(04-06-2024, 12:44 PM)Jerome Wrote: Seems like the start of LGM and transitional phase between badarositan->zarzian.

A late TMRCA means G formed much later?(Or did it rexpand much later)?

(04-06-2024, 06:48 AM)Jerome Wrote: Can you run these stats with chg (zlaty,Bacho,chg) included as a control for iran_n?

Also, couldn't slight SSA in iran_n be skewing the results?

I think basal was the Egyptian upper paleolithic people like nazlet khater and the early ahmarian people.

Egypt was in Africa and E could split from there and spread in both Africa and Levant.
It would also explain E in iberomaurisian.

And why Natufians show more diverse clades than iberomaurisians.

(04-06-2024, 10:12 PM)kolompar Wrote:

Code:

South_Africa_2000BP.SG    Bulgaria_BachoKiro_LatePleistocene    Georgia_Satsurblia.SG    Iran_GanjDareh_N    0.001017909    0.000535645    1.900344389    0.05738794    360878
South_Africa_2000BP.SG    Laos_Hoabinhian.SG    Georgia_Satsurblia.SG    Iran_GanjDareh_N    0.001143852    0.000705403    1.621558166    0.104897986    211180
South_Africa_2000BP.SG    China_Tianyuan    Georgia_Satsurblia.SG    Iran_GanjDareh_N    0.000858186    0.000645933    1.328599747    0.183980056    325619
South_Africa_2000BP.SG    Czechia_Bohemia_UP_HG    Georgia_Satsurblia.SG    Iran_GanjDareh_N    0.000276817    0.000627995    0.440794438    0.659361821    388100

(03-18-2024, 12:18 AM)TanTin Wrote: Now let exclude Altai and Cameroon, so we can see more details for the tested individuals.



As we may see here in this example: Turkey are below the 0-line. So they have more shared markers with Altai Neanderthal, than Cameroon. 
All the rest  are above 0-line. Laos is the 0-reference line.

(03-23-2024, 09:16 PM)TanTin Wrote: The results with V52 1240k  are similar, but not better.

(04-07-2024, 09:14 AM)Jerome Wrote:

(04-06-2024, 10:12 PM)kolompar Wrote:

Code:

South_Africa_2000BP.SG    Bulgaria_BachoKiro_LatePleistocene    Georgia_Satsurblia.SG    Iran_GanjDareh_N    0.001017909    0.000535645    1.900344389    0.05738794    360878
South_Africa_2000BP.SG    Laos_Hoabinhian.SG    Georgia_Satsurblia.SG    Iran_GanjDareh_N    0.001143852    0.000705403    1.621558166    0.104897986    211180
South_Africa_2000BP.SG    China_Tianyuan    Georgia_Satsurblia.SG    Iran_GanjDareh_N    0.000858186    0.000645933    1.328599747    0.183980056    325619
South_Africa_2000BP.SG    Czechia_Bohemia_UP_HG    Georgia_Satsurblia.SG    Iran_GanjDareh_N    0.000276817    0.000627995    0.440794438    0.659361821    388100

Interesting how bacho kiro has more affinity to iran_n over satsurblia than zlaty Kun does.

Does this support some kind of crown Eurasian input in iran_n?
Or does that mean that bacho kiro and iran_n share more of common components in exclusion of chg?

Or a slightly higher east Eurasian input(hoab,etc) in iran_n than chg?
It could fit well if bacho kiro had east Eurasian affinities.


East African affinity in iran_n seems convincing,but the commenter 'Matt' on Eurogenes blog got much different results in his runs, difference between chg and iran_n wrt mota dosent seem that great here.



"f4(Cameroon_SMA.DG, Ethiopia_4500BP.DG; Iran_GanjDareh_N, X) for the following populations is (order of Z score):

Turkey_N, Z: 2.43, 1050123 SNPs
Turkey_Epipaleolithic, Z: 2.29, 815047 SNPs
Spain_MLN, Z: 2.16, 1042707 SNPs
Russia_Afanasievo, Z: 1.64, 1045181 SNPs
Serbia_IronGates_Mesolithic, Z: 0.982, 1049935 SNPs
China_Tianyuan, Z: 0.831, 860301 SNPs
China_AmurRiverLPaleolithic_19k, Z:0.644, 670024 SNPs
Russia_Ust_Ishim.DG, Z: 0.242, 1051361 SNPs
Georgia_CHG.SG, Z: -0.00673, 1049631 SNPs
Russia_Kostenki14, Z: -0.608, 1028916 SNPs"

Here's the link https://eurogenes.blogspot.com/2023/09/the-caucasus-is-semipermeable-genetic.html?m=1

Maybe his shum laka outgroup is changing it?
Also,pinarbasi has more east African affinity than iran_n according to his runs?



The Chad rohlfsen guy there found more mota affinity in pinarbasi than chg too.

result: Chimp Mota Turkey_Epipaleolithic Georgia_Kotias_UP -0.000884 -1.380 12746 13005 293027

(04-07-2024, 11:28 AM)Jerome Wrote: Dosent this refute lazaridis conception of basal eurasian as needed to account for lower Neanderthal Ancestry?
Maybe deselection against Neanderthal alleles could explain that??

Why else is basal eurasian even needed now?

There's also the fact that iran and central Asia was full of Neanderthals(warsawi,Dodekatym-2) so the area being full of basal eurasians dosent make sense.
Any basal eurasian living there would end up with lots of Neanderthal Ancestry which defeats the purpose of basal itself.

(04-07-2024, 11:28 AM)Jerome Wrote: Could you add Kostenki,afontovaGora,Tutkaul and Tyumen_HG here, dosent this show WHG as having more Neanderthal than MA1?
And iran_n has more Neanderthal affinity(2.16) than ust ishim(1.87)?

Dosent this refute lazaridis conception of basal eurasian as needed to account for lower Neanderthal Ancestry?
Maybe deselection against Neanderthal alleles could explain that??

Why else is basal eurasian even needed now?

There's also the fact that iran and central Asia was full of Neanderthals(warsawi,Dodekatym-2) so the area being full of basal eurasians dosent make sense.
Any basal eurasian living there would end up with lots of Neanderthal Ancestry which defeats the purpose of basal itself.

(04-07-2024, 11:28 AM)Jerome Wrote: Could you add Kostenki,afontovaGora,Tutkaul and Tyumen_HG here, dosent this show WHG as having more Neanderthal than MA1?
And iran_n has more Neanderthal affinity(2.16) than ust ishim(1.87)?

Dosent this refute lazaridis conception of basal eurasian as needed to account for lower Neanderthal Ancestry?
Maybe deselection against Neanderthal alleles could explain that??

Why else is basal eurasian even needed now?

There's also the fact that iran and central Asia was full of Neanderthals(warsawi,Dodekatym-2) so the area being full of basal eurasians dosent make sense.
Any basal eurasian living there would end up with lots of Neanderthal Ancestry which defeats the purpose of basal itself.

(03-31-2024, 04:00 PM)TanTin Wrote:

Short video: 
https://www.youtube.com/watch?v=vXOyVG-LNoA

(03-25-2024, 12:48 AM)Desdonas Wrote:

(03-24-2024, 10:25 PM)kolompar Wrote: The Z score for Natufian is lower simply because less SNPs, less certain result. The f4 estimates itself look correct. But what's going on in South Africa?
I find it much less likely that OoA humans stopped and contemplated for thousands of years in Eurasia. I think they must have had some huge technological advantage that allowed them to overtake other humans very quickly, and the conditions for OoA were a short, rare one-off event.

The linked pnas paper (graph is shown below) mentions that OoA occurs at about 80kya, followed by "Arabian Standstill". This clearly requires the back migration of E and D2 (D0) into Africa, and if it is true, we may see the genetic adaptation/related alleles in Africans significantly. So then it may become conflictive. Anyway, a single OoA without back migration is more parsimonious.

However, if a single OoA occured at 50kya (even not 55-60kya), there would be no time left for the genetic adaptation mentioned in the paper. So, either there is a bias in the research of the paper, or the ages of CT, DE, and D may be older than expected. I remember that some studies and graphs suggest that the ages of DE (Yap) and D (CTS3946 level) may reach 73-71 kya, and if the initial OoA population size is smaller, then 10,000 to 20,000 years may be enough for the "Arabian Standstill".

Finally, I believe that the replacement of Neanderthals and Denisovans was largely due to the diseases carried by the OoA population. It is known to all that the migration route of Oceanians is through South Asia and Southeast Asia, but the entire southern route region lacks IUP tools. Southeast Asia and Southern China maintain the ancient pebble-tool industry.

(03-25-2024, 02:46 PM)Rozenfeld Wrote: This study may be relevant for your discussion:

(03-25-2024, 02:45 PM)Rozenfeld Wrote: https://www.nature.com/articles/s41467-024-46161-7

The Persian plateau served as hub for Homo sapiens after the main out of Africa dispersal

    Leonardo Vallini, Carlo Zampieri, Mohamed Javad Shoaee, Eugenio Bortolini, Giulia Marciani, Serena Aneli, Telmo Pievani, Stefano Benazzi, Alberto Barausse, Massimo Mezzavilla, Michael D. Petraglia & Luca Pagani

Nature Communications volume 15, Article number: 1882 (2024)

Abstract

A combination of evidence, based on genetic, fossil and archaeological findings, indicates that Homo sapiens spread out of Africa between ~70-60 thousand years ago (kya). However, it appears that once outside of Africa, human populations did not expand across all of Eurasia until ~45 kya. The geographic whereabouts of these early settlers in the timeframe between ~70-60 to 45 kya has been difficult to reconcile. Here we combine genetic evidence and palaeoecological models to infer the geographic location that acted as the Hub for our species during the early phases of colonisation of Eurasia. Leveraging on available genomic evidence we show that populations from the Persian Plateau carry an ancestry component that closely matches the population that settled the Hub outside Africa. With the paleoclimatic data available to date, we built ecological models showing that the Persian Plateau was suitable for human occupation and that it could sustain a larger population compared to other West Asian regions, strengthening this claim.

Note: there are no new data in this paper, they analyze already published data.

(04-07-2024, 10:14 PM)kolompar Wrote:

(03-31-2024, 04:00 PM)TanTin Wrote:

Short video: 
https://www.youtube.com/watch?v=vXOyVG-LNoA

I'm skeptical of these methods I don't understand
Here is the paper:
https://www.science.org/doi/10.1126/sciadv.aax5097
So it's only West Africans which is plausible as other methods also indicated it. They have CSFS for other populations too in the supplements so we can check out how much it makes sense.

(03-25-2024, 12:48 AM)Desdonas Wrote:

(03-24-2024, 10:25 PM)kolompar Wrote: The Z score for Natufian is lower simply because less SNPs, less certain result. The f4 estimates itself look correct. But what's going on in South Africa?
I find it much less likely that OoA humans stopped and contemplated for thousands of years in Eurasia. I think they must have had some huge technological advantage that allowed them to overtake other humans very quickly, and the conditions for OoA were a short, rare one-off event.

The linked pnas paper (graph is shown below) mentions that OoA occurs at about 80kya, followed by "Arabian Standstill". This clearly requires the back migration of E and D2 (D0) into Africa, and if it is true, we may see the genetic adaptation/related alleles in Africans significantly. So then it may become conflictive. Anyway, a single OoA without back migration is more parsimonious.

However, if a single OoA occured at 50kya (even not 55-60kya), there would be no time left for the genetic adaptation mentioned in the paper. So, either there is a bias in the research of the paper, or the ages of CT, DE, and D may be older than expected. I remember that some studies and graphs suggest that the ages of DE (Yap) and D (CTS3946 level) may reach 73-71 kya, and if the initial OoA population size is smaller, then 10,000 to 20,000 years may be enough for the "Arabian Standstill".

Finally, I believe that the replacement of Neanderthals and Denisovans was largely due to the diseases carried by the OoA population. It is known to all that the migration route of Oceanians is through South Asia and Southeast Asia, but the entire southern route region lacks IUP tools. Southeast Asia and Southern China maintain the ancient pebble-tool industry.

I'm not convinced by that paper at all, not sure if they can even detect the sweeps well. Just look at fig 1, looks very European biased and even there the variation is so large (unless I'm misunderstanding what it's showing). Then even if they got that right there's no reason it would all be OoA adaptation and even less reason it would be during an Arabian standstill, that's just what they wanted to see into it. There could have been selection already in a separated population back in Africa, and I feel like the OoA bottleneck itself could also show as such a hard sweep.

(03-25-2024, 02:46 PM)Rozenfeld Wrote: This study may be relevant for your discussion:

(03-25-2024, 02:45 PM)Rozenfeld Wrote: https://www.nature.com/articles/s41467-024-46161-7

The Persian plateau served as hub for Homo sapiens after the main out of Africa dispersal

    Leonardo Vallini, Carlo Zampieri, Mohamed Javad Shoaee, Eugenio Bortolini, Giulia Marciani, Serena Aneli, Telmo Pievani, Stefano Benazzi, Alberto Barausse, Massimo Mezzavilla, Michael D. Petraglia & Luca Pagani

Nature Communications volume 15, Article number: 1882 (2024)

Abstract

A combination of evidence, based on genetic, fossil and archaeological findings, indicates that Homo sapiens spread out of Africa between ~70-60 thousand years ago (kya). However, it appears that once outside of Africa, human populations did not expand across all of Eurasia until ~45 kya. The geographic whereabouts of these early settlers in the timeframe between ~70-60 to 45 kya has been difficult to reconcile. Here we combine genetic evidence and palaeoecological models to infer the geographic location that acted as the Hub for our species during the early phases of colonisation of Eurasia. Leveraging on available genomic evidence we show that populations from the Persian Plateau carry an ancestry component that closely matches the population that settled the Hub outside Africa. With the paleoclimatic data available to date, we built ecological models showing that the Persian Plateau was suitable for human occupation and that it could sustain a larger population compared to other West Asian regions, strengthening this claim.

Note: there are no new data in this paper, they analyze already published data.

Nice of them to try to contribute to the thread but I don't think derived allele sharing with Tianyuan/Kostenki is a particularly informative model in 2024. I guess we can celebrate the 10 year anniversary of their publication but for scientists it might be a good idea to reconsider it and look for something new? The paleoclimate data looks interesting though.