The PCA method is flawed according to a study

In a recent post I discussed a study that questioned the validity of D-statistics; today I will explore two research papers that look into PCA or Principal Components Analysis, a statistical tool widely used in genetics and anthropology, which, according to two papers, may be biased, subjective, and flawed.

What is PCA?

Principal Components Analysis or PCA is a tool used to analyze data. It can be simplified as a method that concentrates, or reduces this data into two dimensions, where the data can be plotted and patterns, or structure identified. Points closer to one another should be similar and associated, those that are more distant in the plot are assumed to be more weakly (or not at all) linked.

You can obtain different information from samples taken from a population, and if there are, say 15 different variables measured for a given sample, it is very complex to pair up the variables and compare the samples to reach a conclusion.

Suppose you are studying bacteria, both pathogens and benign ones, and have defined fifteen variables, collecting data for each of them (length, width, thickness, rugosity, motility, lifespan, etc.). Your goal is to evaluate the influence of these factors on bacterial virulence. It would be impossible unless you could somehow simplify the data without losing information. Imagine if you could concentrate those 15 variables (or 15 dimensions) into just two, it would be much easier to visualize differences or similarities for your analysis.

PCA does just that. Using statistical formulas and computer power it condenses these variables into two main ones, "Principal Components" PC1 and PC2 without losing information, and plots them in a 2-dimensional chart.

Below is a simplified graph showing how three variables, that form a three dimensional space can be compressed into two Principal Components. The points (one sample is equal to one point), are graphed into a three dimensional space, with the three variables, x, y, and z defining their position.

As you can see, the first line (blue) is drawn along the region with most variability in the samples. A second line is drawn perpendicular to it (red). The First Principal Component is PC-1, the other is the Second Principal Component or PC-2. The data is theb "transformed" into a new, 2-D chart, where each point is one of the original samples from the original dataset.

I won't go into statistic, but the transformation is based on evaluating how the variance of the variables of the dataset (how "far" they are from the mean value of the total set), and how they change together (covariance). An example of covariance could be: alchol intake in oz. and driving ability (the higher the intake, the lower the ability to drive).

This analysis results in one main Component PC-1, which reproduces the highest variance, followed by all other perpendicular components ranked by importance. Of these, the second (PC-2) component is chosen.

We should take into account that since PC-1 is more important than PC-2 the differences along the PC-1 axis are greater than those along the PC-2 axis even if the "distance" between points is the same.

Below is a real example from a paper on human population genetics.

PCA global populations. Adapted from Geleta et al, Deep Variational Autoencoders for Population Genetics September 2023 doi:10.1101/2023.09.27.558320

The Africans seem to be most distant from all other groups and compact (more similar with each other), while West Asians are widely spread out along PC-1 (showing intra-population differences); Oceanians seem to form another compact group.

The method is faulty

Thhhe first article criticizing this PCA method is Principal Components Analysis fails to recover phylogenetic structure in hominins, by Levi Y. Raskin, et al., bioRxiv doi: https://doi.org/10.1101/2025.10.31.685754 🔓 (it has been published now in the American Journal of Biological Anthropology doi: 10.1002/ajpa.70306; Vol 190, no. 3: e70306. https://doi.org/10.1002/ajpa.70306.🔒). The authors analyzed studies using "morphometric data" (lengths, widths, angles, distances, thicknesses of bones, skulls, specimens) and found that "...PCA trees inferred from traditional morphometric data were identical to the sampled tree in 0.11% of datasets when we only considered PC axes 1 and 2, and in 2.9% of datasets when we considered all axes. No PCA tree inferred from any of the 2,400,000 shape datasets was identical to the sampled tree, regardless of the number of axes."

Only 11 out of 1000 trees produced by PCA methods with 2 dimensions were valid! And using more dimensions, the success ratio was less than three percent!

This questions the validity of conclusions reached using PCA methods: "Phylogenetic interpretations of the hominin fossil record based on proximity in PC space are inherently flawed and likely to be erroneous. Arguments in the hominin systematics literature based on PCA should therefore be reevaluated using phylogenetically-informed alternatives."

The authors are terminant. Those were best case scenarios. In real studies, bias and missing data could make matters even worse. The paper concludes that "PCA is fundamentally ill-suited and unreliable for inferring hominin evolutionary relationships from morphological data. Studies of hominin systematics that incorporate, and especially those that rely on, PCA as a means of inferring morphological and phylogenetic affinity should therefore be revisited."

This is relevant because many PCA charts using morphometric data assume that those hominins who are closer to each other in the chart, are related in the family tree and belong to a similar lineage. But it seems that this may not be the case. Below is an example of a morphometric PCA (Fig. 6 in Source); in the caption the text says "... High-scoring test subjects cluster together, suggesting cranial morphological similarity between them...":

Another Critical Voice: PCA and its use in genetic studies

An earlier paper published Aug. 29, 2022 by Elhaik E. Principal Component Analyses (PCA)-based findings in population genetic studies are highly biased and must be reevaluated (Sci Rep. 2022; 12(1):14683. doi: 10.1038/s41598-022-14395-4. PMID: 36038559; PMCID: PMC9424212), questioned the validity of conclusions obtained by using PCA. Elhaik is highly critical about its applicability to genetic studies and suggests that they are unreliable, and lead to false interpretations.

"...We demonstrate that PCA results can be artifacts of the data and can be easily manipulated to generate desired outcomes. PCA adjustment also yielded unfavorable outcomes in association studies. PCA results may not be reliable, robust, or replicable as the field assumes. Our findings raise concerns about the validity of results reported in the population genetics literature and related fields that place a disproportionate reliance upon PCA outcomes and the insights derived from them. We conclude that PCA may have a biasing role in genetic investigations and that 32,000-216,000 genetic studies should be reevaluated."

This work looks into the population PCAs, like the one shown furhter up (Africans, Europeans, Asians, etc). It notes that the PCA charts place the populations along the corners of an imaginary triangle: Africans, Europeans, and East Asians on each vertex of the triangle. And this is assumed to be the result of the migration out of Africa, followed by separate divergence and mutations. A conclusion widely accepted by geneticists. However, Elhaik says it isn't so: "Here we show that the appearance of continental populations at the corners of a triangle is an artifact of the sampling scheme since variable sample sizes can easily create alternative results as well as alternative “clines”."

This study states that "PCA can be used to generate conflicting and absurd scenarios, all mathematically correct but, obviously, biologically incorrect and cherry-pick the most favorable solution. This is an example of how vital a priori knowledge is to PCA. It is thereby misleading to present one or a handful of PC plots without acknowledging the existence of many other solutions, let alone while not disclosing the proportion of explained variance."

The manipulation implied by the author is that the outcome of the PCA chart is controlled by the scholar who already "knows" what the chart should reflect "By manipulating the choice of populations, sample sizes, and markers, experimenters can create multiple conflicting scenarios with real or imaginary historical interpretations, cherry-pick the one they like, and adopt circular reasoning to argue that PCA results support their explanation".

Closing comments

PCA is a valid statistical tool, with ample use in marketing, segmentation of customers, in facial recognition, in finance, climate modelling, medicine, and engineering (predictive maintenance, quality control). But, it seems that it use in the fields of anthropology and genetics is not robust or reliable.

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

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 © 

Out of Africa vs. Multiregional evolution - an 1988 perspective

Thirty eight years ago, back in 1988, BBC Radio 3 transmitted a program called "And Then There Was Us" it was hosted by Colin Tudge, who interviewed different scientists who discussed the then new theory of an Out of Africa origin of mankind, in contrast with the multiregional theory that proposed an interconnected evolution of humans from an ancient, archaic, group of hominins. Shahin Rouhani and Mark Stoneking supported the former, and Milford Wolpoff, the latter. You can read the full transcription of the program online: And Then There Was Us Et puis nous sommes apparus by Emma E. Bird, Julia Galway-Witham, Chris Stringer, First published: 15 January 2026 https://doi.org/10.1111/1467-9655.70025.

I will share a few snippets with my comments.

Diversity and antiquity

This is the explanation of why diversity meant an "older" population, which in fact is wrong. All humans share an equally ancient genome, from teh Amazonian hunter-gatherer to the Pygmy in Congo. We all have the same age in our genes. Yet Mark Stoneking said the following: "We calculated the actual average number of mutational differences within each population-within the individuals belonging to Africa, within individuals belonging to Asia, and so forth-and then also between populations. What we found was that Africans, on the whole, were by far the most variable of the human populations that we surveyed. They were about twice as variable as the other populations. So, if these mutations are neutral (if they are just accumulating in a more-or-less steady rate over time), then the more variability, the more mutational differences a population possesses and the older it is. The inference is that the African population is the oldest."

But mutations are not neutral, and they accumulate at variable rates, others are lost, others revert, but we are all at an equal distance from our common ancestor. (I have written several posts on the variability of mutation rates). Diversity, as observed by Stoneking can also come from admixture with archaics, within Africa, adding diversity to a population that was initially less diverse.

Admixture with other hominins

At that time, admixture with other lines of hominins was unthinkable, mixing of Neanderthals and Humans was not an option, they were considered different species. But Wolpoff thought differently:

Colin Tudge: In short, the Noah's Ark, or Garden of Eden hypothesis seems to have the issues sewn up. Modern human beings arose in Africa about 200,000 years ago; they spread from there, displacing all pre-existing humans in all the rest of the world, until, by about 35,000 years ago, they were the only humans left on Earth. As they took over the world, they grew apart, at least in outward appearance, to form the present-day races. All very neat.
By contrast, on the face of it, Milford Wolpoff's idea has an unlikely feel. It explains, well enough, why the modern races look so different; after all, he believes they descended from populations of human beings who began to diverge a million years ago. But it apparently fails to explain how the races have remained so similar once you get beneath the surface, and why they are all so obviously capable of interbreeding. All the different groups indeed would have had to evolve along strictly parallel lines, from the time that they were all heavy-boned and small-brained, to the time of universal gracility and braininess. But, such criticism, he feels, is based on misunderstanding.
Milford Wolpoff: The idea of races, or sub-divisions of humanity becoming isolated and separate early in their evolution, isn't really where I'm focused. My contention is that they have become separated, but not isolated. In fact, I believe, that if human populations ever were truly isolated for long periods of time – time in the thousands of years – they would become different species, so there would be a different species in Africa, in Asia, in Europe. They could no longer interbreed with each other, they would evolve in their own directions, and we would never be telling this story because it wouldn't be relevant.
The fact that humanity never speciated, in my mind, shows definitively that there always was a fairly high level of gene flow between populations. Now, gene flow doesn't necessarily mean population movement, although often it does mean exactly that. Gene flow can mean the exchange of wives, mating networks with villages next door to each other, or tribes next door, who regularly exchange mates, so that the genes in one area can spread to another.
However, there is more to it than that. Gene flow alone really would not account for this. The changes that have occurred across human evolution are ones that largely are the consequence of human behaviour. For instance, the decrease in robustness comes as a consequence of the more efficient use of tools, tools for preparing foods, tools for hunting, tools for making your life easier; tyre-jacks to lift the car so you don't have to do it yourself. These tools would spread much more rapidly than genes, we know they did, and human populations then responded to these by changing in similar ways in different places. Brain size is the most important of these because brains almost certainly evolve and respond to the increasing complexity of behaviour. Increasing complexity of behaviour can pass from one society to another as quickly as they talk to each other, and believe me, talk to each other they did.
Colin Tudge: You would have a kind of parallel evolution, wouldn't you? Although it would not be as stark as people would suggest.
Milford Wolpoff: You know the thing about parallel evolution is that parallel evolution really only clearly works between species where there is no gene interchange. The definition of parallelism is when a feature in two descendant species evolves from a single different feature in a common ancestor. It would be as though the canines of a common ancestor were large and two descendant species both independently develop small canines. That is parallelism. It works as a definition because there is no possibility that there is gene exchange between these two species. Once there is gene exchange, then it is not clear that the two features of the two descendants work independent of each other. Consequently, I don't think that parallelism really applies.
Colin Tudge: No one can doubt Milford Wolpoff's suggestion that ancient human beings might have exchanged genes, which in practice may mean exchanging wives. The question that bothers Shahin Rouhani is whether there could have been enough exchange to have kept all the different groups on the same evolutionary course.
Shahin Rouhani: If you work out how much gene flow you would require for such a thing to take place-that is you have a constant amount of gene flow throughout a grade of tribes extending from South Africa to southeast Asia-then you come up with some problems. One of the things you come up against is that, supposing an advantageous mutant appears in South Africa, how long will it take before this mutant spreads all the way to southeast Asia? Well, if you put in a reasonable set of parameters, you get numbers like 100,000 years, or 400,000 years, for such a spread to take place. This means that if one has something like a million years only to wait for archaic Man to change into modern Man, then you can only accumulate two, three, or at most ten, advantageous mutants. The morphological differences, which we do observe in the fossil record, are so immense. Much larger brain capacity and lack of brow-ridges would require quite a few genes, and they cannot simply be changed by a handful of genes.
Colin Tudge: But Milford Wolpoff isn't one to stay on the defensive. The Noah's Ark model demands that the emerging group of modern humans, Homo sapiens sapiens, simply replaced all the peoples who were inhabiting the various niches of Europe and Asia. In particular – I say ‘in particular’ only because it's the most famous example – the sapiens sapiens people known as ‘Cro-Magnons’ are supposed to have simply swept aside the Neanderthals, who were so well entrenched in western Europe. That, says Professor Wolpoff, really is implausible.
Milford Wolpoff: It seems to me that the idea that an invading population would not incorporate females as they overcame an indigenous population is behaviour that is not even un-human, it's un-animal. No vertebrate really acts like that. I like to use Tasmania – the poor Tasmanians – as an example of replacement because I think it's a good example. When Europeans came to Tasmania and replaced the Tasmanians, who were said to be extinct, in fact they mixed with them. So, the Tasmanians are said to be extinct only because there are no pure-bred Tasmanians left, but many inhabitants of that island can trace their ancestry one, two, or even three grandparents to Tasmanian natives, and not to Europeans. The real replacement here was one with a massive amount of admixture, and people living on Tasmania will always show the influence of genes from the people who were presumably replaced by the Europeans. If Tasmania is a model, it means that the Neanderthals had a significant genetic input to modern populations – if there were invading populations to begin with. If Tasmania isn't a model, then I don't see what possibly could be.
Colin Tudge: If it's the case that the Cro-Magnons interbred with the Neanderthals, then of course the Neanderthal genes are still around and there ought to be people around with Neanderthal features. Who are they and where are they?
Milford Wolpoff: Well there are some right here in this room, I am afraid to say...
...
Colin Tudge: However, the notion that Neanderthals and modern humans interbred assumes that [these] the two, though different, belong to the same species; that they were both merely versions of Homo sapiens. This indeed is the common assumption, that all Homo sapiens who have lived in the past 300,000 or so years, in all their variety, have been of just one species. Indeed, that Homo erectus, who prevailed for a million years before, was also just one species. It's a nice thought, but actually it's an idea whose roots are religious rather than scientific, fitting in as it does with the human conceit that the line of evolution that led to us was without major diversion, that our unfolding was somehow inevitable. But, in modern science there is no room for such conceit. Chris Stringer sees evidence of deep divisions and indeed diversions among the humans of the past."

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Ninth of July Trivia

Today is Argentina's Independence Day, we became an independent nation on July 9th, 1816, while still fighting against our Colonial Metropolis, Spain, and the Royalists in other parts of South America. Brazil, the US, UK, Portugal, and the then independent Kingdom of Hawaii all recognized our independence by 1823, but Spain would take until 1857 to acknowledge it.

You will find a street or avenue named 9 de julio (9th of July) in every town, city, and village in Argentina. The one in Buenos Aires, with its obelisk celebrating the city's 400th anniversary is shown below (it is one city block wide, a strip 3.8 km (2.4 mi) long by 100 m (330 ft) wide was razed to make way for it, between 1936 and 1986.

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

Denisovan and Neanderthal alleles in Africans at higher levels than in non-Africans

We usually hear that the modern humans, left Africa and, in Eurasia encountered their relatives, the Neanderthals and Denisovans, mating with them and sharing genes. This resulted in non-Africans having snips of genetic material from both ancient groups, with different levels depending on their geographic locations (Denisovan is higher in Oceanians, South eastern, and Eastern Asians, and Native Americans, while Neanderthal is higher among Europeans and Western Asians). Africans, on the other hand have almost zero introgression of Neanderthal genes (the little they have came from mixing with Eurasians who back-migrated into Africa after the OOA event), and zero Denisovan content. The Denisovans never made it back into Africa.

A paper I just read says the opposite! Africans have higher levels of Denisovan and Neanderthal genes than non-Africans.. This paper is ten-years-old (Povysil G, Hochreiter S. IBD Sharing between Africans, Neandertals, and Denisovans. Genome Biol Evol. 2016 Dec 1;8(12):3406-3416. doi: 10.1093/gbe/evw234. PMID: 28158547; PMCID: PMC5381509) and contradicts the history of migration and admixture mentioned further up. Let's see what this paper says and how it explains the higher level of Denisovan and Neanderthal genes in Africans.

p>First, the data, below is Table 1 from Povysil and Hoechretier, 2016. Unfortunately, the table does not include Native Americans! and therefore these are always underrepresented in research articles!

Original caption: Note.—The column labeled “Chr.” gives the chromosome, and “Neandertal” and “Denisovan” group IBD segments matching the Neandertal and Denisovan genomes, respectively. “ALL” gives the total number of IBD segments matching the respective ancient genome, “EAS”, “SAS”, “EUR”, and “AFR” report the number of matching IBD segments shared exclusively by East Asians, South Asians, Europeans, and Africans, respectively, and the percentage compared to the total number of IBD segments matching the respective ancient genome.

Ancient admixture within Africa?

The authors extracted Identical By Descent or IBD segments from genetic data of the 1000 Genomes Phase 3 dataset. They found two types of IBD segments that are shared between modern human beings and also with our ancestors, the Neanderthals and the Denisovans. These are the "longer" and the "shorter" segment types.

The long segments are those found in Eurasians, and the ones shared with Neanderthals and Denisovans are found at higher frequencies in Southern and Eastern Asians. Long segments seem to be related to admixture events outside of Africa.

The short segments, on the other hand, are shared by Africans, and for this reason, the authors believe that they represent ancient "events involving ancestors of humans and other ancient hominins within Africa."

The paper says that shorter segments are "presumably older than longer ones, the segments we extracted reveal events from the very distant past. We found short IBD segments that match the Neandertal and/or Denisovan genome and are shared mainly by Africans. These segments may either stem from a common ancestor with subsequent incomplete lineage sorting or more likely from an interbreeding of ancestors of humans and other ancient hominins within Africa."

They found a surprisingly high frequency of archaic short segments in the sexual X chromosome (that in men is inherited from their mothers, and in women, one part of their pair comes from their mothers, and the other from their fathers): "...chromosome X, on which segments that are shared by Africans and match the Neandertal and/or Denisovan genome were even more prominent. Our results indicate that interbreeding with other hominins was a common feature of human evolution starting already long before ancestors of modern humans left Africa."

The logical explanation for this high frequency of archaic genes in Africans is that they met and bred with these people within Africa. But, this goes against the hypothesis that Africa had highly a structured population with many small, isolated groups, that only occasionally met, and that each of them harbored a high diversity which, when they finally blended, led to the current diversity encountered in Africa. The paper says the following:

"One interpretation of our results is that ancestors of humans and ancient hominins interbred within Africa. The hypothesis of ancient substructures in Africa with limited gene flow between subpopulations of hominins does not contradict this interbreeding. Neandertals and Denisovans could be more closely related to Africans than to out-of-Africa populations because of more interactions between their ancestors. In this case, since the ancestors of Africans and Neandertals/Denisovans were not clearly separated, this could be considered “admixture” rather than “interbreeding”.

So, the limited number of Denisovan or Neanderthal alleles in non-Africans would be the outcome of the bottleneck, and founder effect that took place as they left Africa, carrying a limited subset of the original Neanderthal and Denisovan genes.

The second explanation is similar, but is pushed further back in time. The shared genes are due to a common-origin of Neanderthals, Denisovans and Modern Humans:

"Another interpretation of the extensive IBD sharing between Africans and ancient genomes is that these shared IBD segments originate from a common ancestor of Neandertals/Denisovans and humans. They can only be found in modern Africans due to incomplete lineage sorting. According to this scenario, the detected IBD segments arose first in the population that existed prior to the ancient separation of Neandertals, Denisovans and modern humans, but were relatively rare. Consequently they survived in both archaic humans and in present-day Africans, while drifting to a very low frequency in non-Africans.

The authors analyze this hyptothesis and note that Africans carrying the Neanderthal-Denisovan genetic snippets either carry all of them (there are over 20 of these "rare variants") or none! This presents the improbable situation that all the other people (who carried intermediate ammounts of these alleles) died out leaving no descent. The paper suggests a way out: populations were separated.

"In our opinion, it is unlikely that, for thousands of IBD segments, only these extremes survived while all the intermediate cases died out completely. Consequently, we assume that the source population was separated from all the other populations for a long time and, therefore, acquired such a high number of mutations. We do not know, whether the separated population was already a Neandertal, a Denisovan, their ancestor, or a different hominin. We cannot rule out, that the IBD segments also existed in ancestors of modern Eurasians and were lost due to strong genetic drift. However, our results suggest an interbreeding within Africa that involved a population that was isolated for an extended period of time. This early interbreeding can still be detected via IBD segments that are shared between Africans and Neandertals and/or Denisovans.

The alternative that the African alleles are due to a back-to-Africa migration is discarded because Africans have exclusive alleles not found elsewhere and they are found in all Africans, suggesting a wide distribution.

This study also found a high level of "segments shared between South Asians and Neandertals and/or Denisovans than between other non-African populations and these ancient genomes." This, has been proven time and time again over the past ten years. Interestingly, the authors speculate about the reason for this prevalence of Denisovan genes and offer three explanations. All current papers focus on expanation #1, ignoring the other two, but we should not forget that there are other alternatives that explain the Denisovan introgression in Oceanians and Southeast Asians: "Recent investigations found that South Asians share a surprisingly high amount of DNA with the Denisovan genome (Sankararaman et al. 2016). In our analysis the amount is even higher. Possible explanations for this finding are as follows: (1) additional interbreeding events with ancestors of South Asians, (2) introduction of IBD segments from ancient genomes into other non-African populations via South Asians and not directly, and (3) combinations of bottlenecks, genetic drift, and different selective pressures."

Closing Remarks

Africans seem to have ancient lineages of Denisovan and Neanderthal alleles. An admixture that possibly took place in Africa, within the continent. How does this tally with current theories of an exclusive outside of Africa admixture? It is thought provoking to imagine introgression within Africa, because it alters the timelines of the admixture dates proposed in the different admixture papers (see my post with links to all my posts on admixture and introgressions).

It is a pity that this paper, like most papers, ignores data from Amerindians. Including them would probably uncover furhter research aveneues.

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

High African diversity despite population bottlenecks. Why? (archaic admixture in Africa)

Higher diversity is normally associated with a effective populaton size, and that is why the Out of Africa migrants are said to have a lower diversity: they moved in a small group and this carried less diversity than the original population (a founder effect and a bottleneck for the migrants),

However, a paper published in Nature by Jakobsson et al., 2025 studied the evolution of modern humans using genetic information garnered from "ancient southern African genomes" and found that the African population size wasn't all that big. In fact it was the same size as the Out of Africa band!

Below I quote the relevant passage in the paper, my comments in brackets, and I highlighted some interesting parts of the text:

"Long-term large population size
... Heterozygosity (HO) for ancient southern Africans (mean across genomes; HO = 0.80 × 10−3) was similar to other ancient Africans, only surpassed by an ancient western African individual (HO = 0.93 × 10−3), indicating a large Holocene population size in southern Africa. A multiple sequentially coalescent approach shows that the effective population size (Ne) was large for several hundred thousand years, up to Ne ≈ 30,000 around 200 ka, similar to other African groups. The large Ne at ≥300 ka for all humans was potentially caused by population subdivision. [interesting! so small populations divided into many give the appearance of a large Ne when in fact it isn't] We note a decline in Ne for ancient southern Africans from around 100–50 ka, to Ne ≈ 10,000 by the Last Glacial Maximum (20 ka), similar to non-African groups and the ancient northern Africans [So at the time of the supposed Out of Africa Event 100,000 to 50,000 years ago southern & northern Africans and non-Africans had the same population size! So where is the OOA bottleneck?]
Runs of homozygosity (ROH, where greater numbers and total length of ROH segments indicate a smaller population size) show that the ancient southern Africans were at the upper tail of the distribution of modern-day Africans, but less extreme than most non-Africans—a pattern attributed to the out-of-Africa bottleneck. [homozygosity is attributed to small populations, and inbreeding, loss of diversity or heterozygosity. So the supposed most ancient humans, the South African San people have the highest ROH among Africans — but lower than non-Africans.] This indicates a smaller population size (relative to, for example, western African groups) in the relatively recent history of each individual, but still larger compared with non-Africans and ancient northern Africans. Most ancient southern Africans are shifted towards greater total segment ROH length without affecting the total number of ROH segments, in particular the Great Brak River (2,355–2,310 cal. bp) and the Matjes River 1 (7,845–7,690 cal. bp) individuals [this date is extremely recent! well after the OOA event]. This pattern indicates a smaller recent ancestral population size, possibly with elements of inbreeding, indicating isolation and fragmentation among ancient southern Africans during the Holocene. Ancient southern Africans south of the Limpopo River therefore consisted of a large, stable population for many millennia, with a modest decline since around 50 ka, and a possible fragmentation and further decline during the Holocene."

Admixture with archaics!

As usual the paper also points out that: "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." The isolation would mean that an archaic form of humans didn't admix with the others and carried ancient, unshared alleles. The admixture option seems more plausible.

When discussing diversity, the authors note that: "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." Indeed, introgression from archaics.

Notice how reluctant mainstream scholars are. Instead of digging deeper into the archaic admixture hypothesis, they set it aside. In this case, the authors seem to agree with this option, but, politely wrote: "Irrespective of cause, the many variable amino acid-altering sites among the ancient southern Africans point towards a genetic model in which different protein variants can be combined to viable outcomes... The many Homo sapiens-specific variants found in southern African genomes point to a combinatorial genetic model of human evolution in which there are many possible combinations of genetic variants that lead to ‘genetically modern’ Homo sapiens." Yes, a combination brought about by mating with archaics within Africa.

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

Higher mutation accumulation in Europeans vs. Africans

Another paper mentioning different mutation rates in Africans and non-Africans!

The paper by Mallick, S., Li, H., Lipson, M. et al. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature 538, 201–206 (2016). https://doi.org/10.1038/nature18964, reported that "Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence."

The branch-length issue

This reminded me of a recent post I wrote about Short branch lengths in Africans for Y-chromosomes. Branch lengths are linked to accumulated mutations (the lenght of a branch is the number of mutations in it) so if we start from the fork where Africans and non-Africans split, the branch of Africans is shoreter because it has accumulated fewer mutations, while the non-African one is longer, as it has more accumulated mutations. In that post I asked "...but we are all the same age and equally distant from our common ancestor. So why do the Africans have fewer mutations? Do Eurasians accumulate more mutations?"

I also went back to reread a recent post Mutation rate is faster in Africa where I mentioned different studies suggesting that a higher diversity in Africans (measured by their heterozygosity) promoted a higher mutation rate or μ. But Mallick, Li and Lipson et al. in their 2016 paper suggest otherwise. I quote them below and highlight their findings, which seem to baffle them:

"More mutation accumulation in non-Africans than in Africans
The SGDP data provide an opportunity to compare the rates at which mutations have accumulated across populations. We restricted our analyses to samples for which our genotypes are likely to be most reliable ... We pooled samples by region to increase power, and for all pairs of regions, computed the expected number of positions where, if we picked a random chromosome from both, region A would mismatch chimpanzee and region B would be identical to chimpanzee (or vice versa). If the rate of accumulation of mutation has been the same since the two populations diverged, these numbers are expected to be equal. However, when we compute the ratio of mutations on one lineage or the other since separation, we find a subtle (average of 0.5%) but significant excess of mutations in nonAfricans relative to sub-Saharan Africans. Because any difference must reflect events since non-African / African population divergence which is a less than a tenth of average genetic divergence, this implies a greater difference in mutation accumulation rates since population divergence (~5%). We were concerned that these results might be biased by the fact that the human genome reference sequence is more closely related to non-Africans than to Africans, or by higher levels of heterozygosity in Africans, as both these issues could make detection of divergent sites in Africans more difficult. However, we replicated the findings after remapping to chimpanzee, which is equally distant to all present populations, and after restricting analyses to the X chromosome in males (males only have a single X chromosome, and so this procedure avoids bias due to different error rates in detecting heterozygous genotypes in populations with different rates of heterozygosity). These observations are most likely to be explained by acceleration in the rate of mutation accumulation in non-Africans, since the same signal appears in comparisons to sub-Saharan Africans related in different ways to non-Africans. It is known that the rate of CCT>CTT mutations differs across human populations. However, this particular mutation class was found to be enriched relative to Africans in Europeans but not in East Asians, and thus cannot explain our signal. One of several possible explanations for these findings is a decrease in the generation interval in non-Africans compared to Africans since separation..."

What is going on?

Mallick, S., Li, H., Lipson, M. et al. affirm that mutations accumulate at a higher rate in non-Africans than within Africa, this does not mean that mutation rates (μ) are different, it means that the mutations are fixed differently. It is also higher among Europeans than East Asians. To explain it they propse that non-Africans have a shorter "generation time": they are mating at a younger age than Africans so they accumulate more generations in a given span of time, and therefore more mutations than Africans in the same period.

Generation Time

I am surprised because other research has shown that longer generation times lead to more mutations because "each additional year of paternal age results in an average of 3.9 × 10⁻¹⁰ more mutations per base per generation (Source) and hunter-gatherer people nowadays have longer generation ages (32.3 years for fathers) than sedentary groups and because older fathers accumulate more mutations, if Africans are mating at an older age, there will be more mutations. There is something that isn't adding up here!

A similar viewpoint was reported by Wang and Obbard, 2023: "Our analysis also shows that mutation rates increase significantly with increasing generation time... The relationship we observe between generation time and per-generation mutation rate could therefore be a consequence of either a greater number of cell divisions or of accumulating damage over time." Which makes sense.

However, not all agree, research conducted by Lewin and Eyre-Walker, 2025 confirms that mutation rate (μ) and generation time are inversely correlated (longer generation time = lower mutation rate; and shorter generation time = higher mutation rate).

Due to these conflicting findings, until consensus is reached, for the time being I will leave generation times out of the matter and look for other plausible causes for the higher number of mutations in non-Africans vs. Africans.

Other causes explaining higher accumulation of mutations

Effective population size or Ne. Wang and Obbard, 2023, also notice that "populations with larger Ne tend to have a lower mutation rate even after accounting for their shorter generation times." Africans are said to have a larger initial Ne due to the bottleneck effect that affected those leaving Africa, a small subset of the large original population. The authors suggest that if "... species with small Ne tend to have a longer generation time, and a longer generation time causes higher mutation rates then a higher μ in species with low Ne could be driven by a mechanistic generation-time effect." Since Eurasians seem to have both factors (small Ne and low generation times) is seems logical that their mutation rate is higher.

Besides the effective population size and generation time, there are more possible explanations for the shorter branch in Africans and the longer one in Eurasians are: natural selection, that removes noxious mutations, so looking back from the present, the mutations never seem to have taked place because they were not fixed. Reduced DNA repair mechanisms, one group has a less efficient repair mechanism for mutations and these tend to accumulate in comparison to another group with a more efficient repair system.

The increased TCC→TTC mutation rate in Europeans

This factor is mentioned in Mallick, S., Li, H., Lipson, M. et al. as a possible explanation. But, what does it really mean? I will quote from Harris and Pritchard, 2017, who studied the matter.

Our DNA is made up of two backbones, the intertwined helixes linked by "steps" like a ladder, made from bases called Guanine (G), Cytosine (C), Thymine (T) and Adenine (A). Guanine always links to Adenine G—A, and Thymine with Cytosine (C—T) bonds. Looking at the steps of one side of the helix you will see a sequence like "ATCGATTGAGCTCTAG", and opposing it, on the other strand the complementary bases: "GCTAGCCAGATCTCGA".

Research has shown that "European people experience more mutations within certain DNA motifs (specifically, the DNA sequences ‘TCC’, ‘TCT’, ‘CCC’ and ‘ACC’) than Africans or East Asians do." Why?

Harris and Pritchard propose that "the rate of TCC→TTC mutations increased dramatically ∼15,000 years ago and decreased again ∼2000 years ago... [and] hypothesize that this mutation pulse may have been caused by a mutator allele that drifted up in frequency starting 15,000 years ago, but that is now rare or absent from present day populations." They go on to explain the cause: " At this time, we cannot exclude a role for nongenetic factors such as changes in life history or mutagen exposure in driving these signals. However, given the sheer diversity of the effects reported here, it seems parsimonious to us to propose that most of this variation is driven by the appearance and drift of genetic modifiers of mutation rate."

So it seems that it is due to a chance appearance of genes that regulate mutation rates.

A curious yet interesting fact is that the same effect of TCC→TTC mutation increase is observed in East Asian cattle! It appeared in two separate mammal groups, indicine cattle, derived from the Bos taurus indicus and humans but outside of Africa (Talenti, et al., 20216)

A challenge to the "stable" molecular clock

Harris, 2015 also looks into the TCC→TTC subject and says that explaining the cause is beyond the scope of the paper. However, Harris concludes that "Even if the overall European mutation rate increase was small, it adds to a growing body of evidence that molecular clock assumptions break down on a faster timescale than generally assumed during population genetic analysis. It was once assumed that the human lineage’s mutation rate had changed little since we shared a common ancestor with chimpanzees, but this assumption is losing credibility due to the conflict between direct mutation rate estimates and molecular-clock-based estimates. Although this conflict might have arisen from a gradual decrease in the rate of germline mitoses per year as our ancestors evolved longer generation times, the results of this paper indicate that another force may have come into play: change in the mutation rate per mitosis. If the mutagenic spectrum was able to change during the last 60,000 years of human history, it might have changed numerous times during great ape evolution and beforehand."

I agree, mutation rates are variable, and conclusions based on a constant rate will be wrong.

Notice how different papers find opposite effects (faster mutation rates in Africans, or in Europeans), and don't quite understand the reason!

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

Oldest Homo Sapiens Sites in the Old World

The map below caught my attention while reading a new article by Zhang et al., 2026 it shows the oldest sites where Homo sapiens remains have been found.

Two things surprised me: (1) Despite Africa being touted the "Cradle of Mankind", 40% of the sites over 100 ky are found in Eurasia. (2) Of the 50 to 30 ky sites, 3 are found in Africa, and the other 14 are in Eurasia and Australia. Of course, the map shows partial information, so there are more sites in Africa, but it is suprising to notice such a prevalence of sites outside of Africa.

Fig. 1. Examples of early H. sapiens fossils older than 100 ka (red circles) and younger specimens dating to 50–30 ka ago (yellow circles) in Africa, Eurasia and Oceania. Fig 1 from Zhang et al., 2026

The oldest H. sapiens fossil outside of Africa is from the Greek Cave of Apidima where Apidima 1 skull was found (210,000 years old); see Harvati et al. 2019.

The second oldest is the 190,000-year-old jawbone from the Misliya Cave in Israel, reported by Hershkovitz et al, 2018.

The oldest African site is the Irhoud, Morocco, reported by Hublin et al, 2017, and dated to 315±34 kya. However these hominins have a mix of archaic and modern features that make some scholars wonder if it is a human or another hominin: "[They] have a facial morphology very similar to extant H. sapiens, as well as endocranial volumes that fall within the contemporary range of variation. However, their braincase shapes are elongated rather than globular, suggesting that distinctive features of brain shape, and possibly brain function, evolved within H. sapiens." (Scerri et al., 2018).

The next two African specimens are equal to, or younger than the Eurasian specimens!: Both from Ethiopia, the 195,000-year-old remains from Omo Kibish, and 160,000-year-old bones from Herto. A 2022 paper pushes the dates further back in time to ~230 kya. However, note that they may not be modern humans at all: "The Herto hominids are morphologically and chronologically intermediate between archaic African fossils and later anatomically modern Late Pleistocene humans. They therefore represent the probable immediate ancestors of anatomically modern humans. Their anatomy and antiquity constitute strong evidence of modern-human emergence in Africa." (White et al., 2003).

What is Anatomically Modern Human?

The key issue in my (layman's) opinion is that there seems to be no clear definition of what an Anatomically Modern Human is. Someone who looks like us even though they may not yet have developed behaviors similar to ours.

With a handful of deformed and partial remains (a pice of jaw here, a skullcap there, a few teeth over there) it is impossible to decide if those people who differ from us, and also between themselves, are the norm, or probably outliers of populations that had large intra-population variability.

Does a globe-shaped skull imply more homo-sapiens-similarity than a human-like jaw? Where is the line? Does an oblong skull like the ones found in Morocco count as humans or not? A mossaic of features is human? or primitive? What do archaeologists think about this?

We know that brain size evolved in homo species, and this growth influenced the shape of the skull as different areas of the brain developed, pushed by genetic changes and natural selection. More complex cognitive abilities appeared, the stone tools used by homo individuals gradually changed, improving, becoming more efficient in the use of knapped stone. Acheulean tools of erectus were used for over 1.5 million years, unchanged. Then came Mousterian, Levallois and microblades in a faster sequence of improvement mirroring the changing behavior of our ancestors. The discovery of fire, clothing, use of bone, wood, complex tools, needles, fishooks, symbols engraved on small objects, rock art, burials, all reflect behavioural growth as brains developed.

This evolution led from small skulls, with slanted faces, massive jaws, no chins, heavy browridges, to current gracil, rounded skulls, chins, and high forehads over flat faces.

Is there a sharp line between Modern Humans and "the rest"?

Pearson, 2008 looked into this matter in a detailed paper that ponders the archaic and modern morphology, the reasons for variability (evolutionary adaptation, genetic drift, and the shortcomings of the statistical and biological approaches to the subject.

A very interesting research article by Simon Neubauer, Jean-Jacques Hublin, and Philipp Gunz, 2018, analyzed the shape of the skulls and brains, as well as their size. Contemporary human beings have globular (balloon-shaped) brains with an upright forehead and a prominent parietal, the area occupied by the cerebellum is larger and rounded. Or faces are flat. On the other hand, the homo people before us had slanting faces, and elongated brains. (see image comparing a Human and a Neanderthal skull and brain, from Fig. 1 in the 2018 paper above. The authors compared different parameters of brains and skulls of Homo erectus, Neanderthals, and "Humans" from three periods: (1) very early specimens (200-300 kya) from Morocco and Ethiopia, (2) later people from the Middle East and East Africa (100-130 kya), and (3) more recent humans 35-10 kya. The images below show how they align using Principal Component Analysis:

Fig. 2 bgPCA of endocranial shape (top) and Fig. 4 bgPCA of endocranial form (bottom). Arrows show the Evolutionary trends of shape changes in archaic and modern individuals are shown as regressions on geologic age. Simon Neubauer, Jean-Jacques Hublin, and Philipp Gunz, 2018

Clearly, there is an evolution from primitive to modern features, with group (2), which included these samples: three from the Levant, Skhul V, Qafzeh 6 and Qafzeh 9 ages 115 ky, and one from Africa, the Ngaloba LH 18 skull from Laetoli, Tanzania (120 kya), closest to moderns and group (3), the latter aged 10 to 30 kya, have brains and skulls that are definitely modern.

Even Anatomically Modern Humans, as they dispersed across the globe following the OOA events carried different skull shapes that can still be identified in contemporary people, and have been used to suggest two migrations and two routes into Eurasia (the "two layer" hypothesis). One comprising Papuans and Oceanians following a South Asian route shares elongated skulls with Africans, the other across Central Asia into Siberia, Europe and East Asia has globular skulls, Europeans have compact jaws, Native Americans and NE Asians share large skulls, higher faces and cranial vaults with tighter foreheads (see Matsumura et al., 2022 and Matsumura et al., 2019).

Even modern humans carry introgressions that modified their skull shape (Neanderthals), as reported by Goovaerts et al., 2025, which has added diversity to non-Africans. Human chins are linked by genes to the flatter face of Homo sapiens. Reearch by Schuch et al., 2025 found that slower and shorter growth after birth, and bone reorption during childhood is a distinctivly human feature, found in all modern humans and absent in Neanderthals, that leads to gracile faces lacking Neanderthal prognathism (jaw protrusion).

Scerri et al., 2018, discusses and questions the orthodox notion that modern humans evolved and emerged within one single, specific population located in a particular region of Africa. The paper aruges that fossils from the early days of humans are very different, and the genetic evidence pointing at a very deep and ancient population structure within Africa (I have mentioned this in other posts, involving isolation, small groups, archaic interbreeding and mutation rates that are different to non-Africans) also supports a multiregional origin involving separate populations, an "African Multi-regionalism."

These isolated popualtions in different environments evolved separately at different paces, and this would explain why they show a combination of archaic and modern traits (they were boxed off in different regions of Africa by very dry deserts and dense tropical jungles —n mountains or glaciers in Africa— and faced different environmental challenges). This article also puts forward some unanswered questions and suggests directions for future research:

"Resolving the speciation of H. sapiens and the character of ancestral populations represents a crucial first step in understanding the emergence of the morphological features that diagnose our species during the later Middle Pleistocene
...
Finally, were some of our anatomical traits inherited from transitional African forms before they became extinct? The range of dates for H. naledi and H. heidelbergensis confirms the late survival of at least two archaic species in Africa. The size and environmental diversity of Africa, particularly the poorly investigated forested regions, may have permitted the late survival of more archaic species as well as of early forms of H. sapiens. These discoveries have fuelled speculations that H. sapiens may have interbred with archaic species in Africa itself. Distinguishing admixture between species from the reintegration of diverse H. sapiens lineages represents a major challenge, with significant taxonomic implications.
...
while a globular braincase does seem to represent a synapomorphy of extant H. sapiens, can it be effectively characterized for application to the fossil record? We emphasize that H. sapiens is a lineage with deep and likely diverse African roots that challenge our use of terms such as ‘archaic H. sapiens’ and ‘anatomically modern humans’. Unless they can be operationalized with more clearly defined traits, such categories will have declining value. Diagnostics of H. sapiens must reflect trajectories of evolution rather than static views of our species – which has changed, and continues to change, at various scales."

Into Africa

I believe that it is possible that the homo group leading to Modern humans probably evolved in the Middle East, and moved into Africa from there. However, this notion is contrary to what science believes is the correct approach to our ancestry, and outlined above by Scerri et al. I have the feeling that Chinese scholars will continue their push to have humans appear and evolve in Eastern Asia. Future publications and research will show us how these ideas develop.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2025by Austin Whittall © 

Human Genetic Diversity: Some Maps

The global human diversity map that I included in my previous post came without any reference to source or scientific backing, so it isn't reliable. I decided to search for something better and came across the three maps shown below.

They come from Figure 2, in the 2009 paper by Romero, I., Manica, A., Goudet, J. et al. How accurate is the current picture of human genetic variation?. Heredity 102, 120–126 (2009). https://doi.org/10.1038/hdy.2008.89

Interpolation of estimates of genetic diversity (HS) for short tandem repeats (STRs) (a), indels (b) and single nucleotide polymorphisms (SNPs) (c). The intensity of the red colour represents the genetic diversity obtained with an inverse distance-weighted (IDW) interpolation on landmasses. Blue dots represent the 54 populations from the H971 subset of the HGDP-CEPH data set. (d) The difference in genetic diversity between African and European populations for the three classes of markers. Error bars report standard deviation.. Fig. 2 in Romero, Manica, Goudet et al.

The map does not include data for Australia, South America appears with the lowest diversity for all three indicators, SNPs, indels, and SNPs, however, Africa has a low scoer in indels as you can see in (b).

I also found the source of the original map, it was published by Luca Pagani, as his thesis (online here, Through the layers of the Ethiopian genome: a survey of human genetic variation based on genome-wide genotyping and re-sequencing data. July 2013, DOI:10.17863/CAM.13969, Thesis for: PhDAdvisor: Toomas Kivisild). The map (shown again, below) is captioned "Pattern of genetic diversity in worldwide human populations. The distribution of STR diversity in worldwide human populations, adapted from the literature (Colonna et al. 2011), shows a higher diversity in African populations and a decline with the distance from Africa (each black dot represents a sampled population). The observed pattern fits with the proposed single African origin with subsequent migrations out of Africa proposed by Stringer and Andrews in 1988."

Colonna et al, (2011), cited by Pagani has several maps in his paper as Fig. 1 (Colonna, V., Pagani, L., Xue, Y. et al. A world in a grain of sand: human history from genetic data. Genome Biol 12, 234 (2011). https://doi.org/10.1186/gb-2011-12-11-234), where Pagani was a co-author.

I wonder what the plesiosaur in the Pacific stands for (?) it appears in the four maps of the 2011 paper.

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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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