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 © 

San (Khoisan) and Europeans

Following my previous post on similarities between San people in southern South Africa, and Europeans, I read a paper about the San (Khoisan) and their "antiquity". It reports them as an ancient population that retained a large effective population while that of other groups fell (i.e. other Africans, Europeans, Asians, and the Out of Africa migrants).

The paper published in Nature in 2014 by Kim et al., (Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history). The image below shows how Ne (effective population) evolves over time (oldest to the right), for San, African Yoruba, Europeans, and Asians. As you can see all groups (actually, the ancestors leading to each of these populations) have similar population sizes till 100,000 years ago when a dramatic drop in population sizes occurs. I don't understand how they obtained Ne values for hominin populations 2 to 4 million years ago, this was the days of Australopiths and probably Homo habilis.

Effective population sizes for San, Africans, Asians and Europeans. Fig. 3 a in Kim et al., 2014

This drop in effective population size is attributed to climate changes within Africa. The paper includes a series of maps as Fig. 12 in its Supplementary Material to explain the process. They can be seen below:

Modern humans originated in Africa (a), blue circle in South Africa seems to imply an origin there, though the paper does not specify the location. Then these people spread north (b), the orange oval marks the new territories. Then came the climate change (c) around 150 or 100 kya. Drought in western and central Africa hit the humans there in central, western, and eastern Africa, but spared the San people in the southern part of Africa. This coincided with a fragmented population (structured) with isolated groups that did not interact with each other (see the different dots and colors on the map, marking these groups). Populations declined central and western Africa, and when the ancestors of Non-Africans (green arrows) (d) migrated Out of Africa (OOA), they carried this lower Ne, and it dwindled even more due to bottlenecks and founder effects as they advanced into Eurasia. The San, however, kept their population intact.

The authors reconstruction of this period is summarized as follows: "After the earliest split, between the ancestral Khoisan and non-Khoisan populations ~100–150 kyr ago, the ancestral Khoisan population maintained their high genetic diversity, while the effective population size of the non-Khoisan continued to decline for 30~120 kyr ago and lost more than half of its diversity. The ‘Out of Africa’ migration ~40–60 kyr ago accounts for the observed population split between African and non-African populations, and the subsequent smaller effective population size of non-Africans compared with non-Khoisan Africans."

Comments

However, and interestingly, as pointed out in my previous post, the San and Europeans share several unique allele variants that are ancestral (found also in Neanderthals and Denisovans) whcih confer lighter pigmented skin than that found among the remaining Africans and also South Asians and Australo-Melanesians, who carry a later (derived) mutation for darker pigmentation.

How does this similarity between a specific OOA group and San people tie in with the evolution and migration sproposed by Kim et al.?

Not well. We would have to imagine a group that split from the San, moved north, lived in isolation in Central Africa, then survived the climate crisis there, moved north, left Africa, surviving the founder effect, bottlenecks and genetic drift, established themselves in Europe and somehow managed to keep their skin-color alleles intact. While all the other groups in Africa mutated and adopted a dark skin set of alleles. Too complex to be the explanation.

The San (Khoisan or bushmen) have always intrigued me since the 1980s movie "The Gods Must Be Crazy", I was taken aback by their pale skin and oriental factions. So different from the usual African features. People living in the deserts of Namibia with a hunter-gatherer culture in the 20th century! I have never found a paper explaining their similarity with East Asians. I will explore this strange trait in a coming post.

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

David Reich interview (Worth watching) on OOA and more!

Harvard geneticist David Reich gave a long interview which can be seen in video online here It includes a transcript from where I extracted the text that I share below.

Reich, born in 1974 is Professor of Genetics, Harvard Medical School and Professor of Human Evolutionary Biology who has specialized in population genetics and the genetics of ancient humans. His laboratory has sequenced the genes of over 16,000 people. He is a leader in this field so his opinion about Out of Africa and diversity, population structure and the braids that linke Neanderthals, Denisovans, and modern humans are indeed interesting.

Out of Africa needs a "Copernican Readjustment"

I liked the comparison of a Ptolemaic vs. a Copernican viewpoint for the Out of Africa theory. Reich says (talking about Neanderthals, Denisovans and modern humans) the following:

" When these lineages interacted with each other at different periods of time. But the standard model we have right now is really almost hard to believe. So the standard model right now is that modern humans are a distant cousin of Neanderthals and Denisovans, who are most closely related. Neanderthals and Denisovans stemmed from a common ancestor maybe half a million years ago, which separated earlier from the ancestors of modern humans. But actually, maybe there's some alternative way of thinking about what happened that can really change our vision of the relationships amongst these groups and make it sort of the Copernican readjustment where we say, well, maybe, maybe the maybe the solar system revolves around the sun, and the Earth is a satellite of that. And maybe, maybe that's how it looks. And so I kind of feel that we're missing a trick and that there's something there, and that maybe if we come up with a different model, it will be much more plausible."

On Out of Africa, replacement, and our origins

In another podcast from 2024 (Online here - Dwarkesh Podcast) Reich has some interesting comments (I give the approx. time he says them, also see the transcript):

• Time: 2:05 min. He says the model is implausible, and mentions the Copernican analogy.
• Time: 5:20 min. "Profoundly different models may actually explain the data" in a more plausible manner. At 8 min he adds that each new study is accreted onto the "Standard" (orthodox) model like patches.
• Time: 9:30 min. "in a period of 2 million to 500 thousand years ago I think it is not at all clear where the main ancestors leading to modern humans were, there were humans through many parts of Eurasia and many parts of Africa... I think there's been an assumption where Africa has been at the center of everything."
• Time: 13:00 min. Several hundreds of thousands of years ago a lineage gets into the Middle East and mixes there with the ancestors of Neanderthals.
• Time: 14:00 min. In Africa there were hundreds of small populations with low diversity, almost going extinct, but seen as a whole, their added diversity, and random occasional admixing created the current high diversity of modern humans.
• Time: 52:00 min. Humans changed a lot over the past 2 million years, but then looking back at the past 200 ky, Africans, Oceanians and Eurasians are very similar, only in the past 10,000 years do we see an acceleration of evolution due to selection in Western Eurasia which is baffling: "There's a kind of disconnect... It's a very confusing situation. It feels like we don't really understand what's going on, but there's a lot to learn."
• Time: 1 h 04 min. Replacement of populations are disruptive events, when a Y-chromosome lineage is compeltely replaced by another, yet the mtDNA did not change, it means the men were wiped out and women had no choice about their mates "It wasn't friendly, peaceful, or nice."
• Time: 1h 16 min. "you might argue that non-Africans today are Neanderthals who just have waves and waves of modern humans from Africa mixing with them. Who are the ancestors?... actually the proportion of non-Africans ancestors who are Neanderthals is not 2%. That’s the proportion of their DNA in our genomes today if you're a non-African person. It's more like 10-20% of your ancestors are Neanderthals... It’s not even obvious that non-Africans today are modern humans. Maybe they're Neanderthals who became modernized by waves and waves of admixture."
• Time: 1 h 26 min. "The evidence that our lineage was mostly in Africa is based on an assumption, a kind of inertial idea, that our lineage must have always been in Africa because Africa is the center of human history. But if you look at the archaeological evidence, it's not incredibly clear. If you look at the genetic evidence, we have many early branches from Eurasia and only one from Africa. You have complexity and branching in Eurasia that's sampled in the DNA record, DNA from Denisovans, DNA from unknown archaic lineages that contributed to Denisovans, Neanderthals. All of those are represented in the Eurasian record, not in the African record. Part of that is the fact that ancient DNA is preserved in Eurasia. Maybe there's a period when our lineage resides in Eurasia. It's not obviously wrong. That hypothesis is out there as a possibility."
• Time: 1 h 32 min. On what is lacking in the field: "The basic answer is that we need DNA from Africa. We need old DNA from 50,000 years ago, 100,000 years ago, 200,000 years ago, from all over Africa. Because it's super clear that our lineage is complicated within Africa. There's archaic forms in the archaeological record. Modern human data is extremely substructured, with evidence of having come together from many different lineages, which must have been different archaic forms in Africa contributing to people living today. Having that would crack our understanding of how modern human lineages braided together and relate to the other archaic lineages we have data from. That's obviously extremely helpful."

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

The Three Out Of Africa Migrations

I came across research by J. H. Relethford, who in a paper published in Nature in 2008 cites Templeton's work about the different expansions of our ancestors out of their African homeland.

The Archaeological Evidence

The fossil evidence shows that H. georgicus and H. erectus lived in Eurasia roughly 1.7 million years ago, and that there were different hominins in that region since then. The remains of H. heidelbergensis, Neanderthals and Denisovans also show evolution and possibly other out of Africa events around 600 ky ago. Finally our own branch, H. sapiens left Africa possibly twice, an early, "failed" migration around 250-100 ky ago and the final move that established modern humans around the world ~60 ky ago. At least, that is the official account.

The Genetic Confirmation

What is interesting is that genetic analysis done by Templeton confirms these dates. Again, I wonder if this fit between the data in the genes and the bones and stones is real, or was somehow eased with the foreknowledge of what had to be confirmed...

Below Is what Relethford wrote, including his citation of Templeton:

"The most comprehensive of these analyses has been performed by Templeton (2005, 2007) who examined 25 DNA regions: mtDNA, Y chromosome DNA, 11 X-linked markers and 12 autosomal markers using a 6-Myr-old date for the human–chimpanzee divergence for calibration. Using a method known as nested-clade phylogeographic analysis, Templeton found that 15 of these markers showed evidence of geographic expansion. The estimated ages of range expansion vary significantly across these markers and do not fit a model of a single expansion, but instead cluster into three groups: (1) an expansion out of Africa 1.9 Myr ago (95% CI=0.99–3.10 Myr), (2) an expansion out of Africa 650 000 years ago (95% CI=390 000–970 000 years ago) and (3) an expansion out of Africa 130 000 years ago (95% CI=9600–169 000 years ago)."

These three events coincide with the H. georgicus and H. erectus, the Neanderthal, and the H. sapiens migrations! I find the confidence intervals rather large (0.9 to 3.1 million years for erectus, 390-970 ky for Neanderthals and 9.6 to 169 ky for us). Such large intervals reveal a high uncertainty in the statistical analysis.

Is this a Coincidence? or do genetics and hard archaeology agree with solid evidence?

Relethford warns that: "Given the large confidence intervals typical of coalescent analysis, this correspondence should be taken as suggestive and not conclusive, but the apparent congruence of the fossil and genetic records is interesting and deserves continued attention, particularly as data on more low-recombination DNA regions become available."

Note that word of caution about Templeton's findings. John Henry Relethford originally was a staunch supporter of the Multiregionalism theory (humans evolved in parallel in the Old World and intermingled) and rejected the initial Out of Africa theory which suggested a total replacement of other hominins by modern humans as they marched across Eurasia, wiping them out. He later shifted to a compromise theory (Mostly Out of Africa) where there was an interplay between African H. sapiens and the hominins in Eurasia. He was concerned with the fate of these Eurasian people.

Alan Templeton on the other hand adopted a rigid position against the replacement Out of Africa theory, criticizing it. His papers reflect this (see above), and he continued with another paper in 2013, and again in 2023, supporting his point of view.

Templeton wrote a very interesting critique about some statistical tools, and admixture trees, which will be the subject of a future post.

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

Neutral Theory of Genetic Evolution and Out Of Africa

The main backing for the Out of Africa theory is the Genetic Neutrality Theory.

The arguments of an African origin of modern humans and our dispersal across the globe is supported by the high genetic diversity found in modern African populations, with lower diversity elsewhere, and a gradient or cline in diversity that reflects less diversity as distance to the African homeland increases. Both of these factors are expected according to the Neutrality Theory.

Starting with a highly diverse population, if a small group from that population migrates (into Eurasia), it can only feasibly carry with it a sub-sample of the original diversity. This is known as a Founder Effect, the founders of a new population carry fewer genes than the population from which they split from.

This happened time and time again, as sub-sub-groups split from the main population and moved into Europe, Eastern, Northern, and Southern Asia, Melanesia, Australia, Polynesia, and across North America, and then, into South America.

The Neutral Theory states that each split reduces genetic diversity.

Genetic Heterozygosity

Heterozygosity is a measure of diversity. Each person receives genes from their parents, that code for different proteins and produce traits. Those who have two different varriants (alleles) of a specific gene, one inherited from each parent are heterozygous. If the alleles are identical, they are homozygous.

The image below shows two parents (both are heterozygous) each carrying two different variants A and a. The probability for passing them on to the next generation is simple there are four possible combinations, each has a 25% probability of occurring:

Hetero and Homozygosity. Copyright © 2026 by Austin Whittall

The chances are that two of the offspring will carry Aa alleles, and will therefore be heterozygous, while the other two will receive the same allele from each parent and be either AA or aa, carrying two identical copies. This makes them homozygous.

As we can see, a population that is 100% heterozygous as become 50% homozygous and 50% heterozygous. All the possible combinations of those homozygous and heterozygous genes are shown below:

Combinations of alleles. Copyright © 2026 by Austin Whittall

As you can see 25% of each variant (AA, aa, Aa, and aA). So why would heterozygosity decrease? Suppose only aa homozygous couples mate, the chance of this happening is 1 in 16, or AA mate, again, 1 in 16. So 2:16 or, 1:8 chance of only homozygous mating and offspring. But... if these offspring meet and mate aa with AA, they would have a 100% heterozygous descent. This is true for large populations, but for smaller groups the founder effects and bottlenecks can reduce the allele diversity.

Genetic Bottlenecks

The argument of loss of heterozygosity, or its equivalent, increase in homozygosity is based on genetic bottlenecks, where a small sub-population splits and carries with it the homozygous variant, say only aa or only AA. Losing the possibility of reintroducing the lost allelle. This is a 1 in 16 chance.

Other causes of heterozygosity loss are natural catastrophes, war, and disease. But, why would such events affect the heterozygous individuals more than the homozygous. Wouldn't they be random, and therefore have an equal chance of impacting on hetero- and homozygous individuals?

Regarding the root population. There is the chance that the root from which a population split off from suffered some event that eliminated a large swath of it, while the migrating sub-population in another geographic location was not affected by it. Wouldn't that lower the heterozygosity of the basal group and make the sub-population appear as "enriched"?

Genetic Drift

Both Founder effect and Bottlenecks are part of process called Genetic Drift. As we saw, genetic drift takes place when random events, by chance modify which alleles passed on by parents to their offspring. They also include not only non-reproduction of certain individuals due to war, disease, natural catastrophes, but also loss of genetic variation due to people who don't reproduce because they die before mating, choose not to do so, etc. Genetic Drift isn't driven by evolution. The random changes may or may nor provide adaptations to a changing environment, so they may or not be acted upon by the forces of natural selection.

A sub-population may lose certain alleles, or others may become Fixed reaching a 100% frequency in the population due to chance events.

Mutations and Natural Selection

Random mutations take place, and modify the alleles, natural selection may also work, favoring the survival of individuals with alleles that provide adaptative benefits.

But, what about mutations, that happen by chance, that have a deleterious effect? Some mutations may have harmful consequences. The Neutral theory says that some deleterious mutations may rise to high frequencies in small populations due to fixation promoted by genetic drift. But, why wouldn't people carrying unfavorable genes be affected by natural selection, causing them and their descent to die out?

The Neutral Theory of Molecular Evolution

It was the creation of Motoo Kimura, who in 1968 proposed that at a molecular level, mutations are caused by random genetic drift. These mutations are neutral from a selective point of view. They aren't affected by natural selection.

Kimura has been criticized, for instance Kern and Hahn (2018), argue that modern, genome-scale data demonstrates far more evidence of adaptive evolution than the neutral theory allows, suggesting that natural selection (both positive and negative) shapes much of the genome.

As mutations take place by chance, the probability of them being neutral, deleterious, or beneficial would seem equivalent. So, why assume they are neutral? A beneficial mutation even if it is rare would confer an evolutionary advantage for those carrying it, and modify the population beyond what neutral models suggest.

Linked Selection. The loci (or addresses) that mark the location (locus) of a gene in our DNA isn't independent and isolated. Some genes or DNA sequences located close together on the same chromosome are inherited together, as a unit, during meiosis (linked chromosomes).

Selective Sweep is when an allele that improves the fitness of its carrier increases in frequency due to natural selection, is accompanied (hitchhiking) by other genes linked to it by physical proximity on the DNA strand are also increased in frequency even though they may be neutral. Finally, Background Selection is similar and has the opposite effect: deleterious alleles are removed by natural selection and neighboring neutral alleles are lost too, due to physical proximity to the harmful variants.

These examples show that "neutrality" is not necessarily true.

Molecular Clock

Kimura's theory states that neutral mutations took place at a constant speed, accumulating over time at the same pace. However, this is not true.

However mutations don't appear in a uniform manner in all loci along the genome, they arise unequally, and the probability of fixation depends on where they arise in the genome. This modifies how the clock ticks (Source). Furthermore, substitutions depend on population size, and generation overlap (Source).

Generation time is also an important factor: is it 20 or 30 years? 25? or 18? Over 10,000 generations this means a time scale that can vary from 180,000 to 300,000 years!

Back-Mutations and Recurrence Not Allowed

Kimura's theory, at least when applied in practice, has three axioms that are not true:

1. Infinite sites, it assumes that each mutation takes place at a site that has never mutated before.
2. No back-mutations, changes happen in one direction A → G. Which will never again flip back G → A
3. No Recurrence, in practice there are multiple mutations that take place at the same site. The neutral theory does not accept it, there can't be multiple mutations at identical loci in different lineages.

A paper gives a great example of why and how a back-mutation can have positive effects (here showing how a base C = Cytosine mutates to T = Thymine and back):

"...simple back-mutation is expected to generate slightly advantageous mutations. For example, let us imagine that a site is fixed for C, and that a new T mutation occurs that is slightly deleterious with a disadvantage of −s. Let us imagine that this T mutation spreads through the population and becomes fixed. If a new C mutation then occurs at this site, it will be slightly advantageous with an advantage of +s, unless the relative fitnesses of the C and T alleles have changed. Such a change in fitness could occur because of a change in the environment or the fixation of mutations at other sites which have epistatic interactions with the alleles at a site of interest."

Americas: Great Dying

Regarding Amerindian diversity, we know that up to 90%, or more, of the Native Americans died during the century that followed European "discovery". Disease, war, famine, social disruption, force labor, etc. killed tens of millions of Amerindians. Lineages died out, massively. This is the unique and most massive genocide (albeit unplanned) in the history of humanity. How can we know the number of unique, diverse, divergent alleles that were wiped out during this event? In 1491, America probably presented a far more diverse genetic structure than it does now.

And this brings us to the other point: African "diversity".

African Diversity... is it real?

Finally, and this will be the subject of a future post, do modern Africans reflect the genetic makeup of ancient Africa 100,000 or 75,000 years ago? Is a modern Nigerian, Gambian, Angolan African representative of the ancient population from which the Out of Africa migrants split? Have other events taken place within Africa, isolated from the sub-population that migrated into Eurasia? Admixture with archaic hominins after the OOA event, admixture between many separate and formerly isolated hunter gatherer sub-populations could have led to a modern highly diverse African population, while the original OOA root was far less diverse.

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

Did Humans admix with Neanderthals? Paper in Nature says NO

Research published in Nature on Dec. 13, 2024 suggests, as its title says, that some models used by scientsts may lead to assume the existence of false introgressions. The word spurious used in the title means "based on false reasoning or information that is not true, and therefore not to be trusted". The paper can be found online: Tournebize, R., Chikhi, L. Ignoring population structure in hominin evolutionary models can lead to the inference of spurious admixture events. Nat Ecol Evol 9, 225–236 (2025). https://doi.org/10.1038/s41559-024-02591-6🔒

A preprint free version is available on line in Biorxiv 🔓

The paper's Abstract is quoted below:

"Abstract
Genomic and ancient DNA data have revolutionized palaeoanthropology and our vision of human evolution, with indisputable landmarks like the sequencing of Neanderthal and Denisovan genomes. Yet, using genetic data to identify, date and quantify evolutionary events—such as ancient bottlenecks or admixture—is not straightforward, as inferences may depend on model assumptions. In the last two decades, the idea that Neanderthals and members of the Homo sapiens lineage interbred has gained momentum. From the status of unlikely theory, it has reached consensus among human evolutionary biologists. This theory is mainly supported by statistical approaches that depend on demographic models minimizing or ignoring population structure, despite its widespread occurrence and the fact that, when ignored, population structure can lead to the inference of spurious demographic events. We simulated genomic data under a structured and admixture-free model of human evolution, and found that all the tested admixture approaches identified long Neanderthal fragments in our simulated genomes and an admixture event that never took place. We also observed that several published admixture models failed to predict important empirical diversity or admixture statistics, and that we could identify several scenarios from our structured model that better predicted these statistics jointly. Using a simulated time series of ancient DNA, the structured scenarios could also predict the trajectory of the empirical D statistics. Our results suggest that models accounting for population structure are fundamental to improve our understanding of human evolution, and that admixture between Neanderthals and H. sapiens needs to be re-evaluated in the light of structured models. Beyond the Neanderthal case, we argue that ancient hybridization events, which are increasingly documented in many species, including with other hominins, may also benefit from such re-evaluation."

Notice how the authors criticise the models used ("mainly supported by statistical approaches that depend on demographic models minimizing or ignoring population structure [but, ignoring] population structure can lead to the inference of spurious demographic events ").

The authors assumed that there were two population groups. One named metapopulation M_A tht generated a second one, M_B between 9 Million years ago and 500 ky. This created two populations (Bipartite structure) within Africa. Then, some individuals from the M_B group left to colonize Europe and Asia splitting some 650 ky ago from the remaining populations that stayed in Africa. Those who went to Eurasia became the metapopulation M_N, originating the Neanderthals or Hn population. The African metapopulations M_A and M_B evolved into Homo sapiens (Hs). Later Hs left Africa and colonized Eurasia forming an M_C metapopulation there. The paper states that "the new Hs Eurasian metapopulation M_C with the African Hs metapopulation M_B (itself connected to the Hs metapopulation M_A). Note however that none of the Hs metapopulations (M_A, M_B and M_C) ever exchanged gene flow with the Hn metapopulation (M_N). In brief, our model does not allow admixture between Hs and Hn."

Therefore this study suggests that instead of actual mating between Homo sapiens and Neanderthals, as a means by which genetic material was shared by both groups, the common fragments of genetic material may have originated in ancestral populations that split and carried them with them through time with no need for admixtwure.

Below is Fig. 1 from the paper, and the original caption is the following: "Simplifed representation of the 1D structured model considered in this study. Time flows from top (past) to bottom (present), with an initial metapopulation M_A consisting of nA (=10) demes exchanging migrants with their neighbours. At some point in the past, the rightmost deme of M_A founds a new metapopulation M_B of nB (=10) demes, with which it will continue exchanging migrants till the present. Later, the rightmost deme of M_B founds the metapopulation M_N of nN (=10) demes which will become Neanderthals. The MN metapopulation will never exchange migrants with any other deme from the other metapopulations. Closer towards the present, the rightmost deme of M_B founds M_C which corresponds to the expansion of H. sapiens towards Eurasia. White feet represent the sampled populations (not the specific demes) for respective sampling times. The location of the sampled demes (within the corresponding metapopulations) is a random variable... Fifty individuals are sampled in M_A and in M_C to represent modern-day YRI and CEU samples respectively. For the Neanderthals (M_N), one individual is sampled at 50 kya."

Fig. 1 in the Biorxiv preprint. Source

Comments

Interesting indeed! Could these admixture events be mere artifacts of these black-box statistical models used by scholars? I have posted some critical comments on these models in the past (See: Some thoughts about the tools used in genetic admixture analysis, Biases in Genetic Models that are generally overlooked). I favor admixture, yet, I also consider that the software used by scientists may not accurately reflect the real population dynamics of our ancestors.

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

Asian vs. African origin of Humans and the "inverted" phylogenetic tree of Shi Huang

I have mentioned Shi Huang in two previous posts (Out of China? in 2019 and On Neanderthals in America and the Out of China Hypothesis in 2025).

I love how he inverts the phylogenetic trees, from a root in Africa and youngest brances in East Asia, Europe, and America, to one rooted in Asia, with a youngest African branch, going against the consensus of the Out of Africa theory.

This posture is similar to what I suggested in a post nearly 8 years ago, "On the direction and root of phylogenetic trees" (April 2018): "When I see a phylogenetic tree (also known as an evolutionary tree), I always wonder why do we believe that those branches, trunk and the root which anchors it, are correct. I ask myself why is it assumed that the mutation took place in one direction and not the other. And this trivial question is fundamental because the branches open up from other branches based on the differences between the DNA as you move along them." (sorry for quoting myself). The post included the image below.

Two different trees built from the same genome samples. Copyright © 2018 by Austin Whittall

In today's post I mention another paper co-authored by Shi Huang: Ancient Y chromosomes confirm origin of modern human paternal lineages in Asia rather than Africa, Hongyao Chen, Ye Zhang, Shi Huang. bioRxiv 2020.03.10.986042; doi: https://doi.org/10.1101/2020.03.10.986042

The paper includes the following figure, which, as you can see, inverts the root of the Y-chromosome tree, from Africa to Asia, and places Africa in the newest branch.

Figure 1. Y chromosome phylogenetic trees of modern humans. Only major branches and representative SNPs are shown with branch lengths not to scale. The tree topology was built without making use of any ancient DNAs. A. The Out of East Asia model. B. The Out of Africa model.. Source

They argue in this paper that "The mutation pattern in the ancient Y chromosomes as revealed here confirms the expectation that ancient haplogroups should mutate in only a fraction of the sites that define a haplogroup they belonged to. Two observations here confirm the Asia model and invalidate the Africa model. First, only haplogroups specific to the Asia model showed the expected mutation pattern in ancient samples. Second, the genetic reality that a haplogroup, be it ancient or present, should not carry mutations found in basal haplogroups to which they do not belong is only met by the Asia model but not the Africa model."

Interesting and controversial, and also, not peer reviewed either.

By the way, Shi Huang expands this idea in a paper published one year ago: Examining models of modern human origins through the analysis of 43 fully sequenced human Y chromosomes, Shi Huang. bioRxiv 2023.11.09.566475; doi: https://doi.org/10.1101/2023.11.09.566475. In it he uses the same inverted trees to argue against the Out of Africa theory and support his Out of East Asia theory.

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

HHV6 - Human betaherpesviruses and the peopling of America

Human herpesvirus (HHV-6) has to haplotypes, A-6 and B-6, interestingly the virus can merge into human genes, blending into our DNA (the scientific term is that it "can integrate into the germline"). Roughly 1% of the global population (around 80 million people) carry the DNA of this virus inside one of their chromosomes, in each of the cells of their bodies. Scientists have asked themselves if this "integration" is ancient, or recent, and if it is still happening as people get infected with the virus.

Roughly 90% of humans are seropositive to HHV-6B, because as infants we are exposed to the virus (Roseola Infantum, also known as the Sixth Disease).

Research by Aswad A, et al. (2021) (Evolutionary History of Endogenous Human Herpesvirus 6 Reflects Human Migration out of Africa. Mol Biol Evol. 2021 Jan 4;38(1):96-107. doi: 10.1093/molbev/msaa190. PMID: 32722766; PMCID: PMC7782865.) explored the history of the virus and its "integration".

The "integrated" virus, which forms part of the chromosome, is passed on to the offspring of carriers, and this inherited chromosomally integrated HHV-6 (iciHHV-6). If the integration was ancient, it was passed down along thousands of generations in a parents-to-children line.

The inherited-integrated iciHHV-6 has been found in several chromosomes like number 17 and 22.

Aswad et al., built a phylogenetic tree of the circulating HHV-6 variants A and B (that cause Roseola) and the integrated virus snips inside human chromosomes. The authors state that "the ancestral circulating strains that resulted in these particular independent integration events are not among the known currently circulating strains sampled here. Similarly, the integrated HHV-6A is not acting as a reservoir for ongoing production of circulating strains... In contrast to HHV-6A, the tree for HHV-6B revealed a more entangled topology between circulating and endogenous genomes..."

They found that some clades mirror geographic origin: "among the iciHHV-6A sequences, we observed that individuals from clades A2 and A4 are exclusively European or North American... HHV-6B clades B3–6 and B8 are similarly homogenous and likely represent orthologous integrations in white Europeans and North Americans (and one Australian). This suggests that for each of these clades, those now carrying the virus share a common ancestor who was also European, and thus the virus integration event occurred prior to the diaspora of ancestors of these individuals; the virus thus likely integrated before the colonial era."

"our analysis also revealed a previously unidentified Native American carrier of iciHHV-6B, who possesses an HHV-6B sequence distinct from the other North American samples. Instead, this sequence is almost identical to the iciHHV-6B genome of a Maasai Kenyan sequence uncovered through our SRA mining, and a previously identified Pakistani sample (Zhang et al. 2017) (figs. 2 and 4)."

They then explain how this rare shared variant appeared in America, Asia, and Africa, a Native American who shares "integrated" sequence with a Kenyan and a Pakistani!:

"Unlike the ancestral European integrations, the last common ancestor of these individuals would have been before humans migrated out of Africa (50–100,000 years ago). The observation that they also resolve near the base of the tree further supports this interpretation, as does the fact that the most closely related sequence outside this clade is a circulating strain isolated from a Ugandan patient..."

By "resolve near the base of the tree" they mean that this specific branch is close to the root, and therefold, older than the other branches. As it is similar to the strain of an African (Ugandan), the Out of Africa logic suggests that the root of the tree is based in Africa. Below is the tree and this branch is highlighted.

HHV-6B phylogenetic tree (detail). Fig 2. in Aswad et al.

However, as you can see in the image, not only is a "similar African" strain located at the root, there are three other Ugandan and three D.R.Congo subjects there too, all black-Africans but... one, closest to the root, is a WHITE NY U.S.A. sample!

The authors propose that an ancient ancestor in the distant past (~100 ky ago) before humans left Africa, underwent this "integration" of the virus into one of his or her chromosomes, and this bit of DNA passed on, unscathed, through countless generations, ending up in a Native American, a Pakistani, and a Kenyan Maasai. The tree below is Fig. 4 B, in their paper:

The age of this "integration" was estimated "to be ∼85,000–342,000 years old (depending on the mutation rate used)." Then it says "The Native American is a reference individual used in a South American study on the influences on physical appearance (Chacon-Duque et al. 2018)" Chacón-Duque's paper says that they "examined data for over 500,000 autosomal SNPs typed in more than 6,500 individuals born in Brazil, Chile, Colombia, Mexico and Peru." So, it does include Mexicans, from North America, and the rest of the samples are from South America. Notice that there was only one (1) sample in 6,500 who carried this integrated variant of HHV-6B. A very low frequency indeed!

The data used by Chacon-Duque also noted a high prevalence of African genes (slave trade) in Latin Americans: "~22% of the individuals studied show more than 5% sub-Saharan African ancestry." Which backs my suggestion of African introgression in the Native American sample of "integrated" HHV-6B .

Discussion

The Native American sample's origin isnt' clear in the paper, in one part it says that this sample differs from "the other North American samples", implying that it is North American.

The idea is interesting. However, considering all the bottlenecks that Amerindians have gone through including the founding effect of Beringia, and the loss of 90% of the Native American DNA due to disease, and strife during the conquest and discovery period 1492-1700s, it is difficult to believe that a trait that is now only found in 1% of human beings, managed to survive among Native Americans.

That it is shared by Old World people like the Maasai and the Pakistani could be possible, but the Amerindian carrying this genetic material seems to stretch the odds. Furthermore, no signs of this unique integration is found in Europe or the rest of Asia. What happened to those who carried the gene into Pakistan, and across Asia into America? They left no descent?

Could it be possible that an escaped African slave brought by the Portuguese or Spaniards to South America admixed with natives and passed on this chunk of HHV "integrated" into one of his genes?

It seems a more reasonable explanation.

The tree branch that holds all three samples shows that the closest to the root is the Pakistani, followed by the Amerindian and then, the Kenyan. Shouldn't the Kenyan be closer to the African root?

What is interesting is how the data is "adapted" to the preconceptions of an OOA move some 50-100 kya. Shouldn't the data independently show if that date is correct? Notice the wide window they calculated, a four-fould spread between lower and upper limits" ∼85,000–342,000 years old (depending on the mutation rate used).

It could have originated outside of Africa: We could also imagine a scenario where a Homo antecessor living in Eurasia 700,000 years ago, picked up the virus and it "integrated" into one of its chromosomes, his descent spread Denisovans and Neanderthals, and from there admixing with a modern humans ended up in Pakistan and America, and others crossing Gibraltar (see this post) reintroduced it into Africa. Somehow it didn't survive among those who would later become Europeans, and if these migrants took a northern route, it could have also avoided Eastern and Southern Asians, leaving no trace there.

It could have originated earlier among H. erectus and spread back into Africa with them, and possibly into America in an ancient peopling wave 500,000 years ago. Much later, once modern humans left Africa they could have intermixed in Pakistan, and (no need for them to carry it across Beringia), mated with H. erectus who carried the "integrated" virus, in America.

There are no records of "integrated" virus in ancient Amerindian (or Old World) samples. These would be important as they could help clarify the migration patterns of the virus inside our ancestors' chromosomes.

Let's see what future research discovers.

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

Hominins that predate the Human-Denisovan-Neanderthal split , from Morocco

A paper published yesterday (January 7, 2026) in Nature investigated some fossil remains found in a site (Grotte à Hominidés) at a quarry in Morocco, not far from the city of Casablanca. They belong to hominds who appear to be "basal" to modern H. sapiens, Neanderthals, and Denisovans. The authors date them to around 773,000 years ago and state that these remains reinforce "the case for an African rather than a Eurasian ancestry of H. sapiens."

This is the paper: Hublin, JJ., Lef&egravE;vre, D., Perini, S. et al. Early hominins from Morocco basal to the Homo sapiens lineage. Nature (2026). https://doi.org/10.1038/s41586-025-09914-y

This date is very close to the date when modern humans, Neanderthals and Denisovans split and went different ways, which is believed to have taken place between 550 and 765 thousand years ago.

The paper also suggests that they may be related to the Homo antecessor (TD6) whose remains have been found in Atapuerca, Spain, and whose remains have been dated to 950-770 ka. Though the Morccan remains and the Atapuerca fossils are similar, they also differ.

The Morocco fossils, named ThI-GH (from Thomas Quarry I, Grotte à Hominidés) combine modern and primitive traits. The site, excavated between 1994 and 2015 has produced Acheulean tools (typical of H. erectus), more primitive than the stone knapping techniques developed later by the Neanderthals.

The age of the remains

The authors analyzed the sediments in which the fossils were found, employing magnetostratigraphic tecniques that compare the sediments with the record of polarity reversals of the Earth's magnetic field, and found that "our analysis indicates hominin ages younger than 990 ka (top of Jaramillo) and close to the MBT at a nominal age of 773 ± 4 ka."

However, other tests find a younger age: "Optically stimulated luminescence (OSL) dating, performed in unit SU4 on cemented sands provided age estimates of 420 ± 34 ka and 391 ± 32 ka, of the same order as the ages obtained from OH2 to OH5. OSL ages appear to be inconsistent with the evidence that these formations belong to at least three glacioeustatic cycles and, for this reason, can be disputed. Combined electron-spin resonance (ESR) and U-series dating methods applied directly to an isolated hominin tooth from SU4 resulted in an estimated age of 501 ka +94 ka/−76 ka. The same method yielded ages ranging from 591 ± 103 ka to 538 ± 52 ka on three well-preserved herbivore teeth from SU4...

Below I quote the paper's relevant parts with my comments in brackets.

"These hominins cannot be directly compared with later specimens, such as the Kabwe or Bodo skulls, which have been tentatively assigned to H. heidelbergensis. Not only do these specimens differ substantially in age, but they also lack preservation of comparable anatomical parts. Our analysis suggests that the ThI-GH hominins probably belong to an evolved form of H. erectus sensu lato in North Africa, much as H. antecessor does in Europe.
[These hominins appear to be "evolved" Homo erectus - Homo antecessor group!]
However, the ThI-GH hominins offer an interesting contrast to both the Spanish fossils and the considerably older fossils from Tighennif (Algeria), which are likely to date to at least 1,000 ka. The fossil mandibles from Tighennif appear more primitive, larger and more robust than both the European H. antecessor and the northwest African ThI-GH fossils. The Spanish and Moroccan fossils share several features in their teeth and mandibles. Both groups display a combination of archaic and derived features reminiscent of later hominins. These similarities revive the question of possible exchanges across the Strait of Gibraltar during the EP. Nevertheless, the ThI-GH hominins are different from the TD6 hominins.
[Since the Strait of Gibraltar was breached by the sea during the Zanclean Flood about 5.33 million years ago (that eliminated the dry-land bridge between Europe and Africa as the Mediterranean basin filled up with water from the Atlantic, the "exchanges across the Strait of Gibraltar during the EP" or Early Pleistocene means that these people built watercraft to navigate the Strait of Gibraltar!]
The origin of H. sapiens, and the precise timing of the divergence of its ancestral populations from the Neanderthal–Denisovan clade, remain subjects of debate. Anatomical evidence has at times been used to argue for a split predating 800 ka and even for an alternative Asian ancestry of our species. In this context, the Maghreb fossils are key to understanding the diversification of MP [Mid Pleistocene] hominins. The morphology of the ThI-GH hominins places them close to the split between the African and Eurasian lineages. Our findings not only align with the phylogenetic structure inferred from palaeogenetic data but also highlight the Maghreb as a pivotal region for understanding the emergence of our species, reinforcing the case for an African rather than a Eurasian ancestry of H. sapiens."

The exchange across Gibraltar could be considered as an Out of Africa, for Homo erectus who entered Europe and evolved into Homo antecessor there, or probably a route into Africa from early hominins who (like those found in Dmanisi and the Caucasus) peopled Europe and returned via Spain to Africa across Gibraltar.

The authors seem intent on proving an African origin for "our species" and mention this twice in their paper. I am not so certain this paper suggestss an African origin for modern humans, it only describes hominins with an archaic-modern mossaic of features similar to those of H. erectus and H. antecessor, both of which are Eurasian!

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

All Y-chromosome haplogroups outside of Africa originated in East Asia

A paper published in December 2019 (Early replacement of West Eurasian male Y chromosomes from the east. Pille Hallast, Anastasia Agdzhoyan, Oleg Balanovsky, Yali Xue, Chris Tyler-Smith bioRxiv 867317; doi: https://doi.org/10.1101/867317) suggested that the Y chromosome of ALL non-Africans was replaced by lineages that originated in East Asia!

Published in bioRxiv it hasn't been peer reviewed and can be read in full. The summary of this idea is given in the abstract:

"phylogenetic analyses of haplogroup C, D and FT sequences, including very rare deep-rooting lineages, together with phylogeographic analyses of ancient and present-day non-African Y-chromosomes, all point to East/South-east Asia as the origin 50,000-55,000 years ago of all known non-African male lineages (apart from recent migrants). This implies that the initial Y lineages in populations between Africa and eastern Asia have been entirely replaced by lineages from the east, contrasting with the expectations of the serial-founder model."

So, this paper says that instead of splitting into different haplotypes close to Africa, say in the Middle East after leaving it, human Y-chromosomes began diversifying in Eastern Asia. Then these haplogroups replaced any others that may have appeared to the west of them.

Below is the map shown in this paper's Figure 3, mentioned in the following quote from the same paper.

"In a simple model of gradual human expansion from Africa to Asia and Oceania without subsequent continental-scale reshaping, we would expect the initial divergences in the Y-chromosomal phylogeny to have occurred in geographical locations close to Africa, and the present-day Y-chromosomal phylogeography to reflect this history by showing the presence of the early-diverging lineages within C, D and FT now being located geographically in Central/West Asia (Figure 3a). In stark contrast, the observed distributions of these lineages all lie further to the East, suggesting that their early divergences occurred in the East...
How then can the present-day Y-chromosomal phylogeography be reconciled with an out-of-Africa expansion? The simplest explanation is that initial western Y chromosomes have been entirely replaced by lineages from further east, perhaps on more than one occasion. "

Interesting version of an "Out of China" theory. Yet, it retains the original notion of H. sapiens leaving Africa and originating there.

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

An Eurasian origin for Homo Sapiens (2021 paper)

I found an interesting paper published four years ago (Árnason, Ú. The unidirectional phylogeny of Homo sapiens anchors the origin of modern humans in Eurasia. Hereditas 158, 36 (2021). https://doi.org/10.1186/s41065-021-00197-7) that provides an analysis showing that Homo sapiens sapiens or modern humans originated in Eurasia!!

The author summarizes his "Out of Eurasia" findings as follows: He identified "potentially four translocations of modern humans from Eurasia into Africa, the earliest taking place ≈ 250,000 years before present, YBP. The results were in accordance with the postulates behind OOEH [Out of Eurasia Hypothesis] at the same time ... they lent no support to the OOAH [Out of Africa Hypothesis].

The paper places Homo erectus at the base of the nuclear DNA tree: "Homo erectus, He, has been placed at the root of the tree consistent with He entering Eurasia from Africa > 2 million years ago". The following image appears with the caption that is given below.

Fig. 1 in Arnason (2021). Source

Fig. 1. Captioned: "The nuDNA phylogeny leading to Hss, Homo sapiens sapiens. Blue: Eurasian lineages. Red: African lineages. H. erectus has been placed at the root of the tree in accordance with the artefact sequence related to the Eurasian existence of He 2,12 MYBP. The divergence between Hs, H. sapiens, and Ha, H. antecessor, has been dated to ≈ 850,000 YBP, that between Hss and Hsn, H. s. neanderthalensis, to ≈ 800,000 YBP and that between Lund and Mbuti/San to ≈ 250,000 YBP. Hsn divides into Hsnn, Neanderthals proper, and Hsnd, Denisova, with Hsnn dividing further into SH-Hsnn (Hsnn at Sima de los Huesos) and Hsnn*, a branch arising as the result of the mtDNA introgression that took place from Hss into Hsnn* ≈ 500,000 YBP". Where Hsn is Neanderthal, HSnd, Denisovan.

Fig. 2 in Arnason (2021). Source

Fig. 2's Caption reads: "The mtDNA relationships of Hs demonstrating the paraphyly of the African Hss populations as resolved by PPA. Blue: non-African taxa; red: African taxa. Hsnn*: Hsnn other than SH-Hsnn. The arrowheads signify the mtDNA introgression that gave rise to Hsnn*. The limitation of Hsnn to Eurasia places the mtDNA introgression in this continent, reversing the direction of Hss evolution behind OOAH. The Hss part of the tree underlines the phylogenetic continuity among non-African populations and the paraphyly of the African populations including the two Yoruba [1]. AuAb: Australian aborigines; PNG: Papua New Guinean; Han: Chinese; Lund: The first described non-chimaeric human mtDNA molecule [19]; French: A European, as representing previous genomic findings"

An interesting hypothesis that has surely been torn apart by those who support the OOA theory. Nevertheless, since 2021, findings in China have provided some additional support to the notion that there were evolved humans in Asia at least 200,000 years ago besides the Denisovans.

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

On why modern humans succeeded in their Final Out of Africa migration

A paper published in Nature (Hallett, E.Y., Leonardi, M., Cerasoni, J.N. et al. Major expansion in the human niche preceded out of Africa dispersal. Nature 644, 115–121 (2025). https://doi.org/10.1038/s41586-025-09154-0) on June 18, 2025, explains why the final Out Of Africa event, 50,000 years ago, was the successful one.

The premise of the paper is that human beings in Africa adapted to living in different environments within the continent (deserts, savannas, grasslands, and jungles) expanding their niche. They could face the weather, and survive in different habitats. It was this flexibility, not tools or special genes that allowed them to expand and move out of Africa. In the authors words:

"The expansion of the human niche beginning around 70 ka in Africa is driven by a gradual increase in human preference for forest and desert biomes, allowing them to expand into regions that were previously rarely populated: (1) forests of West Africa, (2) forests of Central Africa and, eventually, (3) arid Saharan regions and semi-arid Sahelian regions of North Africa. This increased ability to adapt to new habitats, ranging from the extremes of equatorial forests to arid deserts, would have allowed these populations of humans the ecological flexibility to tackle a range of new environmental conditions encountered during the expansion out of Africa, allowing them to succeed where earlier migrations out of Africa had previously faltered. The expansion of the human niche in Africa starting around 70 ka, therefore, offers an explanation for the successful worldwide expansion of human populations about 50 ka"

The previous Out of Africa migrants that survived

I disagree with this point of view.

It is clear that a first wave of Homo sapiens didn't survive. They left Africa 100 ky ago.

But, we have the Denisovan and Neanderthals thriving for hundreds of thousands of years in freezing Eurasia, from Tibet to Spain. In a climate that never existed in Africa (glacial ice and extremely low temperatures). Yet, they were extremely well adapted to their niche, with tools, social structures, and flexibility to hunt and survive.

They had been preceded by the Homo erectus, and probably Homo habilis by at least 1 million years in their migration into Eurasia. And H. erectus lived there, and prospered for hundreds of thousands of years adapting to tropical climes in Indonesia and freezing winters in Northern China.

Luck and Chance

Perhaps the demise of these other groups was not dictated by modern human "flexibility" adapting to African ecological niches, which gave them tools to survive. We were lucky. It was just chance and good fortune that allowed small groups of hominins to survive the deadly environment (drought, wild beasts, volcanic eruptions, disease, infections, lack of food, etc.)

Human Beings almost became extinct 900 ky ago

See these articles published in Sept. 2023: "Did our ancestors nearly die out?" (Nick Ashton, Chris Stringer, Science 381,947-948 023).DOI:10.1126/science.adj9484) commenting "Genomic inference of a severe human bottleneck during the Early to Middle Pleistocene transition" (Wangjie Hu et al., Science 381, 979-984 (2023).DOI:10.1126/science.abq7487). Hu et al point out that:

"Results showed that human ancestors went through a severe population bottleneck with about 1280 breeding individuals between around 930,000 and 813,000 years ago. The bottleneck lasted for about 117,000 years and brought human ancestors close to extinction"

Our ancestors were reduced from almost 100,000 individuals to a mere 1,280 individuals some 900,000 years ago, and this went on for 117,000 years. It was touch and go. This dreop in population was caused by climate change with glaciations becoming long-term events, cooling the oceans and provoking drought which in turn affected the animals in Africa, Europe and Asia.

Then, population recovered and a speciation event took place, and the ancestor of modern humans, Neanderthals and Denisovans appared, around 750 to 550 ky ago.

Ashton and Stringer add that " Europe was probably completely depopulated after a previously unrecognized cold phase about 1,100,000 years ago" (https://www.science.org/doi/10.1126/science.adf4445) this event eliminated the first hominins to people Europe 1.5 Ma, the the Sima del Elefante people, perhaps descended from the Dmanisi hominins from Georgia (1.8 MA). "these extreme conditions led to the depopulation of Europe, perhaps lasting for several successive glacial-interglacial cycles." It was only later (1 Ma - 900 ky) that Europe was repopulated "by Homo antecessor, which may have been a more resilient species with evolutionary or behavioral changes that allowed survival under the increasing intensity of glacial conditions."

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

Archaic admixture into Africans

The article I mention in this post was published in Feb. 2020 (Recovering signals of ghost archaic introgression in African populations by Sriram Sankararaman and Arun Durvasula Science Advances 12 Feb 2020:Vol. 6, no. 7, eaax5097 DOI: 10.1126/sciadv.aax5097). It reports an " archaic introgression into four West African populations. Our analyses ... indicate that these populations derive 2 to 19% of their genetic ancestry from an archaic population that diverged before the split of Neanderthals and modern humans".

The authors "estimate that the archaic population split from the ancestor of Neanderthals and modern humans 360 thousand years (ka) to 1.02 million years (Ma) B.P. and subsequently introgressed into the ancestors of present-day Africans 0 to 124 ka B.P. contributing 2 to 19% of their ancestry."

Could African "diversity" often used to justify the continent as the cradle of mankind be due to this introgression?

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2020 by Austin Whittall © 

The Y chromosome of Neanderthals

A paper published in Science (The evolutionary history of Neanderthal and Denisovan Y chromosomes by Martin Petr et al. SCIENCE 25 SEP 2020 : 1653-1656), reports that "interbreeding between early humans and Neanderthals and selection replaced the more ancient Denisovian-like Y chromosome and mitochondria in Neanderthals".

The paper includes this tree:

Caption for image: "A) Neighbor-joining tree estimated from the Y chromosome genotype calls, excluding C-to-T and G-to-A polymorphisms, rooted with a chimpanzee as the outgroup (14). Numbers show bootstrap support out of 100 bootstrap replicates. Terminal branch lengths are not informative about the ages of specimens (Fig. 1A), owing to differences in sequence quality. (B) Estimates of TMRCA between Y chromosomes along the x axis and a panel of 13 non-African Y chromosomes. Each dot represents the TMRCA with a single non-African Y chromosome, with error bars showing 95% CI from a resampling of branch counts (14). Black horizontal lines show the mean TMRCA calculated across the full non-African panel (dashed lines) with resampling-based 95% CI (solid lines) (14).".

I have written about Neanderthal Y chromosome in two posts (May 2014 and May 2018), so I found this paper really intersting.

It suggest that:

• Denisovans, Neanderthals and Humans lie on three separate phylogentic branches ("the Denisovan Y chromosomes form a separate lineage that split before Neanderthal and modern human Y chromosomes diverged from each other (Fig. 2A). Notably, all three late Neanderthal Y chromosomes cluster together and fall outside of the variation of present-day human Y chromosomes"). This is what one would expect.
• Split dates: "The two Denisovan Y chromosomes split from the modern human lineage around 700 ka ago ... By contrast, the three Neanderthal Y chromosomes split from the modern human lineage about 370 ka ago". Which also seems quite normal to me.
• They conclude that "The Denisovan–modern human Y chromosome TMRCA estimates agree with population split times inferred from autosomal sequences, suggesting that the differentiation of Denisovan Y chromosomes from modern humans occurred through a simple population split"
• And find the 370 ky TMRCA too recent for the Neanderthal Y chromosome. They authors write: "By contrast, the young TMRCA of Neanderthal and modern human Y chromosomes and mtDNAs suggest that these loci have been replaced in Neanderthals through gene flow from an early lineage closely related to modern humans."

So they concluded that a line of modern humans admixed into Neandethals, and they completely replaced Neanderthal Y chromosomes and that is why the split seems so recent. Instead of reflecting the older age they expected. This is summarized as "Autosomal genomes show that Neanderthals and Denisovans are sister groups that split from modern humans between 550 thousand and 765 thousand years (ka) ago. By contrast, the mtDNAs of Neanderthals and modern humans are more similar to one another [time to the most recent common ancestor (TMRCA) of 360 to 468 ka ago] than to the mtDNAs of Denisovans."

They add: "We conclude that the Y chromosomes of late Neandertals represent an extinct lineage closely related to modern human Y chromosomes that introgressed into Neanderthals between ~370 and ~100 ka ago. The presence of this Y chromosome lineage in all late Neanderthals makes it unlikely that genetic changes that accumulated in Neanderthal and modern human Y chromosomes before the introgression led to incompatibilities between these groups".

Now, they only sampled 3 male Neanderthals. Perhaps a larger sample may result in a different outcome. An introgression 370 ka would mean that these humans "closely related" modern humans left Africa -assuming the Out Of Africa theory is correct- 370 ka in an ancient migration and mated with Neanderthals. Since their Y chromosome is distinct from ours, these "closely related" people must have died out in Eurasia.

But looking at the tree and the dates, why conclude an admixture from "closely related" humans into Neanderthals? An admixture that erased old Neanderthal Y chromosomes?

Occam's razor approach suggests: the Neanderthals have a different Y chromosome to us and to Denisovans (fig. above, B) it lies on a different branch. Which ratifies the conclusion. So is the age an issue? 370 ka is too recent?

Why not look into the assumptions that lead to this date? Such as the mutation rate (they estimated 7.34 × 10⁻¹⁰ per base pair per year) or the age they adopted for the "oldest Y lineages" (A00): ~249 ka ago.

I am agree with the authors when they state " Furthermore, we predict that the ~400-ka-old Sima de los Huesos Neanderthals should carry a Y chromosome lineage more similar to that of Denisovans than to that of later Neanderthals", it is reasonable, and does not impact on their supposed Y chromosome replacement theory. Sima de los Huesos chromosomes may also have evolved into what we find in later Neanderthals.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2020 by Austin Whittall ©