniparental markers are the Y-chromosome, which follows a strict paternal inheritance, and mitochondrial DNA (mtDNA), which follows a strict maternal inheritance.
Based on the aforementioned uniparental marker analysis, Lipson et al (2022) find that (a) specimens from Kenya and Tanzania have haplotypes/haplogroups associated with East Africa; (b) those from Malawi and Zambia have haplogroups associated with ‘some ancient and present-day Southern African people,’ especially those still engaged in foraging; and (c) one individual from Malawi and [maybe] one from Kenya carries haplogroups of present-day central African foragers. In the past, these haplogroup populations were much more widespread than they are today.

Researchers identified three dinct ancestries, with a dinct geographical structure: one in East Africa, one in southern Africa (not to be confused with South Africa) and another in Central African rainforests. The genetic structures remained highly stable and localised vis-à-vis their geographies, and there was limited gene flow. These dinct genetic structures have since been masked over the last 5000 years migrations driven the transition to sedentary agriculture, and even more so in the recent past due to imperialism and changing socio-politics. Therefore, it is difficult to reconstruct demographic changes in the past from modern DNA alone and is, therefore, tap into ancient DNA wherever possible.
The three ancestries – central African, Eastern and Southern – are -and-large present from southwestern Kenya to southeastern Zambia. 16 kya, all these three components were present in Malawi and, 7 kya, in Tanzania.
While the three ancestries are present in different proportions, ‘geographical proximity remains the strongest predictor of genetic similarity.”  It shows that these groups were essentially separated 200 kya but came in contact with each other 80-50 kya. This led authors to conclude that long-range movements of people were probably rare in terminal Pleocene/Holocene. The same is evidenced signals in the admixture analysis, that examines the amount of connectedness between two gene pools: admixture graphs showed high genetic relatedness at a localised level but not over long dances. For instance, within the three ancestries, individuals in one cluster showed ‘excess allele sharing, even beyond what would be expected from having similar ancestry proportions.’
These lineages, after 10 kya, were possibly brought together fragmenting forests and expanding grasslands, that left more room for people to move around.
The archaeological record sits well with the genetic evidence. Most records of material culture can be dinctly identified in space and time (‘regionalisation’). Even linguic data suggests a transition towards local interactions – to this day, foraging communities in central, eastern and southern Africa speak languages belonging to different families (they do bear some similarities, of course).
‘Our genetic results confirm that trends toward regionalisation extended to human population structure, suggesting that decreasing gene flow accompanied changes in behaviour and possibly language,’ researchers argue.
The author is a research fellow at the Indian Institute of Science (IISc), Bengaluru, and a freelance science communicator. He tweets at @critvik