Thursday, July 19, 2012

Interpreting New Iranian Y-Chromosomal Data (Grugni et al.)


Introduction


A new study on Iranian Y-Chromosomes released just yesterday has, to my satisfaction, adequately sampled every major ethno-linguistic group as well as determining inter-provincial variation between them. Grugni et al. sampled 938 unrelated Iranian men from 15 ethnic groups (including Assyrians, Zoroastrians and Turkmen) in 14 provinces across the country.


Abstract

"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."

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Interpretation of Results

Iranian Y-SNP Frequencies

Data from the original study can be found opposite. In addition, several contour maps showing the frequency of select Y-DNA Haplogroups found across the country are shown along the right. Armenians, Zoroastrians and Assyrians from Tehran, as well as Afro-Iranians from Hormozgan province, are excluded. Note that updated ISOGG nomenclature was applied wherever deemed appropriate (refer to SNP's for clarification of status). Frequency ranges shown on maps are from 0-100%. Please note the maps are only intended to depict general trends rather than specific figures. Refer to the figures from the study (above) for these.


- Consistent with anthropological data and historical records from South Iran, the Y-DNA Haplogroups with frequencies greater in Africa than Eurasia (B-M60 and E2-M75) peak in Hormozgan province. 

- Over half a dozen para-Haplogroups (C*-M216, F*-M89, H*-M69, IJ*-M429, J2*-M172, L*-M61, NO*-LLY22g, Q1*-P36.2 and R*-M207) were found scattered across Iran. Although the presence of para-Haplogroups within a region are often taken as an indicator of a lineage's antiquity there, both their consistency and correspondence with downstream younger clades must be considered before such a conclusion is made. As such, I do not consider H*-M69, NO*-LLY22g or C*-M216's presence in this cohort to indicate anything other than Iran's position as a geographic crossroad. The remaining ones (particularly J2*-M172, L*-M61 and R*-M207) require further investigation to elucidate whether Iran does stake the claim to the origins of each.

- Further to the above, it is likely that the R*-M207 reported in this paper is in fact R2*-M479 based on the dated SNP array used.

- C5-M356 makes a sporadic appearance across Iran. A mysterious clade with a spotty distribution across much of Eurasia. In the region, it is more commonly associated with the Indian Subcontinent.
Iranian J1c3-PAGE08

- Haplogroup G makes a strong appearance with, in my opinion, enough clade diversity to validate an origin in Iran or a close-by region. This is partially supported by its' presence in every ethnic group, albeit through different subclades.

- Although IJ*-M429 has finally been found, Grugni et al.'s decision not to publish STR data does not give us the means to determine if the two Mazandarani and Persian men are in fact related within a genealogical timeframe. The significance of this find in Iran will have to remain pending.

The lacklustre SNP definition in the Y-DNA I found in Iran (Gilaki, Bandari, Kurdish and Armenian populations between I1-M253 and I2-M438) dissuades strong conclusions regarding the development of I-M170 relative to IJ*-M429's discovery. The lack of STR's prevents us from ascertaining whether these are recent contributions from Europe or not, or whether there is any European connection to begin with.

- Both the frequency and subclade diversity of Haplogroup J2-M172 (as well as the presence of J2*-M172 and J2a*-M410 across the country) makes Iran a strong candidate for the origin of this lineage.

The strong presence of J1c3-PAGE08 is one of the surprising finds of this study. With an absence only amongst Assyrians from Azarbaijan province and a peak in Khuzestani Arabs (31.6%), I speculate this is an early Near-Eastern pastoralist nomad marker that is only accentuated in Khuzestani Arabs because the L147.1 marker (J1c3d), which is commonly associated with the expansion of Semitic languages (particularly Arabic in literature) was not tested here. Otherwise, it would be difficult to reconcile medieval Arabic admixture among Iran's Zoroastrians being comparable (and often greater) than Azeris, for instance, as Azerbaijan hosted Arab garrisons following the Sassanid collapse.

- Haplogroup Q presents with a very distorted picture. 42.6% of Turkmens belonging to Q1a2-M25 is not in agreement with Wells et al.'s The Eurasian Heartland: A continental perspective on Y-chromosome diversity, where Haplogroups J, N, R1a and R1b predominated, suggesting either an extensive Founder effect has taken place (i.e. regionalisation of certain branches from a common Oghuz Turk pool) or the Golestani Turkmen values have experienced a more generic form of genetic drift.
On the matter of Turkic affinities, Azeri's from Azarbaijan province have greater subclade variation than all other ethnic groups. However, the total frequency is either comparable (or less) than Persians nationwide. As it stands, if one were to presume Haplogroup Q in Iran was of Turkic origins, it would appear their contribution to the Persian and Azeri genepools is comparable despite linguistic differences. Although more data would certainly flesh this matter out, this diversity combined with the presence of N-M216 among Iran's Azeri population certainly gives a genetic basis for their linguistic heritage.

Haplogroup R1a1a-M17 is regularly found at frequencies greater than 15% across Iran, contrary to the assertion made by Dr. Wells one decade ago regarding the limited samples he obtained, again from The Eurasian Heartland: A continental perspective on Y-chromosome diversity ;

Iranian G2a-P15
"Intriguingly, the population of present-day Iran, speaking a major Indo-European language (Farsi), appears to have had little genetic influence from the M17-carrying Indo-Iranians."

It is somewhat ironic, however, to note that the Persians from Fars province presented one of the lowest R1a1a-M17 frequencies observed in this study. Whether sampling chance is an issue here, or the sparsity of M17 is indeed a reality, is an open question.

- The presence of both R1a1-SRY1532.2 (shown as R1a* due to old nomenclature) and R1b*-M343 repeat the presence of these para-Haplogroups in the region, indicating West Asia was from whence Haplogroup R1-M173 began differentiating into the two primary subclades we see today in Eurasia.

Haplogroup R1b1a2a-L23 is more frequent in the north and west of the country, which (together with its' presence in the furthest southern and eastern poles at ~3%) suggests it likely moved in an overall south-easterly direction via diffusion, probably during the Neolithic.

- The distribution of Haplogroup R2a-M124 is, much like C5-M356, irregular. Contrary to what is shown in Haber et al.'s research, R2a is not more common in the east of the country. Instead, it can be found amongst Esfahani Persians at a frequency of 9.1%. That Iran's R2a frequency achieves its' peak in the centre of the country is reminiscent of Sahoo et al.'s A prehistory of Indian Y chromosomes: Evaluating demic diffusion scenarios;


The sensationalist question of the hour; what accounts for the spike in R2a-M124 that has been picked up in Central Iran for the past half decade?

- Finally, Haplogroup T-M70 enjoys a frequency of 10.1% amongst Assyrians from Azarbaijan province, whilst also being more common among Persians across the country and Iranians from the western periphery of the country (Azeris and Kurds). This would suggest, therefore, an at least passive but deep association with ancient Near-Eastern cultures.


Criticisms of Paper

Despite the rich sampling pool, I have several immediate criticisms;

Iranian J1-M267
  • There are some issues with the sampling strategy employed by this paper. For instance, the Assyrians (Christian non-Arab Semitic-speaking minority) are represented by 39 men, although Persians from Esfahan (a major Iranian city) are by 11 only. 
  • Inadequate haplotype data has been released; the only offering is 8-STR's from select lineages (e.g. J1*-M267) which were used for variance analysis.
  • Furthermore, a maximum of 10 Y-STR's were analysed, rendering some of their variance calculations questionable at such a low resolution. This also does away with the possibility of MRCA and intra-subclade age calculations.
  • Grugni et al. have approached Haplogroup R1a1a-M17 in a similar vein to past studies (e.g. Haber et al., see Showcasing of Y-DNA Variation Among Afghan Ethnic Groups) by not referring to current data concerning the structure of R1a1a. As with Haber et al., R1a1a-M458 is taken as the "European" strain, despite research undertaken by the R1a1a and Subclades Y-DNA Project revealing the apparent schism between the upstream Z283 and Z93 SNP's being far more informative in this regard.
  • Haplogroup R1b1a2*-L23 is considered as a "West Eurasian" paternal contribution to the Iranian plateau rather than the possibility it may have originated within or in proximity to the country's western zone. 
  • As shown in Interpretation of Results, Grugni et al.'s use of dated nomenclature poses problems for those who may not be intimately familiar with recent Y-SNP Tree changes by ISOGG.

Acknowledgements

Map of Iran courtesy of D-Maps.com.

Tuesday, July 17, 2012

The Secrets of Central Asia: Chapter II - The Nomads of West Siberia

Introduction

Molodin et al. have conveniently released an exciting paper just days ago, revealing the convergence and possible origins of maternal lines in several West Siberian sites across different points of time.

The authors made the following conclusions based on the data they had gathered;

"We therefore consider the appearance of the Haplogroup T-lineage as the most likely genetic marker of the Andronovo migration wave to the region....
Apparently, the Andronovo group... assimilated the aboriginal... population, from which it obtained these East-Eurasian mtDNA haplogroups. Obviously, there was reciprocal genetic contact between the migrant and indigenous groups in the region.
...These [autochthonous] components were represented by the Eastern Eurasian haplogroups A, C and Z, and the Western Eurasian haplogroup U5a. On the other hand, the results also reveal some changes in the mtDNA pool structure throughout the Bronze Age. Some of these changes, which point to migration waves to the West Siberian forest steppe zone, are in agreement with the archaeological and anthropological evidence. The most relevant migration waves occurred during the Middle Bronze Age (represented by the migration of the Andronovo culture, probably marked by Haplogroup-T lineages) and the transition from the Bronze to the Iron Age (represented by the migration from the south, marked by the U1a, U3 and H haplogroup lineages)."

[PDF]

In this blog entry, these conclusions reached are scrutinised together with the deeper ancestral associations of these haplogroup lineages with modern (and other ancient) populations.


The Original Paper's Findings

A total of 92 ancient DNA (aDNA) haplotypes in the form of mitochondrial DNA (mtDNA) were retrieved from five sites stratified across seven distinct archaeological periods in a fixed portion of West Siberia known as the Baraba forest-steppe, lying between the network formed between the Irtysh and Ob rivers. These haplotypes were obtained from Hypervariable Region 1 (HVR1) of mtDNA and are included in the original study (shown as Table 3). 

Sampling Sites in Babara Forest-Steppe

As no burial remains have been found dating to the Pleistocene (11th-12th millenium BC) in or around the Baraba forest-steppe, which is the earliest period where anatomically modern humans reached this region, the ultimate origins of the Early Bronze Age lineages are left open to interpretation. Nonetheless, below is a summary of each archaeological culture showcased in the paper, as well as relevant extracts from the literature. [1]


Ust-Tartas (4000-3000 B.C.)

The inhabitants of the earliest grave-containing Baraba prehistoric culture appeared to be Caucasoid-Mongoloid hybrids based on anthropological data whose distribution spanned the swathe of forest from Karelia and the Baltic through to the Ural region. Numerous Russian sources have previously described this concept as the Northern Eurasian Anthropological Formation (e.g. Bunak V.V.). Additionally, a comparison with the nearby Comb-pit Ware culture revealed enough anthropological similarities to suggest the individuals of Ust-Tartas were likely to be autochthonous and not recent migrants.

Extent of the N. Eurasian Anthropological Formation
Of the 18 mtDNA haplotypes retrieved, East Eurasian lineages (A, C, D, Z) comprised a slight majority (11/18). The authors noted "widely distributed root haplotypes" for Haplogroups C and D, which presumably indicates greater antiquity of both in the region. The two individuals belonging to haplogroup A "[represent] a subcluster that is apparently characteristic of West Siberia and the Volga-Ural Region". There was surprise at the presence of Haplogroup Z based on its' absence in modern inhabitants of West Siberians, a topic explored later in this entry.
The seven West Eurasian mtDNA Haplogroups belonged entirely to U, comprising of U2e, U4* and U5a1. The authors recalled the findings of several other recent studies on ancient DNA, stating it likely belonged to "Eastern, Central and Northern European hunter-gatherer groups". [1] 

Besides affirming previous literature concerning the migration corridor between East Europe to East Asia, the haplotypes also complement the anthropological data concerning their status as Mongoloid-Caucasoid hybrids.


Odinovo (3000 B.C.) and Krotovo (Early, 2000 B.C.)

Both of these cultures, regardless of stage, represent a fairly linear continuity from the populations and traditions of the Ust-Tartas culture before them.

The Odinovo culture succeeds Ust-Tartas, although it is viewed as a synthesis between it and the Comb-Pit Ware archaeologically. Anthropological kinship between it and contemporary Baraba findings also confirm the autochthonous nature of Odinovo. However, it differs from its' antecedents in grave objects, funeral rites and the presence of bronze artefacts belonging to the Seima-Turbino cultural phenomenon, a short-lived (2200-1700 B.C.) but "striking" package of metallurgical  goods originating around the Sayan-Altai region in South Siberia that was oriented westwards towards Europe. [2]

In turn, the Krotovo culture is partially derived from Odinovo, although it isn't without its' own influences from adjoining regions. As well as "strikingly different" funeral rites, [1] new archaeological features, including items fashioned out of chalcedony, jaspilite and enstatite, point toward interactions of some degree with the Petrovo culture found further south in Kazakhstan, where the nearest deposits of these materials lie. It is worth noting the physical type of the Krotovo people revealed no significant changes, remaining in-line with the previous autochthonous type.

A total of 16 mtDNA haplotypes were recovered from both Odinovo and the Early Krotovo stage. The spectrum of mtDNA Haplogroups remain unaltered from the Ust-Tartas samples, supporting the archaeological record of continuity. 

The paper goes on to elaborate on the discrepancy between the mtDNA results and the archaeological features of Krotovo by stating "our data did not allow us to detect any Central Asian genetic influence". [1] Several possible explanations which may be considered;
  1. New material items from Petrovo accompanied a male-mediated migration towards Krotovo, resulting in some level of cultural assimilation
  2. In support of the above, the Petrovo culture natives may have themselves been a southward extension of the "Northern Eurasian Anthropological Formation" and belong to the same basic physical type as Ust-Tartas, Odinovo and Krotovo individuals further north, making any inter-culture interactions difficult to infer
  3. Some mode of transmission between Krotovo and Petrovo took place (trade, "package diffusion")

Further information is needed to ascertain which is more probable, including (but not restricted to) Y-Chromosomal data from all concerned cultures for evidence of (dis)continuity between Odinovo and Krotovo through southern influence, as well as anthropological data from Petrovo to determine if they were indeed of the same basic physical type.

The summation of the evidence provided, however, indicates material items from further south were brought northwards into the Baraba forest-steppe after 2000 B.C., but these cultural changes do not reflect in the native maternal lineages, implying less overt processes (or male-mediated migration) were causative.


Krotovo (Late, 1750 B.C.) and Andronovo (1500 B.C.)

The next significant period of Baraban history comes with the arrival of semi-nomadic pastoralists whose origins lay further to the west. We are, of course, referring to the founders of the Andronovo archaeological complex, whose Indo-European language, culture and even ideology had eventually infiltrated deep into the Iranian plateau and Indian subcontinent through their utilisation of both horse and chariot. [3]

Schematic Tree of mtDNA Haplogroups  Found
Within Baraba, despite the Krotovo population coexisting with these newcomers for a length of time (presumably due to their occupancy of different pastoralist niches), we see evidence of a shift from Seima-Turbino to Andronovo with regard to their material traditions. Andronovan dominance is also reflected in the eventual northward displacement of some Krotovo natives based on archaeological data. [1] However, cranioanalysis presents a more complicated picture; the presence of an "autochthonous Mongoloid" variant not typically seen in the Baraba steppe-forest, differing from the hybrid type seen for hundreds of years prior, may suggest the two were not in direct contact and Andronovan influence was exerted by proxy of other native groups who were displaced northwards and east following their assimilation. This is anecdotally supported by Keyser et al.'s discovery of one Andronovo male (specimen S07) from near Krasnoyarsk in South Siberia carrying Y-DNA Haplogroup C*. [4] It is worth stating the physical type of those from Andronovo are commonly described as "Variants of three proto-Europoid types " with minor Mongoloid. [1]

40 mtDNA haplotypes from Late Krotovo (1750 B.C) and Andronovo (1500 B.C.) sites and time periods were taken.  As expected, the same spectrum of mixed West-East Eurasian lineages made an appearance, except for the strong introduction of one new Haplogroup.

In both Late Krotovo and Andronovo, Haplogroup T reaches a stable frequency of 15% in both despite being completely absent in 34 earlier haplotypes. The authors cite this as direct genetic evidence of Andronovan influence on Late Krotovo and postulate this lineage was, as a result, a major contingent in the Andronovo culture's spread.

All of these events precede the Irmen culture (1400-900 B.C.), the eventual successor to Andronovo. Those Irmen individuals found in the Baraba region were found to be predominantly Caucasoid and practiced a mixed economy of agriculture and animal husbandry. Only data from the Late stage (900-800 B.C.) was considered in the study.


Baraba (Late, 1000 B.C.)

The Late Baraba culture is a consequence of a Krotovo-modified Andronovo successor (known as Suzgan) interacting with the Irmen culture (described above). This was a particularly tumultuous period in West Siberian prehistory with tribes continuously coalescing unto one another, forming new identities in the process.

Anthropological data from the Late Baraba culture painted a far more diverse picture than over the previous three millennia. The authors noted that, contrary to the general insignificance of gender on physical type, the men were found to be more similar to a "Southern Eurasian Anthropological Formation", whereas females were closer to the Andronovan derivatives in North Kazakhstan. 

Only five mtDNA haplotypes were recovered from this period. Haplogroups A and C once again were represented, as was U5b and T, indicating the previous assimilation events had been maintained uptil this point. 


Irmen (Late, 900-800 B.C.)

From 1000 B.C. onwards, a complex set of migrations took place in West Siberia between the cultures formed by this point. Archaeologists attribute this to ecological changes involving climatic cooling across the region. 

The last sampled site is the Late Irmen culture, which is a continuation of the Irmen culture proper described earlier in this entry. The intricate interactions between cultures of this period are evident through multi-plural settlements in the archaeological record here.

The final 14 mtDNA haplotypes were, unexpectedly, a complete departure from the partial continuity that we have seen since Ust-Tartas uptil Late Baraba. Almost all belonged to West Eurasian lineages, such as Haplogroups J, K and W. The study had suggested the ultimate origins of these lineages came from further south, in the vicinity of West Kazakhstan and West Central Asia (Turkmenistan and Uzbekistan likely implied). This suggestion will be assessed in detail later in this entry.


Confirmation of the 'Migration Corridor'?

It is remarkable to finally find genetic evidence of the migration corridor, an archaeological concept mentioned several times in Vaêdhya, firmly imprint it in such a definitive way (visit North European Component Variation within the Eurasian Heartland for additional information). 

As it stands, we can now safely conclude that prehistoric hybridisation between hunter-gatherer Paleo-European populations and those from along the East across the Eurasian steppe. The crossover of both along opposing ends of this corridor has been supplemented with aDNA and anthropological evidence, with the finding of a near-equal hybrid population midway between the two poles all but confirming what the raw results have already revealed. Therefore, the connection between Northeast Europe and East Asia through the Eurasian steppe (even before Proto-Indo-European's formation) can no longer be considered a hypothesis, but a verified reality of demic prehistory. If supported with autosomal DNA (auDNA) from similar gravesites, it will drastically alter our perception of the migrations that happened afterwards, as well as doing away with over-simplified models of how certain languages and cultures permeated across Eurasia.


Afanasievo: Without a trail?

It is interesting to note that, despite covering over 3,000 years of prehistory, there is yet to be a trace of the Afanasievo culture, the earliest known offshoot of Yamnaya in the east, across this territory. Under the Eurasian steppe theory, the Afanasievo culture is connected with pastoral nomads who spoke an early (proto) form of the Tocharian branch, an extinct Centum Indo-European language which subverts the Centum:Satem isogloss in Eurasia. [5] The only attested connection between Afanasievo and the Baraba forest-steppe is through interactions between its' successor culture, the Karasuk, with the easternmost of the early Irmen. [1]

The question that persists is thus; where is the Afanasievo trail from Yamanaya through to the Urals and their final archaeological seat in South Siberia? Why have none of the Baraba forest-steppe cultures shown any indication of influence, be it cultural or anthropological, of Caucasoid pastoral nomads before those of Andronovo? 

To arrive at one likely answer, Frachetti's Pastoralist Landscapes and Social Interaction in Bronze Age Eurasia clarifies the material culture and mode of living in Central Asia during the Bronze Age;

"The calibrated C14 dates of Afanas'evo material are generally slightly earlier than those taken from Yamnaya contexts in the western steppe, which complicates a diffusionist explanation of the emergence of pastoralists in the eastern steppe. Although their origins may be obscure, communities associated with Afanas'evo materials still represent the earliest mobile pastoralists east of the Ural Mountains... [their] incipient strategy of cattle and sheep/goat herding, supplemented by hunting and fishing.
The Afanas'evo subsistence economy might best be characterized as a mixed or transitional form between hunting/fishing and localized pastoralism, arising from local antecedents or combining native strategies with diffused domestic innovations among local populations.
...Perhaps the strongest evidence that divides the Yamnaya and Afanas'evo pastoralists in the mid-fourth millenium BCE is the discontinuity of pastoral economic strategies among societies living between these territories."
[6]

If the Afanasievo culture was itself a combination of local hunting strategies and farming practices with their origins further west in the Yamnaya despite differing with contemporary societies above the Black and Caspian seas, one can postulate the Afanasievo people would have likely intermingled with native cultures in South Siberia whilst retaining their core pastoral attributes, and such an event would have occurred some time earlier. 
The Afanasievo bearers needn't travel through the Baraba forest-steppe neither; the maps shown in Chernykh's The “Steppe Belt” of stockbreeding cultures in Eurasia during the Early Metal Age, for instance, show a straight trajectory from the Urals to the Sayan-Altai region out of clarity rather than a factual basis. Little is currently known about the journey taken by these nomads, but the findings of this paper do help in confirming the founders of Afanasievo did not stray along the northern rim of the forest-steppe towards South Siberia.


References

1. Molodin VI, Pilipenko AS, Romaschenko AG, Zhuravlev AA, Trapezov RO. Human migrations in the southern region of the West Siberian Plain during the Bronze Age: Archaeological, palaeogenetic and anthropological data. 2012. Retrieved from here: http://www.degruyter.com/dg/viewbookchapter.fullcontentlink:pdfeventlink/contentUri?t:ac=books$002f9783110266306$002f9783110266306.93$002f9783110266306.93.xml [Last Accessed 17th July 2012]

2. Chernykh E. The “Steppe Belt” of stockbreeding cultures in Eurasia during the Early Metal Age. Trabajos De Prehistoria. 2008;65:73-93.

3. Kuz'mina EE. The Origin of the Indo-Iranians. Koninklijke Brill NV, Leiden, The Netherlands. 2007.

4. Keyser C, Bouakaze C, Crubézy E, Nikolaev VG, Montagnon D. Ancient DNA provides new insights into the history of south Siberian Kurgan people. Hum Genet. 2009;126:395–410.

5. Anthony DW. The Horse, the Wheel, and Language: How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World. Princeton University Press. 2007.

6. Frachetti MD. Pastoralist Landscapes and Social Interaction in Bronze Age Eurasia. University of California Press, Ltd. 2008.