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Denisova and Neanderthal ancestry in the world populations - Printable Version

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Denisova and Neanderthal ancestry in the world populations - TanTin - 05-07-2024

There are many publications regarding Denisovan and Neanderthals.
We know lot about  Neanderthals and we still know very little about  Denisovans.

Now with the available genetic information we may do many additional tests and to check further what are the connections between current world populations and ancient  Neanderthals and  Denisova.

[Image: Neanderthal_at_AMNH.jpg]

RE: Denisova and Neanderthal ancestry in the world populations - TanTin - 05-07-2024

DOI: 10.1126/science.aao626

Denisova and Neanderthals are the first to diverge from the main tree. 
But they don't break all the connections to human tree. There would be several interactions between Humans and Denisova/Neanderthals.

RE: Denisova and Neanderthal ancestry in the world populations - TanTin - 05-07-2024

Now let me try to  show how connected are Humans and Neanderthals / Denisova.

Here is a list of 300 snips.
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These are some snips from 23 CHR. (X-chr).

We do a simple count: how many of these snips are matching to Denisova3.

This will tell us in general who are the most Denisovan-related individuals.
 And here are some results:

Show Content


RE: Denisova and Neanderthal ancestry in the world populations - TanTin - 05-07-2024

Now the same 300 snips can be visualized on the PCA. 
I am adding a color to each individual, the color is matching to the number of snips that match the Denisova3.
We have the max number for Denisova. And you may see the other groups.  The Neanderthals as we know share the most  or the highest number of snips with Denisova. And then we have some surprises: there are many Africans who have the highest number of shared snips with Densiova/Neanderthals.

At the same time there are some Africans, who do not share such number of snips. Just the opposite: some Africans have a very low number of shared snips with Densisova/Neanderthals.. 
Here I am using some  ESN.SG  individuals for my test, but they are not the only one. There are also few other groups with low archaic number of snips.

RE: Denisova and Neanderthal ancestry in the world populations - TanTin - 05-07-2024

Here is the list of the individuals with the lowest number of shared snips compared to Denisova:
(less than 50 shared snips from 300 in total)
Show Content


RE: Denisova and Neanderthal ancestry in the world populations - TanTin - 05-07-2024

The existence of such low-Neanderthal low-Denisova africans is more or less contradicting to our expectations.
We do find such low-archaic Africans, but then we find lot higher archaic-mixed Europeans, Asians and Australians ?

All started from Africa,  those in the root should have closer connection to the archaic hominoids. Unless if the mix was at later time.
But we don't see much proofs for such later mix.  So other processes and explanations are also possible.

My suggestion , or attempt for explanation: 
There could be some ancient African population which stayed isolated from the rest for many 10x thousands of years.
As a result of such isolation and as a result of some "selection" process , the archaic features were rejected during the selection process and these group became more distant from Neanderthal / Denisova . 

Рespectively such group became the basic populations  the base for the later Modern Humans.
At some later time this isolated group started to migrate and to mix with other groups in Africa and Ouside of Africa.

However we see also the existence of high Neanderthal/Denisova africans.  bab001/ baa001 are also example for such high Neanderthal/Denisova Africans.

RE: Denisova and Neanderthal ancestry in the world populations - TanTin - 05-07-2024

example

RE: Denisova and Neanderthal ancestry in the world populations - TanTin - 05-15-2024

https://www.biorxiv.org/content/10.1101/2024.05.13.593955v1

Neandertal ancestry through time: Insights from genomes of ancient and
present-day humans

Leonardo Nicola Martin Iasi, Manjusha Chintalapati, Laurits Skov, Alba Bossoma Mesa, Mateja Hajdinjak, Benjamin Marco Peter, Priya Moorjani

doi: https://doi.org/10.1101/2024.05.13.593955

RE: Denisova and Neanderthal ancestry in the world populations - CLTVTE - 05-16-2024

(05-15-2024, 05:09 PM)TanTin Wrote: https://www.biorxiv.org/content/10.1101/2024.05.13.593955v1

Neandertal ancestry through time: Insights from genomes of ancient and
present-day humans

Leonardo Nicola Martin Iasi, Manjusha Chintalapati, Laurits Skov, Alba Bossoma Mesa, Mateja Hajdinjak, Benjamin Marco Peter, Priya Moorjani

doi: https://doi.org/10.1101/2024.05.13.593955

Some peculiarities on the Denisovan ancestry were reported in “Ancient DNA indicates human population shifts and admixture in northern and southern China”: “Table S3. Admixture proportion of Denisovan-related ancestry using f4-ratios. (…) Though we find a significant archaic admixture proportion for Yumin, Liangdao1, and DevilsCave_N, in no case is the result significant for transversions only. This suggests that we do not detect Denisovan-related archaic admixture in these ancient and presentday Asians and any significant result likely reflects shared characteristic ancient DNA damage.”

On the other hand, a technology, which was used by the Neanderthals, was the Levollois technology. The presence of the Levollois technology from the Guanyindong Cave of the Guizhou Province of South China ca. 170 000 years ago was refuted:

A refutation of reported Levallois technology from Guanyindong Cave in south China
Feng Li, Yinghua Li, Xing Gao, Steven L Kuhn, Eric Boëda, John W Olsen
https://academic.oup.com/nsr/article-pdf/6/6/1094/38917025/nwz115.pdf

The authors stated that:

“One of us (Y.-H.L.) has recently studied the Guanyindong assemblage from a technological perspective. This study showed that production of flakes in the Guanyindong lithic industry was characterized by opportunistic selection of natural technical characteristics on one part of the block to be worked, rather than by the strategic preparation of striking platforms and flaking surfaces. The exploited and unexploited portions of the cores have no apparent association. Different parts of one nucleus may have been flaked if they bore appropriate characteristics, but modifications of various parts of the core are essentially unrelated. Such nuclei exhibiting as ‘additive structure’ are fundamentally distinct from Levallois cores, which reflect an ‘integrated structure’ [9,10]. Occasionally, this approach can produce flakes that superficially resemble Levallois products, but it is a much simpler and less well-organized procedure. A similar situation has been discovered at Zhoukoudian Locality 15, where a few Levallois-like pieces were struck from discoid cores, not from genuine Levallois cores [11].”

U-series dating of Locality 15 at Zhoukoudian, China, and implications for hominid evolution
September 2004 Quaternary Research 62(2): 208-213
DOI:10.1016/j.yqres.2004.06.004
https://www.researchgate.net/publication/43448737_U-series_dating_of_Locality_15_at_Zhoukoudian_China_and_implications_for_hominid_evolution

“This paper reports U-series dates on speleothem samples from Locality 15 at Zhoukoudian, one of the richest Paleolithic sites in northern China. The age of the lower part of Layer 2 is securely bracketed between 155,000 and 284,000 yr. The underlying Layer 3 dates back at least 284,000 yr. Layer 4, further below, should be older still, possibly by a cycle on the SPECMAP time scale before 284,000 yr ago. These ages, much greater than the previous estimates of 110,000-140,000 yr from U-series and electron spin resonance dating of fossil teeth, suggest that Locality 15 was broadly contemporaneous with Locality 4 (New Cave) and with the uppermost strata of Locality 1 (Peking Man site). The physical evolution and cultural development evidenced by the timing of the Zhoukoudian localities are in line with the opinion of Chinese anthropologists for a regional transition from Homo erectus to archaic Homo sapiens.”