Ancient DNA indicates 3,000 years of genetic continuity in the Northern Iranian Plate

[RCO]

Ancient DNA indicates 3,000 years of genetic continuity in the Northern Iranian Plateau, from the Copper Age to the Sassanid Empire

Ancient DNA indicates 3,000 years of genetic continuity in the 1 Northern Iranian Plateau, from the Copper Age to the Sassanid 2 Empire 3  4 Motahareh Ala Amjadi1,2, Yusuf Can Özdemir1,2, Maryam Ramezani3, Kristóf Jakab2, 5 Melinda Megyes2, Arezoo Bibak4, Zeinab Salehi3, Zahra Hayatmehar5, Mohammad 6 Hossein Taheri6, Hossein Moradi7, Peyman Zargari8, Ata Hasanpour9, Vali Jahani10, 7 Abdol Motalleb Sharifi11, Balázs Egyed12, Balázs Gusztáv Mende2, Mahmood 8 Tavallaie13, Anna Szécsényi-Nagy

https://www.biorxiv.org/content/10.1101/...l.pdf+html

  Abstract 34 35 In this study, we present new ancient DNA data from prehistoric and historic populations 36 of the Iranian Plateau. By analysing 50 samples from nine archaeological sites across 37 Iran, we report 23 newly sequenced mitogenomes and 13 nuclear genomes, spanning 38 4700 BCE to 1300 CE. We integrate an extensive reference sample set of previously 39 published ancient DNA datasets from Western and South-Central Asia, enhancing our 40 understanding of genetic continuity and diversity within ancient Iranian populations. A new 41 (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. The copyright holder for this preprint this version posted February 4, 2025. ; https://doi.org/10.1101/2025.02.03.636298 doi: bioRxiv preprint 2 Early Chalcolithic sample, predating all other Chalcolithic genomes from Iran, 42 demonstrates mostly Early Neolithic Iranian genetic ancestry. This finding reflects long-43 term cultural and biological continuity in and around the Zagros area, alongside evidence 44 of some western genetic influence. Our sample selection prioritizes northern Iran, with a 45 particular focus on the Achaemenid, Parthian, and Sassanid periods (355 BCE–460 CE). 46 The genetic profiles of historical samples from this region position them as intermediates 47 on an east-west genetic cline across the Persian Plateau. They also exhibit strong 48 connections to local and South-Central Asian Bronze Age populations, underscoring 49 enduring genetic connections across these regions. Diachronic analyses of uniparental 50 lineages on the Iranian Plateau further highlight population stability from prehistoric to 51 modern times. 

Finally, after almost 20 years waiting for the results, our J1-FGC6064 line was documented in Ancient DNA from Northern Iran around the Caspian Sea !
Dia de Glória !

[Qrts]

New samples from Mazandaran, Gilan, Khuzestan, Lurestan and Semnan. I see some Neo-Elamite period samples in there! Fascinating!

[RCO]

Three new samples from our J1-FGC6064 lineage, the first ancient DNA from our clade, Liarsangbon, Amlash, Gilan Iran_North
Three Parthian samples:
IRN23 and IRN25, a pair of genetically identical/twin individuals from Liarsangbon 200BCE to 100AD - J1-FGC6141 J1-FGC6069
IRN31 also from Liarsangbon 50BCE to 65 AD - J1-FGC6142

The interred bodies were  buried on their left side in small chambers cut into bedrock; the burials contained  numerous artifacts, including pottery, weapons and jewellery (Figure 3). South of  the cemetery, some architectural remains were also found. Thee cemetery was used during the Parthian period as confirmed by two radiocarbon dates obtained for dentin  collagen (skeleton 95502: 38 BCE– 123 CE, skeleton 96303: 45 BCE– 80 CE,

Human remains from Liarsangbon, Iran, 2016-2017 April 2019Bioarchaeology of the Near East 13(2019):49-53
https://www.researchgate.net/publication..._2016-2017

In the ancient DNA article:

551 We demonstrated a strong Iranian Neolithic and CHG substrate in the historical-period
552  samples from northern Iran, where these genetic components persisted in the pre-
553  Medieval era. We confirmed the continuity from the Chalcolithic-Bronze Age into this
554  period in northeastern Iran, despite this area hosting part of the Silk Road, which
555  facilitated extensive human movement. Bronze Age Steppe ancestry remained relatively
556  minor during the historical period in northern Iran. Instead, the historic period population
557  of the northern Iranian Plateau exhibited strong genetic affinities with the Chalcolithic and
558  Bronze Age communities of Turkmenistan, and northeastern-eastern Iran, forming
559  homogeneous groups in our analyses as a part of the described east-west cline. As only
560  one Iron Age genome is available from Turkmenistan, and there are none from the
561  northeastern Iranian Plateau, further sampling is necessary to investigate the dynamics
562  of this era, particularly to determine whether contacts between the two regions were
563  sustained or disrupted after the Bronze Age.

470 Evaluating other possible source populations, we demonstrate through f4-statistics in the
471 form of f4(CHG, Test, Samara_EBA_Yamnaya, Mbuti.DG) and qpAdm models, that the
472 BA Steppe affinities is only apparent due to shared CHG-related ancestries, which were 
473 previously defined in the BA Steppe communities (represented in our dataset with
474 Samara_EBA_Yamnaya

552 We demonstrated a strong Iranian Neolithic and CHG substrate in the historical-period
553 samples from northern Iran, where these genetic components persisted in the pre-
554 Medieval era. We confirmed the continuity from the Chalcolithic-Bronze Age into this
555 period in northeastern Iran, despite this area hosting part of the Silk Road, which
556 facilitated extensive human movement. Bronze Age Steppe ancestry remained relatively
557 minor during the historical period in northern Iran. Instead, the historic period population
558 of the northern Iranian Plateau exhibited strong genetic affinities with the Chalcolithic and
559 Bronze Age communities of Turkmenistan, and northeastern-eastern Iran, forming
560 homogeneous groups in our analyses as a part of the described east-west cline. As only
561 one Iron Age genome is available from Turkmenistan, and there are none from the
562 northeastern Iranian Plateau, further sampling is necessary to investigate the dynamics
563 of this era, particularly to determine whether contacts between the two regions were
564 sustained or disrupted after the Bronze Age.

supplemental

The macro-haplogroups J1 and J2 originate from the western parts of the Persian Plateau and  its surroundings, where they formed approximately 20,000 and 31,600 years ago, respectively  (Singh et al., 2016; Sahakyan et al., 2021). We report their sub-lineages in the Persian Plateau,  which sheds light on their persistence in the region, leading to their discovery in the historical  groups. We discovered two rare Y-DNA haplogroups, J1a2a2a~ in Liarsangbon (J-FGC6141 or  J-FGC6031, https://www.yfull.com/tree/J-FGC6031/ ) and J2b2a2a~ in Marsin Chal (J FGC61903 or J-Y28235, https://www.yfull.com/tree/J-Y28235/) (for more information see  Supplementary Table S4). These two sub-lineages have formed around the Neolithic period  (mean 9100-8100 and 7200-6500 years BP respectively, taken from the calculations in FTDNA  Discover and YFull), however they are not common in the mentioned databases. To our  knowledge, previously published ancient samples either did not trace downstream enough on  the phylogenetic tree or belonged to different or sister branches compared to the two J sub haplogroups identified here. Given the presence of these sub-haplogroups in modern Middle  Eastern populations within the same databases, the limited detection in ancient samples is  likely a result of the relatively small number of published ancient genomes from the region.

[billh]

Is there nothing pre 4th century BC on here? Quite disappointing. Also, I'm not sure if continuity is the right term, Clear influx of something ANF-rich between historical and medieval period, and loss of AHG (Andamanese?). Possibly mesopotamian migration under Sassanids. And it's a pretty small transect of 3000 years.

The lack of R1a in historical samples is interesting too.

[Mithra]

Looks like the Greek scenario for the Persian and Parthian Empire samples. No R1 and minor steppe ancestry.

Is the data available?

[HurrianFam]

Looks like the Greek scenario for the Persian and Parthian Empire samples. No R1 and minor steppe ancestry.

We just got 4 more R1 Greeks from Yediay et al

Crucially, haplogroup R1b-M269 (R1b1a1b) or downstream
only appears in individuals from Mycenaean contexts, with a
single exception: a Late Minoan individual who is an outlier
due to high steppe ancestry. Despite this, only the very rare
subhaplogroup R-PF7558 (R1b1a1b2) has been found so far
in Bronze Age Greece. This is a sister lineage of dominant R-
L51 and the R-Z2103 found in Yamnaya, and is with all
likelihood also connected with the Bronze Age spread of
steppe ancestry. Among the newly generated individuals,
however, we report here the occurrence of four individuals
from three different sites in Bronze Age Greece carrying the
R-Z2103 lineage. All four of them can be placed in the R-
Z2110 (R1b1a1b1b3a1, Z2103 > M12149 > Z2106 > Z2108 >
Z2110) branch; similar to previously published Yamnaya
individuals, who belong to R-Z2108. Additionally, one Early
Bronze Age individual (CGG_2_103620) from Moldova
reported in this study whose autosomes can be modelled
totally with Yamnaya source also carries the same
subhaplogroup (R-Z2108, R1b1a1b1b3a). We date the R-
Z2108 lineage to coalesce at 5.70 (95% confidence interval,
5.03–6.49) kya, which is consistent with a dispersion during
the Bronze Age.

[Mithra]

@HurrianFam

Maybe I was a bit vague. I was referring to the samples from this newly published paper but nevertheless very interesting samples from Yediay et al.

[Арсен]

and how did it get to Portugal/Brazil? if it was carried by steppe ancestors, it would probably be more common among other Indo-Europeans with greater steppe ancestry, but it is mainly found among the Portuguese

[Granary]

Looks like the Greek scenario for the Persian and Parthian Empire samples. No R1 and minor steppe ancestry.

Is the data available?

I mean not really, there is plenty of foreign ancestry in Myceneans if you don't assume the donor population is 100% Yamnaya-like

[Mithra]

Looks like the Greek scenario for the Persian and Parthian Empire samples. No R1 and minor steppe ancestry.

Is the data available?

I mean not really, there is plenty of foreign ancestry in Myceneans if you don't assume the donor population is 100% Yamnaya-like

The same is true for Iranians, the donor population probably looked like the Iron Age Turkmenistan sample referred to in the paper, which is essentially a Yaz-culture sample. The original steppe ancestry was diluted however. 

I expected a lot of R1a at least from the Achaemenid period and higher steppe ancestry than modern Iranians. This seems to not be the case as it stands now. The expectations looked like the Greek scenario before the first ancient DNA was published. I do however expect R1a in future sampling from the Iranian plateau. It would be miracle if there wasn’t any.

[billh]

Our analyses reveal that everyone out of the seven historical-period individuals yielding sufficient genome-wide data can be modelled either with one of these prehistoric groups as a single source or in a two-way model with an additional western Iranian source. In group-based analyses, shotgun genomes, such as those of the Marsin Chal and Liarsangbon groups (n=2 in each) can also be modelled with the same sources. However, the proportions of the northwestern IA components with elevated ANF/Levant-related ancestries are more prominent in Liarsangbon (Supplementary Table S14). IA Hajji Firuz is the only additional western source that provides plausible models for all historical groups. Using this source, Marsin Chal can be modelled with 78% BA Shah Tepe and additional ~22% IA Hajji Firuz, while for the Liarsangbon group these amounts are 37% BA Shah Tepe and 63% IA Hajji Firuz. The combined group, referred to as Iran_North_Historical, produces similar results and can be modelled with 52% BA Shah Tepe and 48% IA Hajji Firuz-type contributions (Supplementary Table S14). We interpret these findings as evidence that the genetic profiles of historical-period groups of the northern Iranian Plateau reflect their position along the broader east-west genetic cline, rather than resulting from specific admixture
events.

Does anyone know if Hajji Firuz IA is Yamnaya-Derived or CWC-derived? I know the close-by IA Hasanlu samples are Z2103-rich with no R1a and apparently Hajji-Firuz IA is also Z2103. Obviously there Z2103 is present in Srubnaya/PII though as well

[nomad01]

Our analyses reveal that everyone out of the seven historical-period individuals yielding sufficient genome-wide data can be modelled either with one of these prehistoric groups as a single source or in a two-way model with an additional western Iranian source. In group-based analyses, shotgun genomes, such as those of the Marsin Chal and Liarsangbon groups (n=2 in each) can also be modelled with the same sources. However, the proportions of the northwestern IA components with elevated ANF/Levant-related ancestries are more prominent in Liarsangbon (Supplementary Table S14). IA Hajji Firuz is the only additional western source that provides plausible models for all historical groups. Using this source, Marsin Chal can be modelled with 78% BA Shah Tepe and additional ~22% IA Hajji Firuz, while for the Liarsangbon group these amounts are 37% BA Shah Tepe and 63% IA Hajji Firuz. The combined group, referred to as Iran_North_Historical, produces similar results and can be modelled with 52% BA Shah Tepe and 48% IA Hajji Firuz-type contributions (Supplementary Table S14). We interpret these findings as evidence that the genetic profiles of historical-period groups of the northern Iranian Plateau reflect their position along the broader east-west genetic cline, rather than resulting from specific admixture
events.

Does anyone know if Hajji Firuz IA is Yamnaya-Derived or CWC-derived? I know the close-by IA Hasanlu samples are Z2103-rich with no R1a and apparently Hajji-Firuz IA is also Z2103. Obviously there Z2103 is present in Srubnaya/PII though as well

Hasanlu samples fall into Armenian-specific subclades, Hajji Hiruz is geographically close so it could be the same case.

[RCO]

and how did it get to Portugal/Brazil? if it was carried by steppe ancestors, it would probably be more common among other Indo-Europeans with greater steppe ancestry, but it is mainly found among the Portuguese

I have the hypothesis of the Iranic Alans in NW Portugal because the time and location do fit well together. I have a dataset of samples in our Portuguese and Brazilian J1-FGC6035 clade modal STRs and a few Big Y. The clade was one historical lineage from the Entre-Douro-e-Minho, close to the space of the documented Alans in Western Lusitania and the formation of the Suebi Kingdom with the capital in Braga, Southern Gallaecia, after the "Barbarian invasions" in the fall of the Roman Empire. The J1-FGC6035 definitely had local Warlords to have had a good expansion and local phylogenetic ramifications in the first centuries of the Portuguese Reconquista, Northern Portugal was a fierce warzone space against the Caliphate and the creation of the Portuguese frontier in Iberia and the Conquest of the Brazilian wilderness, as a high status Brazilian Portuguese mainstream lineage.

[RCO]

Does anyone know if Hajji Firuz IA is Yamnaya-Derived or CWC-derived? I know the close-by IA Hasanlu samples are Z2103-rich with no R1a and apparently Hajji-Firuz IA is also Z2103. Obviously there Z2103 is present in Srubnaya/PII though as well

There are 12 R1b samples found in Iran from the Iron Age (Lazaridis et al. 2022).

During the same period at Hasanlu in Northwest Iran, many individuals have no trace of Eastern hunter-gatherer ancestry at all despite the  presence of R-M12149 there, suggesting  that the initial association of this lineage with Eastern hunter-gatherer ancestry on the steppe had vanished as R-M12149 bearers reproduced with Southern Arc individuals without Eastern hunter-gatherer ancestry.

[billh]

Looks like the Greek scenario for the Persian and Parthian Empire samples. No R1 and minor steppe ancestry.

Is the data available?

I mean not really, there is plenty of foreign ancestry in Myceneans if you don't assume the donor population is 100% Yamnaya-like

The same is true for Iranians, the donor population probably looked like the Iron Age Turkmenistan sample referred to in the paper, which is essentially a Yaz-culture sample. The original steppe ancestry was diluted however. 

I expected a lot of R1a at least from the Achaemenid period and higher steppe ancestry than modern Iranians. This seems to not be the case as it stands now. The expectations looked like the Greek scenario before the first ancient DNA was published. I do however expect R1a in future sampling from the Iranian plateau. It would be miracle if there wasn’t any.

It is possible that when we get early Achaemenid samples, or better yet Mede samples, there will be more R1a. 

Does anyone know if Hajji Firuz IA is Yamnaya-Derived or CWC-derived? I know the close-by IA Hasanlu samples are Z2103-rich with no R1a and apparently Hajji-Firuz IA is also Z2103. Obviously there Z2103 is present in Srubnaya/PII though as well

There are 12 R1b samples found in Iran from the Iron Age (Lazaridis et al. 2022).

During the same period at Hasanlu in Northwest Iran, many individuals have no trace of Eastern hunter-gatherer ancestry at all despite the  presence of R-M12149 there, suggesting  that the initial association of this lineage with Eastern hunter-gatherer ancestry on the steppe had vanished as R-M12149 bearers reproduced with Southern Arc individuals without Eastern hunter-gatherer ancestry.

Yes, what I was wondering is whether their steppe DNA (among the samples that had some) was Yamnaya-like or CWC-like, as I suspect the HajjiFiruz/Hasanlu samples are actually some sort of Armenian-descended population or something else