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 © 

Ancient split between Homo sapiens and Homo Longi clades: 1.325 Ma

Today's post looks into a new paper published a few days ago, on September 25, 2015 in Science, (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)

Th Yunkian 2 skull, Hubei Provincial Museum. Image credit Gary Todd

The authors restored and rebuilt an ancient skull, the Yunxian 2 cranium that had been distorted and compressed. They found that this cranium shows a mosaic of archaic features that " suggest that it is an early member of the Asian H. longi clade, which includes the Denisovans and is the main part of the sister group to the H. sapiens clade. Both the H. sapiens and H. longi clades have deep roots extending beyond the Middle Pleistocene and probably experienced rapid early diversification. Yunxian 2 may preserve transitional features close to the origins of the two clades."

The Yunxian 2 cranium is ancient -0.94 to 1.10 million years (Ma)- and the authors suggest it is close to the last common ancestor to the Homo sapiens and the Homo longi clades, one in Africa and the other in Asia.

This is a major shift in our current knowledge. This specimen pushes the split between modern humans and other hominins further back in time to 1.325 million years ago. The split between these two clades and Neanderthals is also pushed back in this paper to 1.379 Ma.

Hominin phylogenetic tree. From the article in Science

The tree above shows archaic hominins (top) followed by the Neandrthal, H. longi and H. sapiens clades.

Over the next few days we will be posting about the complex panorama of ancient humans in Southern, Eastern and Southeastern Asia.

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

John Hawks on the Misliya jawbone

Below I quote John Hawks on the importance of the Misliya cave jawbone. His opinion is very interesting. Read his full post here.

(See my Previous post on this jawbone, which places modern humans outside of Africa some 177,000 to 194,000 years ago, far earlier than previously thought).

Hawks wrote:

"...There is a major change underway in how we understand “out of Africa”. I don’t think the traditional framing of “out of Africa” is very effective anymore, as leaving Africa is a tiny event, repeated many times over the last several hundred thousand years.
In the context of other discoveries, I think that “modern human” has lost much of the meaning it may once have had.
The big questions concern what was happening inside Africa, where many genetically diverse populations existed and interacted. How many ancestral populations gave rise to the growing population of modern humans after 100,000 years ago? How many African-derived people were involved in mixture with Neandertals 250,000 years ago, or 120,000 years ago? Did African-derived humans make it to China, or to Java, before 100,000 years ago?
Those are open questions, with some evidence pointing toward faster, more widespread dispersal, more mixture, and repeated genetic replacements."

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

An intersting paper on the NON AFRICAN orign of mankind

Seems it is an Out of Asia after all...

This is a very interesting -at least it goes against the grain of most orthodox papers, positing an out of Asia orign of mankind- paper: WORLD SCIENCE EN ROUTE FROM OUT-OF-AFRICA TO OUT-OF-AMERICA: FIRST STOP IS OUT-OF-ASIA.

By the way, Happy 2017!! I have the feeling that this year will bring us surprises galore, and not only from some Neanderthals (with my apologies to our great and dignified ancestors) who have recently taken up their lodging in Washington DC.

May reason, sensible discussion of ideas, open-mindedness and above all, Western values such as respect, freedom to dissent, freedom of religion, thought and above all, freedom of speech, prevail above any populist sleazy politicians and their demagoguery. On both sides of the Anglo-Saxon Atlantic (i.e. Brexit supporters). Respect, chivalry and rationality must prevail over bigotry, prejudice and Medieval witch-hunting. Racism belongs with the 1940s fascists, not in the XXIst century.

And if you post any insidious comments I will publish them even if I disagree -of course-, no foul language please.

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

HPV16 and Humans, Neanderthals, Denisovans and the Out Of Africa theory

Short comment. I have just read this paper: Transmission Between Archaic and Modern Human Ancestors During the Evolution of the Oncogenic Human Papillomavirus 16 by Ville N. Pimenoff, Cristina Mendes de Oliveira and Ignacio G. Bravo. Mol Biol Evol (2016), doi: 10.1093/molbev/msw214, First published online: October 7, 2016.

I am trying to see how it fits in with a non African origin of mankind because the authors are trying to fit their finding that the oldest and most diverse haplogroups of HPV 16 are not found in Africa, but out of it (the African variants of HPV are newer and less diverse) within the Out of Africa theory. And it may not be the case.

Above a map showing distribution of the main clades and below. Some quotes from the paper:

"HVP16A (fig. 2) (is), the most basal HPV16 lineage, in all continents and in all indigenous populations, except in sub-Saharan Africa"

"Moreover, for indigenous populations in South America, for instance, the increased presence of HPV16A lineage variants has been proposed to reflect the influence of recent European occupation (Picconi et al. 2003). However, such a rapid selective sweep of the putative pre-Columbian HPV16 genetic diversity would require strong selection forces for the viral dynamics in very short time scale, which are not compatible with our current understanding of PV evolution"

These Amerindians always have some oddity regarding their genetics, don't they?

"...most common HPV16A lineage haplotypes were observed mostly in Eurasian populations while most common HPV16B, C and D lineage haplotypes were observed mainly in African populations...
Neanderthals/Denisovans may have carried essentially the ancestral HPV16A. Evolution of HPV16 genomes in ancestral Hominin populations remaining in Africa, instead, would have lead to HPV16B and CD lineages (fig 4). The virtual absence of HPV16B outside Sub-Saharan Africa is parsimoniously explained if in the last out-of-Africa expansion, the modern human ancestors that left Africa probably lost the ancestral HPV16B lineage by a lineage sorting event ..."

And the above is the theory put forth by the authors to explain the anomaly of less diverse HPV in Africa vs. the Rest of the World.

"After the modern human dispersal, the HPV16CD ancestor generated in allopatry the HPV16C lineage in the populations remaining in Africa, and the HPV16D lineage in the populations outside Africa (fig. 4). During their expansion in Europe and in Asia, modern human ancestors experienced limited admixture with Neanderthal and Denisovan populations, and were exposed to the HPV16A lineage, most likely through sexual contact..."

But this is all conjectures, there is no physical evidence of HPV in Denisovans or Neanderthals:

"... there is hitherto no evidence of the presence of any PV sequences from ancient human samples. Indeed, we analysed the currently available Neanderthal and Denisovan pre-assembly sequence data, and we could not find any significant traces of any known HPVs in these data sets"

"... that the HPV16A1-3 lineage predominated in Europe, South Asia and Central/South America, and was also present in all other continental subgroups, albeit with very low prevalence in sub-Saharan Africa (fig. 2). HPV16A4 was the most prevalent lineage in East Asia and was also present in North America, but was virtually absent elsewhere. Variants B and C were largely restricted to Africa and were especially prevalent in Sub-Saharan Africa, although they were also observed in North America. Variant D was present in all continents, displaying low prevalence in Sub-Saharan Africa, and the highest frequency in Central/South America.·"

Why is "D" highest in the Americas if it is supposed to have originated in Africa (see further up)... slave trade by Europeans? We'd need to see Karitiana or Coya, Pima haplogroups...

Then we have the time frame!! (rather wide): "Depending on substitution rate priors, divergence times of extant HPV16 lineages showed to be between 260 kya and 4.8 Mya"... early enough to be older than our oldest relatives. It may also leave the window open for an Homo Erectus migartory event into Asia carrying the ancestral HPV16A root. And the diversity issue also seems odd: "Although HPV16A was thus always the basal clade, divergence within HPV16A showed to be lower than within HPV16BCD" So the oldest group with A type haplos are less diverse among them than the BCD are.. maybe some ancient bottleneck in the A groups?.

And the diversity again: " East Asian and Central American HPV16 isolates showed higher average number of pairwise differences compared with sub-Saharan African isolates, even after accounting for intralineage diversity.", what? something in America more diverse than in Sub-Saharan Africa... why?

"... although HPV16A is the oldest lineage, the tmrca for the HPV16BCD variants (197kya, 95% 121-291kya) was older than the tmrca for the HPV16A lineage (88kya, 95% HPD 50 – 134kya), and the HPV16A lineage encompasses less genetic diversity than the sister HPV16BCD lineages." This is odd, again the diversity issue (bottleneck) but the split is younger in the "oldest" lineage?? That sounds odd.

I will keep on trying to make sense of this, and post later on this finding.

New 03 Nov. 2018, following a recent paper published two days ago, I have added a new post on this subject: HPV Neanderthals, Africans and the early peopling of America

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

An even earlier Out Of Africa 2.6 MyA.

A very early out of Africa may have taken place if the paper by Anne Dambricourt Malassé et al., Anthropic activities in the fossiliferous Quranwala Zone, 2.6 Ma, Siwaliks of Northwest India, historical context of the discovery and scientific investigations (Comptes Rendus Palevol, doi.org/bb7c) is correct.

Though it is behind a paywall, the abstract clearly states that: "This paper presents the historical context and the rigorous scientific process, which has led to the acknowledgment that some bones, dating back to the Latest Pliocene, present intentional and precise cut marks made by sharp edges in quartzite and an intelligence, which knew the anatomy of the bovid carcasses. Our pluridisciplinary works support anthropic activities 2.6 Ma ago in the sub-Himalayan floodplain and the probability of finding hominin fossils in the Quranwala Zone. ".

Now 2.6 million years ago is long before any Homo erectus moved out of Africa (their oldest Asian remains have been dated at 1.8 Ma). Or perhaps they did migrate but much earlier. Or were their predecessors, the Homo habilis the first to leave Africa. Perhaps the H. habilis evolved into H. erectus in Asia and these back migrated into Africa...

The point is that this site in Siwalik hills is about 300 kilometres north of New Delhi, India, well in the heart of Southern Asia, and it is a clear indication that human origins are much more complicated than we once believed.

Also, it gives us about 1 million additional years for those archaic people, to reach America...

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2016 by Austin Whittall © 

Language diversity and the peopling of America

For years I have wondered why do Native American people speak so many languages? They supposedly reached the New World recently (i.e. 15,000 years ago) yet evolved over 40% of the global languages! A figure higher than that found in Africa, the "cradle of Mankind".

Africans have had the time (they are supposedly the oldest humans) and the advantage of not going through bottlenecks (I do imagine that bottleneck that wipes out genetic diversity does the same to languages... kill the speakers and the language dies), so they should have evolved most languages than any other group of humans. But they have not.

The diversity of Languages: highest in America. From [1]

Then we have the island of divesity in New Guinea has the highest language diversity in the whole world! 820 languages out of a global total of around 7,000. That is 1 language every 820 Papuans.

I found that quite reasonable, the island is a jungle, with many mountain ranges that isolate populations and keep them from mixinng. New Guinea has been considered as one of the first places reached by mankind during our epic trek out of Africa.

But America is different, we are newcomers. The Papuans had 50 ky to develop their languages, the Amerindians less than 15 ky. So how do we explain this?

To make matters worse, America's native population fell to half or even less during the period of discovery and conquest. How many languages were wiped out before even being discovered? Even so, it has the highest global language diversity.

The origin of languages

Human beings speak, and we are all aware that Chinese and English sound different, that Spanish, Italian and French may seem similar but are also different. We are humans and speak different languages despite having a common origin.

An early attempt to explain this can be found in the Bible (Genesis 11: 1- 9): "... But the Lord came down to see the city and the tower the people were building. 6 The Lord said, 'If as one people speaking the same language they have begun to do this, then nothing they plan to do will be impossible for them. 7 Come, let us go down and confuse their language so they will not understand each other.'" So God made us all speak different languages by an act of his almighty power. Neat and simple.

But we now know that humans originated longe before any ziggurats were built in Mesopotamia. Language is something that arose tens of thousands of years ago. According to Chomsky, Tattersall, Bolhuis and Berwick (2014), "The faculty of language is likely to have emerged quite recently in evolutionary terms, some 70,000–100,000 years ago" [3]. Of course (I have posted on this before) that date range is not inferred from language studies, it is taken from the date suggested by anthropologists as the date of emergence of Modern Homo sapiens. So if that date was not correct, then the date given for the origin of languages is also incorrect.

In fact, our next of kin, the Neanderthals, could and did speak: "From the consilience of evidence from anatomy, archeology, and DNA, one can conclude that some language abilities, if not necessarily full modern syntactic language, were present in Neanderthals" so perhaps the ability to speak in Neanderthals predates that in humans. [4]

Daniel Nettle [2] suggests that people living near the Equator live easier lives regarding food supply and can split into smaller groups, which favours creation of new languages: "Where the climate allows continuous food production throughout the year, small groups of people can be reliably self-sufficient and so populations fragment into many small languages. Where the variability of the climate is greater, the size of social network necessary for reliable subsistence is larger, and so languages tend to be more widespread."

And this makes sense, as you can see in the map below, language diversity is highest close to the warm equatorial areas:

The diversity of Languages: location of highest densities. A. Whittall

Interesting, but this explains the evolution of languages during the last 11,000 years after the discovery of agriculture. I cannot imagine a large society of hunter-gatherers all speaking the same language, but one of farmers and tax collectors does make more sense.

But how fast do languages evolve? Take Australian English and English English or American English. They Aussies and Americans split from the mother tongue between 250 and 400 years ago, and did keep in touch with the distant British Metropolis yet evolved distinct stress and intonation for the same words. Something similar has happened with Spanish in the different Latin American countries and Spain over the past 500 years. But change has been small perhaps due to the lack of isolation.

The image above, from L. Luca Cavalli-Sforza & Marcus W. Feldman clearly shows that American languages are different to those in Asia, the "source" of the Native Americans' ancestors. This is surely conveniently explained by the "Beringian standstill" (how convenient) which allowed the future Amerindians to differentiate from those remaining behind in Asia.

Last but not least, I usually read that all indicators of genetic diversity fall as you move away from Africa, a clear indication of an African origin for all human beings. But, this is not seen in the case of human language diversity. Why?

I do believe that we should look into language diversity as an indicator of an older origin for mankind as a whole and for an earlier date for the peopling of America.

For those interesting in reading about this subject in depth, German Dziebel has written about linguistic diversity in support of his Out of America theory. Read More, and see an analysis of it here.

Sources

[1] Mobility and Ancient Society in Asia and the Americas, pp 117-126, chapter " How America Was Colonized: Linguistic Evidence. Johanna Nichols
[2] Explaining Global Patterns of Language Diversity, Daniel Nettle, journal of anthropological archaeology 17, 354–374 (1998) article no. AA98032
[3] Bolhuis JJ, Tattersall I, Chomsky N, Berwick RC (2014) >How Could Language Have Evolved? PLoS Biol 12(8): e1001934. doi:10.1371/journal.pbio.1001934
[4] Language Abilities in Neanderthals By:Johansson, S (Johansson, Sverker) ANNUAL REVIEW OF LINGUISTICS, VOL 1 Book Series: Annual Review of Linguistics Volume: 1 Pages: 311-332 DOI: 10.1146/annurev-linguist-030514-124945 Published: 2015

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

An earlier dispersal of Modern Humans or an Asian origin for mankind?

A very interesting paper by Liu, W. et al. in Nature The earliest unequivocally modern humans in southern China http://dx.doi.org/10.1038/nature15696 (2015) reports having found modern human teeth in Southern China that are at least 80,000 years old, and up to 120,000 years old. This is clearly at odds with other papers that suggest a much later "Out Of Africa" event.

The Abstract reads:

"The hominin record from southern Asia for the early Late Pleistocene epoch is scarce. Well-dated and well-preserved fossils older than ~45,000 years that can be unequivocally attributed to Homo sapiens are lacking. Here we present evidence from the newly excavated Fuyan Cave in Daoxian (southern China). This site has provided 47 human teeth dated to more than 80,000 years old, and with an inferred maximum age of 120,000 years. The morphological and metric assessment of this sample supports its unequivocal assignment to H. sapiens. The Daoxian sample is more derived than any other anatomically modern humans, resembling middle-to-late Late Pleistocene specimens and even contemporary humans. Our study shows that fully modern morphologies were present in southern China 30,000–70,000 years earlier than in the Levant and Europe. Our data fill a chronological and geographical gap that is relevant for understanding when H. sapiens first appeared in southern Asia. The Daoxian teeth also support the hypothesis that during the same period, southern China was inhabited by more derived populations than central and northern China. This evidence is important for the study of dispersal routes of modern humans. Finally, our results are relevant to exploring the reasons for the relatively late entry of H. sapiens into Europe. Some studies have investigated how the competition with H. sapiens may have caused Neanderthals’ extinction (see ref. 8 and references therein). Notably, although fully modern humans were already present in southern China at least as early as ~80,000 years ago, there is no evidence that they entered Europe before ~45,000 years ago. This could indicate that H. neanderthalensis was indeed an additional ecological barrier for modern humans, who could only enter Europe when the demise of Neanderthals had already started."

In the article (by some odd miracle I was granted Online access to the article by the nature.com content sharing initiative) it mentions that: "This evidence could support different origins and/or dispersal routes for modern humans across Asia". And indeed it does. Here we have humans in China 80 to 120 kya while they failed to reach Europe until 35 to 75 kya. The authors attribute this to the fact that: "... the possibility that H. Neanderthalensis was for a long time and additional barrier for modern human's expansion...".

An article by E. Callaway also in Nature includes this interesting comment: "Although Hublin says there is a good case that the Daoxian teeth are older than 80,000 years, he notes that several of the teeth have visible cavities, a feature uncommon in human teeth older than 50,000 years. “It could be that early modern humans had a peculiar diet in tropical Asia,” he says. “But I am pretty sure that this observation will raise some eyebrows." Martinon-Torres says her team plans to look more closely at the cavities and the diet of the Daoxian humans by examining patterns of tooth wear."

Dental cavities are much older than mankind. Cavities have been found in a distant relative, the Paranthropus robustus, that lived in Africa 2 million years ago. However the bacteria that causes tooth decay seems to have become more prevalent among humans after the invention of agriculture. Perhaps because it provided more carbohydrates in the diet, a good source of sugars for the tooth-decay bacteria. Nevertheless, a diet with plenty of fruit in subtropical China could also cause cavities.

The idea of an ancient dispersal out of Africa and admixture in Asia with even more archaic migrants is not new and has recently received support (see: Early modern human dispersal from Africa: genomic evidence for multiple waves of migration (2015), Francesca Tassi, Silvia Ghirotto, Massimo Mezzavilla, Sibelle Torres Vilaça, Lisa De Santi, Guido Barbujani. doi: http://dx.doi.org/10.1101/022889). However others have contended that dispersal took place only recently (See: Levantine cranium from Manot Cave (Israel) foreshadows the first European modern humans (2015), Israel Hershkovitz, et al., Nature 520, 216–219 (09 April 2015) doi:10.1038/nature14134) some 60 to 40 thousand years (kyr) before present (BP) as demonstrated by the former oldest remains of modern H. sapiens outside of Africa at Manot Cave (Western Galilee, Israel) dated to 54.7 +/- 5.5 kyr BP.

There has been another paper by Wu Liu et al., (2010). (Human remains from Zhirendong, South China, and modern human emergence in East Asia, PNAS 19201–19206, doi: 10.1073/pnas.1014386107) which clearly states that: "...The Zhiren Cave human remains, securely dated to at least 100 kya (early MIS 5), therefore represent the oldest evidence of derived modern human morphology in East Asia....The age and morphology of the Zhiren Cave human remains support a modern human emergence scenario for East Asia involving dispersal with assimilation or populational continuity with gene flow. It also places the Late Pleistocene Asian emergence of modern humans in a pre-Upper Paleolithic context and raises issues concerning the long-term Late Pleistocene coexistence of late archaic and early modern humans across Eurasia."

So, how did these modern humans reach China 80 to 120 Kya? Did they leave Africa even earlier? Did they originate outside of Africa?

Apparently the old peopling wave some 130 kya proposed by Hugo Reyes-Centeno, Silvia Ghirotto, Florent Détroit, Dominique Grimaud-Hervé, Guido Barbujani, and Katerina Harvati ( Genomic and cranial phenotype data support multiple modern human dispersals from Africa and a southern route into Asia. PNAS, April 21, 2014 DOI: 10.1073/pnas.1323666111) is a fact. The South Asian route could explain an early modern H. sapiens in south China.

But there was admixing with other archaic people in Asia, the Denisovans are one of those groups, and did mix into the ancestors of Melanesians.

An early 130 kya wave of humans may have also headed north and then west, into America, reaching the New World 100,000 years earlier than what is now currently accepte...

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

Into Africa gaining strength

A paper pubished in Science (Gallego Llorente et al., 2015. Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent, Science DOI: 10.1126/science.aad2879 two days ago, reveals what has been suspected for some time: All Africans have a Eurasian component in their genes.

The abstract says so clearly:

Characterizing genetic diversity in Africa is a crucial step for most analyses reconstructing the evolutionary history of anatomically modern humans. However, historic migrations from Eurasia into Africa have affected many contemporary populations, confounding inferences. Here, we present a 12.5x coverage ancient genome of an Ethiopian male (‘Mota’) who lived approximately 4,500 years ago. We use this genome to demonstrate that the Eurasian backflow into Africa came from a population closely related to Early Neolithic farmers, who had colonized Europe 4,000 years earlier. The extent of this backflow was much greater than previously reported, reaching all the way to Central, West and Southern Africa, affecting even populations such as Yoruba and Mbuti, previously thought to be relatively unadmixed, who harbor 6-7% Eurasian ancestry.

As it is behind a pay wall, I checked the web and found the following additional data:

• "the scientists believe up to 25% of the DNA of modern Africans can be traced back to this event."
• "... if you go to the corners of Africa, all the way to West Africa or South Africa, even populations that we really thought were purely African have 5-6% of their genome that dates back to these western Eurasian farmers."
• "...it is also interesting to discover now that even sub-Saharan Africans have a bit (0.3-0.7%) of Neanderthal ancestry."

Who knows, perhaps this is the first step into a serious analysis of the real roots of mankind, and may lead to a revision of the conclusions of another recent paper (L. Pagani, 2015, Tracing the Route of Modern Humans out of Africa by Using 225 Human Genome Sequences from Ethiopians and Egyptians Cell):

"... the Ethiopian and Egyptian genomes showed different patterns. In particular, the Egyptian0 genomes displayed a more recent split from both the West African (21,000 years ago) and the non-African (55,000 years ago) genomes than did the Ethiopian genomes (37,000 and 65,000 years ago, respectively). This suggests a higher similarity between non-African and Egyptian components than between non-African and Ethiopian components, which is consistent with the fact that Egypt is the last stop on the way out of Africa. Such split dates also hint at a recent interaction between Egyptians and West Africans..."

They too noticed a similarity between Egyptian and Eurasian genes, but their conclusions are different.

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

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 ©