U7 in Rostov Scythians

I found it quite interesting that in terms of mtDNA, the Rostov Scythians studied by der Sarkissian resembled closely the Shugnans of Tajikistan, who speak an eastern Iranian language. The author finds links between the Scythians and the "Central Asian Corridor", in particular with respect to mtDNA haplogroup U7.

This "Central Asian Corridor" sensu der Sarkissian (Iraq, Iran, Pakistan, India) seems to touch Frachetti's Inner Asian Mountain Corridor (shown below) in the region of the Pamirs.

Interestingly, the Sughnans belong, anthropologically to the Pamir-Ferghana type, which was also called Central Asian interfluvial type, the rivers in question being the Oxus and Jaxartes (Amu Darya and Syr Darya). And, of course, between these two rivers was the heartland of the Bactria Margiana Archaeological Complex, which I have previously linked with the Indo-Iranians.

Wells et al. studied Y-chromosomes of Sughnans, Yagnobis and other Iranic survivals of Tajikistan more than 10 years ago, and it will be very well worth revisiting them with newer methods. The area east of the Caspian and west of the IAMC intersects so much history, that any data from from it (new or ancient) would be extremely useful.

In my own experiments there has been an unambiguous "South Asian" genetic component in almost all Iranic peoples, even the westernmost Kurds. While the interpretation of this component is not easy, it does point to a genetic relationship between its possessors and Central/South Asia, with notable contrasts between Kurds/Iranians and their non-Iranic Armenian/Anatolian/Caucasian neighbors.

The occurrence of mtDNA haplogroup U7 in the Rostov Scythians is also consistent with a link between the Iranian nomads who penetrated into Europe with the area east of the Caspian, and it is also, of course, consistent with the narrative of Herodotus who recorded the migration of the Scythians into Europe.

There is a widely held theory that the origin of the Indo-Iranians are to be sought in eastern Europe. That theory appears inconsistent both with the "South Asian" autosomal signal in Iranic groups, and with the mtDNA evidence. Consider, again, the evidence of der Sarkissian:

Now, if Rostov Scythians were primarily descended from Mesolithic West Eurasians or even Bronze Age ones, then we would expect them to cluster at the "top", approaching the northern Europeoid extrema of PWC and Bronze Age Altai (ALT-BA). On the contrary, their position is well to the "south" of all European Bronze Age groups, and intermediate between Europeans and Iron Age Asian groups from south Siberia and Kazakhstan (KUR-IA, KAZ-IA). Again, this is compatible with an east-west migration during the Iron Age.

It might be worth speculating on the possible autosomal history of the steppe, for which the mtDNA evidence complements others: I offer that the long-term trend will be one of diminishing "North European", increasing "West Asian" and "East Eurasian" influences across the Neolithic-Bronze-Iron Age boundaries. At the western end of the steppe, there may also be "Mediterranean"/Sardinian-like infusions from the Balkans and Central Europe, although these clearly did not influence Inner/South Asia (where Mediterranean components shrink to non-existence), and Europe proper was mostly the recipient rather than the emitter of populations to Asia. Hopefully, autosomal data to test this conjecture will be made available in the coming years.

Iron Age Pazyryk mtDNA

The term "Scythian" is often used to describe a whole host of unrelated peoples across time periods, a practice that is not new but was also applied by the classical writers who were not well acquainted with the world of Eurasian nomads.

The distinction between "west" and "east" in terms of genetics and geography was not always very concordant. East Eurasian mtDNA has been uncovered as far west as Ukraine, and West Eurasian mtDNA well to the east of Europe, in Siberia and eastern Central Asia. The former was extended in the boreal zone of north Eurasian hunter-gatherers, while the latter in the intermediate steppe zone. The results of this paper might suggest that the Europeoid zone extended only up to the Altai, but a previous study discovered mtDNA U5a in Lake Baikal, well to the east of this region. A temporal transect of a particular region, such as the one reported here may help  elucidate not only the mixing of west/east types --which seems to be ancient across the northern parts of Eurasia-- but also the kinds of elements involved. For example, haplogroups K and J which are well-represented in the Iron Age results presented in this paper (especially the former), made their first appearance in the transition to the Iron Age in the Baraba forest-steppe zone to the west during the same time. The picture is still muddy, but a few patterns have begun to emerge: first U's, followed by T's during Andronovo horizon, followed by a wide assortment of lineages during the "Scythian" Iron Age. As I've written before, I strongly suspect that the last stratum originated in the area east of the Caspian sea, where the likely Proto-Indo-Iranian homeland existed, and where a segment of the BMAC population "went nomad" after the desiccation of their homeland.

PLoS ONE 7(11): e48904. doi:10.1371/journal.pone.0048904

Tracing the Origin of the East-West Population Admixture in the Altai Region (Central Asia)

Mercedes González-Ruiz et al.

Abstract

A recent discovery of Iron Age burials (Pazyryk culture) in the Altai Mountains of Mongolia may shed light on the mode and tempo of the generation of the current genetic east-west population admixture in Central Asia. Studies on ancient mitochondrial DNA of this region suggest that the Altai Mountains played the role of a geographical barrier between West and East Eurasian lineages until the beginning of the Iron Age. After the 7th century BC, coinciding with Scythian expansion across the Eurasian steppes, a gradual influx of East Eurasian sequences in Western steppes is detected. However, the underlying events behind the genetic admixture in Altai during the Iron Age are still unresolved: 1) whether it was a result of migratory events (eastward firstly, westward secondly), or 2) whether it was a result of a local demographic expansion in a ‘contact zone’ between European and East Asian people. In the present work, we analyzed the mitochondrial DNA lineages in human remains from Bronze and Iron Age burials of Mongolian Altai. Here we present support to the hypothesis that the gene pool of Iron Age inhabitants of Mongolian Altai was similar to that of western Iron Age Altaians (Russia and Kazakhstan). Thus, this people not only shared the same culture (Pazyryk), but also shared the same genetic east-west population admixture. In turn, Pazyryks appear to have a similar gene pool that current Altaians. Our results further show that Iron Age Altaians displayed mitochondrial lineages already present around Altai region before the Iron Age. This would provide support for a demographic expansion of local people of Altai instead of westward or eastward migratory events, as the demographic event behind the high population genetic admixture and diversity in Central Asia.

Link

rolloff analysis of South Indian Brahmins as Armenian+Chamar

The first analysis of this population showed that there were negative f3(Brahmin; X, Y) signals when X were a variety of West European, Balkan, and West Asian population, and Y either the Chamar or North Kannadi. In the first analysis I used Orcadians and North Kannadi. I have now carried out a new rolloff analysis on 470,559 SNPs, using Armenians_Y and Chamar_M as the reference populations.

The exponential fit can be seen below.

The admixture date is 142.814 +/- 15.010 generations, or 4,140 +/- 440 years, which seems to correspond quite well with commonly accepted dates for the formation of Indo-Iranian.

I have previously observed that:

These patterns can be well-explained, I believe, if we accept that Indo-Iranians are partially descended not only from the early Proto-Indo-Europeans of the Near East, but also from a second element that had conceivable "South Asian" affiliations. The most likely candidate for the "second element" is the population of the Bactria Margiana Archaeological Complex (BMAC). The rise and demise of the BMAC fits well with the relative shallowness of the Indo-Iranian language family and its 2nd millennium BC breakup, and has been assigned an Indo-Iranian identity on other grounds by its excavator. As climate change led to the decline and abandonment of BMAC sites, its population must have spread outward: to the Iranian plateau, the steppe, and into South Asia, reinforcing the linguistic differentiation that must have already began over the extensive territory of the complex.

Quite possibly, as the West Asian element began mixing with the Sardinian-like population in Greece, another branch of the Indo-Europeans made its appearance east of the Caspian, in the territory of the BMAC, admixing with South Asian-like populations. Thus, it might seem that the Graeco-Aryan clade of Indo-European broke down during the Bronze Age, with one branch heading off to the Balkans, and another to the east. 

This scenario would also explain how the likely J2-bearing population associated with the earliest Proto-Indo-Europeans may have acquired the contrasting pattern I have previously described: the western (cis-Caspian) population would have admixed with R1b-bearers who occupy the "small arc" west and south of the Caspian, while the eastern (trans-Caspian) populations would have admixed with R1a-bearers who occupy the "large arc" in the flatlands north and east of the Caspian. It would also explain how the "western" branch (Graeco-Armenian) would have picked up Sardinian-like "Atlantic_Med" admixture, which is absent in the "eastern" Indo-Iranian branch.

At the same time, this scenario would explain the lack of "North European" admixture in the "western" branch (since this was shielded by the Caucasus and Black Sea from the northern Europeoids who may have lived north of these barriers), and explain it in the "eastern" branch (since the BMAC agriculturalists were in contact with presumably northern Europeoid groups inhabiting the steppelands, unhindered by any major physical barriers). (The relative absence of this admixture in the Graeco-Armenian branch may be advanced on the strength of its absence in Armenians, the evidence of a Sardinian-like Iron Age individual from Bulgaria, and the historical-era timing of admixture for the Greek population.)

It would be interesting to carry out similar experiments on Iranian groups, to see if they, too, present a similar pattern of admixture.

Visualizing admixture differences with ACD tool

Vaêdhya has created a new ACD tool that allows one to visualize differences between sets of populations in terms of admixture components. He also posts two examples of the application of his tool on data generated by myself in the Dodecad Project, as well as by the Harappa Project.

 I have speculated about the origins of Indo-Iranians before, noting that the evidence links even the Kurds with a "South Asian" component; in subsequent higher-resolution analysis, such as the K12b, it appeared that this component was related to the Gedrosia component. In any case, the evidence is clear about the links of different Iranian and Indo-Aryan groups, so it is nice that this can be made evident with the ACD tool and data from the Harappa Project. Notice the excess of the Baloch (~Gedrosia) component in Kurds and Iranians in contradistinction to the Indo-European Armenians and Semitic Assyrians. It is fairly clear to me that the Iranian ancestral homeland is to be sought to the east, with the Bactria-Margiana Archaeological Complex (BMAC) being a good candidate for its location.

In a second plot, Vaêdhya uses Dodecad data to contrast patterns of differences in Northeastern Europe. Here, too, the patterns are clear, with Finns, and secondarily Russians showing an excess of Siberian ancestry relative to Poles. This is, no doubt, due to the Finnic element, which links Finns, and the Uralic substratum in Russians with Siberia. A second contrast is between Finns and Russians/Poles. The latter have more of the Caucasus component, a probable legacy of the Bronze Age Indo-European invasion of Europe. A final contrast is the higher Atlantic_Med element in Poles, which suggests an excess of early Neolithic farmer ancestry, or, admixture with West European populations such as Germans and others who possess more of this component than Slavs.

Huge study on Y-chromosome variation in Iran (Grugni et al. 2012)

This is the equivalent of a box of candy for anyone interested in Eurasian (pre-)history. I will have digest all the goodies within, and post any of my comments as updates to this post.

UPDATE I: Here is the table of haplogroup frequencies for easy reference:

One of the most interesting finds is the presence of a few IJ-M429* chromosomes  in the sample. Haplogroup IJ encompasses the major European I subclade, and the major West Asian J subclade. The discovery of IJ* chromosomes is consistent with the origin of this haplogroup in West Asia; it is widely believed that haplogroup I represents a pre-Neolithic lineage in Europe, although at present there are no Y chromosome-tested pre-Neolithic remains.

There is also a wide assortment of Q and R in Iran. While some of these may be intrusive (e.g., the 42.6% of Q1a2 in Turkmen, likely a legacy of their Central Asian origins), the overall picture appears consistent with a deep presence of these lineages in Iran. This is especially true for haplogroup R where pretty much every paragroup and derived group is present, excepting those likely to have originated recently elsewhere.

UPDATE II: From the paper:

Although accounting only for 25% of the total variance, the first two components (Figure 3) separate populations according to their geographic and ethnic origin and define five main clusters: East-African, North-African and Near Eastern Arab, European, Near Eastern and South Asian. The 1stPC clearly distinguishes the East African groups (showing a high frequency of haplogroup E) from all the others which distribute longitudinally along the axis with a wide overlapping between European and Arab peoples and between Near Eastern and South Asian groups. The 2ndPC separates the North-African and Near Eastern Arabs (characterized by the highest frequency of haplogroup J1) from Europeans (characterized by haplogroups I, R1a and R1b) and the Near Easterners from the South Asians (due to the distribution of haplogroups G, R2 and L). Iranian groups do not cluster all together, occupying intermediate positions among Arab, Near Eastern and Asian clusters. In this scenario, it is worth of noticing the position of three Iranian groups: (i) Khuzestan Arabs (KHU-Ar) who, despite their Arabic origin, are close to the Iranian samples; (ii) Armenians from Tehran (THE-Ar), whose position, in the upper part of the Iranian distribution, indicates a close affinity with the Near Eastern cluster, while their position near Turkey and Caucasus groups, due to the high frequency R1b-M269 and other European markers (eg: I-M170), is in agreement with their Armenia origin; (iii) Sistan Baluchestan (SB-Ba) that clusters with its neighbouring Pakistan.

UPDATE III: There are lots of little details in the haplogroup distribution that make historical sense. For example, C3 exists in Assyrians from Azarbaijan, and both C*, C3, and O exists in Zoroastrians from Yazd. It is often forgotten that before the spread of Islam, and quite time thereafter, Inner Asia was teeming with Zoroastrians and Nestorian Christians. It seems quite likely that these outliers represent a legacy of these communities.

UPDATE IV: I have a feeling that Razib will take exception with this statement: "Ancient Persian people were firstly characterized by the Zoroastrianism. After the Islamization, Shi'a became the main doctrine of all Iranian people."


UPDATE V: This confirms my observation from the recent studies in Afghanistan, that there is an inverse relationship of J2a and R1a in Iranian-speaking groups, with an excess of the latter among the eastern Iranians, and of the former among the Persians. From the paper:

Among the different J2a haplogroups, J2a-M530 [46] is the most informative as for ancient dispersal events from the Iranian region. This lineage probably originated in Iran where it displays its highest frequency and variance in Yazd and Mazandaran (Figure 2). Taking into account its microsatellite variation and age estimates along its distribution area (Tables S3 and S7), it is likely that its diffusion could have been triggered by the Euroasiatic climatic amelioration after the Last Glacial Maximum and later increased by agriculture spread from Turkey and Caucasus towards southern Europe. The high variance observed in the Italian Peninsula is probably the result of stratifications of subsequent migrations and/or of the presence of sub-lineages not yet identified. Of interest in the M530 network (Figures 2 and S3) is the presence of a lateral branch that is characterized by a DYS391 repeat number equal to 9. Differently from previous observations [46], this branch is not restricted to Anatolian Greek samples being shared with different eastern Mediterranean coastal populations. The M530 diffusion pattern seems to be also shared by the paragroups J2a-M410* and J2a-PAGE55*. In addition, the variance distribution of the rare R1b-M269* Y chromosomes, displaying decreasing values from Iran, Anatolia and the western Black Sea coastal region, is also suggestive of a westward diffusion from the Iranian plateau, although more complex scenarios can be still envisioned because of its non-star like structure.

Of course, the idea that the diffusion of J2a related lineages ties in with early agricultural expansions has been with us for a long time, but it is time to abandon it. First of all, as we have seen, J2a diminishes greatly as we head towards South Asia; it certainly doesn't look like the lineage of the multitude of agricultural settlements that sprang up along the southeastern vector soon after the invention of agriculture. Second, it is lacking so far in all ancient Y chromosome data from Europe down to 5,000 years ago. It seems much more probably that J2 related lineages spread from the highlands of West Asia much later. 


The "age estimates" are the result of using the inappropriate "evolutionary mutation rate", and become even older because of the inclusion of the DYS388 marker that is very stable in many haplogroups but very mutable within haplogroup J. On the left you can see frequency, Y-STR variance, and haplotype network structures for various J-related groups.


It is unfortunate that there is no progress in the phylogeographic assessment of R1a in this paper. There have been substantial discoveries of SNPs within this haplogroup as a result of commercial testing; however there is clearly an ascertainment bias in the newer discoveries, as almost all these SNPs have been detected in Europeans. The new paper confirms the high levels of Y-STR variance in India, Pakistan, and Iran. Together with the cornucopia of related paragroups in Iran, there is little doubt that this haplogroup originated in the general area of Central/South Asia.


Personally, as I have stated before, I would relate this R1a with Neolithic peoples living east of the Caspian, in contrast to the R1b bearers who lived west and south of it. These two populations came under the influence of the Indo-Europeans and spread in different directions. The Indo-Iranians were then initially the mixed descendants of the Indo-Europeans and the R1a old agricultural population, and were formed in the territory of the Bactria-Margiana Archaeological Complex. 


This also explains the contrast between Iranian and Armenian groups: the latter mostly lack the R1a lineage, contrasting with all Iranian groups (even their Kurdish neighbors) who possess it. Conversely, Iranian groups, and especially eastern Iranians and Indo-Ayrans lack the R1b lineage. This is due to the fact that neither R1a nor R1b were originally part of the Indo-European community, but their geographical position was such that they came under the influence of the Indo-Europeans when the latter began their expansion.


UPDATE VI: I have created my own dendrogram using the Y-haplogroup frequencies and the hclust package of R (default parameters):

From top to bottom, one can identify some clusters:

• Eastern Europe, further broken down into Balkans and Slavic+Hungary
• West Asian/Caucasus
• Iranian Proper
• Arab

These correspond largely to the clusters identified by the authors, with India and the Turkmen sample emerging as the clear outliers. I omitted the Ethiopian samples, since E-M78 was not resolved phylogenetically, causing the Ethiopians to group with the likely E-V13 from the Balkans.

UPDATE VII: I have also run MCLUST over the haplogroup frequency data over the MDS representation of the distance matrix. The maximum number of 10 clusters occurred with 5 MDS dimensions retained. Population assignments in the 10 clusters can be found in the table below:

Iran/Azerbaijan_Gharbi+Tehran_(Assyrian)	1
Iran/Lorestan_(Lur)	1
Iran/Tehran_(Armenian)	1
Iran/Azerbaijan_Gharbi_(Azeri)	2
Iran/Hormozgan_(Bandari+Afro-Iranian)	2
Iran/Hormozgan/Qeshmi	2
Iran/Khorasan_(Persian)	2
Iran/Kurdistan_(Kurd)	2
Iran/Sistan_Baluchestan_(Baluch)	2
Pakistan	2
Iran/Fars+Isfahan_(Persian)	3
Iran/Gilan_(Gilak)	3
Iran/Yazd+Tehran_(Zoroastrian)	3
Turkey/Central	3
Turkey/East	3
Turkey/West_	3
Iran/Golestan_(Turkmen)	4
India	4
Iran/Khuzestan_(Arab)	5
Egypt_(Arab)	5
Iraq/Baghdad	5
Oman	5
Saudi_Arabia	5
Tunisia	5
United_Arab_Emirates	5
Iran/Mazandaran_(Mazandarani)	6
Iran/Yazd_(Persian)	6
Balkarian	6
Georgia	6
Albania	7
Greece	7
Bosnia	8
Croatia	8
Slovenia	8
Czech_Republic	9
Hungary	9
Poland	9
Ukraine	9
Iraq_(Marsh_Arab)	10
Qatar	10
Yemen	10

We can ignore cluster #4 which consists of the two outliers (India + Turkmen). The rest of the clusters seem relatively coherent. Notice, for example, the Arabian cluster #10, Balkan cluster #8, Eastern European cluster #9, Greek-Albanian cluster #7, Mixed Arab cluster #5.

PLoS ONE 7(7): e41252. doi:10.1371/journal.pone.0041252

Ancient Migratory Events in the Middle East: New Clues from the Y-Chromosome Variation of Modern Iranians

Viola Grugni et al.


Knowledge of high resolution Y-chromosome haplogroup diversification within Iran provides important geographic context regarding the spread and compartmentalization of male lineages in the Middle East and southwestern Asia. At present, the Iranian population is characterized by an extraordinary mix of different ethnic groups speaking a variety of Indo-Iranian, Semitic and Turkic languages. Despite these features, only few studies have investigated the multiethnic components of the Iranian gene pool. In this survey 938 Iranian male DNAs belonging to 15 ethnic groups from 14 Iranian provinces were analyzed for 84 Y-chromosome biallelic markers and 10 STRs. The results show an autochthonous but non-homogeneous ancient background mainly composed by J2a sub-clades with different external contributions. The phylogeography of the main haplogroups allowed identifying post-glacial and Neolithic expansions toward western Eurasia but also recent movements towards the Iranian region from western Eurasia (R1b-L23), Central Asia (Q-M25), Asia Minor (J2a-M92) and southern Mesopotamia (J1-Page08). In spite of the presence of important geographic barriers (Zagros and Alborz mountain ranges, and the Dasht-e Kavir and Dash-e Lut deserts) which may have limited gene flow, AMOVA analysis revealed that language, in addition to geography, has played an important role in shaping the nowadays Iranian gene pool. Overall, this study provides a portrait of the Y-chromosomal variation in Iran, useful for depicting a more comprehensive history of the peoples of this area as well as for reconstructing ancient migration routes. In addition, our results evidence the important role of the Iranian plateau as source and recipient of gene flow between culturally and genetically distinct populations.

Link