The history of humans in Africa (a new preprint)

The research article posted on July 28, 2026 in non-peer-reviewed bioRxiv, titled Ancient tree-topologies and gene-flow processes among human lineages in Africa, by Gwenna Breton et al. (doi: https://doi.org/10.1101/2024.07.15.603519) looked into the evolution of human beings inside Africa. The authors sampled the genes of different African populations and using AI ("extensive simulations and machine-learning Approximate Bayesian Computation (ABC)"), they compared different models to explain how our species evolved in that continent over the past couple of million years. The paper reports that the best-fitting model is one where "tree-like population histories with long periods of drift separated by short pulses of unidirectional gene-flow better explain the data than continuous gene-flow."

It should be noted that the authors state that their model did so "Without invoking archaic admixture"

The paper notes that instead of repeated migrations of populations, that lead to intermingling, the best models are those with "instantaneous gene-flow processes." This implies that isolated populations co-existed in Africa and time to time they quickly exchanged alleles: " ...our results unambiguously favor an evolutionary history of African lineages ancestral to a variety of Central and Southern African populations where Homo sapiens populations experienced long periods of isolation and drift, followed by short periods of possibly asymmetric gene-flow, which may in turn have induced some reticulations among lineages"

The first modern humans, according to this paper, were the Khoe-San (KS) people who are now found in South Africa and Botswana, they split from a basal lineage between 265,000 and 398,000 yearws ago. Then the rainforest hunter gatherers of Western Africa split from those of Central Africa (called RHG and RHGn, respectively, in the paper), between 127,000 and 190,000 years ago.

These findings differ from those of Ragsdale, A. P. et al., (2023) and the authors note that their dates are olde than the 110,000-135,000 year timeline for the KS split given in that study, and attribute the differenct to Ragsdale et al's use of "very ancient genetic structures, long before Homo sapiens emergence, a feature that is unspecified in our scenarios which considered simply a single ancestral population in which all extant lineages ultimately coalesce."

They agree that there are limitations to their study and that a "large effective population ancestral to all extant populations here investigated" could have existed, and future studeis should look into "very ancient substructures and reticulations within our ancestral population, prior to the original divergence between Southern and Central African populations." The authors also note that "where the ancestors of extant Khoe-San populations lived at that time remains unknown and is nevertheless needed to further elaborate possible scenarios for the causes of the genetic divergence here inferred... similarly as above for the Northern and Southern Khoe-San populations divergence, where the ancestors of extant Eastern and Western Rainforest Hunter-Gatherers lived remains unknown..."

We tend to consider modern Africans as being the same as the ancient ones, those living 100,000 or 200,000 years ago. But, they were not the same. There is a vast space of time of thousands of generations of people during which the genes accumulated mutations, admixing with archaics, and evolving under the pressure of natural selection. The paper recognizes these factors: "... Central African Rainforest Hunter-Gatherer and Southern African Khoe-San populations have had, respectively, extensive time for selection processes, including adaptive introgression processes, to have influenced independently both groups of populations as well as populations within each group separately."

Archaic admixture

The authors state that there is no need to invoke archaic introgression to account for the diversity in the genetic makeup of the Central and South African people. In fact, they "... did not explore possible contributions from unsampled lineages, whether from non-Homo sapiens or from ancient “ghost” human populations, and therefore cannot formally evaluate such possibilities."

But they know that archaics contributed even though they don't say so: they acknowledge that their method can be used to evaluate "scenarios comprising possible contributions from ancient or ghost unsampled populations; where the burden of proof lies on showing that scenarios with archaic admixture fit specific parts of the data significantly better than scenarios without such archaic admixture."

Interestingly, regarding the archaics and their contribution to modern Africans, the authors note that there is no ancient DNA available from ancient African fossils and that this lack of data is a handicap: "In any case, the complexification of scenario-specifications to account for possible past “archaic” or “ancient” introgressions will not fundamentally solve the issue of the current lack of reliable ancient genomic data older than a few hundreds or thousands of years from Sub-Saharan Africa 3,110,111. Indeed, analogously to archaic admixture signals that were identified outside Africa only when ancient DNA data were made available for Neanderthals and Denisovans, we imperatively need to overcome this lack of empirical ancient DNA data in Africa to formally test whether, or not, ancient human or non-human now extinct lineages have significantly contributed to shaping extant African diversity." I am convinced that when hard data is obtained from African fossils, there will be many interesting surprises.

Another finding is that the mixing after long periods of isolation took place around the time of the purported Out of Africa migration of modern humans: "Interestingly, we found strong indications for almost synchronic events of introgressions having occurred during the Last Interglacial Maximum in Africa 73, between ∼85,000 and ∼135,000 years ago... They involved gene-flow between lineages ancestral to Khoe-San populations and ancestors of Rainforest Hunter-Gatherer neighbors on the one hand and, on the other hand, between lineages ancestral to Khoe-San populations and the lineage ancestral to all Rainforest Hunter-Gatherers... we estimated that the instantaneous gene-flow event between the ancestral Rainforest Hunter-Gatherers lineage and that of their extant neighbors seemingly occurred synchronically to the genetic Out-of-Africa. This would imply that possible climatic and ecological shifts at that time may not have only induced population divergences and displacement, but may also have triggered population gene-flow."

This also implies that there was a blending of isolated populations, that contributed diversity to those remaining inside of Africa while another population that migrated out of Africa carried fewer alleles, and less diversity with them (see my post On the Diversity of Africans). It also implies that the Khoisan people were split from the rest, and isolated in Southern Africa with their genetics "enriched" by intermingling with other formerly isolated groups. Did they also interact with archaics like the Homo naledi?

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2026 by Austin Whittall © 

Much Older divergence dates for Denisovans, Humans, and Neanderthals: Implications

I have already posted about this, reporting it last October: The dates for the splits between the different archaic groups has revised in a paper published in Science last September. Research by Xiabo Feng et al., 2025 suggests that a skull unearthed in China known as Yunxian 2 belongs to an Asian group of hominins known as Homo longi, which encompasses the Denisovans (the clade's name is relatively new and was created to formalize the diverse remains from the Middle Pleistocene of East Asia, including Denisovans). It places the split between humans and Denisovans at 1.32 million years ago (Ma) and proposes that Neanderthals split even earlier: 1.38 Ma. The Homo sapiens are much older than previously assumed: 1.02 Ma.

This is the article: Xiaobo Feng et al., The phylogenetic position of the Yunxian cranium elucidates the origin of Homo longi and the Denisovans. Science 389, 1320-1324 (2025). DOI:10.1126/science.ado9202.

Today's post will look into the implications of these earlier dates for our lineage.

A very early split with a different sequence to it

The accepted view is that the ancestor of modern humans and the group leading to Neanderthals and Denisovans split first, and then, Neanderthals and Denisovans separated into two different groups in Eurasia, Neanderthals heading west, into Europe and the Caucasus while Denisovans headed east into Siberia, Tibet, Southern, Southeastern and Eastern Asia. This paper upends that notion. The Neanderthals split first, then humans and Denisovans (called Longi clade in this article) split.

The authors, considering the very old age of Yunxian2 (~1 million years old) push the roots of Human-Neanderthal/Denisovan split further back ("deeper"): "Both the H. sapiens and H. longi clades have deep roots extending beyond the Middle Pleistocene and probably experienced rapid early diversification." The current dates for the Human - Neandersovan split is around 500,000 to 700,000 years ago, this paper suggests it is older: ".The origin of the longi clade can be inferred to be about 1.2 Ma, slightly older than the Yunxian fossils. The origin of the sapiens clade is estimated to be about 1.02 Ma, also close to the age of Yunxian. The divergence between the longi clade and the sapiens clade is at about 1.32 Ma. The monophyletic Neanderthal clade, widely thought to be sister to H. sapiens, diverged from the longi and sapiens clades at about 1.38 Ma in our analysis."

The paper includes the following dated phylogenetic tree (click here for full size image or click on the image below to enlarge it):

Fig. 4. Phylogeny and divergence time of the 57 selected fossil operational taxonomic units from the genus Homo.
The topology of the tree was the majority consensus of the most parsimonious trees from the parsimony analysis in TNT (34). The divergence time was inferred from the Bayesian tip-dating analysis in MrBayes 3.2 (35). Branch lengths are proportional to the division age in thousands of years (Ka). Numbers at the internal nodes are the median ages, and the blue bars indicate the 95% highest posterior density interval of the node ages. The red half-brackets on the right indicate the ranges of the Neanderthal, longi, and sapiens clades. The numbers in red highlight the ages of division of the three clades. Yunxian is also highlighted in red. Xiabo Feng et al., 2025

The shape of the skull is interpreted by this paper as having a "mosaic morphology, which retains plesiomorphies seen in H. erectus/H. ergaster, Kabwe, and Petralona while developing apomorphies shared with H. longi and H. sapiens" Indeed, Homo erectus present in Eurasia since ~2 million years ago is surely linked to the root of the Denisovan (Longi) clade.

Implications

Neanderthal Dispersal

By having Neanderthal split first, 1.38 Ma, we can imagine the pre-longi/sapiens group remaining in Africa and the Neanderthals heading out of Africa into Eurasia. This clade includes the Sima de los Huesos (SH in the phylogenetic tree, above) specimen, which is old, and linked to Neanderthals, and places it as an early split of that clade. Mainstream Neanderthals appear 781 to 600 kya.

Adopting a position embraced by Chinese scholars (and government), they move Neanderthals further away from modern humans, and place Denisovans (H. longi) closer to us; after all, Neanderthals are Western Eurasians, and Longi are East Asian (Chinese!).

See Qiang Ji, 2021 version for Western consumption, and the Chinese version in The Innovation, Qiang Ji et al., 2021 from which the following image was taken, showing the Neanderthals displaced by Longi as our sister clade:

Graphical abstract . Qiang Ji et al., 2021

However Qiang Ji et al., (2021) in their detailed phylogenetic, dated tree (Fig. 4), give later dates than >Xiabo Feng et al., 2025: ~1 Ma for the Neanderthal split, 949 kya for the Denisovan-Human split, and 770 ky for the root of H. sapiens. See below, highlight is mine. Note: OTU = operational taxonomic unit, a name used for genetically similar creatures, analog to a species definition.

" Harbin cranium and H. sapiens shared a common ancestor at ∼949 ka (1,041.41–875.25 ka). The Neanderthal-H. sapiens divergence time in our analysis was ∼1,007 ka (1,114–919 ka). This estimation falls in the range based on mtDNAs for the split between the basal Neanderthal (Sima de los Huesos) and the H. sapiens lineage, but is much older than the estimation based on nuclear DNAs for the splits between the Neanderthal and H. sapiens lineages. However, it is possible that this younger estimated divergence date is an artifact of statistical averaging between “super-archaic” and “recent gene flow” events. The common ancestor of the H. sapiens OTUs included in our analysis is as old as ∼770 ka (922–622 ka), suggesting that the H. sapiens clade has a much deeper origin time than previously estimated. The Eurasian H. sapiens OTUs share a common ancestor ∼416 ka (534–305 ka) old. Outside of Africa, however, the earliest known H. sapiens fossil is only ∼210 ka."

Qiang Ji et al., 2021 suggest that "Sympatric isolation of small populations combined with stochastic long-distance dispersals is the best fitting biogeographical model for interpreting the evolution of the Homo genus...multi-lineages of Homo coexisted in Africa, Europe, and Asia during the Middle and Late Pleistocene. These Homo lineages probably had a strong capability of dispersing for long distances, but remained in relatively small and isolated populations." Sympatric isolation means that even though they shared the same overlapping territory, they evolved separately, not because of physical barriers, but by other ones (genetic, environmental, adaptative, reproductive, specializations), that keep them apart.

What would keep Neanderthals, who during the later period 120-50 kya spanned Western Eurasia from Altai to Portugal, from moving on into America. They could have skirted the Denisovans (who seem to be more adapted to temperate and tropical climates) by living in colder, glacial spots, in Europe and Asia. They could have gone across West-Central Siberia, Northern Siberia and Northeastern Siberia to Bering, and into America. Nobody digs deep enough to find remains 1.3 million years old!. I am not joking, sediments deposit at a rate of 0.10 to 0.12 mm/year (Source) that is 14 times smaller than 1/16th of an inch. Over one million years it represents 120 m of sediment (393 feet). Archaeologists have only scraped the surface (of course, when digging in areas scoured by previous erosion, or by river banks, other elements factor in, recucing sediment buildup.

Neanderthals, well adapted to ice-cold climates, could have easily reached America 1.38 Ma.

Denisovans

The phylo tree built by Xiabo Feng et al., 2025, follows the line set by Qiang Ji. It has older dates, and places the Homo Antecessor at the base of the Denisovan tree, H. antecessor is a Western European specimen, discovered in Atapuerca, Spain. This suggests a very wide territory for Denisovans.

Although their presence has been described in the temperate and tropical parts of Asia, like the Philippines, Sunda, Southern and Southeastern Asia, they also lived in Tibet, and overlapped Neanderthals in Denisova Cave, Altai, Russia, further north, in colder climes, ~200 kya. The Harbin individual, ~146 kya lived in Northeastern China which even nowadays is cold. Xijung Ni et al., 2021, state, regarding the Harbin remains that "the northerly location of the Harbin site also has implications for Middle Pleistocene human adaptive capabilities, since, even in the present interglacial, this region has winter temperatures averaging more than 16°C below zero [3.2°F] The very large size of the Harbin individual (as judged from the size of the cranium) may indicate physical adaptation to such conditions."

This suggests that they too could have moved northeast towards Beringia. Did they reach America 1.32 Ma?

Humans

Homo sapiens is pushed back 700,000 years, from the commonly accepted date of 300 kya to one million years ago. In Africa, alone, isolated from the Denisovans and Neanderthals who left them for Eurasia.

The Gap in the fossil record

The oldest members of the human branches are the Irhoud, the 300 ky old human from Morocco, the Tabun 2 person from Israel, and Florisbad a H. Heidelbergensis from South Africa. But there is a gap of 700,000 years between them and the split date with Denisovans!

Xijung Ni et al., 2021 who proposed an older than the commonly accepted date for the split "(∼416 ka (534–305 ka) old", yet much shorter than the 1 million years proposed by Xiabo Feng et al., 2025, wonder why there is such a gap between the first fossils and the split date. The team favors an African origin for Homo sapiens offers the following explanation:

"There is a large time gap between the hypothetical common ancestor of Eurasian H. sapiens and the actual fossil record, from the Bayesian tip-dating analysis. One plausible hypothesis is that the ancestral population of Eurasian H. sapiens may have diversified in Africa for many millennia before they dispersed into Eurasia. Genetic studies on ancient DNA suggest that the initial genetic exchanges between Neanderthals and H. sapiens occurred between 468 and 219 ka, or between ∼370 and 100 ka, and the introgression may have originated through gene flow from an African source. Interestingly, not only does the estimated time of the introgression event between Neanderthals and H. sapiens roughly overlap our prediction for the age of the common ancestor of Eurasian H. sapiens, but the African origin of the introgression is also consistent with our African ancestral population hypothesis."

Perhaps the fossil record is incomplete because we haven't found the specimens. Humans are intelligent so they were not easy prey or caught in quicksand, they were surely buried. So, unless we dig deep enough in the right places and find burials, we won't find them.

I believe that there was "diversification" within Africa as ancient archaics that indeed lived in Africa (H. naledi) and others admixed with Africans not too long ago, providing them with divergent alleles. But, why imagine an African origin at all?

Middle Eastern Origin of Modern Humans

Below is a possible and probable sequence for the origin of modern humans outside of Africa following the timeline given further up.

The first to enter Eurasia were H. erectus, from the Horn of Africa in Ethiopia, across the Middle East to the Caucasus where we find them in Dmanisi, Georgia. The map below (Map 1) shows the source and the destination, as well as a tentative migration route (red arrow). I deliberately painted their territories in different colors, they would become isolated and mutations would differentiate African from Eurasian erectus.

Map 1. Erectus leaves Africa . A. Whittall ©2026

Then, 1.9 to 1.7 Ma., H. erectus migrated westwards into Europe, and east, along southern Asia into Southeast Asia, Sunda, and China. Their remains have been found in Eurasia. In Africa, they must have also migrated though we have no evidence (poor fossilizing conditions in tropical Africa). Map 2 reflects these migrations and the color changes denote evolving differences between the groups. Ice and mountain ranges guide their migration

Map 2. Erectus migrates across Eurasia and Africa . A. Whittall ©2026

Map 3 shows separate evolution of the H. erectus clades ~1.5 Ma., splitting in smaller groups, losing territory in the north as the Ice Ages progress, living in more isolation, and moving to better regions (arrows). Some groups become extinct. All differentiate and diverge. Asian, European, and Africans remain isolated, perhaps some interchange in Gibraltar between North Africa and Spain. Erectus people move into Northern China. The group in the Middle East will become relevant in the following phase.

Map 3. Erectus diversify, and evolve across Eurasia and Africa . A. Whittall ©2026

In Map 4 the evolved Eurasian ancestors of Denisovans, Neanderthals, and Modern Humans located in the Middle East (yellow-black star) see the Neanderthals move out, north and west into Europe and the Caucasus and replacing the other descendants of erectus there, possibly leading to the Sima de Los Huesos individual. Their territories are colored yellow.

The H. erectus in the Far East have modified their territories, becoming extinct in some sites, and evolving. The African descent of the erectus are still living in small groups, moving around the continent, diversifying, evolving. Color changes imply changes in the populations.

Map 4. Neanderthal dispersal (their territory in yellow). A. Whittall ©2026

Map 5 below shows the split that took place 1.38 Ma, centered in the Middle East (star) with Denisovans heading west along a southern coastal route into Asia, the same followed by erectus over 600 ky before them, and their inroads into erectus territories in Sunda and East Asia. They also crossed Neanderthal regions heading towards Central Asia (Altai) mingling with them. The pink color marks Denisovan areas. Africans continue splitting into isolated groups, some very archaic, exchanging genes occasionally. They are many very divergent groups, some are more archaic than the rest.

Map 5. Denisovan dispersal (their territory in pink). A. Whittall ©2026

The final move is the one involving modern humans (Map 6, below) shows how modern humans spread, 1 million years ago, from the Levant, into Africa, admixing with the until then isolated, separated, divergent, archaics there. Into Europe admixing and replacing Neanderthals, and west into Asia. The orange color marks their initial territory as they advance on Neanderthals (yellows) and Denisovans (pink) admixing along the way.

Map 6. Modern Humans dispersal into Africa and across Eurasia (their initial territory is colored orange). A. Whittall ©2026

This, at least, is my take on the subject. Of course, fossils are needed to validate it, and further (improved) genetic tools and models are necessary too.

A very early appearance of humans, would imply that mutation rates are slower than currently estimated, only 1/3 of the accepted rate (because it would have taken 1 My instead of 0.3 My for our species to evolve. With modern humans around 1 My ago, they could have also moved on, into America at any time over the past million years. The problem is, that nobody is looking for such ancient signs.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2026 by Austin Whittall © 

Diversity in Africa. Some explanations on why it is so diverse

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 ♥.

Human genetic diversity map (not sure how it was made). Source

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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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2026 by Austin Whittall © 

On some misconceptions regarding mutations and "antiquity"

This website in an attempt to explain DNA diversity that allows us to identify "older" genomes from more "recent" ones, says the following:

"There are parts of your (our) genome where random mutations won’t generally kill you. Random mutations tend, therefore, to accumulate there. Since have some pretty decent estimates for how often random mutations occur, comparing the mutations in two different populations lets us estimate how long ago they split. For example, let’s suppose you get one random mutation per hundred years, and we’re comparing two populations that split 300 years ago and haven’t seen each other since. Population A should have gotten 3 mutations during that 300 years, and Population B should have gotten 3 mutations. So if we look at a third population, C, and find that they have 5 mutations that they don’t share with A or B, then we conclude that C split off from some ancestral population 500 years ago. We can reconstruct this as: 600 years ago, there was a group called ABC, but 500 years ago, it split into Group AB and Group C. 300 years ago, Group AB split into Group A and Group B."

Sounds great, so clear, so logical... but... This is a typical explanation for diversity in Africa vs. out of Africa and to put it bluntly, it is Wrong!!. And this is why:

It says there was an ancestral group, ABC which split 500 years ago into AB and C. Since the split, group C accumulated 5 mutations. And group AB split 300 years ago. Each sub group, A and B, accumulated 3 mutations each, which made them different. So as C has 5 mutations but A and B only 3 each, C is "older" than A or B. Did you see the mistake in this logical explanation?

The error is that although they postulate a random mutation every 100 years, the group AB which split from ABC 500 years ago did not accumulate any mutations from then until the split of A and B 300 years ago.

AB group did not accumulate a single mutation over 200 years, but C did, it added 2.

Then, A split from B, and both of them kept on mutating at 1 mutation every hundred years. Final score: C = 5 mutations and A & B only 3.

Actualy AB would have accumulated mutations over those 200 years, different mjtations from those of C. In fact all groups A, B and C would have accumulated 5 mutations over those 500 years.

All humans are equally ancient, we all carry the original DNA, and after we split into separate groups, our random mutations led us to split apart a bit more, but we all have roughly the same amount of mutations, unless, of course these mutations are not random, but are mobilized by selection, but that will be discussed in another post.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

On the molecular "Clock" and divergence of humans, chimps and gorillas

I have written several posts on my doubts about the molecular "clock" used to calculate events such as the split between Homo sapiens and Neandertal or the Out Of Africa event. (see some examples here and here), today I came across a recent paper that proposes an earlier date for the split between humans, chimps and gorillas.

This notion had been put forth by Langerbraber et al., (2012) Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution [Vol. 109 no. 39 15716–15721, doi: 10.1073/pnas.1211740109], who calculated a split date for Humans, Chimpanzees and Gorillas between 9.35 and 20 million years ago vs. the commonly accepted figure of 6.69 Mya (see Table 2 in their paper).

The more recent work, by David Begun of the University of Toronto in Canada, suggests that the Dryopithecus apes which lived in Europe 12.5 million years ago are part of the great apes and that this moves the chimp-human split back to 10 Mya.

This will mean, if proven true by other studies, that the dates of other more recent events will have to be reviewed, and that the reliability of molecular clocks should not be taken for granted.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2015 by Austin Whittall ©