Sima de los huesos is now.... closer to Neanderthals than Denisovans!

Earlier this year I wrote a post about the Sima de los Huesos remains and its possible linkeage to Homo erectus. I was commenting on a paper that had sequenced the mtDNA of the remains from this Spanish site and found it "to be closer to Denisovan mtDNA than to Neanderthal ⁄ Human mtDNA. This is quite hard to explain: how did Denisovans get more of this mtDNA than the Neanderthals did considering that Denisovans are located in Altai while Neandertals are located in between Spain and Altai?".

Well it appears that the mtDNA was closer to Denisovans, but today I read another article (DNA from Neandertal relative may shake up human family tree, by Ann Gibbons, Science 11.Sep. 2015) which says that:

After 2 years of intense effort, paleogeneticist Matthias Meyer of the Max Planck Institute for Evolutionary Anthropology has finally sequenced enough nuclear DNA from fossils of a tooth and a leg bone from the pit to solve the mystery. The task was especially challenging because the ancient DNA was degraded to short fragments, made up of as few as 25 to 40 single nucleotides. (Nucleotides—also known as base pairs—are the building blocks of DNA.) Although he and his colleagues did not sequence the entire genomes of the fossils, Meyer reported at the meeting that they did get 1 million to 2 million base pairs of ancient nuclear DNA.
 
They scanned this DNA for unique markers found only in Neandertals or Denisovans or modern humans, and found that the two Sima fossils shared far more alleles—different nucleotides at the same address in the genome—with Neandertals than Denisovans or modern humans. “Indeed, the Sima de los Huesos specimens are early Neandertals or related to early Neandertals,” suggesting that the split of Denisovans and Neandertals should be moved back in time, Meyer reported at the meeting...

This is very interesting since it pushes the ancestors of Denisovans and Humans split from the linage leading to Sima de los Huesos earlier than expected. But also, (because that explains how the mtDNA that is closer to Denisovans was found in Sima de los Huesos remains) they did interbreed after they split apart.

The allegory of an evolutionary tree is not the best way to describe our origins. It is more like a tree with criss-crossing branches that split from a common trunk much earlier than expected.

The early splitting is no problem from my point of view, in fact I have written some posts about an earlier origin of humans, but it is a problem for those who base their "molecular clocks" and adjust them based on dates which, are in fact quite wrong. The process can be summarized as follows:

We look at populations (say Amerindians) and jot down their haplogroup markers, and we assume that they mutated when they reached America and then, we guess the date they entered America (say 15 kya). With this we calibrate our clock. We again look at the humans closest to Africa and jot down their haplogroups markers, and once again guess the date these people's ancestors left Africa (say 70 kya), and again calibrate our clock. We take another look at the oldest fossils of AMH in Africa (195 kya) and jot down the most divergent African haplogroups' markers, we recalibrate our clock again. But, as you can see, there are many assumptions in all of this (the dates and, above all, the assumption that these haplogroups are specifically human and mutated recently < 200 ky!).

But what if the origin of H. sapiens was not 200 kya but 300 or 350 kya? this alters the mutation rates, so America could have been peopled much earlier...

More findings will help us understand this better.

A closing thought

The common mtDNA shared by Denisovans and Sima de los Huesos but not the nuclear DNA could be explained as follows:

• Archaic population lives in Eurasia (H. erectus?) with its specific DNA and mtDNA they are the ancestors of Denisovans and a pre-Sima de los Huesos people.
• A later wave of proto-Neandertal reach Europe, they are more successful and breed with the native women of pre-Sima de los Huesos stock. The original mtDNA is preserved in their offspring, but the nuclear DNA is now admixed with proto-Neandertal. After many generations we have a European lineage with mtDNA similar to the original stock and therefore shared with Denisovans, but a DNA which will be more like that of Neanderthals.

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

An even older Out of Africa event (270kya)!!

A paper published in Nature, by Cosimo Posth et al, published in Nature looks into the odd discrepancy in the age of the split between Modern Human and Neanderthal genomes

The date of the split between humans and Neanderthals differs when you consider their nuclear or their mtDNA:

• Nuclear DNA says that humans and Nearnderthals split some 765,000 to 550,000 years ago
• Mitochondrial DNA or mtDNA says we split 365,000 to 400,000 years ago

I believe that discrepancies are what makes science leap forward (like the problems caused by the "ether" theory that led to relativity and quantum physics). And a gap like this of several hundreds of thousands of years is a big discrepancy. Either the dating is all wrong and has to be reviewed (ie. mutation rates and so forth), or the current ideas on the migration and origin of Homo sapiens are incorrect.

The paper looks into the mtDNA extracted a "complete mtDNA of an archaic femur from the Hohlenstein–Stadel (HST) cave in southwestern Germany. HST carries the deepest divergent mtDNA lineage that splits from other Neanderthals ∼270,000 years ago..."

This date of 270 kya is actualy the average, the real divergence date between HST and all other Neanderthals (95% HPD) is between 316 and 219 kya. The Altai Neanderthals split from the other Neanderthals some ∼160,000 years ago (95% HPD of 199 - 125 kya).


This paper tries to explain the genetic incongruence of Sima de los Huesos (see my post Sima de los Huesos remains, Neanderthals, Denisovans and their nuclear and mtDNA), the remains from Sima de los Huesos in Spain which are 430 ky old, have mtDNA that resembles that of Denisovans more closely than that of the Neanderthals. But, their nuclear DNA is more similar to that of Neanderthals than to Denisovan nuclear DNA.

The authors write (Bold is mine) that the nuclear DNA (nDNA) "... from the Sima de los Huesos site... confirmed their closer affinity to the Neanderthal lineage, suggesting that at least by ∼430 ka, Neanderthals and Denisovans had already diverged. However, in contrast to genome-wide data, the Sima de los Huesos mtDNA was found to branch off with the deeply divergent Denisovan mtDNA lineage. The phylogenetic discrepancies could be reconciled if the mtDNA of early Neanderthals was indeed Denisovan-like and was subsequently replaced by a more derived mtDNA lineage.".

This "derived mtDNA" got into the Neanderthals through " a genetic introgression event from African hominins into the early Neanderthal population that gave rise to the ‘Late Pleistocene’ Neanderthal mtDNA lineage".

This introgression took place long ago, and came from " an African source, which we constrain taking place more than ∼270 ka". In other words the paper suggests an Out of Africa event over 270,000 years ago which admixed human mtDNA into Neanderthals, mtDNA which replaced the older mtDNA -i.e. Denisovan and Sima de los Huesos hominin, with a new lineage, the "African mtDNA that evolved into the Late Pleistocene Neanderthal mtDNA type". And this "new" mtDNA spread from the HST Neanderthal in Germany to all others, including Sidron in Spain and eastwards all the way to Altai. Thousands of kilometers from the Atlantic to Siberia.

Furthermore, they estimate that "if Ne (effective population) was <5,000 units, a mean temporal interval of 300 ka is sufficient for an incoming mtDNA lineage below 0.1% in frequency to drift up to fixation." in other words, a very small initial input of "African genes".
But looking at this theory with a critical eye, we must point out that Neanderthals were spread out over a very wide area, which makes it very difficult for this replacement to take place in the whole population.

Furthermore a different explanation can be found: if modern humans were already outside of Africa i.e. in Asia, and they mixed with the Neanderthals outside of Africa -no Africans involved in the introgression. They would have had plenty of time to admix over a wide area, and this would also explain why there was an Ancient gene flow from early modern humans into Eastern Neanderthals 100,000 years ago as suggested by Martin Kuhlwilm et al, in Nature, Feb. 2016. DOI:10.1038/nature16544.

So instead of suggesting an earlier migration (it actually took place 1.8 Mya when Homo erectus left Africa for Asia) why not think about H. sapiens living in Eurasia and mixing with Neanderthals?

I wonder how this ties in with the Oldest Homo sapiens remains dating back to 315,000 years ago, found in Morocco?
 
Sources

(1) Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals, Cosimo Posth, Christoph Wißing, Keiko Kitagawa, Luca Pagani, Laura van Holstein, Fernando Racimo, Kurt Wehrberger, Nicholas J. Conard, Claus Joachim Kind, Hervé Bocherens & Johannes Krause. Nature Communications 8, Article number: 16046 (2017). doi:10.1038/ncomms16046.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2017 by Austin Whittall ©

Were Denisovans the last Homo erectus?

My previous post mentioned the new findings regarding Denisova admixture in Homo sapiens, and the two theories proposed to explain how Denisovan DNA spread between Austronesians and East Asians - Native Americans.

I believe that sooner or later we will find out that the elusive Denisovans are no others than Homo erectus. And I base my suspicions on two facts:

Erectus were alive in South East Asia about 40 kya. This was proved by Yokoyama Y, Falguères C, Sémah F, Jacob T and Grün R, in their paper (2008) Gamma-ray spectrometric dating of late Homo erectus skulls from Ngandong and Sambungmacan, Central Java, Indonesia. J Hum Evol. 2008 Aug;55(2):274-7. doi: 10.1016/j.jhevol.2008.01.006. Epub 2008 May 14., the team concluded that: "we establish[ed] minimum age estimates of around 40ka, with an upper age limit of around 60 to 70ka. This means that the Homo erectus of Java very likely survived the Toba eruption and may have been contemporaneous with the earliest Homo sapiens in Southeast Asia and Australasia..

The 400 ky Sima de los Huesos remains from Spain also hint at this. The mtDNA of the remains from this Spanish site was sequenced and found to be closer to Denisovan mtDNA than to Neanderthal ⁄ Human mtDNA. This is quite hard to explain: how did Denisovans get more of this mtDNA than the Neanderthals did considering that Denisovans are located in Altai while Neandertals are located in between Spain and Altai? The authors offer 4 explanations, and I believe that their fourth is correct: bold font is mine [1]

A fourth possible scenario is that gene flow from another hominin population brought the Denisova-like mtDNA into the Sima de los Huesos population or its ancestors. Such a hominin group might have also contributed mtDNA to the Densiovans in Asia. Based on the fossil record, more than one evolutionary lineage may have existed in Europe during the Middle Pleistocene. Several fossils have been found in Europe as well as in Africa and Asia that are close in time to Sima de los Huesos but do not exhibit clear Neanderthal traits. These fossils are often grouped into H. heidelbergensis, a taxon that is difficult to define, particularly with regard to whether the Sima de los Huesos hominins should be included. Furthermore, there may have been relict populations of still earlier hominins, notably those classified as Homo antecessor, which share some morphological traits with Asian Homo erectus and have been found just a few hundred metres away from Sima de los Huesos in Gran Dolina.

[1]

Home erectus left Africa (or maybe even originated out of Africa, in Asia from H. Habilis who had migrated earlier, and some of them returned to Africa later, generating the African erectus.) 1.8 Mya. They had plenty of time to move across Eurasia, fromm Indonesia to China to, why not?, Spain. Surely they originated more "modern" versions as time passed, the Homo antecessor and later H. heidelbergensis could be some of them. As well as Denisovans.

Maybe they even marched all the way to the New World.

Later, when modern H. sapiens moved into their territories they admixed, in varying degrees. This admixture must depend on the population ratios of migrants and residents. We have therefore a high content of Denisovan gene flow in Austronesia, and also in East Asia and the New World. But they may have been the result of separate admixture events.

Orthodoxy requires that the Humans marching into America be the result of a split that took place in Asia. And if these future Amerindians were the only ones to enter America, then they had to admix with Denisovans in Asia. But neat theories are not the way Nature works. The history of our genetic makeup is much more complex. And it may involve admixture in the New World, both with Neandertals and Denisovans

Sources

[1] Matthias Meyer, Qiaomei Fu, ,et al., A mitochondrial genome sequence of a hominin from Sima de los Huesos, Nature 505, 403–406 (16 January 2014) doi:10.1038/nature12788

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

Sima de los Huesos remains, Neanderthals, Denisovans and their nuclear and mtDNA

A very interesting paper published in Nature (Matthias Meyer et al.) has confirmed that the Sima de los Huesos remains, that are 430 ky old, have mtDNA that resembles that of Denisovans more closely than that of the Neanderthals. But, their nuclear DNA is more similar to that of Neanderthals than to Denisovan nuclear DNA.

Since the Sima de los Huesos hominins are supposed to be the ancestors of Neanderthals it is reasonable that their nuclear DNA is similar to that of Neanderthals and different from Denisovans. But why is the relationship regarding mtDNA exactly the opposite?

The paper offers three explanations:

1. The Sima de los Huesos people had two very diverging mtDNA types, one leading to Neanderthals the other to Denisovans, and these samples are of the first kind.
2. Some "other" hominin contributed its mtDNA to both Denisovans and Sima de los Huesos people
3. The original proto Neanderthal mtDNA was inherited by their Neanderthal descent but was completely diluted by later inflow of Neanderthal mtDNA from Africa, which we find in more recent Neanderthals.

In science, the breakthroughs come from finding the correct answer to discrepancies like these. So it is very exciting and who knows what will eventually be learned from this!.

Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall © 

Atapuerca Sima de los Huesos remains were closer to the Neanderthals

Four and a half years ago I posted about a site in Spain, known as Atapuerca (What Science is all about), in it, I mentioned two studies that came to different conclusions: one stated that the human remains there resembled Neanderthals, the other that they were closer to the Denisovans than to the Neanderthals.

Today I read a paper that was published on Nov. 30, 2018 and which states that the teeth of remains from Atapuerca's Sima de los Huesos site shows that they had a close relationship to the later Neanderthal groups found in Europe.

The paywall protected abstract says:

"Enamel and dentin patterns have awakened a considerable interest in phylogenetic studies. However, almost nothing is known about the dental tissue proportions of European Pleistocene hominins, apart from Neanderthal populations. This study aims to assess the three-dimensional dental tissue proportions of permanent canines belonging to the extensive sample of hominin teeth at Sierra de Atapuerca (Spain) through the use of microtomographic techniques. Our results show that early and middle Pleistocene populations from Atapuerca exhibit large coronal and root dentine dimensions, as well as a thinly enamelled pattern, which has been traditionally considered an autapomorphic Neanderthal trait. Therefore, these results might support an early enamel thickness decrease which is already observed 800 kyr ago in Homo antecessor and maintained in later groups such as Sima de los Huesos and Neanderthal populations during the middle Pleistocene."

This is important because it shows that the Sima de los Huesos remains had a close relationship with the Homo neanderthalensis.

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

HST and Scladina Neanderthals

A A recent paper by Stephane Peyregne et al., (Nuclear DNA from two early Neandertals reveals 80,000 years of genetic continuity in Europe, Science Advances 26 Jun 2019: Vol. 5, no. 6, eaaw5873 DOI: 10.1126/sciadv.aaw5873) looked into the mitochondrial DNA (mtDNA) of some ancient European remains and compared them to that of modern humans, Neanderthals and Denisovans.

What they found is indeed interesting, and unexpected.

The team sampled the remains of two Neanderthal people, which lived roughly at the same time (some 125,000 years ago), relatively close to each other in Western Europe: a male femur (thigh bone) discovered in the Hohlenstein-Stadel Cave, Germany, back in 1937 -this sample was named HST. They also analyzed a jaw bone belonging to a girl found in 1993 in Scladina, Belgium.

The mtDNA of the Scladina girl and the HST man, both from Western Europe, were most similar to the mtDNA of the Altai Neandertal (from the Altai region in Asia), 3,300 miles (5.300 km) west of Scladina and Hohlenstein-Stadel.

Their mtDNA was quite different from the mtDNA of later European Neanderthals that lived in the same region 80,000 years later.

HST and its unique mtDNA

The HST an carried mtDNA that was very different from that of all other Neanderthals, it had more than 70 mutations that distinguish it from the others' mtDNA. The bone was dated to approximately 124 kya. (62 to 183 kya), but its mtDNA split from that of other humans 270 kya.

The girl's remains are of a similar age: 127 kya (95 to 173 kya) but her mtDNA was more similar to that of an Asian Altai Neanderthal.

In fact both Scladina and the Altai Neanderthal grouped together in a branch of their own, with HST at the root and all other later Neanderthals on a separate branch.

The image below shows the branch that groups the Scladina girl with Atai Neanderthals and the HST Branch (inside the red square). As you can see, they are quite differentiated from that of all the other Neanderthals and Modern Humans (we are shown on the upper part of the diagram).

MtDNA of Neanderthals, Sima de los Huesos, Denisovan and Modern Humans

The fact that these three older Neanderthals are grouped together (see red square in image above) means that they share a common lineage of mtDNA; they all lived more or less at the same time (some 125 kya) and spanned a wide geographic area from the North Sea to the Altai in Siberia.

All more recent Neanderthals who lived roughly 40,000 years ago (green square in the image above) shared a common ancestor who lived some 97 kya, and belong to a branch that diverges from that of these three older Neanderthals.

These "modern" Neanderthals' mtDNA is derived from that of the "older" group.

The interesting part is that the Denisova Neanderthal (see "Denisova 11" in the image) which lived 90 kya in the Denisova cave in Central Asia, and is a hybrid of Denisovan father and a Neanderthal mother, has mtDNA which is closer to the more recent Neanderthals of Western Europe than to the Altai Neanderthal that lived in that same Denisova cave! 120,000 years ago.

This means that the ancient mtDNA of Altai Neanderthals was replaced by the "new" mtDNA shared by Denisova 11 and all other modern Neanderthals, so these later western European Neanderthals migrated east into Siberia and repopulated the Altai.

What about the Nuclear DNA?

The team looked into the nuclear or autosomal DNA of both Scladina and HST specimens and compared them with that of other Neanderthals.

They found that from a nuclear DNA point of view HST and Scladina were "more closely related to Vindija than they are to the Altai Neandertal". Vindija is a cave in Northern Croatia.

We see that all Neanderthals, old and recent share a common root for their nuclear DNA, but there are two branches: one with the Altai Neanderthal, and the other with all the other Neanderthals.

So it may be reasonable to suppose that all known Neanderthals (old and recent) share a common origin, and that it split as they migrated into Western Europe (HST and Scladina) and Siberia (Altain Neanderthals), this explains their branching.

Regarding the Atai Neanderthal, (see Prüfer K, Racimo F, Patterson N, et al. The complete genome sequence of a Neanderthal from the Altai Mountains, Nature. 2014;505(7481):43–49. doi:10.1038/nature12886) it was found to be (see Figure 2b in that paper) on the most diverged and basal branch within Neanderthal's nuclear DNA and therefore furthest away from the Vindjia specimens).

See image below, which I adapted from (here) and Fig. 2 of Peyregne et al.; it depicts the Nuclear DNA branching.

So we can imagine a very early migration of Neanderthals into Siberia (ancestral to Altai Neanderthal) who did not leave descendants.

The Western Neanderthal population (which included HST and Scladina) had settled Europe 125 kya and its descendants later migrated across Eastern Europe, entered Asia and settled in the Altai region replacing this eastern population in Asia.

The very odd HST mtDNA

The very divergent mtDNA carried by HST split from that of all other Neanderthals some 270,000 years ago. This is far older than expected by the team (they'd estimated less than 150 kya).

And they believe that this is due to the fact that "HST carries some ancestry from a genetically distant population.".

They propose two scenarios:

1. "Admixture between Neandertals and ancestors or relatives of modern humans could explain the origin of this later Neandertal mtDNA... If several mtDNAs were introduced into the Neandertal population by such a putative gene flow, then the deeply divergent mtDNA in HST may represent the remnants of the mitochondrial diversity of this introgressing population... This would imply that this admixture into Neandertals occurred later than the previously suggested lower boundary of 270 ka ago".
2. "An alternative source for the deeply divergent mtDNA in HST could be an isolated Neandertal population, for example, a population that separated from other Neandertals before the glacial period preceding HST and Scladina (~130 to 190 ka ago...). Such an isolated population may have preserved the mtDNA that was later re-introduced during a warmer period between 115 and 130 ka ago (the “Eemian” period) when these populations met again and gene flow resumed."

Discussion

I ask: Can we reasonably expect a group to remain in isolation for 15,000 to 75,000 years and maintain their mtDNA without mutations? This "isolated group"notion is identical to the Beringian Standstill Hypothesis which states that the humans who would people America remained isolated in Beringia for tens of thousands of years.

But the Beringian mutated while the isolated Neanderthals did not! This is weird, same situation and two different outcomes:

The Beringians suffered mutations that gave their descent, the modern Native Americans a distinctive mtDNA that is not found in Asia is said to have arisen during the "standstill": after their ancestors left Asia, but before they dispersed into the Americas.

Yet the isolated ancestors of the Neanderthals retained their original mtDNA without anyn mutations.

So in one case it is mtDNA "stasis" and in another "mutation". You can't have it both ways. One or other or perhaps even both theories are wrong.

In this context, the admixture theory seems reasonable, but why should we have to assume admixture? Let's read it in the paper's words:

"It seems unexpected that HST carries an mtDNA lineage that diverged ~270 ka ago from other mtDNAs, given the recent population split times from the Vindija ancestors and the low levels of genetic diversity in the nuclear genomes of Neandertals".

In other words, as their nuclear genome is very similar to that of the Vindija Neanderthals, who lived 80 ky later than HST, their mtDNA can't be 270 ky old.

They add:

"An explanation could be related to a replacement of mtDNAs in Neandertals that has been suggested to explain the discrepancy between the mtDNA divergence time (<470 ka ago) and the population split times based on nuclear DNA (>520 ka ago) between modern humans and Neandertals.
The Sima de los Huesos hominins, and perhaps other early Neandertals, carried mtDNAs that shared a common ancestor with Denisovan mtDNAs more recently than with those of modern humans, whereas later Neandertals carried mtDNAs that shared a more recent common ancestor with the mtDNAs of modern humans.
Admixture between Neandertals and ancestors or relatives of modern humans could explain the origin of this later Neandertal mtDNA".

We see that once again there is a discrepancy between mtDNA and nuclear DNA divergence dates, you'd expect both to be the same age. In this case it is 470 ky vs. 520 ky.

In a previous post on this subject (Sima de los huesos is now.... closer to Neanderthals than Denisovans!) I gave an explanation for this conundrum as follows:

The common mtDNA shared by Denisovans and Sima de los Huesos but not the nuclear DNA could be explained as follows:

• A native archaic population lives in Eurasia (descendants of H. erectus?) with its specific autosomal DNA and mtDNA; they are the ancestors of Denisovans and a pre-Sima de los Huesos people.
• A later wave of proto-Neandertal reach Europe, they are more successful and breed with the native women (kill the men and keep the women) of the native pre-Sima de los Huesos stock.

The original archaic mtDNA is preserved in their offspring -since it is transmitted by the mothers to their children-, but the nuclear DNA is now admixed with that of the proto-Neandertals.

After many generations we have a European lineage with mtDNA similar to the original ancient stock (Homo erectus?) and therefore shared with Denisovans, but a nuclear DNA which will be more like that of Neanderthals which were formed by this admixture.

A similar event must have taken place with the Neanderthals.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2019 by Austin Whittall © 

Neanderthal and Denisovans split around 750 Kya

This paper: Early history of Neanderthals and Denisovans, by Alan R. Rogers, Ryan J. Bohlender, and Chad D. Huff (PNAS September 12, 2017. 114 (37) 9859-9863; published ahead of print August 7, 2017. https://doi.org/10.1073/pnas.1706426114), has some interesting insights into Neanderthal diversity and population size. Below we quote from this paper

"Discussion
These results contradict current views about Neanderthal population history. For example, Prüfer et al. estimate that the Neanderthal population was very small—declining toward extinction. This view receives additional support from research showing elevated frequencies of nonsynonymous (and presumably deleterious) mutations among Neanderthals. This abundance of deleterious alleles implies that drift was strong and thus that population size was small. Yet our estimate of Neanderthal population size is large—in the tens of thousands."

So the authors find that the neanderthal population was large!. They then try to find common ground with other authors, adding:

"To reconcile these views, we suggest that the Neanderthal population consisted of many small subpopulations, which exchanged mates only rarely. In such a population, the effective size of the global population can be large, even if each local population is small. A sample from a single subpopulation would show a misleading signal of gradual population decline, even if the true population were constant. Furthermore, there is direct evidence of large genetic differences among Neanderthal populations. Finally, the rich and widespread fossil record of Neanderthals is hard to reconcile with the view that their global population was tiny. We suggest that previous research has documented the small size of local Neanderthal populations, whereas our own findings document the large effective size of the metapopulation that contributed genes to modern humans."

All of which makes perfect sense. They then address the timing of Neanderthal-Denisovan split:

"...As discussed above, our results also disagree with previous estimates of the Neanderthal–Denisovan separation time. On the other hand, Meyer et al. show that 430 ky-old fossils from Sima de los Huesos, Spain are more closely related to Neanderthals than to Denisovans. This implies an early separation of the two archaic lineages. Our own estimate—25,660 generations, or 744 ky—is earlier still. It is consistent with the results of Meyer et al. but not with those of Prüfer et al., as discussed above. The cause of this discrepancy is unclear. Prüfer et al. use the pairwise sequentially Markovian coalescent (PSMC) method, which may give biased estimates of separation times in subdivided populations..."

So they find a rather old (almost 750,000 years ago) split between Neanderthals and Denisovans.

In their introductory comments they mentioned some competing theories

"Around 600 kya, Europe was invaded by large-brained hominins using Acheulean stone tools. They were probably African immigrants, because similar fossils and tools occur earlier in Africa. They have been called archaic Homo sapiens, Homo heidelbergensis, and early Neanderthals, yet they remain mysterious. They may have been ancestors of Neanderthals and modern humans, or ancestors of Neanderthals only, or an evolutionary dead end. According to this last hypothesis, they were replaced later in the Middle Pleistocene by a wave of African immigrants that separated Neanderthals from modern humans and introduced the Levallois stone tool tradition to Europe."

Regarding the above, the authors write:

"Our results shed light on the large-brained hominins who appear in Europe early in the Middle Pleistocene. Various authors have suggested that these were African immigrants. This story is consistent with genetic estimates of the separation time of archaics and moderns. Our own results imply that, by the time these hominins show up in European archaeological sites, they had already separated from Denisovans. This agrees with Meyer et al., who show that the hominins at Sima de los Huesos were genetically more similar to Neanderthals than to Denisovans. It also agrees with Hublin, who argues that Neanderthal features emerged gradually in Europe, over an interval that began 500–600 kya."

And, they conclude:

"It appears that Neanderthals and Denisovans separated only a few hundred generations after their ancestors left the modern lineage. During the intervening interval, the Neanderthal–Denisovan lineage was small. After separating from Denisovans, the Neanderthal population grew large and fragmented into largely isolated local groups. The Neanderthal metapopulation that contributed genes to modern humans was much larger than the local population of the Altai Neanderthal fossil."

Denisovans admixed with Africans

Among their findings is corroboration of what we already know: "...yn is more common than xn —Neanderthals share more derived alleles with Europeans than with Africans. This suggests gene flow from Neanderthals into Europeans", and then, a startling finding: "More surprisingly, xd is more common than yd. The same pattern appears in all four combinations (YRI.CEU, YRI.CHB, LWK.CEU, and LWK.CHB) of African and Eurasian populations in our analysis. This pattern suggests gene flow from Denisovans into Africans..." (bold mine). This is unexpected: Denisovan admixture into Africans! Maybe it reflects an Out of Asia episode into Africa...

The fact that the Neanderthals were a large population split into sub-groups is very interesting because it is the opposite to what has been widely proclaimed until now: that they were a small, inbred group on the verge of vanishing when they mingled with modern humans...

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

An earlier Human - Neanderthal split? (400,000 years earlier!)

Aida Gómez-Robles published a paper in Science Advances three days ago (May 15, 2019 - Dental evolutionary rates and its implications for the Neanderthal–modern human divergence, Vol. 5, no. 5, eaaw1268 DOI: 10.1126/sciadv.aaw1268) in which she finds evidence that "support[s] a pre–800 ka last common ancestor for Neanderthals and modern humans unless hitherto unexplained mechanisms sped up dental evolution in early Neanderthals".

This is really remarkable, as it pushes the conventionally accepted date of divergence back in time from 400 to 800 thousand years ago.

This far older age was worked out by studying ancient Neanderthal teeth from the Sima de los Huesos site in Spain.

Gomez-Robles compared fossilised teeth from archaic hominins such as Australopithecus afarensis, Australopithecus africanus, Paranthropus robustus, Paranthropus boisei, and ancient ones such as Homo habilis, Asian specimens of H. erectus, a Sima de los Huesos H. neanderthalensis and of course, us: Homo sapiens, Other Neanderthal teeth from different sites in Europe were deliberatel left out of the comparative study.

The idea behind the comparison was to see how the shape of teeth in hominins changed over time. Gomez-Robles found that they evolve, and do so at a steady pace. This let estimate when each of these species split from each other.

The conclusion: "The simplest explanation of the results presented in this study is that Neanderthals and modern humans diverged before 0.8 Ma ago", our Last Common Ancestor (LCA) with Neanderthals dates back to 800,000 years ago.

Gomez-Robles goes on to spell out the implications of this more ancient split:

" If the phenotypic LCA of Neanderthals and modern humans was older than 800 ka, this would imply that all fossil hominins younger than this age are no longer valid candidates to occupy this ancestral position. Some fossils younger than this age, however, are frequently considered to be part of the last common ancestral species to Neanderthals and modern humans. These fossils, usually ascribed to Homo heidelbergensis, include European and African specimens, such as Mauer, Arago, Petralona, Bodo, Kabwe, etc., and maybe even some Asian specimens. If Neanderthals and modern humans diverged earlier than 800 ka ago, then all these fossils have to be related either to Neanderthals or to modern humans, or they can be part of a sister lineage to both of them. These fossils, however, cannot be ancestral to Neanderthals and modern humans because they would postdate their evolutionary divergence. An evolutionary relationship between these fossils and both Neanderthals and modern humans would be possible only if they were part of an older ancestral species that persisted in time as a relic species after the actual split of both lineages. Effectively, this scenario would mean that the H. heidelbergensis fossils are part of a sister group to Neanderthals and modern humans but that the evolutionary change from their putative ancestral populations did not involve speciation."

Of course, there are confounding factors that can explain the structural differences in teeth without requiring such an older age, for instance: the teeth evolved quicker in a small population of Neanderthals, isolated from other human groups, making them seem older while they are actually only 400 Ky old.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2019 by Austin Whittall © 

Neanderthals actually came from Human Beings! (March 2026 paper says)

A very interesting suggestion was prepublished on March 13 in Biorxiv by David Reich, 2026, it is work in progress, and a model, but its title tells it all: Hypothesis: A modern human range expansion ~300,000 years ago explains Neandertal origins.

Trying to explain why the split date between the human lineage and Neanderthals differs when you consider nuclear DNA (765-550 kya) or mtDNA (365-400 kya), or why the original Y chromosome of Neanderthals appears to have vanished, and what we have found is so similar to ours, and that their mtDNA is remarkably similar to ours, Reich suggests that they are a population that arose from modern humans introgression with archaics in Europe. This also explains some incongruent dates and other oddities found in the Atapuerca Sima de los Huesos remains. Simple hypothesis that is very similar to the proposal maed by Cosimo Posth published in Nature, which I commented in a post back in 2017 (An even older Out of Africa event (270kya)!!). Posth suggested that African inflow was "responsible for providing the mtDNA to the Late Pleistocene Neanderthals might have been an even earlier Middle Pleistocene gene flow from Africa, occurring in a time interval that we date between 413 and 268 ka... The temporal corridor for this introgression event between 460 ka and 219 ka is compatible with the evidence of archaeological similarities between Africa and western Eurasia during the Lower to Middle Paleolithic transition39 and potentially may explain the dissimilarities in Middle Paleolithic industries between eastern and western Eurasia. Environmental changes across this time span might have facilitated a hominin expansion out of Africa and potentially spread cultural innovations such as the Levallois technology into Eurasia." Reich developed the concept. Below is the Abstract of Reich's paper

"Abstract.
This paper demonstrates the feasibility of the hypothesis that Neandertals formed when a population using recently developed Levallois stone tool technology expanded between 400-250 thousand years ago (ka). In Europe, their range expansion into an area with Sima de los Huesos-like people led to massive introgression of local archaic genes producing a population with around 95% archaic ancestry (Neandertals); if this range expansion was sex-biased it would provide a simple explanation for why Neandertals retain modern human lineage Y chromosomes or mitochondrial DNA. In Africa, interbreeding with local archaic humans led to more modest archaic admixture and the deep substructure detected in all modern humans today. This proposal explains four previously perplexing similarities of modern humans and Neandertals—sharing of mitochondrial DNA, Y chromosomes, Levallois tools, and 300-200 ka date of formation by mixture—even while Neandertals and Denisovans cluster genome-wide."

This is the paper: Hypothesis: A modern human range expansion ~300,000 years ago explains Neandertal origins David Reich. bioRxiv 2026.03.11.711219; doi: https://doi.org/10.64898/2026.03.11.711219.

This paper is interesting because it also mentions humans mixing with archaics inside of Africa, a source of diversity:

"... ancestors of all modern humans including sub-Saharan Africans were deeply substructured, due to the coming together a few hundred thousand years ago of lineages that began diverging a million or more years ago. For example, ref. 16 models modern human ancestry as largely derived from a mixture of about 80% from a lineage that was most closely related to Neandertals and Denisovans, and 20% from a lineage that diverged from it around 1.5 million years ago, with the two coming together around 300 ka. The remixture is estimated to date to around the same time as the genetically inferred interbreeding of modern humans and archaic humans in the ancestors of Neandertals 300-200 ka. This raises the possibility that these mixtures in Europe and Africa had related causes: a range expansion of a successful population interbreeding with local archaic groups. In Europe, there was massive introgression of local genes because barriers to producing viable offspring were few. In Africa, the mixture was with a more divergent archaic lineage, result in a lower γ (cross-group interbreeding rate), and less introgression..."

This is the reference "ref. 16" cited above: Cousins T, Scally A, Durbin R, (2025) A structured coalescent model reveals deep ancestral structure shared by all modern humans. Nat Genet 57, 856–864.

Comments

I am surprised at the different conclusions that the same datasets of human genes and fossils produce (some are mutually exclusive): humans and Neanderthals are the same, humans and Neanderths split after the Denisovans split, Denisovans and humans split after the Neanderthal split, dates that range from 500 to over 1 million years, introgressions all over (Denisovan to Neanderthal to Human, Human to Neanderthal, Denisovan to Human, one or more lineages of superarchaics introgressing into different hominins). Surely they can't all be right.

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

What Science is all about

A micro mini post

The latest paper on Neanderthals is one dealing with crania found at the Sima de los Huesos site in Atapuerca, Spain: Seventeen skulls were pieced together and showed a mixture of archaic and Neanderthal features. These people, were the ancestors of Neanderthals (maybe not their direct ancestors, but somewhere in their past!). They were dated to 430 kya.

But this brought to my mind another paper on Sima de los Huesos, which sequenced DNA from a 400 kya specimen (maybe one of those mentioned above), and found that they were closer to the Denisovans than to the Neanderthals!.

So one paper says the Atapuercan remains are ancestral to Neanderthal, and another says they are closer to Denisovans than to Neanderthals...

This brings me to the title of this post: science is built on discrepancies, on conflicting data. They have to be explained in a clear and rational manner that satisfies all the evidence. I expect more will come from Atapuerca and it will help us understand our human past better.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 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 © 

A critical post on the current methods of genetics when applied to human ancestry

If you have been reading my posts over the last couple of years, you will notice that time and time again I write about the "early peopling of America". The reason for this is, one one hand, because I believe that our ancestral relatives, either Homo habilis, Homo erectus or even the Neanderthals reached the New World long before the 30 - 15 kya window currently accepted by orthodox mainstream science as the date of arrival of modern humans to the Americas. I also believe that H. sapiens reached America much earlier than that date. However, proof in the shape of stones and bones is lacking, or if produced, is dismissed as geofacts (for the tools) or poorly dated. I have the hunch that Acheulian or Mousterian tools are not even found because nobody is on the look out for them as would be the case in the Old World.

Why do I investigate the early peopling of America?

My original objective for looking into archaic humans in America arose from the intriguing posibility that extant populations of these hominins could have survived until recently in the Americas and been the origin of Native American myths regarding wild men, ogres and bigfoots across the continent. The recent survival of the Flores Island hominin is proof that such an idea is not absurd. Unfortunately we have no proof yet, that any of those hominins ever reached the New World.

My dismay regarding research and a Critique

Being an amateur in this subject, I decided to look into the different findings, sites, dates, the pattern of human migrations, the current ideas regarding the evolution of our species and the hard, solid and factual evidence that is behind the current consensus among scholars that dedicate their lives to study these matters.

My research into these matters, with the open mindeness of a person well read in science, with a University degree in engineering and a sceptic but questioning mentality has opened my eyes to the methods of geneticists and archaeologists. Methods which are often surprising becaus they are unquestioning regarding the evidence they base research on. Some papers are based on educated guesses or cite papers which cite other papers that do the guessing and therefore appear well backed by research and proven by peer review.

Most papers on ancestry and haplogroup datings or admixture between modern and archaic humans are dense models based on computer run simulations with pages of statistical formulae and probabilistic assumptions (mutation rates, migratory events) and equations dredged from previous papers, cited again and again. Seldom are these basic axioms questioned or scrutinized with an impartial approach.

Taking all of the above into account it is very logical to assume that they will all produce similar scenarios supporting the currently prevailing Out of Africa theory.

The model of an Out of Africa migration of modern humans, after they evolved in that continent, and then dispersed across the globe, replacing previous migrants without leaving trace of them has evolved since its inception in the early 1990s, was based on weak premises. But it was acclaimed by all and has adapted: it now admits introgression and admixture with archaic hominins in both Africa and Eurasia (though their mtDNA and Y chromosome haplogroups have vanished without a trace but not so their autosomal DNA-funnily nobody really sees this as unusual...). The African origin theory goes mainly unquestioned.

A dissident Voice against "Out Of Africa"
By the way, there is an excellent paper criticising the Out of Africa theory focusing on many of the things that I have pointed out in some of my previous papers: self-fulfilling circular-logic papers where data is bent or tinkered with to prove something (i.e. calibrate a clock based on a date arising from archaeology and then, via complex genetic inferences and hand-picked data, reach that same date and wield it as proof.
It is a very interesting paper and I recommend reading it: Anatole A. Klyosov, (2014) Reconsideration of the “Out of Africa” Concept as Not Having Enough Proof. http://dx.doi.org/10.4236/aa.2014.41004 Advances in Anthropology 2014. Vol.4, No.1, 18-37 February 2014

The Chinese view of the world OOC

I have also come across some Sino-centric papers written by Chinese scientists at Chinese Universities which seem to promote an Out-Of-China origin of modern humans (Well, after all, Chinese invented the compass, paper, the printing press and gunpowder so it is natural to assume that modern humans come from China too). The story goes something like this: [1]

Our darkest and deepest ancestors appeared in Africa, but soon dispersed: H. habilis moved into Asia (Georgia, Sundaland and Nihewan, China), followed later by H. erectus. The latter evolved in Lantian in China to produce H. yunxianensis which back-migrated to West Eurasia 600 kya and originated H. heidelbergensis and later, the Neanderthals. They also trekked back into Africa, where they were the ancestors of H. rhodesiensis and ultimately the Homo sapiens in Africa, replacing in the process the hominins that had evolved in Africa and Europe (H. leakeyi and H. antecessor respectively).

The hominins in China in the meantime kept on evolving, originating archaic humans in China (H. mapaensis in the South and H. daliensis in the North) some 400 kya. The modern H. sapiens left Africa 120 kya and intermixed with the archaic Eurasians in China and India. They were followed by modern H. sapiens 60 kya which kept on admixing and this "led to the emergence of fully modern Chinese hominans by approximately 35,000 ya." [1]. I rest my case.

Please don't misinterpret me; I have nothing against China or science in China, what is more, I do agree on a dynamic model of human evolution with migrations and introgressions, and even with an Eurasian origin of mankind.

The current one with isolated branches either evolving into other hominins or dying stunted is too linear for me. There is no doubt that the branches criss-cross and merge, but the OOC (out of China) theory is a bit too much for me, lacking as it does, solid proof.

An example of Sino-centrism is a recent paper on the sequencing of the DNA from the Tianyuan remains (allegedly 40 kya, but younger according to others). The bones, from a site close to Beijing, China, show a moisaic of modern and achaic features. However its DNA admixture with Neanderthals is similar to current-day populations in the region (and it has no Denisovan genes). The Sino-centric part comes when the paper claims that its mtDNA is "ancestral to present-day haplogroup B" [2], insinuating that it is the "root" of all Amerindian and South East Asian humans belonging to hg. B. Placing a Chinese origin to the dispersal of these people. But we know that this haplogroup arose in West Asia, in the Caucasus, 50 kya, and not in China 10 ky later.

The findings are interesting: admixture if it happened took place long before 40 kya (otherwise Tianyuan would have more Neander or Denisovan admixture since it had less time to dilute). The Phylo Tree.org site indicates that the nucleotide mutations place it in the B6 haplotype within R11'B6 [3], which has a more regional distribution than the other B lineages spread across America and Asia:

• R11'B6 (occasionally also in Japan and South Asia)
  
  • R11 (recorded in Hainan but not in Laos.)
  • B6 (Centred on South China. Recorded in Laos but not in Hainan. )

By the way, the paper explicitly mentions in the mtDNA sequence, a long deleted block at positions 8281-8289 (this is the famous 9bp deletion), which if you search for it in the Phylo Tree page above will turn up 4 times! Meaning it is not so uncommon or perhaps that it is ancestral and the haplogroups should be reviewed to accomodate it in a better way. This is an interesting marker and will be scrutinized in future posts.

Surviving Homo erectus

Despite my misgivings, I do find some papers very interesting, like the one that claims that Homo erectus survived until very recently in Northern China [4]:

The Lantian site, close to Xi'an (renown for its imperial tomb with hundreds human-sized terracota warriors) has unveiled stone artifacts of a clear Acheulean technology. The site is located on the terraces of the Bahie River and its toolage has been dated to the period between 70 and 30 kya. (Wang et al., 2014) [4].

This relatively modern dating (and the type of tools, which includes hand-axes), implies that Homo erectus was alive in the Lantian region "from the early and middle Pleistocene to the later period of the late Pleistocene" [4].

There is also a paper [5] (more below) that hints at a recent introgression, in Africa between archaic humans and modern ones some 37 kya. These archaics had split from our line between 700 and 2,100 kya, meaning they could be any hominin from H. erectus onwards.

But, except these two papers, Homo erectus is seldom mentioned in any of these papers concerning admixture; they are regarded as a dead end, perhaps extinct by the time modern humans reached East Asia. Not many follow up on the clues on the possible admixture from H. erectus into modern humans, as suggested by Prüfer et al., 2013 [6]: that Denisovans carried an introgression from an archaic hominin that split from our line over 1 Mya. (H. erectus perhaps?).

(Well, some do follow up, sort of, as you will see below in point 3 or 4)

And the possibility of H. erectus entering America, migrating across Northeastern Asia is, of course, completely ignored (excuses given: too dim witted to deal with the cold Arctic conditions, not able to navigate, etc.).

Competing Theories are good for Science

But, fortunately for Science, new ideas appear, and they are analysed from different points of view and with different tools; this is good for science and for the advancement of our knowledge.

It seems that almost everyone now agrees that there was admixture between Neanderthals and Modern Humans (While not too long ago -see Herrera et al., 2009 [7], there were serious doubts and scepticism regarding admixture). Then we have the mysterious Denisovans whose genome is found in high proportion of Melanesians and Papuans but not among South East Asians.

We are know asking: Who admixed with who? did Africans admix with Neanderthals? What is the degree of all this admixture?

And the answers differ and even have opposite points of view, as we can see below (from a very small sampling on the matter), and from these differences, Science will grow stronger:

1. Neanderthal DNA Only in Europeans: 3.6% introgression in Europeans with a decreasing cline as you move away from Europe. Neanderthal genes in Africans' (as well as Denisovan presence in Melanesians and Papuans) is not due to admixture but to "the retention of ancient mutations in these populations" [8], that is, the archaic genes survived in them -but, may I ask, why did they disappear in Europeans?
2. 40% More Neanderthal DNA in East Asians (9.6%) than Europeans (6.4%). The Maasai of East Africa have a small but significant fraction of Neanderthal DNA but not through direct contact with them, but with Eurasians humans carrying Neanderthal DNA in them; a "Back into Africa Migration".
   Admixture with Neanderthals happened at least twice or, over a long period of time 50,000 to 80,000 ya., with Europeans splitting off first and therefore being less exposed to Neanderthal genes. [11]
3. Archaic admixture in Africa: "African populations contain a small proportion of genetic material (~2%) that introgressed ~35 kya from an archaic population that split from the ancestors of anatomically modern humans ~700 kya.... [which] introgressed into modern Africans from a now-extinct taxon that may have lived in central Africa." [5]
   This study sets the split between our line and the "archaics" at 1.25 Mya (95% CI, 0.7–2.1 Mya) and an admixture time of 37 kya (95% CI, 1–137 kya). Note the very very large Confidence Intervals. [5]
   When CI are large, I begin to wonder about the soundness of the statistical tools used...
4. Not one, but many introgressions. This one is interesting; it finds "introgressions from two unknown archaic hominins whom diverged with modern humans approximately 859 and 3,464 thousand years ago. The latter unknown archaic hominin contributed to the genomes of the common ancestors of modern humans and Neanderthals. In total, archaic hominin introgressions comprised 2.4% of Eurasian genomes" [9]
   These episiodes of admixture are shown in the image below. The "E" hominin may be H. erectus or even "australopithecines, which inhabited Africa; it was proposed that those hominins might have migrated out of Africa at ~3 Mya" [9]. Note however that "E" does not admix with modern humans either in Africa or Asia, it is an indirect influx via Neanderthals or the unknown X hominin (E_N + N or X arrows) or an admixture with the pre-OOA humans (E_A arrow), which takes us to the case proposed in point 3 of an introgression in Africa.

Figure 3, from [9]

This last paper is interesting but we don't see an admixture between H. erectus and humans in Eurasia, only indirect introgression via Neanderthals or X hominin. In this context, the mtDNA extracted from the remains of Sima de los Huesos, Spain, belonging to a Mid Pleistocene H. heidelbergensis about 300 ky old. may give some clues:

It shows that these archaich Spaniards shared descent with the Denisovans, implying that the Denisovans of Altai and the Sima de los Huesos people formed a clade with a common ancestor some ~800 to 900 kya, which is not the same ancestor of Neanderthals and modern humans. [10]

Could this ancestor be H. erectus who had been in Eurasia for nearly 1 My at that time? or the descendants of Georgian H. habilis? Is there any other candidate from out of Africa at that time?

Interestingly we have the H. heidelbergensis in East Europe which must have extended its range or even migrated into Western and Central Asia to originate our mysterious Denisovans. Did this happen before the appearance of the Neanderthals in the Middle East? or did they overlap?

Now if Neanderthals did not originate from the European H. heidelbergensis as thought until now, where did they evolve? In the Levant, and migrated from there into Europe and West Asia?

Regarding the genesis of these clades, notice that we see very deep splits between mtDNAs not in Africa, but in Eurasia: so much for the OOA. But then, these are mtDNA lineages, what do the autosomal and the Y chromosomes have to say, we have no input yet. But it will be interesting when we do.

And these questions, the migrations and admixtures of our ancestors, take me back to a post (First Asians were not H. erectus) (Sept. 2011), where I mentioned the initial departure of H. habilis from Africa for Georgia in Asia. The image below is an update of the original one from that post.

Hypothetical routes of our ancestors out of Africa. Copyright © 2014 by Austin Whittall

The paths drawn above start with an Out of Africa event, long ago: H. habilis leaves Africa, reaches Asia where it evolves into H. erectus. Some H. habilis reach Indonesia the ancestors of Flores hominin, others may have reached America. The H. erectus cross Europe becoming the ancestors of the Sima de los Huesos people, and also re-enter Africa and they go East too, into South Asia and China. Some march on, into America. The Afro-European hominins evolve into Neanderthal, the Eurasians (now it seems that it is the H. heidelbergensis of Europe) into Denisovans.

They all admix as they criss cross their territories. Somewhere (Africa? Asia? or why not, America?) modern humans appear and also mix with the surviving archaics.

This possible story outlined above, is of course a wild conjecture, with no proof to back it. A fancy tale.

But who knows, maybe if I phrased it using formulae with Greek letters (θ, ρ and so on,) framed with obscure statistical phrases ("the likelihood function f(γ), describing the probability -p(x,y,n)- of the data under different parameter values; and f(z) is the total probability of the data summed and integrated over the parameter space considering a bias scatter ratio in the Bayesian inference based on the...") and ran a Computer program to validate it ("We then ran (n=1,000) simulations on GATACCA® using 150,000 ARGs for each parameter value, storing approximations of the summary statistic distribution, discarding outliers below conformed threshold ratios...")... would someone buy it?

Mind you I am an engineer with a solid foundation in statistics, advanced maths and am particularly fond of quantum mechanics but in all honesty, most genetics papers nowadays are based on statistical simulations.

And we should not forget that simulations are only as robust as the models they are based on, and models tend to oversimplify reality using assumptions that may or may not be correct. The ample confidence intervals informed in many papers is a clear indication of uncertainty in the models and the variability within the sample employed.

Other factors such as migrations influx, population sizes and growth, generation duration and mutation rates also impact on the models' predictions. Explaining anomalies away aducing bottlenecks, founder effects and genetic drifts is like invoking ether for light transmission in the pre-relativity days of modern physics. Predictions should be made and validated by the models to prove reliability.

Thanks for bearing me out!

Sources

[1] Dennis A. Etler, LI Tianyuan, A Multiple Dispersal Hypothesis for Interpreting the Pattern of Hominan Evolution in China
[2] Qiaomei Fu, et al., (2012). DNA analysis of an early modern human from Tianyuan Cave, China. PNAS vol. 110 no. 6 2223–2227, doi: 10.1073/pnas.1221359110
[3] van Oven M, Kayser M., (2009). Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30(2):E386-E394. doi:10.1002/humu.20921. http://www.phylotree.org/
[4] Shejiang Wang et al., (2014). Newly discovered Palaeolithic artefacts from loess deposits and their ages in Lantian, central China. Chinese Science Bulletin Jan- 2014. 10.1007/s11434-013-0105-5
[5] Michael F. Hammer et al., (2011). Genetic evidence for archaic admixture in Africa. PNAS. vol. 108 no. 37 15123–15128, doi: 10.1073/pnas.1109300108
[6] Prüfer K.,et al., (2013). The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505: 43-49.
[7] Kristian J. Herrera et al., (2009). To what extent did Neanderthals and modern humans interact?. Biol. Rev. (2009), 84, pp. 245–257. doi:10.1111/j.1469-185X.2008.00071.x
[8] Lowery RK et al., (2013). Neanderthal and Denisova genetic affinities with contemporary humans: introgression versus common ancestral polymorphisms. Gene. 2013 Nov 1;530(1):83-94. doi: 10.1016/j.gene.2013.06.005. Epub 2013 Jul 19
[9] Ya Hu, et al. (2014). Genome-wide Scan of Archaic Hominin Introgressions in Eurasians Reveals Complex Admixture History. arXiv preprint arXiv:1404.7766
[10] Matthias Meyer et al., (2013). A mitochondrial genome sequence of a hominin from Sima de los Huesos Nature (2013) doi:10.1038/nature12788
[11] Jeffrey D. Wall et al., (2013). Higher Levels of Neanderthal Ancestry in East Asians than in Europeans. Early Online February 14, 2013, doi: 10.1534/genetics.112.148213 Genetics May 1, 2013 vol. 194 no. 1 199-209

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall © 

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

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

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

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

A very early split with a different sequence to it

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

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

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

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

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

Implications

Neanderthal Dispersal

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

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

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

Graphical abstract . Qiang Ji et al., 2021

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

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

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

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

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

Denisovans

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

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

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

Humans

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

The Gap in the fossil record

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

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

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

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

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

Middle Eastern Origin of Modern Humans

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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