Large-Scale Assessment of the Iranian population structure of mtDNA and Y-DNA

[RCO]

Large-Scale Assessment of the Iranian population structure of Mitochondrial and Y-chromosome Haplogroups
 
Neda Mazaheri1,2, Amin Ghahremani1,3, Masoumeh Babazadeh1,3 , Damoun NashtaAli1,3, Seyyed Abolfazl Motahari1,

   The Iranian plateau, strategically positioned as a corridor for population diffusion across Eurasia, holds a pivotal role in elucidating the dynamics of human migrations originating from Africa around 60,000 years ago. Both prehistoric and historic movements of populations between Africa, Asia, and Europe may have been influenced by the unique geographical features of the Iranian plateau. Iran boasts ancient cultures and urban settlements predating some of the earliest civilizations, including the Neolithic revolution in neighboring Mesopotamia. Spanning from the Balkans and Egypt in the west to the Indus Valley in Pakistan and northern India in the southeast, the Iranian plateau encompasses a vast area characterized by incredible ethnocultural diversity. This region served as the origin for numerous mt-DNA/Y-DNA haplogroups that expanded to West Asia, Europe, Siberia, Central Asia, and South Asia. By examining both maternal and paternal haplogroups within the Iranian context, we aim to contribute to the broader narrative of human dispersals and elucidate the role those specific regions, such as the Iranian plateau, played in shaping the observed genetic diversity today. Due to the lack of comprehensive studies on mtDNA /Y-DNA haplogroups in the Iranian population, our study sought to uncover the distribution of haplogroups among Iranian peoples using a large sample size. Our analysis focused on the frequency of ancestral haplogroups in Iran through the examination of large-scale whole-exome sequencing (WES) and SNP microarray data from 18,184 individuals. In our study, we observed 24 mt-DNA super haplogroups in the Iranian population, with the most common haplogroups belonging to West-Eurasian lineages U (20.73%), H (18.84%), J (12.10%), HV (9.22%), and T (8.98%), collectively comprising 69.70% of all Iranian samples. Notably, subclades J1 and U7 emerged as the two most frequent subclades, with frequencies of 11.24% and 7.30%, respectively. We also revealed the presence of 14 distinct Y-DNA haplogroups, with J, R, G, T, and Q emerging as the five predominant lineages. Notably, J2 (including J-L26) exhibited the highest frequency at 35.64%, followed by R1a at 14.68%. also, The detected mtDNA and Y-chromosome haplogroups were clustered into distinct groups that confirmed the heterogenicity of the Iranian population because of various factors including geographic or linguistic ethnic groups. 

Keywords: Iranian Plateau, mt-DNA haplogroup, Y-DNA haplogroup, Whole Exome Sequencing (WES), SNP microarray 

 

https://www.biorxiv.org/content/10.1101/...4.585067v1
https://www.biorxiv.org/content/10.1101/...1.full.pdf


No supplemental ?
Extremely needed investigation, but quite frustrating because they don't show subclades of the major haplogroups ? 

I just want to know about my Y-DNA J1-FGC6064 in Iran ?

[Riverman]

Like mentioned in the E-V13 thread, there seems to be a typo where the author confuses E-V13 with E-M35, because both the frequency and age are wrong for E-V13.

More detailled subclade assignments would be needed to get more out of it.

[RCO]

The investigation must reveal local Iranian SNPs and clades to be relevant.

1 - Iran is the central bulk of J haplogroup with 46.20% of the samples.

2 - J2 - 35.54% of the samples believed origin in Western Iran and its dispersion via Neolithic farmers from the Zagros mountains and northern Mesopotamia across the Iranian plateau to South Asia and Central Asia. Among the observed subclades of J2-M172, the most common include J-L26 (10.54%) and J-M47 (4.47%). - J2 was associated with expanding Neolithic waves to the East (India) and West (Europe)

3 - J1-M267 - 10.66%- likely origins spanning northwestern Iran, the Caucasus, the Armenian Highland, and northern Mesopotamia. In Iran, J1 has been reported to be present in frequencies below 10%, primarily found in regions such as Fars, Zoroastrians from Yazd, Gilan, Assyrians from Azerbaijan, and Khuzestan. Specifically, J1-Page08 is more common in populations residing below the Dasht-e Kevir and Dasht-e Lut desert area (approximately latitude 30°N), reaching its highest frequency among Arab populations in Khuzestan, bordering southern Iraq. with J-P58 observed as the predominant subclade at a frequency of 4.83%. - J1 was more associated with Northwestern Iran, different native areas than J2, the strong correlation between J1 and the CHG-IRAN component and that's the explanation why only J1 was found deep in the steppe and Eastern Europe related to the expansion of Proto-Indo-European in my opinion. There are more Northern non-P58 than Southern P58 in Iran.
What about the "Missing Links in Paternal Haplogroup J1-M267. Filling in the J1-M267 Phylogenetic Gap. Two Mesolithic Clades of Human Y chromosome haplogroup J1-M267: J1-FGC6064 and J1-ZS6599" - https://zenodo.org/records/5528265

4 - R1a is the most frequent subclade within the R haplogroup, with a frequency of 14.48%, followed by R1b at 4.26%, and R2 observed at a very low frequency of 1.5%. Evidence suggests that R1a likely originated in Central Asia or southern Russia/Siberia and, along with R1b, expanded to eastern Europe via Iran and the Caucasus [34]. - What specific R1a clades and what was the relation between other different R1a collateral clades and proportions in Central Asia and India ?

5- R1b (at 4.26%) is believed to have first developed somewhere in northern Iran or southern Central Asia before diffusing to the Fertile Crescent for herding. - What specific R1b clades and what was the relation between other different R1b collateral clades and proportions in the Southern Caucasus, Armenia and Europe ?

6- Why R2 (1.5%) was so small ?

7 - In our report, haplogroup E emerged as the second most common Y-DNA haplogroup, with a frequency of 11.88% (Fig. 2). The majority of this haplogroup belongs to the E-V13 subclade (11.75%), - A mistake or typo here. Haplogroup E arrived from the South and West, it was not native from Iran.

8 - Haplogroup G: emerges as the fourth most common Y-DNA haplogroup in the Iranian population, with a frequency of 6.25% (Fig. 2). Within this haplogroup, G2a is the most frequent sub-clade, accounting for 5.72% of the total sample. It is worth noting that G2b and G1a were also observed at low frequencies in our Iranian samples, at 0.05% and 0.44%, respectively. - G is more frequent to the West in Anatolia

9 - : The T- chrY haplogroup predominantly represented by the T1a sub-clade, was found with a frequency of 4.30% in the Iranian sample. T-L906, with a frequency of 2.08%, is a more frequent sub-lineage of T1a in our Iranian samples

10 - Haplogroup Q: is predominantly represented by the Q2a (Q-M378) subclade, which was found at a frequency of 3.62% in Iranian samples

11 - H (1.93%), C (1.62%), I (0.74%), L (0.63%), N (0.37%), O (0.33%), B (0.19%) and D (0.03%) - I thought L could be more representative in Iran

[rmstevens2]

5- R1b (at 4.26%) is believed to have first developed somewhere in northern Iran or southern Central Asia before diffusing to the Fertile Crescent for herding. 

Who believes that? R1b diffused to the Fertile Crescent for herding?

What evidence is there of that?

[RCO]

Yes, I think they are talking about specific Iranian R1b clades but they must show the SNPs and clades for appraisal and assessment, just like all new evidences for the entire article or nothing new would be pertinent to be investigated there, of course we need more Ancient and Modern Iranian DNA from that central hub in Eurasia.

[rmstevens2]

Yes, I think they are talking about specific Iranian R1b clades but they must show the SNPs and clades for appraisal and assessment, just like all new evidences for the entire article or nothing new would be pertinent to be investigated there, of course we need more Ancient and Modern Iranian DNA from that central hub in Eurasia.

So, that was actually a quote from the paper?

I can see the idea that R1b arose in Central Asia, but there is no indication whatsoever of any R1b diffusion to the Fertile Crescent. 

Personally, I think when R1b formed it was largely ANE.

[Moeca]

The T ydna is 100% purely only from the T1a1 branch ( T-L162 group )

there is no T1a2 or T1a3 ydna

[East Anglian]

The investigation must reveal local Iranian SNPs and clades to be relevant.


11 - H (1.93%), C (1.62%), I (0.74%), L (0.63%), N (0.37%), O (0.33%), B (0.19%) and D (0.03%) - I thought L could be more representative in Iran

Yes, I'm very surprised. One of my closest yDNA matches hails from Birjand. Otherwise they lay either side of Iran.