The contemporary San people in South Africa are usuallyt mentioned as the most basal group of humans, and the most diverse one, that split from all others ~150 ky ago (or more) and are the living proof of the richness in genetic diversity that was lost by those who trekked out of Africa.
By the way, this is the real post 1,000 ♥.
About the image above. Interesting to see how Eastern China, Manchuria, Japan, Korea, Indochina, and Peru in South America are the least diverse! Also how African slave trade extended diversity into Brazil and European colonization into Eastern North America and parts of South America. The map is from reddit, though, so it has no references, source or hard data to back it. May be a fabrication.
However, a very recent paper published on line in Dec. 2025, in Nature, by Mattias Jakobsson et al.,, note that the alleles found in the modern San people are not only due to a large and stable population (large Ne), they also had an introgression from some other, unknown, group of genetically differentiated humans. The authors state that (yellow-bold highlighting is mine):
"Cumulatively, the genomes of the ancient southern Africans show that this group displays many Homo sapiens-specific variants (and variable positions) at amino acid-altering sites, also reflected among the modern-day San people. This observation cannot be explained solely by a large, stable southern African population, which retained derived variants to a greater extent compared with other groups. The ancient southern Africans were probably also isolated from other African groups for long periods. The derived variants unique to southern Africans may also signal low-to-modest gene flow from an unknown/unsampled group of genetically differentiated humans.
Genetic, anthropological and archaeological studies support an African origin of Homo sapiens, but the evolutionary process is debated based on fossils, archaeology and genetics, with Africa harbouring the greatest human genetic diversity, and southern and central African hunter-gatherer groups displaying some of the deepest diverging Homo sapiens lineages. Population stratification between southern Africa (the region south of the Zambezi River) and the rest of Africa probably existed for at least 300 thousand years (kyr), perhaps up to a million years. Such deep stratification may result from admixture with an unknown archaic African group predating the divergence of Homo sapiens from Neandertals and Denisovans, and/or from isolation from other groups.
Average population divergences between individuals representing the ancient southern African group (7 individuals with >7.2-fold genome coverage) to any other individual (ancient and modern-day western, eastern, central, northern Africans and non-Africans) were estimated to around 310–240 ka using a two-by-two site-frequency spectra approach (Supplementary Information 2.17 and Supplementary Data 15–31). Although the exact calibration of chronological population divergence-time estimates depends on model assumptions, mutation-rate assumptions and generation time, these estimates recapitulate findings in which the divergence between ancient southern Africans and all other groups captures the deepest population split-time at around 300 ka (see also Supplementary Fig. 11 for a comparison to modern-day Khoe-San individuals). This approximately 300 ka population-divergence-time estimate is not caused by a deeper partial archaic admixture event per se, but it does not negate such an event either (Supplementary Information 3.11 and Supplementary Figs. 12 and 13)."
This is something that I have mentioned several times in different posts: diversity in contemporary Africans is due to an introgression of highly divergent genes from super archaic hominins that took place recently.
The paper also attributes diversity to isolation and small subpopulations (more on this below).
Cecilia Padilla-Iglesias et al., (2025) in a paper published last May (Pan-African metapopulation model explains Homo sapiens genetic and morphological evolution), explores the possibility of introgression and also how isolation, natural selection (adapting to local environmental challenges) and modest gene flow between separated populations shaped the contemporary highly diverse genetic makeup of Africans:
"Our results are consistent with findings that despite deep genetic divergences, there is evidence for intermittent episodes of gene-flow between all hunter-gatherer lineages. These episodes would have allowed on the one hand the emergence of adaptive cultural and phenotypic variants for local environments during periods of isolation, and on the other, the exchange of such variants during periods of connectivity. Crucially, our model highlights the vast diversity of environments in which the members of our species thrived throughout our evolutionary history, and thus, the adaptive potential of the human foraging niche.
The maintenance of viable population sizes and interconnectedness in the majority of African regions, following their initial settlement by hunter-gatherers, explains the evidence for low levels of historical inbreeding and high genetic diversity indicated by very few short runs homozygosity observed among contemporary and ancient African hunter-gatherers."
So isolation, selection, concentration of diverse alleles, and then exchange between groups shaped the current diversity, but what about archaic introgression? The paper addresses this issue too (MSA is Middle Stone Age):
"Our model reveals that West Africa, and in particular, the area around the Gulf of Guinea as well as Senegal is the region with the highest reconstructed population turnover in the continent and remains isolated for large periods of time throughout our evolutionary history, until the present. This is consistent with the finding of fossils showing very archaic features (and outside of contemporary human variation) as late as 11.2 kya (or 13 kya calibrated) in Iho Eleru, Nigeria, as well as the late persistence of MSA technologies in Saxomununya, Senegal, until a similar time well beyond their disappearance in Southern Africa, Eastern Africa and the Maghreb.
Genetic studies have shown that Southern African Stone Age hunter-gatherers (including those from our sample) despite representing the most diverged human genetic lineages, still share significantly more alleles with eastern Africans (including the present-day Dinka and Mota) than they do with present-day Western Africans (as represented by the Yoruba). These findings have been used alongside findings of some “archaic” morphological features and continued MSA industries in Western Africa in the Holocene to the presence of archaic lineages in the region that have left no direct descendants."
Survival of very old lithic technology from the MSA coupled to archaic cranial features until very recently (11-13 kya) suggests the presence of archaic hominins who surely mated with, and left their genetic imprint in, modern humans in Africa. However, the need to downplay archaic introgression as a source of diversity (God knows why!) leads the researchers to suggest another mechanism (which I didn't quite grasp), yet, they must include the admixture option (highlight, by me):
"However, another possibility leading to this pattern is that the cline of connected groups across the Eastern part of the continent (connecting Eastern and Southern Africa) was not nearly as connected to Western Africa. Our demographic reconstructions show reduced levels of East-West migration compared with East-South migration for the vast majority of evolutionary history. This, together with the fact that we were able to predict the morphological distance between the Iho Eleru specimen and the rest of cranial specimens in our sample, shows that the second scenario is sufficient to explain the observed patterns, though we do not exclude the possibility of small amounts of introgression."
Pontus Skoglund et al., (2017) note the archaic admixture, they found: "... Evidence for a divergent human lineage contributing to western Africans... The deepest diversifications of African lineages were complex, involving either repeated gene flow among geographically disparate groups or a lineage more deeply diverging than that of the San contributing more to some western African populations than to others. "
The authors then mention the hypothesis: "there has been ancient structure in the ancestry of present-day Africans... One scenario consistent with this result could involve ancestry related to eastern Africans (and the out-of-Africa population) expanding into western Africa and mixing there with more basal lineages" This means, archaic, or super-archaic hominins liv
Yet, when confronted with taking a stance, the authors opt for a conventional explanation: "Our genetic data do not support the theory that this putative basal lineage diverged prior to the ancestors of Neanderthals." Meaning they mixed with more recent humans, not those that predate our split with Neanderthals some 600 ky ago.
J. H. Relethford (mentioned in a recent post), wrote an article, published in Nature back in 2008, in which he discussed the "regional diversity" issue very rationally, and offering explanations for the diversity in Africa and how it is a demographic rather than a phylogenetic matter:
"The genetic evidence: regional differences in genetic diversity
Not all living human populations show the same average level of genetic variability, and these differences in present-day diversity can provide us with inferences about our evolutionary history. DNA markers typically show higher levels of genetic diversity (heterozygosity and nucleotide diversity) in sub-Saharan African populations. This observation has been made for mtDNA (Cann et al., 1987), nuclear microsatellite DNA (Relethford and Jorde, 1999) and Alu insertion markers (Watkins et al., 2001). The same observation has been made on measures of variation from phenotypic traits; within-group variances are highest in sub-Saharan African populations for both craniometric measures (Relethford and Harpending, 1994; Manica et al., 2007) and skin color (Relethford, 2000).
Why would one geographic region consistently show higher levels of genetic and phenotypic diversity? One possibility is greater time depth for the accumulation of mutations. The longer a population has been in existence, the greater the number of mutations that will accumulate. Under an African origin model, mutations would accumulate longer in Africa, as any populations dispersing out of Africa would likely be small, and the subsequent founder effect would effectively ‘reset’ the accumulation of mutations in the non-African populations. Thus, a model of an initial African origin followed by dispersals out of Africa at a later point in time would generate the regional differences in genetic and phenotypic diversity that we see today. If correct, the observation of higher African diversity supports the other genetic (and fossil) evidence for an African origin for modern humans, but does not distinguish between an African origin with replacement and an African origin with admixture outside of Africa except to say that if there was any admixture it was not of sufficient magnitude to erase the genetic signature of an African origin.
Furthermore, the fact that the model of accumulated mutations is compatible with the observed genetic data does not mean that it is correct if there are other reasonable interpretations that are also compatible. In the case of genetic diversity, another possible explanation is regional differences in population size, because expected diversity is proportionally related to effective population size. Smaller populations experience more genetic drift and are therefore lower levels of diversity. If the long-term effective population size of Africa were larger throughout most of recent human evolution, then diversity would be greater in Africa than elsewhere, again consistent with our observations of present-day variation. Analyses of craniometric data and microsatellite DNA support this hypothesis (Relethford and Harpending, 1994; Relethford and Jorde, 1999). A larger African population is also consistent with archeological and ecological inferences (Relethford, 2001b; Eller et al., 2004). If higher levels of genetic diversity in sub-Saharan Africa are due to a larger long-term effective population size, then the observation of higher diversity does not provide any resolution about the modern human origins debate. All of the models proposed to date can easily accommodate a larger African population. In this case, genetic data may be telling us more about the demographic, rather than phylogenetic, history of our species."
Again, the higher Ne size and its impact on diversity. If we add introgression and, as mentioned further up, and also isolation in separate groups that evolve due to natural selection, and then admix with each other, it is easy to see what has shaped the diversity of modern Africans.
Nevertheless, Mark Lipson et al., (2022) published in Nature about the effect of many subpopulations: "Furthermore, small subpopulations with limited gene flow could result in low ancestral effective population sizes even if the region’s total population is high. Preservation of genetic diversity through the existence of many subpopulations over long time scales could also be a contributor to the high levels of genetic diversity observed in most present-day sub-Saharan African groups." This questions the need for a high Ne!
Fred W Allendorf, Ola Hössjer, and Nils Ryman (2025) expressed it as follows: "Fragmentation into many, small subpopulations with periods of infrequent gene flow, preserves allelic variation at the expense of heterozygosity. In contrast, fragmentation into a few, large populations maintains heterozygosity at the expense of allelic variation."
The original African pre-Homo sapiens populations were small groups of hominins with little admixing which meant that they had their own unique alleles, but, being small, had lower heterozygosity. When they came together, the outcome was a larger population with higher allele diversity and the sum of all the separate heterozygosities resulting in the current African high diversity.
And, finally the backflow from Eurasia! It contributed genes that may later have been lost as humans marched across the Old World, but were reintroduced into Africa at an early date, enriching the diversity there. A paper by Christopher B. Cole, Sha Joe Zhu, Iain Mathieson, Kay Prüufer, Gerton Lunter in the Covid pandemic year of 2020, boldly stated that "We find evidence for substantial migration from the ancestors of present-day Eurasians into African groups between 40 and 70 thousand years ago, predating the divergence of Eastern and Western Eurasian lineages. This event accounts for previously unexplained genetic diversity in African populations, and supports the existence of novel population substructure in the Late Middle Paleolithic. Our results indicate that our species’ demographic history around the out-of-Africa event is more complex than previously appreciated."
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