The GenArchivist Forum

I am starting this thread as a continuation of the controversial thread over at the ProBoard version of this forum.

G25-coordinates provided by ghurier:

https://genarchivist.freeforums.net/post/4459/thread

ghurier Wrote:Here are few coordinates estimated from the triangulation of some genetic distances provided above (using markov-chain process) :
Should be close enough to real values to play with a PCA.
Disclaimer : I copied the distance values manually, extra uncertainty might be generated if I miscopied some numbers (or if for some reasons I don't have exactly the same G25s for ref-modern-pops than the peoples providing the genetic distances).

OK:I6409,0.029665247,0.13868540,-0.047587444,-0.14426329,-0.0022221347,-0.063518622,-0.014261081,-0.013556098,0.087986490,0.0041161682,-0.0028172711,-0.019512651,0.055365686,0.0068209691,0.0071103512,0.014172621,-0.0011899901,-0.019799603,-0.021658496,0.032836460,-0.0024145371,-0.010472191,-0.0046426664,-0.0034683108,0.0029676763

OMK:I10020,0.011530275,0.13728656,-0.049170061,-0.11359996,0.00099127203,-0.049440638,-0.020387999,-0.0026683728,0.062675346,-0.0081175666,0.0020009024,-0.011293133,0.028314321,0.020438082,0.0095046032,0.0088030027,-0.017175880,-0.0096735594,-0.0038784026,0.00068539449,0.0029141859,-0.015338366,-0.0043286787,-0.0012691466,0.0014364105

MK:I6130,0.053504150,0.13702279,-0.042256778,-0.088577892,0.0016483012,-0.037922341,-0.014478379,-0.0022917330,0.032911256,0.0051009809,0.0091531458,-0.013376381,0.026522487,0.0012096728,-0.0043573045,-0.0011185066,-0.021307803,6.0763451e-05,0.0033831153,0.0024352202,0.0013931869,-0.0017261886,0.0014597641,0.0049339092,0.0086866961

Some results posted by twelve:

https://genarchivist.freeforums.net/thre...ns-g25-new

twelve Wrote:

Results posted by Ajeje Brazorf:

https://genarchivist.freeforums.net/post/4529/thread

Ajeje Brazorf Wrote:Full picture:



The first sample is dated to 2400 BC, but it is not carbon dated, so it may (or may not) be older. It bears the closest resemblance to the Natufian sample I0861.

Is this leak real?

Results on my Neolithic model

Target: MK:I6130
Distance: 2.2291% / 0.02229137
31.4 Levant_Meoslithic
25.0 Anatolian_Neolithic
20.0 Iran_N
15.4 Levant_Neolithic
6.2 Steppe
1.8 SSA
0.2 AASI

Target: OMK:I10020
Distance: 3.6055% / 0.03605479
39.6 Levant_Neolithic
24.8 Levant_Meoslithic
16.4 Iran_N
10.0 Anatolian_Neolithic
5.6 Nilo-Saharian_Pastoralist
3.6 Taforalt

Target: OK:I6409
Distance: 4.0677% / 0.04067728
45.4 Levant_Neolithic
39.6 Levant_Meoslithic
8.4 Iran_N
6.6 Taforalt


These are sims from what I know

*Bump*

I saw it referred that in the Archivist "free forum" which preceded this thread that the 18th dynasty lineage was determined as P312+. Is this confirmed or is this an assumption based on the haplotype which commonly fits P312+ determined ones? 

Second, was it confirmed that some of the genomes from the Middle kingdom had some Italian BB shift to them?

Is there an update on Predynastic and other Early Dynastic-Old Kingdom materials?

According to a 2018 study, Djehutynaht belongs to mtdna U5b2b5. On yfull, the result is refined to U5b2b5a2, and his closest subclade is from modern Lebanon. However, there may be some errors in yfull's age calculation. The Lebanese sample and Djehutynakht only split at 1500BC.

Also, according to yfull, the early epicenter of U5b2b5/U5b2b5a seems to be in Central Europe/Italy, and U5b2b5a2 is a nested subclade. Except a Romanian sample 1450 BP, Balkan/SE Europe does not have its diversity.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5867856/

https://www.yfull.com/mtree/U5b2b5/

https://www.yfull.com/mtree/U5b2b5a2/

I wonder how this uniparental and its related autosomal components entered Egypt. The 2018 study suggests that the introduction is through the Near East route, but this subgroup may show a link to the BB/Italo-Celtic population rather than non-BB-derived groups like Hittites and Balkan-IEs. Somalispot also mentions the Italian BB-like autosomal component in ancient Egypt, except old Kingdom.

Quote:Given limited available data and the fact that U5 is the dominant mitochondrial haplogroup found among hunter-gatherers in Europe [83,84], the recovery of a haplogroup U5b2b5 sequence from the mummy of Djehutynakht raises the question of data authenticity, despite the molecular metrics suggesting otherwise. When the mummy’s mtDNA sequence is viewed in the context of modern mtDNA diversity, however, the observed U5 lineage could potentially reflect interactions between Egypt and the Near East that date as far back as the Predynastic and Early Dynastic periods [85]. Trade between Egypt and the Near East is evidenced by, among other things, ceramic imports to Egypt [86]. In addition, dwellings similar to those found in Palestine suggest some immigration to Egypt from more arid Near Eastern areas from the late Predynastic to the Old Kingdom [85,87]. Both trade and immigration between Egypt and the Near East continued to increase over time. Demand in Egypt for cedar of Lebanon wood (a wood available and harvested in Lebanon and Syria during the MK) led to the further establishment of trade routes between Egypt and the Levant [85,86]. It is interesting, and perhaps not coincidental, that the individual with the mtDNA sequence most similar to Djehutynakht comes from a Lebanese individual.

www.somalispot.com/threads/ancient-egyptian-g25-results.154114/page-5

www.somalispot.com/threads/ancient-egyptian-g25-results.154114/

Ancient U5b2b5 samples:



Leaked info:



How to make images smaller?

It seems that U5b2b5 does have a very SW European origin/epicenter, and may have formed as early as 3800-3400BC. Although this is prior to BB expansion, but the autosomal data and chronology (11-12th Dynasty) suggest the relationship between the arrival of this haplogroup and some BB-related geneflow.

If I understand correctly this story started because people ran Tut's STRs on nevgen (or some similar program) and put R-M269 as a "known SNP". I've done some experiments with Greek STRs from older studies and a lot of the nevgen predictions for R1b were clearly wrong. Basically, if you just put the STRs (with no known SNP) it gives R-M269, if you put R-M269 as a known SNP it predicts western European branches at an unrealistic rate. If I had to guess the huge number of western European testers in the STR database compared to other areas plays a role here. Just putting this here so people don't get disappointed down the road

(12-09-2023, 04:53 PM)pelop Wrote: [ -> ]If I understand correctly this story started because people ran Tut's STRs on nevgen (or some similar program) and put R-M269 as a "known SNP". I've done some experiments with Greek STRs from older studies and a lot of the nevgen predictions for R1b were clearly wrong. Basically, if you just put the STRs (with no known SNP) it gives R-M269, if you put R-M269 as a known SNP it predicts western European branches at an unrealistic rate. If I had to guess the huge number of western European testers in the STR database compared to other areas plays a role here. Just putting this here so people don't get disappointed down the road

Not just Nevgen but anyone who knows about these things who's looked at it says it's R-M269 at least. The first was iGenea who leaked the info back in 2011. Hawass's team lied and slandered iGenea. Ten years later they quietly released the results in a book that costs £200. No journal publication, no press release, no coverage in the media. They know exactly what it is.

(12-09-2023, 05:01 PM)James100 Wrote: [ -> ]

(12-09-2023, 04:53 PM)pelop Wrote: [ -> ]If I understand correctly this story started because people ran Tut's STRs on nevgen (or some similar program) and put R-M269 as a "known SNP". I've done some experiments with Greek STRs from older studies and a lot of the nevgen predictions for R1b were clearly wrong. Basically, if you just put the STRs (with no known SNP) it gives R-M269, if you put R-M269 as a known SNP it predicts western European branches at an unrealistic rate. If I had to guess the huge number of western European testers in the STR database compared to other areas plays a role here. Just putting this here so people don't get disappointed down the road

Not just Nevgen but anyone who knows about these things who's looked at it says it's R-M269 at least. The first was iGenea who leaked the info back in 2011. Hawass's team lied and slandered iGenea. Ten years later they quietly released the results in a book that costs £200. No journal publication, no press release, no coverage in the media. They know exactly what it is.

You should re-read what I wrote. He's R-M269 but downstream predictions are not reliable.

(12-09-2023, 05:30 PM)pelop Wrote: [ -> ]

(12-09-2023, 05:01 PM)James100 Wrote: [ -> ]

(12-09-2023, 04:53 PM)pelop Wrote: [ -> ]If I understand correctly this story started because people ran Tut's STRs on nevgen (or some similar program) and put R-M269 as a "known SNP". I've done some experiments with Greek STRs from older studies and a lot of the nevgen predictions for R1b were clearly wrong. Basically, if you just put the STRs (with no known SNP) it gives R-M269, if you put R-M269 as a known SNP it predicts western European branches at an unrealistic rate. If I had to guess the huge number of western European testers in the STR database compared to other areas plays a role here. Just putting this here so people don't get disappointed down the road

Not just Nevgen but anyone who knows about these things who's looked at it says it's R-M269 at least. The first was iGenea who leaked the info back in 2011. Hawass's team lied and slandered iGenea. Ten years later they quietly released the results in a book that costs £200. No journal publication, no press release, no coverage in the media. They know exactly what it is.

You should re-read what I wrote. He's R-M269 but downstream predictions are not reliable.

Ok. You haven't shown that they're unreliable though.

(12-09-2023, 06:54 AM)Desdonas Wrote: [ -> ]According to a 2018 study, Djehutynaht belongs to mtdna U5b2b5. On yfull, the result is refined to U5b2b5a2, and his closest subclade is from modern Lebanon. However, there may be some errors in yfull's age calculation. The Lebanese sample and Djehutynakht only split at 1500BC.

Also, according to yfull, the early epicenter of U5b2b5/U5b2b5a seems to be in Central Europe/Italy, and U5b2b5a2 is a nested subclade. Except a Romanian sample 1450 BP, Balkan/SE Europe does not have its diversity.

[...]

It seems that U5b2b5 does have a very SW European origin/epicenter, and may have formed as early as 3800-3400BC. Although this is prior to BB expansion, but the autosomal data and chronology (11-12th Dynasty) suggest the relationship between the arrival of this haplogroup and some BB-related geneflow.

Hi,

It is important to remember that TMRCA based on mtDNA are very unsecured :
1. Mutations on mtDNA are uncommon (every ~2500 years in average) due to the small size of the sequence
2. Fixing rate of mtDNA mutations seems to strongly varies with environnement pressure.
Thus it is not necessarly an error considering the very big statistical uncertainty on mtDNA-based TMRCA.

Looking at : https://www.yfull.com/mtree/U5b2b5/
The YF111416 sample (U5b2b5*) is interesting, he has no flag on his mtDNA but this is a male sample.
Looking in the ytree we find him under https://www.yfull.com/tree/J-ZS4757/ with a Morocco flag.

U5b2b-a* have been found 15 kyr BP in Italy.
Thus U5b2b5a only received 2 extra-mutations since U5b2b-a (thus this haplogroup could exists since ~10 kyr BP).
Therefore, the lineage found in Lebanon and Egypt could have arrived there since the Paleolithic.
Finding a basal lineage U5b2b5* in Morocco might indicate that this lineage crossed the Mediteranean sea (From Southern Europe to Northern Africa) at some point during Mesolithic or Neolithic.

Looking at the Y-DNA side, we have R-V88 ( https://www.yfull.com/tree/R-V88/ ) that might be in a similar situation.
Y-DNA based TMRCA are more accurate (mutations are occuring more often, and Y-DNA seems less affected by varying fixing rate).
We see that R-V88 seems to have moved from Europe to Africa around 5600 BCE possibly passing by Sardinia.
U5b2b5 could have followed the same path.
The large amount of U5b2b5a lineages found in Sardinia seems to also favor this possibility.
Under the hypothesis of a co-migration of these Y-DNA and mtDNA lineages, the timing works reasonably for an entrance in north Africa around 7000 ybp :
1. R-Y8447 TMRCA 9100-6200 ybp (95% probability interval)
2. U5b2b5a TMRCA 7200-3300 ybp (95% probability interval)

Therefore, if a relation with a potential BB-culture geneflow cannot be excluded, it is also fairly possible that this lineage arrived around Egypt during the Neolithic (at least R-V88 seems to show that such population movement existed during Neolithic).

(12-10-2023, 07:58 PM)GHurier Wrote: [ -> ]

(12-09-2023, 06:54 AM)Desdonas Wrote: [ -> ]According to a 2018 study, Djehutynaht belongs to mtdna U5b2b5. On yfull, the result is refined to U5b2b5a2, and his closest subclade is from modern Lebanon. However, there may be some errors in yfull's age calculation. The Lebanese sample and Djehutynakht only split at 1500BC.

Also, according to yfull, the early epicenter of U5b2b5/U5b2b5a seems to be in Central Europe/Italy, and U5b2b5a2 is a nested subclade. Except a Romanian sample 1450 BP, Balkan/SE Europe does not have its diversity.

[...]

It seems that U5b2b5 does have a very SW European origin/epicenter, and may have formed as early as 3800-3400BC. Although this is prior to BB expansion, but the autosomal data and chronology (11-12th Dynasty) suggest the relationship between the arrival of this haplogroup and some BB-related geneflow.

Hi,

It is important to remember that TMRCA based on mtDNA are very unsecured :
1. Mutations on mtDNA are uncommon (every ~2500 years in average) due to the small size of the sequence
2. Fixing rate of mtDNA mutations seems to strongly varies with environnement pressure.
Thus it is not necessarly an error considering the very big statistical uncertainty on mtDNA-based TMRCA.

What exactly do you mean by point 2., "environmental pressure"?

(12-11-2023, 03:14 PM)Horatio McCalliste Wrote: [ -> ]What exactly do you mean by point 2., "environmental pressure"?

Natural selection.
For instance, you have a significant increase of the mtDNA fixing rate during the OoA phase.
Which somehow makes sense, as humans needed to adapt to colder environements (a role that you expect mtDNA to contribute).

(12-12-2023, 06:45 PM)GHurier Wrote: [ -> ]

(12-11-2023, 03:14 PM)Horatio McCalliste Wrote: [ -> ]What exactly do you mean by point 2., "environmental pressure"?

Natural selection.
For instance, you have a significant increase of the mtDNA fixing rate during the OoA phase.
Which somehow makes sense, as humans needed to adapt to colder environements (a role that you expect mtDNA to contribute).

Do you mean the massive diversification of mtDNA N and M? I have always found it peculiar how many primary branches there are of N ( around 20) and M (around 50) compared to L3 (Around 7). That is something I feel has been underexplored in popgen research regarding OoA. In a much more attenuated fashion it's sort of true for y-DNA as well, most of CT's splits occurred amongst ancestral Eurasians with just E in Africa.

That is an interesting point regarding body heat/cold environment adaption, that does seem like a good possible explanation M/N diversification, however the earliest branch splitting had to have occurred in Southwest Asia, I'm not really sure if climate was ever cold enough there to drive such a strong evolutionary pressure on the mtDNA in that way?