Steppe Ancestry Estimations in West, Central & South Asia (Ancestral Proportions Method) [Original Work]

Disclaimer
This is largely a re-post, albeit with additional explanations, from a recent ADMIXTURE autosomal run (Eurasia K20) performed at Anthrogenica by the user Kurd. Full technical information and the original files may be found in his original thread. Full acknowledgement is provided to him for the great work. Unless stated otherwise, assume the contents refer to the Eurasia K20 run. This entry may be updated at any time to include further investigations based on future runs. Finally, this entry assumes the mainstream Pontic-Caspian theory for the genesis of the Indo-Europeans to be fully accurate.

Preamble
This entry/repost contains a "quick and dirty" method for a preliminary attempt at deriving their Sintashta admixture levels in West, Central and South Asians based on the Eurasia K20 scores. Given the different admixture histories elsewhere in Eurasia, this probably won't be very informative for users with ancestral backgrounds outside the lands between Kurdistan and the Indo-Gangetic plains. This is especially the case with modern Europeans, who share the same core components with Sintashta, while also deriving their own Indo-European ancestries from different archaeological cultures and time periods.

Establishing the Context
According to this Eurasia K20 run, Sintashta are approximately 62% Yamnaya, 22% EEF, 10% European and 3% SHG_WHG. Sintashta, at present, appear to be the best proxy for the Indo-Iranians that arrived in West and South Asia. The above four components define the majority (94%) of Sintashta's autosomal profile here.

As discussed elsewhere in Anthrogenica (kudos to user Sein for pointing this out), Sintashta should be considered better surrogates for the Andronovo-related waves which reached West, Central and South Asia than the actual Andronovo samples derived from Allentoft et al. 2015. This is due to the Andronovo samples being derived from the extreme northeast of the archaeological horizon (above the Altai, near Afanasievo). Their position opens up the possibility for extraneous admixture from other steppe groups (including early speakers of Tocharian through Afanasievo?).

The user Kurd has previously demonstrated that recent steppe-related admixture may be segregated from other components. While undertaking this exercise, it also looks like Kurd has done an excellent job addressing the "teal" component that defined up to half of Samara Yamnaya and a big chunk of Sintashta. Kurd's K20 is, in my view, the most effective attempt thus far at separating the complicated autosomal overlapping in West and Central Eurasia.

Introducing the Ancestral Proportions Method (APM)
At present, the genetic landscape in West, Central and South Asia presents as a triple conundrum:

1. There is, to date (and with the exception of the poor quality Barcin Neolithic Turkish sample), absolutely no interpretable ancient DNA (aDNA) from any of these regions, or indeed, at any point in this broad area's history. Perhaps the greatest obstacle at present.
2. Autosomal and uniparental marker data from across the region are either inconsistent in sample strategy, or outdated, preventing a knowledge-based approach towards interpreting results.
3. Archaeological evidence is inconsistent across the region; some cultures are well-studied, whereas others have fallen to mirthful speculation or cannot be readily assigned to any particular prehistoric group.

The APM is, in principle, unconcerned with these issues. Instead, it relies on objective data from a single ancient population to discern the numerical degree of overlap with modern populations.

Whether or not Iranians, Punjabis or Nepalis derive the bulk of their ancestry from unrelated group X or Y is beside the point. The sole purpose of the APM is, therefore, to establish whether or not ancient population Z has left any genetic imprint on modern populations A-K, and if so, to what extent. As such, the methodology described here is completely different as it is assymetrical; one-way gene flow across space and time from one ancestral (extinct) population to numerous extant populations. APM or derivative approaches should be considered as supplementary rather than directly competing with symmetrical modelling techniques such as f3 statistics.

The APM was specifically designed to answer the question; to what degree did Sintashta-related populations contribute to the modern groups of West, Central and South Asia? This simple inquiry has a tendency to attract considerable debate and wildly differing estimates in online discussion boards. Today, using the APM and recently generated data from the Eurasia K20 run, I hope to provide one set of estimations completely independent of extraneous modelling factors.

This approach is entirely reliant on high component specificity (e.g. minimal overlap or bleed-over from one component to another). This particular parameter is not within my control in this instance. As such, the outputs from APM here should be considered cautionary preliminary estimates at best, given the potential for ADMIXTURE-related shortcomings in the absence of relevant aDNA. I anticipate this approach will be much more effective at gleaning admixture extents once aDNA from West and Central Asia dating <2200 B.C. are retrieved.

The APM Approach
To contrast against the ADMIXTURE Sintashta scores, two different approaches are utilised together:

1) Direct Overlap (DO): summarised, for each component, the maximum overlap between a given population average and Sintashta's scores are calculated. This is done individually across all four components (Yamnaya, EEF, European, SHG_WHG) with the outputs added. See image below for schematic (conceptual breakdown of how the DO principle works between hypothetical samples 1 and 2, with Components a-d representing the distinct components).

Schematic diagram showing the principle behind Direct Overlap calculation

2) Component Proportions (CP): A single dominating component (frequency > 50%) is considered modal for the ancestral population of choice, with the other values considered as a fraction of this in modern populations. Given the Yamnaya component makes up almost two-thirds of Sintashta, the ratio between a population's and Sintashta's Yamnaya score are calculated and re-applied to the rest.

There are, however, problems with either approach:

1) DO is overinflated the more West Eurasian a population is. For example, several of the Iranian or Kurdish users at Anthrogenica had component scores greater than what is found in Sintashta (e.g. European being 12% in one sample, when it's 10% in Sintashta). This biases the results for Iranians and Kurds greatly, even when absolute value adjustments are set in place, which the formula shows is (it is highly improbable an Iranian with 10% European derived all of it from Sintashta).

2) CP is more accurate given the Yamnaya component appears highly steppe-oriented in Eurasia K20 and can therefore serve as a direct admixture marker. However, some of the South Asians are scoring very low, or almost none of, the other key components found in Sintashta (e.g. EEF). Due to this, CP doesn't fully account for the "missing variation" in South Asians, biasing the results slightly in their favour.

One convenient workaround is undertaking an average of both scores. However. given CP is intuitively more accurate due to the reasonable specificity of the Yamnaya component, a weighted average biased in favour of CP by a ratio of 3:1 was undertaken. The ratio choice in this variant of the APM is arbitrary here. Other variants (2:1, 4:1) would not result in radically different outcomes.

Results
Full results from up to 24 populations are shown in the Data Sink (interactive chart below). Summarised, Pamiri Tajiks are the most Sintashta-derived at 31.9%. North Caucasian (Ossetian) and Central Asian ethnic groups (Pashtuns, Uzbek, other Tajiks, Turkmen) follow at 22-19%. Various other ethnic groups across West, Central and South Asia follow. The lowest scoring population sampled here are the Makrani at 9.2%.

Internal Validation
The output (Data Sink) readily demonstrates strong correlation between DO and CP scores per population (e.g. Tajik Pamiris at 34.20% & 30.8%, Nepalis at 15% & 14.5% and Makrani at 10.2% & 8.7% respectively account for the top, middle and bottom pairs). The only marked deviation between the DO and CP scores were noted in West Asian populations (Armenians, Kurds, Iranians), as mentioned previously. Thus, empirical confirmation of correlation (e.g. Spearman's rank order) is unwarranted here.

Another means of confirming the validity of APM is to confirm Andronovo is a descendant of Sintashta. As the Andronovo archaeological horizon originates from Sintashta directly, one would expect very high (>90%) Sintashta-derived ancestry among them.

This appears to be the case. compared against Sintashta, Andronovo exhibits DO = 83.9%, CP = 97.3%, an average of 90.6% and a weighted average of 92.8%.

Summarised, these two results (dataset-wide correlation, ancestral-immediate successor high overlap) validate the outcomes of the APM.

Closing Thoughts
The results featured in this entry are in line with both broad uniparental marker data, previously published IBD results (unfortunately removed from sources) and are largely (though not fully) compatible with the degree of archaeological input from Andronovo-derived cultures in Asia. As stated previously, due to earlier shortcomings, they should not be considered definitive.

Given the CP here is not exclusively associated with Sintashta, I anticipate this technique will be more accurate if future "steppe"/"Yamnaya"/"Yamanya_related" components are shown to define more of the Sintashta samples. I look forward to extending this method in the near future.

Acknowledgements
Special thanks to the user Kurd from Anthrogenica for making this data available and obliging member inquiries with productive responses, as well as the user Sapporo for generating several of the population averages.

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

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.